# Index

$ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## $

$(String) - Static method in class org.jmol.i18n.GT

## A

a - Variable in class javajs.util.Matrix
a - Variable in class org.jmol.g3d.PrecisionRenderer
a - Variable in class org.jmol.util.SimpleUnitCell
a_ - Variable in class org.jmol.util.SimpleUnitCell
A4 - Class in javajs.util
  A 4 element axis angle represented by single precision floating point x,y,z,angle components.
A4() - Constructor for class javajs.util.A4
  Constructs and initializes a AxisAngle4f to (0,0,1,0).
aaTest1 - Variable in class org.jmol.viewer.TransformManager
aatoken - Variable in class org.jmol.script.ScriptEval
AB - Enum constant in enum class jspecview.common.PanelData.LinkMode
ABC - Enum constant in enum class jspecview.common.PanelData.LinkMode
abcFor(M4) - Method in class org.jmol.symmetry.CLEG.ClegData
abFace - Static variable in class org.jmol.util.Triangulator
ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
AbinitReader - Class in org.jmol.adapter.readers.xtal
AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
AboutDialog - Class in jspecview.application
  The `About Dialog` class is the help | about window for JSpecView.
AboutDialog - Class in org.openscience.jmol.app.jmolpanel
AboutDialog(Frame) - Constructor for class jspecview.application.AboutDialog
  Constructor that initalises the Dialog a parent frame, no title and modality to true
AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
abs - Static variable in class org.jmol.script.T
absolute - Static variable in class org.jmol.script.T
ABSOLUTE - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
AbstractButton - Class in org.jmol.awtjs.swing
AbstractButton(String) - Constructor for class org.jmol.awtjs.swing.AbstractButton
AbstractTableModel - Interface in org.jmol.awtjs.swing
ac - Variable in class org.jmol.adapter.readers.cif.CifReader
ac - Variable in class org.jmol.adapter.readers.simple.InputReader
ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
ac - Variable in class org.jmol.atomdata.AtomData
ac - Variable in class org.jmol.jvxl.readers.JvxlReader
ac - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
ac - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
ac - Variable in class org.jmol.modelset.AtomCollection
ac - Variable in class org.jmol.util.JmolMolecule
accept(File) - Method in class jspecview.java.AwtDialogFileFilter
  Implementation of method from interface `FileFilter`.
accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
accept(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
ACCEPTOR - Enum constant in enum class org.jmol.c.HB
acm - Variable in class org.jmol.viewer.Viewer
acos - Static variable in class org.jmol.script.T
act - Variable in class org.jmol.modelset.Model
  atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
action(String) - Method in interface org.jmol.api.JmolAudioPlayer
action(String) - Method in class org.jmol.util.JmolAudio
  Execute an action from load audio "xxxxx.wav" filter "id=a1 action=xxx"
ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
ACTION_center - Static variable in class org.jmol.viewer.ActionManager
ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
ACTION_count - Static variable in class org.jmol.viewer.ActionManager
ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
ACTION_select - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
actionCommand - Variable in class org.jmol.awtjs.swing.JComponent
actionListener - Variable in class org.jmol.awtjs.swing.JComponent
actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
ActionManager - Class in org.jmol.viewer
ActionManager() - Constructor for class org.jmol.viewer.ActionManager
ActionManagerMT - Class in org.jmol.multitouch
ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
actionPerformed(ActionEvent) - Method in class jspecview.application.PreferencesDialog
  Sets the color of the selected element on the current color button
actionPerformed(ActionEvent) - Method in class jspecview.java.AwtDialogManager
  ActionListener callback
actionPerformed(ActionEvent) - Method in class org.jmol.awt.AwtPopupHelper
actionPerformed(ActionEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
actionPerformed(ActionEvent) - Method in class org.jmol.console.ImageDialog
actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
actionPerformed(String) - Method in class jspecview.js2d.JsDialogManager
  Jmol.Swing.click() callback (via SwingController)
actionRotateBond(int, int, int, int, boolean) - Method in class org.jmol.modelkit.ModelKit
  Actually rotate the bond.
activate() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
activate() - Method in class org.openscience.jmol.app.janocchio.NoeTable
activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
activateQuery() - Method in class jme.JME
active_selections - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
add - Static variable in class org.jmol.script.T
add(float) - Method in class javajs.util.Quat
add(int, V) - Method in class javajs.util.Lst
add(String) - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
add(Map, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
add(M3) - Method in class javajs.util.M3
  Sets the value of this matrix to sum of itself and matrix m1.
add(Matrix) - Method in class javajs.util.Matrix
  add two matrices
add(T3) - Method in class javajs.util.M4
  add to translation
add(T3) - Method in class javajs.util.T3
  Sets the value of this tuple to the vector sum of itself and tuple t1.
add(T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the vector sum of itself and tuple t1.
add(T3i) - Method in class javajs.util.T3i
  Sets the value of this tuple to the sum of itself and t1.
add(SC) - Method in interface org.jmol.api.SC
add(SC) - Method in class org.jmol.awt.AwtSwingComponent
add(SC) - Method in class org.jmol.awtjs.swing.AbstractButton
add(SC) - Method in class org.jmol.awtjs.swing.ButtonGroup
add(Component) - Method in class org.jmol.awtjs.swing.Container
add(JComponent, Object) - Method in class org.jmol.awtjs.swing.JPanel
add(JComponent, GridBagConstraints) - Method in class org.jmol.awtjs.swing.Grid
add(V) - Method in class javajs.util.Lst
  Deprecated.
ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
add2(T3d, T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the vector sum of tuples t1 and t2.
add2(T3, T3) - Method in class javajs.util.T3
  Sets the value of this tuple to the vector sum of tuples t1 and t2.
add3(float, float, float) - Method in class javajs.util.T3
  Add {a b c}
add33(M34) - Method in class javajs.util.M34
addActionListener(Object) - Method in interface org.jmol.api.SC
addActionListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
addActionListener(Object) - Method in class org.jmol.awtjs.swing.JComponent
  Note that it will be the job of the JavaScript on the page to do with actionListener what is desired.
addActions(List) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
addActions(List) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
addActions(List) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
addAlpha(int) - Method in interface javajs.api.GenericColor
addAlpha(int) - Method in class jspecview.java.AwtColor
addAlpha(int) - Method in class org.jmol.awt.AwtColor
addAlpha(int) - Method in class org.jmol.awtjs.swing.Color
addAnnotation(Lst) - Method in class jspecview.common.PanelData
addApplyBtn - Variable in class jspecview.dialog.JSVDialog
addAssembly(String[]) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addAtom(double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
  add a proton to the atom list
addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst, boolean, boolean, byte, BS, float) - Method in class org.jmol.modelset.ModelSet
addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addAtoms(int) - Method in class org.jmol.modelset.Group
addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
  turns this into a SPHERICAL iterator for "within Distance" measures
addAtoms(BS) - Method in class org.jmol.symmetry.UnitCellIterator
addAtomSet(String) - Method in class org.jmol.modelkit.ModelKit
addAtomstoMatrix() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
  Generate noeMatrix and map fields for DistanceJMolecule.
addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addAttribute(SB, String, String) - Static method in class org.jmol.adapter.writers.CMLWriter
addAttributes(SB, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
addBondNoCheck(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addBonds - Variable in class org.jmol.adapter.writers.CMLWriter
addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
addButton(String, String) - Method in interface jspecview.api.PlatformDialog
addButton(String, String) - Method in class jspecview.java.AwtDialog
addButton(String, String) - Method in class jspecview.js2d.JsDialog
addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
addBytes(byte[], int, int) - Method in class javajs.util.ZipData
addCheckBox(String, String, int, boolean) - Method in interface jspecview.api.PlatformDialog
addCheckBox(String, String, int, boolean) - Method in class jspecview.java.AwtDialog
addCheckBox(String, String, int, boolean) - Method in class jspecview.js2d.JsDialog
addCifAtom(Atom, String, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
addCoef(Map, float[], String, float, float, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
addColix(int) - Method in class org.jmol.shapecgo.CGOMesh
addCommand(int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
addCommand(String) - Method in class org.jmol.util.CommandHistory
  Adds any number of lines to the command history
addCommand(String) - Method in class org.jmol.viewer.Viewer
  Adds one or more commands to the command history
addComponent(Component) - Method in class org.jmol.awtjs.swing.Container
addConnectedHAtoms(Atom, BS) - Method in class org.jmol.modelset.BondCollection
addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
addContourPoints(Lst, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
addCouple(int, int, int, int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
addCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
addData(MOCalculation, boolean) - Method in interface org.jmol.quantum.mo.DataAdder
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder11H
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder13I
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder7F
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder9G
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderF
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderG
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderH
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderI
addDialog(int, Annotation.AType, AnnotationData) - Method in class jspecview.common.PanelData
addDisplayedBackbone(Atom, boolean) - Method in class org.jmol.shapebio.Backbone
addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
addEquiv(double[], double[], double[]) - Method in class org.jmol.quantum.NMRNoeMatrix
addExplicitLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addExtension(String) - Method in class jspecview.java.AwtDialogFileFilter
  Adds an extension to the JSpecViewFileFilter
addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
addFunction(ScriptFunction) - Method in class org.jmol.script.ScriptEval
addGroup(Group, int) - Method in class org.jmol.modelset.Chain
addHallOperationCheckDuplicates(M4) - Method in interface org.jmol.symmetry.HallInfo.HallReceiver
  Add a (possibly) new operation, checking for duplicates.
addHallOperationCheckDuplicates(M4) - Method in class org.jmol.symmetry.SpaceGroup
addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
  /// bonding methods //////
addHeader() - Method in class org.jmol.adapter.readers.cif.CifReader
addHeader() - Method in class org.jmol.adapter.readers.cif.MMTFReader
addHeader(String, String) - Method in class jspecview.source.JDXHeader.DataLDRTable
addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addHetero(String, String, String, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addHighlight(double, double, int, int, int, int) - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a `JSVPanel`
addHighlight(double, double, int, int, int, int) - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a `JSVPanel`
addHighlight(double, double, int, int, int, int) - Method in class jspecview.appletjs.JSVApplet
addHighlight(GraphSet, double, double, Spectrum, int, int, int, int) - Method in class jspecview.common.PanelData
  Add information about a region of the displayed spectrum to be highlighted applet only right now
addHistoryWindowDimInfo(String, Component, Dimension) - Method in interface org.jmol.api.JmolAppAPI
addHistoryWindowDimInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.JmolApp
addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
addHydrogenBond(Lst, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
addhydrogens - Static variable in class org.jmol.script.T
addHydrogens(BS, int) - Method in class org.jmol.viewer.Viewer
  / requiring ScriptEvaluator:
addHydrogens(Lst, P3[]) - Method in class org.jmol.modelset.ModelSet
  these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
addHydrogensInline(BS, Lst, P3[], Map) - Method in interface org.jmol.api.JmolScriptManager
addHydrogensInline(BS, Lst, P3[], Map) - Method in class org.jmol.script.ScriptManager
  Add hydrogens to a model
addHydrogensInline(BS, Lst, P3[], Map) - Method in class org.jmol.viewer.Viewer
addImageResource(Object, int, int, int[], boolean) - Method in class javajs.export.PDFCreator
addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.BioResolver
  Get bonding info for double bonds and add implicit hydrogen atoms, if needed.
addInfo(Map) - Method in class javajs.export.PDFCreator
addIntegralRegion(double, double) - Method in class jspecview.common.IntegralData
addInversion() - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
addItemListener(Object) - Method in interface org.jmol.api.SC
addItemListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
addItemListener(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
addItems(String[][]) - Method in class org.jmol.popup.PopupResource
addJDXSpectrum(String, Spectrum, boolean) - Method in class jspecview.source.JDXSource
  Adds a Spectrum to the list
addJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
addJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
  Add using Jmol atom index
addJmolProperties(Properties) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolWindowInfo(String, Component, Point) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Deprecated.
addJmolWindowInnerInfo(String, Component, Dimension) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addLast(V) - Method in class javajs.util.Lst
addLatticeVector(Lst, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
addLatticeVector(Lst, String) - Method in interface org.jmol.adapter.smarter.MSInterface
addListener(PanelListener) - Method in class jspecview.common.PanelData
addListSelectionListener(Object) - Method in class org.jmol.awtjs.swing.JTable
  It will be the function of the JavaScript on the page to do with selectionListener what is desired.
addListSelectionListener(Object) - Method in interface org.jmol.awtjs.swing.ListSelectionModel
addLockedAtoms(SymmetryInterface, BS) - Method in class org.jmol.modelkit.ModelKit
  Only for the current model
addMacrosMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addMagLatticeVectors(Lst) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
addMagLatticeVectors(Lst) - Method in class org.jmol.symmetry.SpaceGroup
addMarks(String) - Method in class jspecview.common.IntegralData
  INTEGRATION MARK list where list is a comma-separated list of ppm1-ppm2 with :x.x added to normalize one of them and starting with 0-0 clears the integration
addMatrix(String, M4, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtJmolPopup
addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtModelKitPopup
addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.popup.GenericPopup
addMenuItem(JMenu, String, char, ActionListener) - Static method in class jspecview.application.ApplicationMenu
addMenuItem(SC, String) - Method in class org.jmol.popup.GenericPopup
addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericPopup
addMeshInfo(IsosurfaceMesh, Map) - Method in class org.jmol.shapesurface.Contact
addMeshInfo(IsosurfaceMesh, Map) - Method in class org.jmol.shapesurface.Isosurface
addMethyl(double, double, double, double, double, double, double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
  Add a methyl group to the atom list
addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
addMOData(int, Lst[], Map[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
addModulation(Map, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
addModulation(Map, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
addMol() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
addMol() - Method in class org.openscience.jmol.app.janocchio.NoeTable
addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
addMolFile(String, int, SB, BS, BS, boolean, boolean, boolean, Quat, boolean) - Method in class org.jmol.adapter.writers.MOLWriter
addMoreUnitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addMouseListener(Object) - Method in interface org.jmol.api.SC
addMouseListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
addMouseListener(Object) - Method in class org.jmol.awtjs.swing.Component
addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNOE(int, int, String, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addNormix(int) - Method in class org.jmol.shapecgo.CGOMesh
addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
  addOp The primary driver of the Reverse Polish Notation evaluation engine.
addOp(SymmetryOperation, String, boolean) - Method in class org.jmol.symmetry.SpaceGroup
addOperation(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
addPeakData(String) - Method in class jspecview.source.JDXReader
addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
addPeakHighlight(PeakInfo) - Method in class jspecview.common.PanelData
addPluginMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
addPopulation(double[]) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
addPrimitiveTransform(String, String) - Method in class org.jmol.symmetry.CLEG.ClegData
addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the given properties to the history.
addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the given property to the history.
addPropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
addRenderer(int) - Method in class org.jmol.export.Export3D
addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
  allows core JavaScript loading to not involve these classes
addRenderer(int) - Method in class org.jmol.util.GData
addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
addRotatedTensor(Atom, Tensor, int, boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.XtalSymmetry
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
addSelectOption(String, String, String[], int, boolean) - Method in interface jspecview.api.PlatformDialog
addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.java.AwtDialog
addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.js2d.JsDialog
addSGTransform(String, String) - Method in class org.jmol.symmetry.CLEG.ClegData
addSites(Map) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AdfReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AmsReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.CsfReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.DgridReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.CsfReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MOReader
  See MopacSlaterReader
addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
addSpecShift(double) - Method in class jspecview.common.Measurement
addSpecShift(double) - Method in class jspecview.common.Spectrum
addSpinLattice(Lst, Map) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
addSpinLattice(Lst, Map) - Method in class org.jmol.symmetry.SpaceGroup
  spin space groups only
addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addStructure(STR, String, String, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
addStructureProtected(STR, String, String, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
addStructureSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
  We must add groups to the proper bsStructure element
addSubSpectrum(Spectrum, boolean) - Method in class jspecview.common.Spectrum
  adds an nD subspectrum and titles it "Subspectrum <n>" These spectra can be iterated over using the UP and DOWN keys.
addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
addTextField(String, String, String, String, String, boolean) - Method in interface jspecview.api.PlatformDialog
addTextField(String, String, String, String, String, boolean) - Method in class jspecview.java.AwtDialog
  / get/set methods ////
addTextField(String, String, String, String, String, boolean) - Method in class jspecview.js2d.JsDialog
  / get/set methods ////
addTo(GenericZipTools, SB) - Method in class javajs.util.ZipData
addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
addTo(T3, float) - Method in class org.jmol.util.ModulationSet
addToken(String, T) - Static method in class org.jmol.script.T
addToList(int, Lst) - Method in class jspecview.common.PanelData
addTracePt(int, Point3fi) - Method in class org.jmol.util.Vibration
addTransform(int, String) - Method in class org.jmol.symmetry.CLEG.ClegData
addTransformLink() - Method in class org.jmol.symmetry.CLEG.ClegData
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
  addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
addTuple(int, P3) - Method in class org.jmol.bspt.Bspf
addTuple(T3) - Method in class org.jmol.bspt.Bspt
  Iterate through all of your data points, calling addTuple
addUniqueControls() - Method in class jspecview.dialog.IntegrationDialog
addUniqueControls() - Method in class jspecview.dialog.JSVDialog
addUniqueControls() - Method in class jspecview.dialog.MeasurementsDialog
addUniqueControls() - Method in class jspecview.dialog.OverlayLegendDialog
addUniqueControls() - Method in class jspecview.dialog.PeakListDialog
addUniqueControls() - Method in class jspecview.dialog.ViewsDialog
addUniqueControls(DialogManager) - Method in class jspecview.dialog.JSVDialog
addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
addUTens(String, float) - Method in class org.jmol.util.ModulationSet
addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
addVectors(float[]) - Static method in class org.jmol.util.SimpleUnitCell
addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
addVertexCopy(T3, float, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
  addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the window informations to the history.
addWindowInfo(String, Component, Point, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
addWindowInnerInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
addWindowListener() - Method in class org.jmol.console.JmolConsole
  /////////////////////////////////////////////////////////////
addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
addXList(Lst) - Method in class org.jmol.script.ScriptMathProcessor
addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
addXMap(Map) - Method in class org.jmol.script.ScriptMathProcessor
addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
addZipEntry(Object, String) - Method in interface javajs.api.GenericZipTools
addZipEntry(Object, String) - Method in class javajs.util.ZipTools
AdfReader - Class in org.jmol.adapter.readers.quantum
  TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
adjustForWindow - Variable in class org.jmol.modelset.Text
adjustRangeMinMax(T3[], float, P3i, P3i, P3, P3, P3i, P3i) - Method in interface org.jmol.api.SymmetryInterface
adjustRangeMinMax(T3[], float, P3i, P3i, P3, P3, P3i, P3i) - Method in class org.jmol.symmetry.Symmetry
adjustRangeMinMax(T3[], float, P3i, P3i, P3, P3, P3i, P3i) - Method in class org.jmol.symmetry.UnitCell
adjustStrut(P3[], int, int, int) - Method in class org.jmol.renderbio.RocketsRenderer
adpmax - Static variable in class org.jmol.script.T
ADPMAX - Enum constant in enum class org.jmol.c.VDW
adpmin - Static variable in class org.jmol.script.T
ADPMIN - Enum constant in enum class org.jmol.c.VDW
adpMode - Variable in class org.jmol.atomdata.AtomData
advanceSpectrumBy(int) - Method in class jspecview.common.JSViewer
advanceSubSpectrum(int) - Method in class jspecview.common.PanelData
advanceSubSpectrum(int) - Method in class jspecview.common.Spectrum
AFLOWReader - Class in org.jmol.adapter.readers.more
  A reader for various AFLOW file types.
AFLOWReader() - Constructor for class org.jmol.adapter.readers.more.AFLOWReader
afterClear - Variable in class jme.JME
AimsReader - Class in org.jmol.adapter.readers.xtal
  FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
AjaxURLConnection - Class in javajs.util
  A method to allow a JavaScript Ajax
AjaxURLConnection(URL) - Constructor for class javajs.util.AjaxURLConnection
AjaxURLStreamHandler - Class in javajs.util
  A method to allow a JavaScript AJAX adapter to deliver web content to JSmol.
AjaxURLStreamHandler(String) - Constructor for class javajs.util.AjaxURLStreamHandler
AjaxURLStreamHandlerFactory - Class in javajs.util
  For handling URL file IO via AJAX in JavaScript version
AjaxURLStreamHandlerFactory() - Constructor for class javajs.util.AjaxURLStreamHandlerFactory
AlchemyReader - Class in org.jmol.adapter.readers.simple
  TRIPOS simple Alchemy reader.
AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
alert(String) - Method in class org.jmol.viewer.Viewer
align - Variable in class org.jmol.modelset.Text
align - Static variable in class org.jmol.script.T
ALIGN_CENTER - Static variable in class jme.JMEUtil
ALIGN_LEFT - Static variable in class jme.JMEUtil
ALIGN_RIGHT - Static variable in class jme.JMEUtil
alignment - Variable in class jme.AtomDisplayLabel
alignment_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
all - Static variable in class org.jmol.script.T
ALL - Enum constant in enum class jspecview.common.PanelData.LinkMode
ALL - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
all_states - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
allconnected - Static variable in class org.jmol.script.T
allEmptyString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
ALLENE - Static variable in class org.jmol.smiles.SmilesStereo
allfloat - Static variable in class org.jmol.script.T
allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
allHs - Variable in class jme.JME
allNaN() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
allNull() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
allocateColix(int, boolean) - Static method in class org.jmol.util.C
allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
allocateExpCouples(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
allocateExpNoes(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.java.AwtPlatform
  /// Image
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.js2d.JsPlatform
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in interface org.jmol.api.GenericPlatform
  // core Image handling
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
  /// Image
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
  Create an "image" that is either a canvas with width/height/buf32 (from g3d.Platform32) or just an associative array with those (image writing
allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
  a simpler option
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
  legacy only
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
  This is the older main access point for creating an application or applet vwr.
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
  old way...
allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
allocMesh(String, Mesh) - Method in class org.jmol.shapecgo.CGO
allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
allocTempEnum(int) - Method in class org.jmol.util.TempArray
allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
allocTempPoints(int) - Method in class org.jmol.util.TempArray
allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
allocTempScreens(int) - Method in class org.jmol.util.TempArray
allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
allow_a_len_1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
allow300 - Static variable in class org.jmol.symmetry.CLEG
  allows 300, 400, 500, 600 instead of p/ l/ r/ f/ could be turned on; this is for Jmol testing
allowAromaticBond(Bond) - Method in class org.jmol.modelset.BondCollection
allowaudio - Static variable in class org.jmol.script.T
allowCapture() - Method in class org.jmol.viewer.Viewer
allowDashed - Variable in class org.jmol.render.MeshRenderer
allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
allowembeddedscripts - Static variable in class org.jmol.script.T
allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
allowgestures - Static variable in class org.jmol.script.T
allowJavaConsole - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
allowkeystrokes - Static variable in class org.jmol.script.T
allowMenu - Variable in class jspecview.common.JSViewer
allowmodelkit - Static variable in class org.jmol.script.T
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.CsfReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
allowmoveatoms - Static variable in class org.jmol.script.T
allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
allowmultitouch - Static variable in class org.jmol.script.T
allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
allowrotateselected - Static variable in class org.jmol.script.T
allowSameName - Static variable in class org.jmol.jsv.JDXMOLParser
allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
allowSignedFeatures - Variable in class org.jmol.popup.GenericPopup
allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
allowSubSpec(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
allSame() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
allTrajectories - Variable in class org.jmol.adapter.writers.CMLWriter
allZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
alpha - Variable in class org.jmol.util.SimpleUnitCell
ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
ALPHA_SHIFT - Static variable in class org.jmol.util.C
ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
AlphaMonomer - Class in org.jmol.modelsetbio
AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
AlphaPolymer - Class in org.jmol.modelsetbio
ALT - Static variable in class org.jmol.util.ColorEncoder
ALT - Static variable in class org.jmol.viewer.binding.Binding
ALT_MASK - Static variable in class org.jmol.awtjs.Event
altArgbsCpk - Static variable in class org.jmol.viewer.JC
altElementCounts - Variable in class org.jmol.util.JmolMolecule
altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
altElementMax - Static variable in class org.jmol.util.Elements
  length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementMax - Variable in class org.jmol.util.JmolMolecule
altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
altloc - Variable in class org.jmol.modelset.Atom
altloc - Static variable in class org.jmol.script.T
altLoc - Variable in class org.jmol.adapter.smarter.Atom
ALTLOC - Enum constant in enum class org.jmol.c.PAL
altLocCount - Variable in class org.jmol.modelset.Model
altType - Variable in class org.jmol.util.Tensor
altVertices - Variable in class org.jmol.util.MeshSurface
am - Variable in class org.jmol.modelset.ModelSet
am - Variable in class org.jmol.viewer.Viewer
ambient - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ambient_occlusion_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ambient_occlusion_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ambient_occlusion_smooth - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ambientocclusion - Static variable in class org.jmol.script.T
ambientOcclusion - Variable in class org.jmol.util.GData
ambientpercent - Static variable in class org.jmol.script.T
amino - Static variable in class org.jmol.script.T
AMINO - Enum constant in enum class org.jmol.c.PAL
AMINO - Static variable in class org.jmol.util.ColorEncoder
AminoMonomer - Class in org.jmol.modelsetbio
AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
AminoPolymer - Class in org.jmol.modelsetbio
AML - Enum constant in enum class jspecview.common.ExportType
AMLExporter - Class in jspecview.export
  class `AnIMLExporter` contains static methods to export a Graph as as AnIML.
AMLExporter() - Constructor for class jspecview.export.AMLExporter
AmpacReader - Class in org.jmol.adapter.readers.simple
  A reader for AMPAC output.
AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
AmsReader - Class in org.jmol.adapter.readers.quantum
  A reader for AMS output subclassing the older AdfReader.
AmsReader() - Constructor for class org.jmol.adapter.readers.quantum.AmsReader
anaglyph_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
anchor - Variable in class org.jmol.awtjs.swing.GridBagConstraints
and(BS) - Method in class javajs.util.BS
  Performs a logical AND of this target bit set with the argument bit set.
andequals - Static variable in class org.jmol.script.T
andNot(BS) - Method in class javajs.util.BS
  Clears all of the bits in this `BitSet` whose corresponding bit is set in the specified `BitSet`.
andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
angle - Variable in class javajs.util.A4
  The angle.
angle - Static variable in class org.jmol.script.T
angle(V3) - Method in class javajs.util.V3
  Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
angle(V3d) - Method in class javajs.util.V3d
angle_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
angle_label_position - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
angle_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
angstroms - Static variable in class org.jmol.script.T
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
animation - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
animation - Static variable in class org.jmol.script.T
animation_duration - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
animationfps - Static variable in class org.jmol.script.T
animationFps - Variable in class org.jmol.viewer.AnimationManager
AnimationManager - Class in org.jmol.viewer
animationmode - Static variable in class org.jmol.script.T
animationOn - Variable in class org.jmol.viewer.AnimationManager
animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
animationThread - Variable in class org.jmol.viewer.AnimationManager
AnimationThread - Class in org.jmol.thread
AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
ANIMFRAME - Enum constant in enum class org.jmol.c.CBK
AnIMLReader - Class in jspecview.source
  Representation of a XML Source.
AnIMLReader() - Constructor for class jspecview.source.AnIMLReader
anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
anisotropy - Static variable in class org.jmol.script.T
anisotropy() - Method in class org.jmol.util.Tensor
  anisotropy = directed distance from (center of two closest) to (the furthest)
Annotation - Class in jspecview.common
  The `Annotation` class stores the spectral x and pixel y values of an annotation text along with its text
Annotation - Class in org.jmol.modelsetbio
Annotation() - Constructor for class jspecview.common.Annotation
Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
ANNOTATION - Enum constant in enum class org.jmol.c.STR
Annotation.AType - Enum Class in jspecview.common
AnnotationData - Interface in jspecview.api
AnnotationParser - Class in org.jmol.dssx
  A parser for output from 3DNA web service.
AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
antialias - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
antialias - Variable in class org.jmol.render.MeshRenderer
antialias - Variable in class org.jmol.viewer.TransformManager
antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
antialiasdisplay - Static variable in class org.jmol.script.T
antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
antialiased - Variable in class org.jmol.viewer.Viewer
antialiasEnabled - Variable in class org.jmol.util.GData
antialiasimages - Static variable in class org.jmol.script.T
antialiasThisFrame - Variable in class org.jmol.util.GData
antialiastranslucent - Static variable in class org.jmol.script.T
aperatureAngle - Variable in class org.jmol.viewer.TransformManager
apertureAngle - Variable in class org.jmol.export.___Exporter
apiPlatform - Variable in class jspecview.common.JSViewer
apiPlatform - Variable in class org.jmol.api.JmolViewer
apiPlatform - Variable in class org.jmol.util.GData
apivot - Static variable in class org.jmol.script.T
apointx - Variable in class jme.JME
apointy - Variable in class jme.JME
apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
app - Variable in class jspecview.appletjs.JSVApplet
appCheckItem(String, SC) - Method in class jspecview.popup.JSVGenericPopup
appCheckItem(String, SC) - Method in class org.jmol.popup.GenericPopup
  Opportunity to do something special with an item.
appCheckItem(String, SC) - Method in class org.jmol.popup.JmolPopup
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericPopup
  Opportunity to do something special with a given submenu is created
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolPopup
AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
appConsole - Variable in class org.jmol.viewer.Viewer
AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
  general entry point
append - Static variable in class org.jmol.script.T
append(String) - Method in class javajs.util.OC
  will go to string buffer if bw == null and os == null
append(String) - Method in class javajs.util.SB
append(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
append(String) - Method in interface org.jmol.console.GenericTextArea
append(String) - Method in class org.jmol.util.JSONWriter
append3(SB, T3) - Method in class org.jmol.adapter.writers.CIFWriter
appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Appends an AtomSetCollection
appendAttrib(SB, Object, Object) - Static method in class javajs.util.XmlUtil
appendB(boolean) - Method in class javajs.util.SB
appendC(char) - Method in class javajs.util.SB
appendCB(char[], int, int) - Method in class javajs.util.SB
appendCdata(SB, String, Object[], String) - Static method in class javajs.util.XmlUtil
  <name></name>" will convert ]]> to ]] >
appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
appendContourTriangleIntersection(int, float, float, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
  appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
appendD(double) - Method in class javajs.util.SB
appendEmptyTag(SB, String, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
appendF(float) - Method in class javajs.util.SB
  note that JavaScript could drop off the ".0" in "1.0"
appendField(SB, String, int) - Static method in class org.jmol.adapter.writers.CIFWriter
appendFontCmd(SB) - Method in class org.jmol.modelset.Text
appendI(int) - Method in class javajs.util.SB
appendKey(SB, String, int) - Method in class org.jmol.adapter.writers.CIFWriter
appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
appendnew - Static variable in class org.jmol.script.T
appendNew - Variable in class org.jmol.viewer.GlobalSettings
appendO(Object) - Method in class javajs.util.SB
appendSB(SB) - Method in class javajs.util.SB
appendTag(SB, String, Object) - Static method in class javajs.util.XmlUtil
  standard <name>data</name>" standard "
appendTagAll(SB, String, Object[], Object, boolean, boolean) - Static method in class javajs.util.XmlUtil
appendTagObj(SB, String, Object[], Object) - Static method in class javajs.util.XmlUtil
  standard data"
appFixLabel(String) - Method in class jspecview.popup.JSVGenericPopup
appFixLabel(String) - Method in class org.jmol.popup.GenericPopup
appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
appGetBooleanProperty(String) - Method in class jspecview.popup.JSVGenericPopup
appGetBooleanProperty(String) - Method in class org.jmol.modelkit.ModelKitPopup
  //////////////// menu execution //////////////
appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericPopup
appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
appGetMenuAsString(String) - Method in class jspecview.popup.JSVGenericPopup
appGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
appGetMenuAsString(String) - Method in class org.jmol.popup.JmolPopup
appletCodeBase - Static variable in class org.jmol.viewer.Viewer
AppletConsole - Class in org.jmol.console
AppletConsole - Class in org.jmol.consolejs
  An interface to Jmol.Console.
AppletConsole() - Constructor for class org.jmol.console.AppletConsole
AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
appletDocumentBase - Static variable in class jspecview.common.JSVFileManager
appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
appletFrame - Variable in class jspecview.app.JSVApp
AppletFrame - Interface in jspecview.api
APPLETID - Enum constant in enum class jspecview.common.ScriptToken
appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
appletName - Variable in class jspecview.common.JSViewer
appletName - Variable in class org.jmol.viewer.Viewer
appletObject - Variable in class org.jmol.util.GenericApplet
appletproxy - Static variable in class org.jmol.script.T
APPLETREADY - Enum constant in enum class org.jmol.c.CBK
appletReadyCallbackFunctionName - Variable in class jspecview.app.JSVApp
APPLETREADYCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
application - Variable in class jme.JME
ApplicationMenu - Class in jspecview.application
  The Main Class or Entry point of the JSpecView Application.
ApplicationMenu(MainFrame) - Constructor for class jspecview.application.ApplicationMenu
apply(Object[]) - Method in class jspecview.dialog.JSVDialog
applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
applyFromFields() - Method in class jspecview.dialog.IntegrationDialog
applyFromFields() - Method in class jspecview.dialog.JSVDialog
applyFromFields() - Method in class jspecview.dialog.ViewsDialog
applyFunc(Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
applyLeftMouse(int) - Static method in class jspecview.app.GenericMouse
applyScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
  Apply the scale factor to the coordinates
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.MMTFReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
applySymmetryBio(Map, boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
applysymmetrytobonds - Static variable in class org.jmol.script.T
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
appRestorePopupMenu() - Method in class jspecview.popup.JSVGenericPopup
appRestorePopupMenu() - Method in class org.jmol.popup.GenericPopup
appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
appRestorePopupMenu() - Method in class org.jmol.popup.JmolPopup
approx(float, float) - Static method in class javajs.util.PT
approx0(float) - Static method in class org.jmol.util.SimpleUnitCell
appRunScript(String) - Method in class jspecview.popup.JSVGenericPopup
appRunScript(String) - Method in class org.jmol.popup.GenericPopup
appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
AppToolBar - Class in jspecview.application
AppToolBar(MainFrame) - Constructor for class jspecview.application.AppToolBar
appUpdateForShow() - Method in class jspecview.popup.JSVGenericPopup
appUpdateForShow() - Method in class org.jmol.modelkit.ModelKitPopup
appUpdateForShow() - Method in class org.jmol.popup.GenericPopup
appUpdateForShow() - Method in class org.jmol.popup.JmolPopup
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
  Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
  (1) setOption --> set setOption true or set setOption false
arc - Static variable in class org.jmol.script.T
ARC - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
area - Static variable in class org.jmol.script.T
areAxesTainted() - Method in class org.jmol.viewer.Viewer
areEqual(Object, Object) - Method in interface org.jmol.api.SmilesMatcherInterface
areEqual(Object, Object) - Method in class org.jmol.smiles.SmilesMatcher
areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
areEqual(SV, SV) - Static method in class org.jmol.script.SV
  For legacy reasons, "x" == "X" but see isLike()
areEqualTest(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
  for JUnit test, mainly
areLinkableX(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
areLinkableY(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
areXScalesCompatible(Spectrum, Spectrum, boolean, boolean) - Static method in class jspecview.common.Spectrum
areYScalesSame(int, int) - Method in class jspecview.common.ViewData
argb - Variable in class org.jmol.awtjs.swing.Color
argbCurrent - Variable in class org.jmol.util.GData
argbNoisyDn - Variable in class org.jmol.util.GData
argbNoisyUp - Variable in class org.jmol.util.GData
argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
argbsCpk - Static variable in enum class org.jmol.c.PAL
  Default table of CPK atom colors.
argbsCpkRasmol - Static variable in enum class org.jmol.c.PAL
argbsFormalCharge - Static variable in class org.jmol.viewer.JC
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
argbsRoygbScale - Static variable in class org.jmol.viewer.JC
argbsRwbScale - Static variable in class org.jmol.viewer.JC
aromatic - Static variable in class org.jmol.script.T
array - Static variable in class org.jmol.script.T
arrayAdd(Object) - Method in class org.jmol.util.JSONWriter
arrayClose(boolean) - Method in class org.jmol.util.JSONWriter
arrayCopyBool(boolean[], int) - Static method in class javajs.util.AU
arrayCopyByte(byte[], int) - Static method in class javajs.util.AU
arrayCopyF(float[], int) - Static method in class javajs.util.AU
arrayCopyI(int[], int) - Static method in class javajs.util.AU
arrayCopyII(int[][], int) - Static method in class javajs.util.AU
arrayCopyObject(Object, int) - Static method in class javajs.util.AU
  note -- cannot copy if array is null! does not copy if length is unchanged
arrayCopyPt(T3[], int) - Static method in class javajs.util.AU
arrayCopyRangeI(int[], int, int) - Static method in class javajs.util.AU
  a specialized method that allows copying from a starting point either to the end or to the middle (color schemes, especially)
arrayCopyRangeRevI(int[], int, int) - Static method in class javajs.util.AU
arrayCopyS(String[], int) - Static method in class javajs.util.AU
arrayCopyShort(short[], int) - Static method in class javajs.util.AU
ArrayDataReader - Class in javajs.util
  ArrayDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with String[] arrays without any further adaptation.
ArrayDataReader() - Constructor for class javajs.util.ArrayDataReader
arrayDiv(Quat[], Quat[], int, boolean) - Static method in class javajs.util.Quat
arrayOpen(boolean) - Method in class org.jmol.util.JSONWriter
arrayToList(SV) - Method in class org.jmol.script.SV
arrow - Static variable in class org.jmol.script.T
ARROW - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
as - Static variable in class org.jmol.script.T
asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
asBoolean() - Method in class org.jmol.script.SV
asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ASCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
ascent - Variable in class org.jmol.render.LabelsRenderer
asFloat() - Method in class org.jmol.script.SV
asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
asInt() - Method in class org.jmol.script.SV
asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
asObject - Variable in class javajs.util.CifDataParser
  A flag to create and return Java objects, not strings.
asPDF - Variable in class jspecview.common.PrintLayout
assign - Static variable in class org.jmol.script.T
assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
  algorithm discussed above.
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
ASSOCIATION - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
asString() - Method in class javajs.util.T3i
asString() - Method in class org.jmol.script.SV
asString() - Method in class org.jmol.symmetry.SpaceGroup
astrType - Static variable in class org.jmol.script.T
asymMatrix - Variable in class org.jmol.util.Tensor
asymmetry() - Method in class org.jmol.util.Tensor
  asymmetry = deviation from a symmetric tensor
async - Static variable in class org.jmol.script.T
async - Variable in class org.jmol.viewer.Viewer
async_builds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
at - Variable in class org.jmol.modelset.AtomCollection
ati_bugs - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
atNos - Variable in class org.jmol.util.JmolMolecule
atokenInfix - Variable in class org.jmol.script.ScriptCompiler
atom - Variable in class org.jmol.minimize.MinAtom
Atom - Class in org.jmol.adapter.smarter
Atom - Class in org.jmol.modelset
Atom() - Constructor for class org.jmol.adapter.smarter.Atom
Atom() - Constructor for class org.jmol.modelset.Atom
ATOM_INFRAME - Static variable in class org.jmol.modelset.Atom
ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
atom_name_wildcard - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ATOM_NOFLAGS - Static variable in class org.jmol.modelset.Atom
ATOM_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.modelset.Atom
atom_type_format - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ATOM_VISIBLE - Static variable in class org.jmol.modelset.Atom
ATOM_VISSET - Static variable in class org.jmol.modelset.Atom
atom1 - Variable in class org.jmol.modelset.Bond
atom2 - Variable in class org.jmol.modelset.Bond
atomCenterOrCoordinateParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
AtomCollection - Class in org.jmol.modelset
AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
AtomCollection.AtomSorter - Class in org.jmol.modelset
AtomData - Class in org.jmol.atomdata
AtomData() - Constructor for class org.jmol.atomdata.AtomData
atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
AtomDataServer - Interface in org.jmol.atomdata
AtomDisplayLabel - Class in jme
AtomDisplayLabel(double, double, String, int, int, int, int, int, int, int, int, FontMetrics, double, boolean) - Constructor for class jme.AtomDisplayLabel
atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
atomExpression(T[], int, int, boolean, boolean, Object[], boolean) - Method in class org.jmol.script.ScriptEval
atomExpressionAt(int) - Method in class org.jmol.script.ScriptEval
atomExpressionAt(int) - Method in class org.jmol.scriptext.ScriptExt
atomExpressionCommand - Static variable in class org.jmol.script.T
atomFormats - Variable in class org.jmol.shape.Hover
atomHighlighted - Variable in class org.jmol.viewer.Viewer
atomicMass - Static variable in class org.jmol.util.Elements
atomicNumber - Variable in class org.jmol.atomdata.AtomData
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
atomicorbital - Static variable in class org.jmol.script.T
atomicSymbols - Static variable in class org.iupac.InchiUtils
atomid - Static variable in class org.jmol.script.T
atomID - Variable in class org.jmol.modelset.Atom
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
  /////////////////////////////////////////////////////////////
ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C2 - Static variable in class org.jmol.viewer.JC
ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C4 - Static variable in class org.jmol.viewer.JC
ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C5 - Static variable in class org.jmol.viewer.JC
ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C5M - Static variable in class org.jmol.viewer.JC
ATOMID_C6 - Static variable in class org.jmol.viewer.JC
ATOMID_C7 - Static variable in class org.jmol.viewer.JC
ATOMID_C8 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_MAX - Static variable in class org.jmol.modelsetbio.BioResolver
ATOMID_N1 - Static variable in class org.jmol.viewer.JC
ATOMID_N2 - Static variable in class org.jmol.viewer.JC
ATOMID_N3 - Static variable in class org.jmol.viewer.JC
ATOMID_N4 - Static variable in class org.jmol.viewer.JC
ATOMID_N6 - Static variable in class org.jmol.viewer.JC
ATOMID_N7 - Static variable in class org.jmol.viewer.JC
ATOMID_N9 - Static variable in class org.jmol.viewer.JC
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
ATOMID_O1 - Static variable in class org.jmol.viewer.JC
ATOMID_O1P - Static variable in class org.jmol.viewer.JC
ATOMID_O2 - Static variable in class org.jmol.viewer.JC
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O2P - Static variable in class org.jmol.viewer.JC
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O4 - Static variable in class org.jmol.viewer.JC
ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
ATOMID_O6 - Static variable in class org.jmol.viewer.JC
ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_S4 - Static variable in class org.jmol.viewer.JC
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
atomindex - Static variable in class org.jmol.script.T
atomIndex - Variable in class org.jmol.atomdata.AtomData
atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
atomIndex - Variable in class org.jmol.shape.Hover
atomIndex - Variable in class org.jmol.shape.Mesh
atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
atomIndex1 - Variable in class org.jmol.util.Tensor
atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
atomIndex2 - Variable in class org.jmol.util.Tensor
AtomIndexIterator - Interface in org.jmol.api
  note: YOU MUST RELEASE THE ITERATOR
AtomIteratorWithinModel - Class in org.jmol.modelset
AtomIteratorWithinModelSet - Class in org.jmol.modelset
AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
atomLabelBoundingBox - Variable in class jme.AtomDisplayLabel
atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
atomLabels - Variable in class org.jmol.adapter.writers.CIFWriter
atomList - Variable in class org.jmol.util.JmolMolecule
atomMapAnyCase - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomMapX - Variable in class jme.AtomDisplayLabel
atomMapY - Variable in class jme.AtomDisplayLabel
atomMolecule - Variable in class org.jmol.atomdata.AtomData
ATOMMOVED - Enum constant in enum class org.jmol.c.CBK
atomname - Static variable in class org.jmol.script.T
atomName - Variable in class org.jmol.adapter.smarter.Atom
atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
atomno - Static variable in class org.jmol.script.T
atomNo - Variable in class org.jmol.quantum.SlaterData
atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
atomPicked(int) - Method in class org.jmol.jsv.JSV
atompicking - Static variable in class org.jmol.script.T
atomproperty - Static variable in class org.jmol.script.T
atomPropertyFloat(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
  called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyInt(Viewer, int) - Method in class org.jmol.modelset.Atom
  called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyString(Viewer, int) - Method in class org.jmol.modelset.Atom
atomPropertyTuple(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
atomPt - Variable in class org.jmol.render.LabelsRenderer
atomRadius - Variable in class org.jmol.atomdata.AtomData
atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atoms - Variable in class org.jmol.adapter.writers.CIFWriter
atoms - Variable in class org.jmol.atomdata.AtomData
atoms - Variable in class org.jmol.minimize.Minimizer
atoms - Static variable in class org.jmol.script.T
atoms - Variable in class org.jmol.shapespecial.Dipole
atoms - Variable in class org.jmol.shapesurface.Contact
atomSerial - Variable in class org.jmol.adapter.smarter.Atom
atomSetAtomCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
  A JFrame that allows for choosing an Atomset to view.
AtomSetChooser(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
AtomSetCollection - Class in org.jmol.adapter.smarter
AtomSetCollection(String, AtomSetCollectionReader, AtomSetCollection[], Lst) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
AtomSetCollectionReader - Class in org.jmol.adapter.smarter
AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
atomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetObject
atomSetInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
AtomSetObject - Class in org.jmol.adapter.smarter
AtomSetObject() - Constructor for class org.jmol.adapter.smarter.AtomSetObject
AtomShape - Class in org.jmol.shape
AtomShape() - Constructor for class org.jmol.shape.AtomShape
atomSite - Variable in class org.jmol.adapter.smarter.Atom
atomsMax - Variable in class org.jmol.adapter.writers.CMLWriter
AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
atomStartEnd - Variable in class org.jmol.adapter.smarter.Structure
atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSymmetry - Variable in class org.jmol.modelset.Atom
atomTensorList - Variable in class org.jmol.modelset.AtomCollection
  /////////////////////////////////////////////////////////////
atomTensors - Variable in class org.jmol.modelset.AtomCollection
atomtype - Static variable in class org.jmol.script.T
AtomType - Class in org.jmol.minimize.forcefield
atomtypes - Static variable in class org.jmol.script.T
atomWarning - Variable in class org.jmol.shape.Halos
atomx - Static variable in class org.jmol.script.T
atomX - Variable in class org.jmol.modelset.Text
atomy - Static variable in class org.jmol.script.T
atomY - Variable in class org.jmol.modelset.Text
atomz - Static variable in class org.jmol.script.T
atomZ - Variable in class org.jmol.modelset.Text
attEcho - Variable in class org.jmol.console.ScriptEditor
attError - Variable in class org.jmol.console.ScriptEditor
attHighlight - Variable in class org.jmol.console.ScriptEditor
attrList - Variable in class jspecview.source.AnIMLReader
attrList - Variable in class jspecview.source.NMRMLReader
atts - Variable in class org.jmol.adapter.readers.xml.XmlReader
AU - Class in javajs.util
AU() - Constructor for class javajs.util.AU
audio - Static variable in class org.jmol.script.T
AUDIO - Enum constant in enum class org.jmol.c.CBK
auto - Static variable in class org.jmol.script.T
AUTO - Enum constant in enum class jspecview.common.IntegralData.IntMode
AUTO - Enum constant in enum class org.jmol.c.VDW
AUTO_BABEL - Enum constant in enum class org.jmol.c.VDW
auto_classify_atoms - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_color_next - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_copy_images - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_defer_atom_count - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_defer_builds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_dss - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_hide_selections - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_indicate_flags - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
AUTO_JMOL - Enum constant in enum class org.jmol.c.VDW
auto_number_selections - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_overlay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
AUTO_RASMOL - Enum constant in enum class org.jmol.c.VDW
auto_remove_hydrogens - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_rename_duplicate_objects - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_sculpt - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_show_lines - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_show_nonbonded - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_show_selections - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_show_spheres - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
auto_zoom - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
autoAddImplicitH - Variable in class org.jmol.smiles.SmilesSearch
autoAnimationDelay - Variable in class org.openscience.jmol.app.JmolApp
autobond - Static variable in class org.jmol.script.T
autoBondBs4(BS, BS, BS, BS, short, boolean, SB) - Method in class org.jmol.modelset.ModelSet
autoCalculate(int, String) - Method in class org.jmol.viewer.Viewer
autoclose_dialogs - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
autoExit - Variable in class org.jmol.viewer.Viewer
autoez - Variable in class jme.JME
autofps - Static variable in class org.jmol.script.T
autoHbond(BS, BS, boolean) - Method in class org.jmol.modelset.ModelSet
  a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
autoHbond(BS, BS, boolean) - Method in class org.jmol.viewer.Viewer
autoIntegrate - Variable in class jspecview.common.JSViewer
autoIntegrate() - Method in class jspecview.common.IntegralData
AUTOINTEGRATE - Enum constant in enum class jspecview.common.ScriptToken
autonumber - Variable in class jme.JME
autoplaymovie - Static variable in class org.jmol.script.T
autoScrolls - Variable in class org.jmol.awtjs.swing.JComponent
autoSelectOnLoad() - Method in class jspecview.common.PeakInfo
  a spectrum which, when loaded, should fire a message to load first peak -- GC for now
autoShowLegend - Variable in class jspecview.common.JSViewer
auxiliaryInfo - Variable in class org.jmol.modelset.Model
AuxNone - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Omit auxiliary information
ave(T3, T3) - Method in class javajs.util.T3
  average of two tuples
average - Static variable in class org.jmol.script.T
AviCreator - Class in org.jmol.image
AviCreator() - Constructor for class org.jmol.image.AviCreator
awaken(boolean) - Method in class jspecview.application.MainFrame
AwtClipboard - Class in jspecview.java
  This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtClipboard - Class in org.jmol.awt
  This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtColor - Class in jspecview.java
AwtColor - Class in org.jmol.awt
AwtColor(int) - Constructor for class jspecview.java.AwtColor
AwtColor(int) - Constructor for class org.jmol.awt.AwtColor
AwtColor(int, int, int) - Constructor for class jspecview.java.AwtColor
AwtColor(int, int, int) - Constructor for class org.jmol.awt.AwtColor
AwtColor(int, int, int, int) - Constructor for class jspecview.java.AwtColor
AwtColor(int, int, int, int) - Constructor for class org.jmol.awt.AwtColor
AwtDialog - Class in jspecview.java
  AwtDialog extends JDialog, interpreting DialogManager's requests in terms of Swing and AWT.
AwtDialog(DialogManager, JSVDialog, String) - Constructor for class jspecview.java.AwtDialog
AwtDialogFileFilter - Class in jspecview.java
  A implementation of the `FileFilter` that filters out all files except those with extensions that are added.
AwtDialogFileFilter() - Constructor for class jspecview.java.AwtDialogFileFilter
  Intialises a `JSpecViewFileFilter`
AwtDialogFileFilter(String[]) - Constructor for class jspecview.java.AwtDialogFileFilter
  Initialises the `JSpecViewFileFilter` with an list of extensions to filter
AwtDialogFileFilter(String[], String) - Constructor for class jspecview.java.AwtDialogFileFilter
  Initialises the `JSpecViewFileFilter` with an list of extensions to filter and a description of the filter
AwtDialogManager - Class in jspecview.java
  just a class I made to separate the construction of the AnnotationDialogs from their use
AwtDialogManager() - Constructor for class jspecview.java.AwtDialogManager
AwtFileDropper - Class in jspecview.java
AwtFileDropper() - Constructor for class jspecview.java.AwtFileDropper
AwtFileHelper - Class in jspecview.java
AwtFileHelper() - Constructor for class jspecview.java.AwtFileHelper
AwtG2D - Class in jspecview.java
  generic 2D drawing methods -- AWT version
AwtG2D - Class in org.jmol.awt
  generic 2D drawing methods -- AWT version
AwtG2D() - Constructor for class jspecview.java.AwtG2D
AwtG2D() - Constructor for class org.jmol.awt.AwtG2D
AwtJmolPopup - Class in org.jmol.awt
AwtJmolPopup() - Constructor for class org.jmol.awt.AwtJmolPopup
AwtMainPanel - Class in jspecview.java
AwtMainPanel(BorderLayout) - Constructor for class jspecview.java.AwtMainPanel
AwtModelKitPopup - Class in org.jmol.awt
AwtModelKitPopup() - Constructor for class org.jmol.awt.AwtModelKitPopup
AwtPanel - Class in jspecview.java
  JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
AwtPanel.RequestThread - Class in jspecview.java
AwtParameters - Class in jspecview.java
AwtParameters() - Constructor for class jspecview.java.AwtParameters
AwtPlatform - Class in jspecview.java
AwtPlatform() - Constructor for class jspecview.java.AwtPlatform
AwtPopup - Class in jspecview.java
AwtPopup() - Constructor for class jspecview.java.AwtPopup
AwtPopupHelper - Class in org.jmol.awt
  all popup-related awt/swing class references are in this file.
AwtPopupHelper(GenericPopup) - Constructor for class org.jmol.awt.AwtPopupHelper
AwtPrintDialog - Class in jspecview.java
  Dialog to set print preferences for JSpecview.
AwtPrintDialog() - Constructor for class jspecview.java.AwtPrintDialog
AwtSwingComponent - Class in org.jmol.awt
  A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.
AwtSwingComponent() - Constructor for class org.jmol.awt.AwtSwingComponent
AwtTree - Class in jspecview.application
AwtTree(JSViewer) - Constructor for class jspecview.application.AwtTree
AwtTreeNode - Class in jspecview.application
AwtTreeNode(String, PanelNode) - Constructor for class jspecview.application.AwtTreeNode
AwtTreePath - Class in jspecview.application
AwtTreePath(Object[]) - Constructor for class jspecview.application.AwtTreePath
axes - Static variable in class org.jmol.script.T
Axes - Class in org.jmol.shape
Axes() - Constructor for class org.jmol.shape.Axes
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
axes2 - Variable in class org.jmol.shape.Axes
axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
axescolor - Static variable in class org.jmol.script.T
axesmode - Static variable in class org.jmol.script.T
axesMode - Variable in class org.jmol.viewer.GlobalSettings
axesmolecular - Static variable in class org.jmol.script.T
axesoffset - Static variable in class org.jmol.script.T
axesorientationrasmol - Static variable in class org.jmol.script.T
AxesRenderer - Class in org.jmol.render
AxesRenderer() - Constructor for class org.jmol.render.AxesRenderer
axesscale - Static variable in class org.jmol.script.T
axesTypes - Static variable in class org.jmol.viewer.JC
axesunitcell - Static variable in class org.jmol.script.T
axeswindow - Static variable in class org.jmol.script.T
axis - Static variable in class org.jmol.script.T
AXIS_A - Static variable in class org.jmol.viewer.JC
axis1color - Static variable in class org.jmol.script.T
axis2color - Static variable in class org.jmol.script.T
axis3color - Static variable in class org.jmol.script.T
axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
axisangle - Static variable in class org.jmol.script.T
axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
axisLabels - Static variable in class org.jmol.viewer.JC
axisNX - Static variable in class org.jmol.viewer.JC
axisNY - Static variable in class org.jmol.viewer.JC
axisNZ - Static variable in class org.jmol.viewer.JC
axisPoints - Variable in class org.jmol.shape.Axes
  [x, y, z, -x, -y, -z] or [a, b, c, -a, -b, -c]
axisType - Variable in class org.jmol.shape.Axes
axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
axisX - Static variable in class org.jmol.viewer.JC
axisXY - Variable in class org.jmol.shape.Axes
axisY - Static variable in class javajs.util.Measure
axisY - Static variable in class org.jmol.viewer.JC
axisZ - Static variable in class org.jmol.viewer.JC

## B

b - Variable in class org.jmol.g3d.PrecisionRenderer
b - Variable in class org.jmol.util.Rgb16
b - Variable in class org.jmol.util.SimpleUnitCell
b - Variable in class org.jmol.viewer.ActionManager
b_ - Variable in class org.jmol.util.SimpleUnitCell
babel - Static variable in class org.jmol.script.T
BABEL - Enum constant in enum class org.jmol.c.VDW
babel21 - Static variable in class org.jmol.script.T
BABEL21 - Enum constant in enum class org.jmol.c.VDW
back - Static variable in class org.jmol.script.T
backbone - Static variable in class org.jmol.script.T
Backbone - Class in org.jmol.shapebio
Backbone() - Constructor for class org.jmol.shapebio.Backbone
backboneBlockVis - Variable in class org.jmol.modelsetbio.Monomer
BackboneRenderer - Class in org.jmol.renderbio
BackboneRenderer() - Constructor for class org.jmol.renderbio.BackboneRenderer
backface_cull - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
background - Static variable in class org.jmol.script.T
backgroundColix - Variable in class org.jmol.export.___Exporter
backgroundColix - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
backgroundcolor - Static variable in class org.jmol.script.T
BACKGROUNDCOLOR - Enum constant in enum class jspecview.common.ScriptToken
backgroundImage - Variable in class org.jmol.util.GData
backgroundmodel - Static variable in class org.jmol.script.T
backlit - Static variable in class org.jmol.script.T
backshell - Static variable in class org.jmol.script.T
bad() - Method in class org.jmol.script.ScriptError
balls - Static variable in class org.jmol.script.T
Balls - Class in org.jmol.shape
Balls() - Constructor for class org.jmol.shape.Balls
BallsRenderer - Class in org.jmol.render
BallsRenderer() - Constructor for class org.jmol.render.BallsRenderer
bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
BannerFrame - Class in org.openscience.jmol.app.jsonkiosk
  A simple class that throws up a white rectangle that has a single centered label.
BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jsonkiosk.BannerFrame
barb - Static variable in class org.jmol.script.T
barDistance - Variable in class org.jmol.modelset.Text
barPixels - Variable in class org.jmol.modelset.Text
barPixelsXYZ - Variable in class org.jmol.modelset.Text
barray - Static variable in class org.jmol.script.T
BArray - Class in javajs.util
BArray(byte[]) - Constructor for class javajs.util.BArray
Base64 - Class in javajs.util
Base64() - Constructor for class javajs.util.Base64
BASE64_TAG - Static variable in class org.jmol.viewer.JC
baseAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
  first atom index for this collection, current modelset.ac
baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
baseBlockSize - Static variable in interface org.apache.tools.bzip2.BZip2Constants
baseBondIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
baseColor - Variable in class org.jmol.jvxl.data.JvxlData
baseFont3d - Variable in class org.jmol.shape.Frank
baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
basemodel - Static variable in class org.jmol.script.T
baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
basepair - Static variable in class org.jmol.script.T
BasePair - Class in org.jmol.modelsetbio
baseStrandOffset - Variable in class org.jmol.renderbio.StrandsRenderer
baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter - Class in org.jmol.adapter.readers.quantum
batch_prefix - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
Bbcage - Class in org.jmol.shape
Bbcage() - Constructor for class org.jmol.shape.Bbcage
BbcageRenderer - Class in org.jmol.render
BbcageRenderer() - Constructor for class org.jmol.render.BbcageRenderer
bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
bbCorner0 - Variable in class org.jmol.util.BoxInfo
bbCorner1 - Variable in class org.jmol.util.BoxInfo
bboxModels - Variable in class org.jmol.modelset.ModelSet
BC - Class in javajs.util
  byte converter
BC() - Constructor for class javajs.util.BC
BCIFReader - Class in org.jmol.adapter.readers.cif
  A very simple Binary CIF file reader extention of MMCifReader extends CifReader.
BCIFReader() - Constructor for class org.jmol.adapter.readers.cif.BCIFReader
BEGIN - Static variable in class org.jmol.shapecgo.CGOMesh
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.util.GData
best - Static variable in class org.jmol.script.T
beta - Static variable in class org.jmol.script.T
beta - Variable in class org.jmol.util.SimpleUnitCell
bfactor - Variable in class org.jmol.adapter.smarter.Atom
bg_gradient - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_image_filename - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_image_linear - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_image_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_image_tilesize - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_rgb - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_rgb_bottom - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bg_rgb_top - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bgcolix - Variable in class org.jmol.modelset.Text
bgcolix - Variable in class org.jmol.render.LabelsRenderer
bgcolixes - Variable in class org.jmol.shape.Labels
bgcolor - Variable in class jspecview.common.PanelData
bgcolor - Variable in class org.jmol.util.GData
BGYOR - Static variable in class org.jmol.util.ColorEncoder
bigEndian - Variable in class javajs.util.OC
BilbaoReader - Class in org.jmol.adapter.readers.xtal
  Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.
BilbaoReader() - Constructor for class org.jmol.adapter.readers.xtal.BilbaoReader
bin - Static variable in class org.jmol.script.T
binary - Static variable in class org.jmol.script.T
BinaryDcdReader - Class in org.jmol.adapter.readers.more
  DCD binary trajectory file reader.
BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
binarydoc - Variable in class org.jmol.jvxl.readers.JvxlReader
binarydoc - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
binarydoc - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
binaryDoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
BinaryDocument - Class in javajs.util
BinaryDocument() - Constructor for class javajs.util.BinaryDocument
binaryOp(T, SV, SV) - Method in class org.jmol.script.ScriptMathProcessor
bind - Static variable in class org.jmol.script.T
bindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
bindAction(String, String) - Method in class org.jmol.viewer.Viewer
Binding - Class in org.jmol.viewer.binding
Binding() - Constructor for class org.jmol.viewer.binding.Binding
bindName(int, String) - Method in class org.jmol.viewer.binding.Binding
BioExt - Class in org.jmol.modelsetbio
BioExt() - Constructor for class org.jmol.modelsetbio.BioExt
BioMeshRenderer - Class in org.jmol.renderbio
BioMeshRenderer() - Constructor for class org.jmol.renderbio.BioMeshRenderer
BioModel - Class in org.jmol.modelsetbio
BioModel() - Constructor for class org.jmol.modelsetbio.BioModel
bioModelset - Variable in class org.jmol.modelset.AtomCollection
  If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning
BioModelSet - Class in org.jmol.modelsetbio
BioModelSet() - Constructor for class org.jmol.modelsetbio.BioModelSet
biomtChainAtomCounts - Variable in class org.jmol.adapter.readers.pdb.PdbReader
bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
bioPolymer - Variable in class org.jmol.shapebio.BioShape
BioPolymer - Class in org.jmol.modelsetbio
  A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers", which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone), Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
BioPolymer(Monomer[], boolean) - Constructor for class org.jmol.modelsetbio.BioPolymer
bioPolymerIndexInModel - Variable in class org.jmol.modelsetbio.BioPolymer
bioPolymers - Variable in class org.jmol.modelsetbio.BioModel
BioResolver - Class in org.jmol.modelsetbio
  a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
BioResolver() - Constructor for class org.jmol.modelsetbio.BioResolver
BioShape - Class in org.jmol.shapebio
BioShapeCollection - Class in org.jmol.shapebio
  When a Cartoon is instantiated with a call to setSize(), it creates an BioShapeCollection for each BioPolymer in the model set.
BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
biosymmetry - Variable in class org.jmol.modelset.Model
BIRTH - Static variable in class com.sparshui.common.TouchState
BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
bis - Variable in class javajs.util.BinaryDocument
bitset - Static variable in class org.jmol.script.T
BLACK - Static variable in class jspecview.common.ColorParameters
BLACK - Variable in class jspecview.common.PanelData
BLACK - Static variable in class org.jmol.util.C
blockdata - Static variable in class org.jmol.script.T
blockID - Variable in class jspecview.source.JDXDataObject
BLUE - Static variable in class jspecview.common.ColorParameters
BLUE - Static variable in class org.jmol.util.C
BMPDecoder - Class in javajs.img
  src: http://www.javaworld.com/article/2077542/learn-java/java-tip-43--how-to- read-8--and-24-bit-microsoft-windows-bitmaps-in-java-applications.html see also: http://en.wikipedia.org/wiki/BMP_file_format Modified by Bob Hanson hansonr@stolaf.edu
BMPDecoder() - Constructor for class javajs.img.BMPDecoder
bo - Variable in class org.jmol.modelset.BondCollection
bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
bond - Variable in class org.jmol.shapespecial.Dipole
Bond - Class in org.jmol.adapter.smarter
Bond - Class in org.jmol.modelset
Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
BOND_AROMATIC - Static variable in class org.jmol.util.Edge
BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
BOND_AROMATIC_MASK - Static variable in class org.jmol.util.Edge
BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_MASK - Static variable in class org.jmol.util.Edge
BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_QUINTUPLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_sextuple - Static variable in class org.jmol.util.Edge
BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.Edge
BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
BOND_H_CALC - Static variable in class org.jmol.util.Edge
BOND_H_CALC_MASK - Static variable in class org.jmol.util.Edge
BOND_H_MINUS_3 - Static variable in class org.jmol.util.Edge
BOND_H_MINUS_4 - Static variable in class org.jmol.util.Edge
BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_2 - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_3 - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_4 - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_5 - Static variable in class org.jmol.util.Edge
BOND_H_REGULAR - Static variable in class org.jmol.util.Edge
BOND_HBOND_SHIFT - Static variable in class org.jmol.util.Edge
BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.Edge
BOND_NEW - Static variable in class org.jmol.util.Edge
BOND_ORDER_ANY - Static variable in class org.jmol.util.Edge
BOND_ORDER_NULL - Static variable in class org.jmol.util.Edge
BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.Edge
BOND_PARTIAL01 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL12 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL23 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL32 - Static variable in class org.jmol.util.Edge
BOND_PYMOL_MULT - Static variable in class org.jmol.util.Edge
BOND_PYMOL_SCALE - Static variable in class org.jmol.util.Edge
BOND_RENDER_MASK - Static variable in class org.jmol.util.Edge
  Extended Bond Definition Types Originally these were short 16-bit values
BOND_RENDER_SINGLE - Static variable in class org.jmol.util.Edge
BOND_STEREO_EITHER - Static variable in class org.jmol.util.Edge
BOND_STEREO_FAR - Static variable in class org.jmol.util.Edge
BOND_STEREO_NEAR - Static variable in class org.jmol.util.Edge
BOND_STRUT - Static variable in class org.jmol.util.Edge
BOND_SULFUR_MASK - Static variable in class org.jmol.util.Edge
bondAtoms(Atom, Atom, int, short, BS, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
BondCollection - Class in org.jmol.modelset
BondCollection() - Constructor for class org.jmol.modelset.BondCollection
bondcount - Static variable in class org.jmol.script.T
bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bondCount - Variable in class org.jmol.modelset.BondCollection
bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
bonded - Static variable in class org.jmol.script.T
BONDING - Enum constant in enum class org.jmol.c.VDW
bonding_vdw_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
bondingradius - Static variable in class org.jmol.script.T
bondingRadius - Variable in class org.jmol.adapter.smarter.Atom
bondingversion - Static variable in class org.jmol.script.T
bondingVersion - Static variable in class org.jmol.util.Elements
bondingVersion - Variable in class org.jmol.viewer.GlobalSettings
BondIterator - Interface in org.jmol.modelset
bondmode - Static variable in class org.jmol.script.T
bondmodeor - Static variable in class org.jmol.script.T
bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
bondorder - Static variable in class org.jmol.script.T
bondpicking - Static variable in class org.jmol.script.T
bondradiusmilliangstroms - Static variable in class org.jmol.script.T
bondRotationCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bonds - Variable in class org.jmol.minimize.Minimizer
bonds - Variable in class org.jmol.modelset.Atom
  MAY BE NULL
bonds - Static variable in class org.jmol.script.T
bondset - Static variable in class org.jmol.script.T
BondSet - Class in org.jmol.modelset
BondSet() - Constructor for class org.jmol.modelset.BondSet
bondtolerance - Static variable in class org.jmol.script.T
booleanparam - Static variable in class org.jmol.script.T
BorderLayout - Class in org.jmol.awtjs.swing
BorderLayout() - Constructor for class org.jmol.awtjs.swing.BorderLayout
bottom - Static variable in class org.jmol.script.T
bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
bottomMargin - Static variable in class jspecview.common.PanelData
boundbox - Static variable in class org.jmol.script.T
boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
boundboxcolor - Static variable in class org.jmol.script.T
BOUNDING_BOX - Static variable in class org.jmol.shapecgo.CGOMesh
boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
boundingBox - Variable in class org.jmol.jvxl.readers.JvxlReader
boundingBox - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
boundingBox - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
boxHeight - Variable in class org.jmol.modelset.Text
BoxInfo - Class in org.jmol.util
  The BoxInfo class holds critical information about boundboxes.
BoxInfo() - Constructor for class org.jmol.util.BoxInfo
boxWidth - Variable in class org.jmol.modelset.Text
boxX - Variable in class org.jmol.modelset.Text
boxXY - Variable in class org.jmol.modelset.Text
boxY - Variable in class org.jmol.modelset.Text
boxYoff2 - Variable in class org.jmol.modelset.Text
bp - Variable in class jspecview.export.AMLExporter
bp - Variable in class jspecview.export.CMLExporter
bpointx - Variable in class jme.JME
bpointy - Variable in class jme.JME
br - Variable in class org.jmol.jvxl.readers.JvxlReader
br - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
br - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
branch - Static variable in class org.jmol.script.T
breakcmd - Static variable in class org.jmol.script.T
brillouin - Static variable in class org.jmol.script.T
BrukerReader - Class in jspecview.source
  A class to read Bruker ZIP files and directories.
BrukerReader() - Constructor for class jspecview.source.BrukerReader
BS - Class in javajs.util
  a fast 32-bit BitSet optimized for Java2Script -- about 25 times faster than java.util.BitSet
BS() - Constructor for class javajs.util.BS
  Creates a new bit set.
bs14 - Variable in class org.jmol.minimize.MinAtom
bsA() - Method in class org.jmol.viewer.Viewer
bsAll - Variable in class org.jmol.adapter.smarter.Structure
bsAll - Variable in class org.jmol.modelset.ModelSet
bsAromatic - Variable in class org.jmol.modelset.BondCollection
bsAsymmetricUnit - Variable in class org.jmol.modelset.Model
  tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.
bsAtoms - Variable in class org.jmol.adapter.readers.xml.CDXMLParser
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bsAtoms - Variable in class org.jmol.minimize.Minimizer
bsAtoms - Variable in class org.jmol.modelset.Model
  Note that this bitset may or may not include bsAtomsDeleted
bsAtomsDeleted - Variable in class org.jmol.modelset.Model
bsBgColixSet - Variable in class org.jmol.shape.Labels
bsBonds - Variable in class org.jmol.adapter.readers.xml.CDXMLParser
bsClickable - Variable in class org.jmol.modelset.AtomCollection
bsColixSet - Variable in class org.jmol.shape.Shape
bsDeleted - Variable in class org.jmol.adapter.readers.molxyz.MolReader
bsDeleted - Variable in class org.jmol.viewer.SelectionManager
bsDisplay - Variable in class org.jmol.shape.MeshCollection
bsDisplay - Variable in class org.jmol.util.MeshSurface
bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
  //////// FILTER /////////////////
bsFontSet - Variable in class org.jmol.shape.Labels
bsFrameOffsets - Variable in class org.jmol.viewer.TransformManager
bsHighlight - Variable in class org.jmol.shape.Halos
bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
bsIgnored - Variable in class org.jmol.atomdata.AtomData
bsKeyModels - Variable in class org.jmol.modelkit.ModelKit
  a bitset indicating the presence of element keys for models; clearing a bit will cause a new key to be produced.
bsKeyModelsOFF - Variable in class org.jmol.modelkit.ModelKit
  tracks models for which the element key has been explicitly set OFF, overriding global SET elementKey ON
bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
bsMinFixed - Variable in class org.jmol.minimize.Minimizer
bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
bsModulated - Variable in class org.jmol.modelset.AtomCollection
bsMolecule - Variable in class org.jmol.shapespecial.Dipole
bsMolecules - Variable in class org.jmol.atomdata.AtomData
bsOrderSet - Variable in class org.jmol.shape.Sticks
bsOut - Variable in class org.jmol.adapter.writers.CIFWriter
bsPartialCharges - Variable in class org.jmol.modelset.AtomCollection
bsPeriod - Variable in class org.jmol.render.AxesRenderer
bsPeriod - Variable in class org.jmol.render.BbcageRenderer
bsPeriod - Variable in class org.jmol.render.UccageRenderer
bspf - Variable in class org.jmol.modelset.AtomCollection
  Binary Space Partitioning Forest
bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
Bspf - Class in org.jmol.bspt
  A Binary Space Partitioning Forest
Bspf(int) - Constructor for class org.jmol.bspt.Bspf
bsPolygons - Variable in class org.jmol.render.MeshRenderer
bsPolygons - Variable in class org.jmol.util.MeshSurface
bsPolygonsToExport - Variable in class org.jmol.render.MeshRenderer
Bspt - Class in org.jmol.bspt
  a Binary Space Partitioning Tree
Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
  Create a bspt with the specified number of dimensions.
bspts - Variable in class org.jmol.bspt.Bspf
bsRenderableAtoms - Variable in class org.jmol.viewer.ShapeManager
bsSelected - Variable in class org.jmol.atomdata.AtomData
bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
bsSelected - Variable in class org.jmol.modelset.MeasurementData
bsSizeDefault - Variable in class org.jmol.shape.AtomShape
bsSizeSet - Variable in class org.jmol.shape.Shape
bsSlabbedInternal - Variable in class org.jmol.viewer.ShapeManager
bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
bsSlabGhost - Variable in class org.jmol.util.MeshSurface
bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
bsStructuredModels - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bsSubset - Variable in class org.jmol.viewer.SelectionManager
bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
bsSymmetry - Variable in class org.jmol.modelset.ModelSet
bsTemp - Variable in class org.jmol.shape.Mesh
bsToArray(BS) - Method in class org.jmol.scriptext.ScriptExt
BSUtil - Class in org.jmol.util
BSUtil() - Constructor for class org.jmol.util.BSUtil
bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
bsVdw - Variable in class org.jmol.minimize.MinAtom
bsVisible - Variable in class org.jmol.modelset.AtomCollection
bsVisible - Variable in class org.jmol.renderbio.BackboneRenderer
bsVisible - Variable in class org.jmol.renderbio.CartoonRenderer
bsVisible - Variable in class org.jmol.renderbio.MeshRibbonRenderer
bsVisible - Variable in class org.jmol.renderbio.RibbonsRenderer
bsVisible - Variable in class org.jmol.renderbio.RocketsRenderer
bsVisible - Variable in class org.jmol.renderbio.StrandsRenderer
bsVisible - Variable in class org.jmol.renderbio.TraceRenderer
bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
btnType - Variable in class org.jmol.awtjs.swing.JMenuItem
bufferSize - Variable in class org.jmol.util.GData
buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
buildStructure(String) - Method in class jspecview.popup.JSVPopupResourceBundle
buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
buildStructure(String) - Method in class org.jmol.popup.PopupResource
BUTTON_MASK - Static variable in class org.jmol.awtjs.Event
BUTTON_MASK - Static variable in class org.jmol.viewer.binding.Binding
button_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
button_mode_name - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
buttonGroup - Variable in class org.jmol.popup.GenericPopup
ButtonGroup - Class in org.jmol.awtjs.swing
ButtonGroup() - Constructor for class org.jmol.awtjs.swing.ButtonGroup
buttonModelkit - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
buttonRotate - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
bValue(T) - Static method in class org.jmol.script.SV
BW - Static variable in class org.jmol.util.ColorEncoder
bwMode - Variable in class jme.JME
BWR - Static variable in class org.jmol.util.ColorEncoder
BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
byteArrayToFloat(byte[], int) - Static method in class com.sparshui.common.utils.Converter
byteArrayToInt(byte[]) - Static method in class com.sparshui.common.utils.Converter
  Converts a byte array to an integer.
byteArrayToInt(byte[], int) - Static method in class com.sparshui.common.utils.Converter
byteArrayToJSON(byte[]) - Static method in class javajs.util.PT
byteArrayToLong(byte[], int) - Static method in class com.sparshui.common.utils.Converter
byteArrayToString(byte[]) - Static method in class com.sparshui.common.utils.Converter
bytePos - Variable in class javajs.img.PngEncoder
BytePoster - Interface in javajs.api
bytesToDoubleToFloat(byte[], int, boolean) - Static method in class javajs.util.BC
  see http://en.wikipedia.org/wiki/Binary64 not concerning ourselves with very small or very large numbers and getting this exactly right.
bytesToFloat(byte[], int, boolean) - Static method in class javajs.util.BC
bytesToInt(byte[], int, boolean) - Static method in class javajs.util.BC
bytesToShort(byte[], int, boolean) - Static method in class javajs.util.BC
bz - Variable in class org.jmol.util.BZone
  overall object
BZip2Constants - Interface in org.apache.tools.bzip2
  Base class for both the compress and decompress classes.
BZone - Class in org.jmol.util
  A class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells.
BZone() - Constructor for class org.jmol.util.BZone

## C

c - Variable in class org.jmol.util.SimpleUnitCell
C - Class in org.jmol.util
  Note: Color table is now in javajs/util/CU.java
C() - Constructor for class org.jmol.util.C
c_ - Variable in class org.jmol.util.SimpleUnitCell
cA_ - Variable in class org.jmol.util.SimpleUnitCell
cache - Static variable in class org.jmol.script.T
cache_display - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cache_frames - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cache_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cache_memory - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cache_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cacheClear() - Method in class org.jmol.viewer.Viewer
cacheFileByName(String, boolean) - Method in interface javajs.api.JSInterface
cacheFileByName(String, boolean) - Method in class jspecview.appletjs.JSVApplet
cacheFileByName(String, boolean) - Method in class org.jmol.util.GenericApplet
cacheFileByName(String, boolean) - Method in class org.jmol.viewer.Viewer
cacheFileByNameAdd(String, boolean) - Method in class org.jmol.viewer.FileManager
cacheGet(String) - Static method in class jspecview.common.JSVFileManager
cacheGet(String, boolean) - Method in class org.jmol.viewer.FileManager
cacheList() - Method in class org.jmol.viewer.FileManager
cachePut(String, Object) - Method in interface javajs.api.JSInterface
cachePut(String, Object) - Method in class jspecview.appletjs.JSVApplet
cachePut(String, Object) - Method in class org.jmol.util.GenericApplet
cachePut(String, Object) - Method in class org.jmol.viewer.Viewer
  JSInterface -- allows saving files in memory for later retrieval
cachePut(String, String) - Static method in class jspecview.common.JSVFileManager
cacheZipContents(BufferedInputStream, String, Map, boolean) - Method in interface javajs.api.GenericZipTools
cacheZipContents(BufferedInputStream, String, Map, boolean) - Method in class javajs.util.ZipTools
CACTUS_FILE_TYPES - Static variable in class org.jmol.viewer.JC
calc(double[][]) - Method in class javajs.util.Eigen
  Check for symmetry, then construct the eigenvalue decomposition
CALC_H_ALLOW_H - Static variable in class org.jmol.modelset.AtomCollection
CALC_H_DOALL - Static variable in class org.jmol.modelset.AtomCollection
CALC_H_HAVEH - Static variable in class org.jmol.modelset.AtomCollection
CALC_H_IGNORE_H - Static variable in class org.jmol.modelset.AtomCollection
CALC_H_JUSTC - Static variable in class org.jmol.modelset.AtomCollection
CALC_H_QUICK - Static variable in class org.jmol.modelset.AtomCollection
CALC_SET - Static variable in class org.jmol.symmetry.CLEG.ClegNode
CALC_SUB - Static variable in class org.jmol.symmetry.CLEG.ClegNode
CALC_SUBP - Static variable in class org.jmol.symmetry.CLEG.ClegNode
CALC_SUPER - Static variable in class org.jmol.symmetry.CLEG.ClegNode
CALC_SUPERP - Static variable in class org.jmol.symmetry.CLEG.ClegNode
calc2or3JorNOE(Viewer, Atom[], String, int) - Static method in class org.jmol.quantum.NMRCalculation
  Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;
calc3JCH(String, double, boolean) - Static method in class org.jmol.quantum.NMRCalculation
calcAllRasmolHydrogenBonds(BS, BS, Lst, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
  only for base models, not trajectories
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.api.JmolViewer
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.modelset.ModelSet
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.viewer.Viewer
calcAveragePoint(P3, P3, P3) - Static method in class javajs.util.Measure
calcAveragePointN(P3[], int, P3) - Static method in class javajs.util.Measure
calcAxis() - Method in class org.jmol.modelsetbio.Helix
calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
calcAxis() - Method in class org.jmol.modelsetbio.Sheet
calcBestAxisThroughPoints(P3[], int, P3, V3, V3, int) - Static method in class javajs.util.Measure
calcBestPlaneThroughPoints(P3[], int, P4) - Static method in class javajs.util.Measure
  Calculate the best ax + by + cz + d = 0 plane through a number of points using a three-step check for the best plane based on normal distance.
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.modelset.ModelSet
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.viewer.Viewer
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
  sets all camera and scale factors needed by the specific perspective model instantiated
calcCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
calcEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
calcJKarplus(double) - Static method in class org.jmol.quantum.NMRCalculation
calcJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
calcNavigationPoint() - Method in interface org.jmol.api.JmolNavigatorInterface
calcNavigationPoint() - Method in class org.jmol.navigate.Navigator
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
  All the magic happens here.
calcNOE(Viewer, Atom, Atom) - Static method in class org.jmol.quantum.NMRCalculation
calcNOEs() - Method in class org.jmol.quantum.NMRNoeMatrix
  calculate the NOESY spectrum at a particular mixing time.
calcNOEs() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
calcNormalizedNormal(T3, T3, T3, T3, T3) - Static method in class javajs.util.Measure
  note that if vAB or vAC is dispensible, vNormNorm can be one of them
calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
  //////////////////////////////////////////////
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
  For reduced density only; coloring is done point by point.
calcPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Fill this plane with data based on the current set of raw data planes.
calcPlaneForMode(P3[], int, P4, char) - Static method in class javajs.util.Measure
  Compact calculation of the best pane using a simple method discussed at https://stackoverflow.com/questions/12299540/plane-fitting-to-4-or-more-xyz-points (A^T A)^-1 A^T B run three times to ensure that at least one is not perpendicular.
calcRasmolHydrogenBonds(BS, BS, Lst, boolean, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
  These are not actual hydrogen bonds.
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
  ///////////////////////////////////////////////
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
calcRopeMidPoints() - Method in class org.jmol.renderbio.RocketsRenderer
calcRotationRadius(int, P3, boolean) - Method in class org.jmol.modelset.ModelSet
calcRotationRadiusBs(BS) - Method in class org.jmol.modelset.ModelSet
calcScreenControlPoints() - Method in class org.jmol.renderbio.BackboneRenderer
calcScreenControlPoints() - Method in class org.jmol.renderbio.CartoonRenderer
calcScreenControlPoints() - Method in class org.jmol.renderbio.MeshRibbonRenderer
calcScreenControlPoints() - Method in class org.jmol.renderbio.RibbonsRenderer
calcScreenControlPoints() - Method in class org.jmol.renderbio.RocketsRenderer
calcScreenControlPoints() - Method in class org.jmol.renderbio.StrandsRenderer
calcScreenControlPoints() - Method in class org.jmol.renderbio.TraceRenderer
calcScreens(float, short[]) - Method in class org.jmol.renderbio.BackboneRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.CartoonRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.MeshRibbonRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.RibbonsRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.RocketsRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.StrandsRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.TraceRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcSelectedGroupsCount() - Method in class org.jmol.modelset.ModelSet
calcSelectedMoleculesCount() - Method in class org.jmol.modelset.ModelSet
calcSelectedMonomersCount() - Method in class org.jmol.modelset.ModelSet
calcSelectedMonomersCount() - Method in class org.jmol.modelsetbio.BioModelSet
calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioPolymer
calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
  sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager4D
calculate - Static variable in class org.jmol.script.T
calculate(M4) - Method in class org.jmol.symmetry.CLEG.ClegData
calculate(T3, boolean) - Method in class org.jmol.util.ModulationSet
  Calculate r_I internal d-space coordinate of an atom.
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolEnvCalc
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
calculate(VolumeData, BS, P3[], Atom[], float[], int) - Method in class org.jmol.quantum.MepCalculation
calculateAllPolymers(Group[], int, int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
calculateAllStructuresExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
calculateAllStuctures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
calculateChirality(BS) - Method in class org.jmol.viewer.Viewer
calculateChiralityForAtoms(BS, boolean) - Method in class org.jmol.modelset.ModelSet
calculateChiralityForSmiles(String) - Method in class org.jmol.viewer.Viewer
calculateCIPChiralityForAtoms(Viewer, BS) - Method in interface org.jmol.api.SymmetryInterface
calculateCIPChiralityForAtoms(Viewer, BS) - Method in class org.jmol.symmetry.Symmetry
calculateCIPChiralityForSmiles(String) - Method in interface org.jmol.api.SymmetryInterface
calculateCIPChiralityForSmiles(String) - Method in class org.jmol.symmetry.Symmetry
calculateDssp(Object[], int, Object, boolean, boolean, boolean, int) - Method in class org.jmol.dssx.DSSP
calculateDssrProperty(String) - Method in class org.jmol.modelset.ModelSet
calculateDSSRStructure(Viewer, BS) - Method in interface org.jmol.api.JmolAnnotationParser
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.AnnotationParser
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.DSSR1
calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
calculateFormalCharges(BS) - Method in class org.jmol.viewer.Viewer
calculateFractionalPoint(float, P3, P3, float, float, P3) - Method in class org.jmol.jvxl.data.VolumeData
calculateGeodesicSurface(BS, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
calculateGeodesicSurface(BS, float) - Method in class org.jmol.shapesurface.Isosurface
calculateHydrogens(BS, int[], Lst, int) - Method in class org.jmol.modelset.AtomCollection
  get a list of potential H atom positions based on elemental valence and formal charge
calculateIntegral() - Method in class jspecview.common.IntegralData
calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
calculateMolecularDipole(int, BS) - Method in class org.jmol.modelset.ModelSet
calculateMolecularDipole(BS) - Method in class org.jmol.viewer.Viewer
calculatePartialCharges(BS) - Method in class org.jmol.viewer.Viewer
calculatePartialCharges(Bond[], int[], Atom[], int[], BS, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
  assign partial charges ala MMFF94
calculatePartialCharges(ModelSet, BS, BS) - Method in class org.jmol.minimize.Minimizer
calculatePointGroup(BS, P3) - Method in class org.jmol.modelset.ModelSet
  ////// atom and shape selecting /////////
calculatePolymers(Group[], int, int, BS) - Method in class org.jmol.modelset.ModelSet
calculateQuaternionRotation(P3[][], float[]) - Static method in class javajs.util.Measure
  Closed-form solution of absolute orientation requiring 1:1 mapping of positions.
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
calculateStraightness() - Method in class org.jmol.viewer.Viewer
calculateStraightnessAll() - Method in class org.jmol.modelset.ModelSet
calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioModelSet
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
  Uses Levitt invalid input: '&' Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
  /////////////////////////////////////////////////////
calculateStructures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
calculateStructures(BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
calculateStructuresAllExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
  allows rebuilding of PDB structures; also accessed by ModelManager from Eval
calculateStruts(BS, BS) - Method in class org.jmol.modelset.ModelSet
  see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
calculateStruts(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
calculateStruts(BS, BS) - Method in class org.jmol.viewer.Viewer
calculateSurface(BS, float) - Method in class org.jmol.modelset.AtomCollection
calculateSurface(BS, float) - Method in class org.jmol.viewer.Viewer
calculateVolume(BS, VDW) - Method in class org.jmol.modelset.AtomCollection
calculateVolumeOrArea(MeshData, BS, boolean, boolean) - Static method in class org.jmol.jvxl.data.MeshData
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
  The number of the calculation being interpreted.
calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
calcVertexPoint(int, int, int, int, P3) - Method in class org.jmol.jvxl.calc.MarchingCubes
calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
callback(String, String) - Method in class jspecview.dialog.IntegrationDialog
callback(String, String) - Method in class jspecview.dialog.JSVDialog
callback(String, String) - Method in class jspecview.dialog.MeasurementsDialog
callback(String, String) - Method in class jspecview.dialog.OverlayLegendDialog
callback(String, String) - Method in class jspecview.dialog.PeakListDialog
callback(String, String) - Method in class jspecview.dialog.ViewsDialog
callbackAD(String, String) - Method in class jspecview.dialog.JSVDialog
callbacks - Variable in class org.jmol.util.GenericApplet
callToJavaScript(String, Object[]) - Method in interface jspecview.api.AppletFrame
callToJavaScript(String, Object[]) - Method in class jspecview.appletjs.JSVApplet
  Calls a javascript function given by the function name passing to it the string parameters as arguments
camera - Variable in class org.jmol.viewer.TransformManager
cameradepth - Static variable in class org.jmol.script.T
cameraDepth - Variable in class org.jmol.viewer.TransformManager
cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
cameraDistance - Variable in class org.jmol.export.___Exporter
cameraDistance - Variable in class org.jmol.viewer.TransformManager
cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
cameraPosition - Variable in class org.jmol.export.___Exporter
cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
cameraSetting - Variable in class org.jmol.viewer.TransformManager
canBeNormalized(V3d) - Static method in class org.jmol.minimize.Util
canBeSquared(double) - Static method in class org.jmol.minimize.Util
canCapCylinders - Variable in class org.jmol.export.__CartesianExporter
cancel - Static variable in class org.jmol.script.T
cancel() - Method in class javajs.util.OC
cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
canConvertTransAbs() - Method in class jspecview.source.JDXDataObject
canDo(int) - Method in class org.jmol.viewer.StateManager
canDoLineTo() - Method in class javajs.export.PDFCreator
canDoLineTo() - Method in class jspecview.common.PDFWriter
canDoLineTo() - Method in class jspecview.java.AwtG2D
canDoLineTo() - Method in class jspecview.js2d.JsG2D
canDoLineTo() - Method in interface org.jmol.api.GenericGraphics
canDoLineTo() - Method in class org.jmol.awt.AwtG2D
canDoLineTo() - Method in class org.jmol.awtjs2d.JsG2D
canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
canDownsample - Variable in class org.jmol.jvxl.readers.JvxlReader
canDownsample - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
canDownsample - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
canIntegrate() - Method in class jspecview.source.JDXDataObject
CANONICAL_DC_LIST - Static variable in class org.jmol.quantum.QS
CANONICAL_DS_LIST - Static variable in class org.jmol.quantum.QS
CANONICAL_FC_LIST - Static variable in class org.jmol.quantum.QS
CANONICAL_FS_LIST - Static variable in class org.jmol.quantum.QS
canonicalizeCleg(String) - Static method in class org.jmol.symmetry.SpaceGroup
  adds :a,b,c;0,0,0 or ;0,0,0; does NOT change :h or :r
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonize - Variable in class jme.JME
canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
canSaveAsJDX() - Method in class jspecview.source.JDXDataObject
canShowSolutionColor() - Method in class jspecview.source.JDXDataObject
canSkipLoad - Variable in class org.jmol.modelset.AtomCollection
canvas - Variable in class org.jmol.console.ImageDialog
cap - Static variable in class org.jmol.script.T
capData(P4, float) - Method in class org.jmol.jvxl.data.VolumeData
cappingObject - Variable in class org.jmol.shape.Mesh
capture - Static variable in class org.jmol.script.T
captureParams - Variable in class org.jmol.viewer.Viewer
carbohydrate - Static variable in class org.jmol.script.T
CARBOHYDRATE - Enum constant in enum class org.jmol.c.STR
CarbohydrateMonomer - Class in org.jmol.modelsetbio
CarbohydratePolymer - Class in org.jmol.modelsetbio
carbohydrates - Variable in class org.jmol.modelsetbio.BioResolver
cardinality() - Method in class javajs.util.BS
  Returns the number of bits set to `true` in this `BitSet`.
cardinalityN(int) - Method in class javajs.util.BS
cardinalityOf(BS) - Static method in class org.jmol.util.BSUtil
  cardinality = "total number of set bits"
CARTESIAN_PRECISION - Static variable in class javajs.util.PT
cartoon - Static variable in class org.jmol.script.T
Cartoon - Class in org.jmol.shapebio
Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
cartoon_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_cylindrical_helices - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_debug - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_discrete_colors - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_dumbbell_length - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_dumbbell_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_dumbbell_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_fancy_helices - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_fancy_sheets - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_flat_cycles - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_flat_sheets - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_helix_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_highlight_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ladder_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ladder_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ladder_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_loop_cap - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_loop_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_loop_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_nucleic_acid_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_nucleic_acid_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_nucleic_acid_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_oval_length - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_oval_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_oval_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_power_b - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_range - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_scale_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_scale_min - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_scale_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_putty_transform - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_rect_length - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_rect_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_refine - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_refine_normals - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_refine_tips - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ring_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ring_finder - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ring_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ring_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ring_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_ring_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_round_helices - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_sampling - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_side_chain_helper - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_smooth_cycles - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_smooth_first - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_smooth_last - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_smooth_loops - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_throw - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_trace_atoms - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_tube_cap - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_tube_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_tube_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoon_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cartoonbaseedges - Static variable in class org.jmol.script.T
cartoonblockheight - Static variable in class org.jmol.script.T
cartoonblocks - Static variable in class org.jmol.script.T
cartoonladders - Static variable in class org.jmol.script.T
CartoonRenderer - Class in org.jmol.renderbio
CartoonRenderer() - Constructor for class org.jmol.renderbio.CartoonRenderer
cartoonribose - Static variable in class org.jmol.script.T
cartoonrockets - Static variable in class org.jmol.script.T
cartoonsfancy - Static variable in class org.jmol.script.T
cartoonsFancy - Variable in class org.jmol.renderbio.BackboneRenderer
cartoonsFancy - Variable in class org.jmol.renderbio.CartoonRenderer
cartoonsFancy - Variable in class org.jmol.renderbio.MeshRibbonRenderer
cartoonsFancy - Variable in class org.jmol.renderbio.RibbonsRenderer
cartoonsFancy - Variable in class org.jmol.renderbio.RocketsRenderer
cartoonsFancy - Variable in class org.jmol.renderbio.StrandsRenderer
cartoonsFancy - Variable in class org.jmol.renderbio.TraceRenderer
cartoonsteps - Static variable in class org.jmol.script.T
casecmd - Static variable in class org.jmol.script.T
casName - Variable in class jspecview.export.AMLExporter
casName - Variable in class jspecview.export.CMLExporter
casName - Variable in class jspecview.source.AnIMLReader
casName - Variable in class jspecview.source.NMRMLReader
casRN - Variable in class jspecview.export.AMLExporter
casRN - Variable in class jspecview.export.CMLExporter
casRN - Variable in class jspecview.source.AnIMLReader
casRN - Variable in class jspecview.source.NMRMLReader
CastepReader - Class in org.jmol.adapter.readers.xtal
  CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.
CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
CAT_ASSEM - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_ATOM_SITE - Static variable in class org.jmol.adapter.readers.cif.CifReader
CAT_ATOM_SITES - Static variable in class org.jmol.adapter.readers.cif.CifReader
CAT_ATOM_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
CAT_CELL - Static variable in class org.jmol.adapter.readers.cif.CifReader
CAT_CHEMCOMP - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_COMPBOND - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_NCS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_OPER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_SEQUENCEDIF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_SHEET - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_STRUCSITE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_STRUCTCONF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CAT_STRUCTCONN - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
catalogStructureUnits(Viewer, SV, int[], Map, Object, Map) - Method in interface org.jmol.api.JmolAnnotationParser
catalogStructureUnits(Viewer, SV, int[], Map, Object, Map) - Method in class org.jmol.dssx.AnnotationParser
  RNA3D --
catalogValidations(Viewer, SV, int[], Map, Map, Map) - Method in interface org.jmol.api.JmolAnnotationParser
catalogValidations(Viewer, SV, int[], Map, Map, Map) - Method in class org.jmol.dssx.AnnotationParser
  Returns a Lst
catchcmd - Static variable in class org.jmol.script.T
cavity - Static variable in class org.jmol.script.T
cavity_cull - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cB_ - Variable in class org.jmol.util.SimpleUnitCell
CBK - Enum Class in org.jmol.c
cbl - Variable in class org.jmol.viewer.StatusManager
CBZip2InputStream - Class in org.apache.tools.bzip2
  An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStream(InputStream) - Constructor for class org.apache.tools.bzip2.CBZip2InputStream
  Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
CBZip2InputStream(InputStream, boolean) - Constructor for class org.apache.tools.bzip2.CBZip2InputStream
  Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
CBZip2InputStreamFactory - Class in org.apache.tools.bzip2
CBZip2InputStreamFactory() - Constructor for class org.apache.tools.bzip2.CBZip2InputStreamFactory
cch - Variable in class javajs.util.CifDataParser
  length of str
cd - Static variable in class org.jmol.script.T
cd(String) - Method in class org.jmol.viewer.Viewer
CDXMLParser - Class in org.jmol.adapter.readers.xml
  A reader for CambridgeSoft CDXML files.
CDXMLParser(CDXMLParser.CDXReaderI) - Constructor for class org.jmol.adapter.readers.xml.CDXMLParser
CDXMLParser.CDXReaderI - Interface in org.jmol.adapter.readers.xml
CDXMLWriter - Class in org.jmol.adapter.writers
  Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the basic necessities for XmlCDXReader.
CDXMLWriter() - Constructor for class org.jmol.adapter.writers.CDXMLWriter
CDXReader - Class in org.jmol.adapter.readers.more
  A reader for ChemDraw binary CDX files.
CDXReader() - Constructor for class org.jmol.adapter.readers.more.CDXReader
ce - Variable in class org.jmol.viewer.ColorManager
cell - Static variable in class org.jmol.script.T
Cell - Class in org.jmol.awtjs.swing
Cell(JComponent, GridBagConstraints) - Constructor for class org.jmol.awtjs.swing.Cell
CELL_TYPE_CONVENTIONAL - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
CELL_TYPE_MAGNETIC_PARENT - Static variable in class org.jmol.viewer.JC
CELL_TYPE_MAGNETIC_STANDARD - Static variable in class org.jmol.viewer.JC
CELL_TYPE_PRIMITIVE - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
CELL_TYPE_SPIN_FRAME - Static variable in class org.jmol.viewer.JC
CELL_TYPE_SPIN_G0 - Static variable in class org.jmol.viewer.JC
CELL_TYPE_SPIN_L0 - Static variable in class org.jmol.viewer.JC
CELL_TYPE_SPIN_MAG_INPUT - Static variable in class org.jmol.viewer.JC
CELL_TYPE_SPIN_MAG_PRIMITIVE - Static variable in class org.jmol.viewer.JC
CELL_TYPE_SUPER - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
cellParamNames - Static variable in class org.jmol.api.JmolAdapter
  ///////////////////////////////////////////////////////////////
cellSlop - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
celshading - Static variable in class org.jmol.script.T
celshadingpower - Static variable in class org.jmol.script.T
CENATT - Static variable in class javajs.api.GenericZipInputStream
CENATX - Static variable in class javajs.api.GenericZipInputStream
CENCOM - Static variable in class javajs.api.GenericZipInputStream
CENCRC - Static variable in class javajs.api.GenericZipInputStream
CENDSK - Static variable in class javajs.api.GenericZipInputStream
CENEXT - Static variable in class javajs.api.GenericZipInputStream
CENFLG - Static variable in class javajs.api.GenericZipInputStream
CENHDR - Static variable in class javajs.api.GenericZipInputStream
CENHOW - Static variable in class javajs.api.GenericZipInputStream
CENLEN - Static variable in class javajs.api.GenericZipInputStream
CENNAM - Static variable in class javajs.api.GenericZipInputStream
CENOFF - Static variable in class javajs.api.GenericZipInputStream
CENSIG - Static variable in class javajs.api.GenericZipInputStream
CENSIZ - Static variable in class javajs.api.GenericZipInputStream
center - Variable in class org.jmol.export.___Exporter
center - Variable in class org.jmol.jvxl.readers.SurfaceReader
center - Static variable in class org.jmol.script.T
center - Variable in class org.jmol.shapespecial.Dipole
center - Variable in class org.jmol.shapespecial.Ellipsoid
center - Variable in class org.jmol.shapespecial.Polyhedron
center - Variable in class org.jmol.util.BZone
center - Static variable in class org.jmol.viewer.JC
center() - Method in class jme.JMEmol
CENTER - Static variable in class org.jmol.awtjs.swing.BorderLayout
CENTER - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
CENTER - Static variable in class org.jmol.awtjs.swing.SwingConstants
centerat - Static variable in class org.jmol.script.T
centerAt(int, int, P3) - Method in class org.jmol.viewer.TransformManager
centerDialog() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
centerDialog() - Method in class org.openscience.jmol.app.janocchio.NoeTable
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
centerings - Variable in class org.jmol.symmetry.WyckoffFinder
centeringStr - Variable in class org.jmol.symmetry.WyckoffFinder
centerParameter(int) - Method in class org.jmol.scriptext.ScriptExt
centerParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
centerParameterForModel(int, int, Object[]) - Method in class org.jmol.script.ScriptParam
CENTIM - Static variable in class javajs.api.GenericZipInputStream
centralAtom - Variable in class org.jmol.shapespecial.Polyhedron
centralize() - Method in class org.jmol.adapter.smarter.AtomSetCollection
centroid - Static variable in class org.jmol.script.T
centroidPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
CENVEM - Static variable in class javajs.api.GenericZipInputStream
CENVER - Static variable in class javajs.api.GenericZipInputStream
CgdReader - Class in org.jmol.adapter.readers.xtal
  A reader for TOPOS systre file Crystal Graph Data format.
CgdReader() - Constructor for class org.jmol.adapter.readers.xtal.CgdReader
cgo - Static variable in class org.jmol.script.T
CGO - Class in org.jmol.shapecgo
  PyMOL Compiled Graphic Object (CGO) meshes
CGO() - Constructor for class org.jmol.shapecgo.CGO
CGO_ACCESSIBILITY_ARRAY - Static variable in class org.jmol.shapecgo.CGOMesh
CGO_COLOR_ARRAY - Static variable in class org.jmol.shapecgo.CGOMesh
cgo_debug - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_dot_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_dot_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_ellipsoid_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_lighting - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_line_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_line_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
CGO_NORMAL_ARRAY - Static variable in class org.jmol.shapecgo.CGOMesh
CGO_PICK_COLOR_ARRAY - Static variable in class org.jmol.shapecgo.CGOMesh
cgo_ray_width_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_shader_ub_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_shader_ub_flags - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_shader_ub_normal - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_sphere_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
CGO_TEX_COORD_ARRAY - Static variable in class org.jmol.shapecgo.CGOMesh
cgo_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cgo_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
CGO_VERTEX_ARRAY - Static variable in class org.jmol.shapecgo.CGOMesh
CGOMesh - Class in org.jmol.shapecgo
CGORenderer - Class in org.jmol.rendercgo
  Something like a PyMOL Compiled Graphical Object, but more interesting!
CGORenderer() - Constructor for class org.jmol.rendercgo.CGORenderer
chain - Variable in class org.jmol.modelset.Group
  required
chain - Static variable in class org.jmol.script.T
Chain - Class in org.jmol.modelset
  A Model is a collection of Chains of Groups of Atoms.
CHAIN - Enum constant in enum class org.jmol.c.PAL
chaincasesensitive - Static variable in class org.jmol.script.T
chainCount - Variable in class org.jmol.modelset.Model
chainID - Variable in class org.jmol.adapter.smarter.Atom
chainID - Variable in class org.jmol.modelset.Chain
  chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
chainMap - Variable in class org.jmol.viewer.Viewer
chainno - Static variable in class org.jmol.script.T
chainNo - Variable in class org.jmol.modelset.Chain
  chainNo is for information purposes only; retrieved by {atoms}.chainNo
chains - Variable in class org.jmol.modelset.Model
chainToUpper(int) - Method in class org.jmol.modelset.AtomCollection
CHANGEABLE_MASK - Static variable in class org.jmol.util.C
changeableColixMap - Variable in class org.jmol.util.GData
changeColixArgb(int, int) - Method in class org.jmol.util.GData
CHAR - Static variable in class org.jmol.shapecgo.CGOMesh
characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlHandler
CHARACTERS - Static variable in class jspecview.source.XMLParser
charAt(int) - Method in class javajs.util.SB
charCodeAt(int) - Method in class javajs.util.SB
chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
check - Static variable in class org.jmol.script.T
check(boolean, boolean) - Method in class org.jmol.renderbio.BioMeshRenderer
check(int, int, int, int, long, long) - Method in class org.jmol.viewer.MouseState
check(String) - Method in class jspecview.dialog.ViewsDialog
CHECK_DIMS - Static variable in class org.jmol.viewer.FileManager
CHECK1 - Static variable in class org.jmol.thread.JmolThread
CHECK2 - Static variable in class org.jmol.thread.JmolThread
CHECK3 - Static variable in class org.jmol.thread.JmolThread
checkAllFieldsPresent(String[], int, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
checkAndRemoveFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkAromaticDefined() - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
checkAtomicSymbol(String) - Static method in class jme.JMEUtil
  Return the JME atoming number associated to the given symbol
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.JvxlReader
  checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
  checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
  checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAutoIntegrate() - Method in class jspecview.common.JSViewer
checkBCIF(byte[], boolean) - Static method in class org.jmol.adapter.smarter.Resolver
checkBoundsMinMax(P3, P3) - Method in class org.jmol.shape.Shape
CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
checkByteCount - Variable in class org.jmol.shape.Mesh
checkcir - Static variable in class org.jmol.script.T
checkColixLength(short, int) - Method in class org.jmol.shape.AtomShape
checkCommandLineForTip(char, String, boolean) - Method in class jspecview.common.JSViewer
checkCompatible(float[], float[], boolean, int, int, int, int) - Method in class org.jmol.symmetry.SpecialGroup
checkConsoleScript(String) - Method in class org.jmol.viewer.Viewer
checkCoordinatesChanged(BS) - Method in class org.jmol.viewer.Viewer
checkCurrentLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
checkEnables() - Method in class jspecview.dialog.JSVDialog
checkEnables() - Method in class jspecview.dialog.ViewsDialog
checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
checkExtension(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
checkFileExists(String, boolean, String, int, boolean) - Method in class org.jmol.script.ScriptEval
checkFileIndex(String, String, String) - Method in class jspecview.common.PeakInfo
checkFileTypeModel(String, String, String) - Method in class jspecview.common.PeakInfo
  type checks true for MS in GC/MS; reverse of checkType
checkFilterAssembly(String, Map) - Method in class org.jmol.adapter.readers.cif.MMCifReader
checkFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkFront(short, short, short) - Method in class org.jmol.render.MeshRenderer
checkFullSyntax(String[], SymmetryInterface, boolean) - Static method in class org.jmol.symmetry.CLEG
  Test nodes and transforms for valid syntax.
checkHalt(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
checkHalt(String, boolean) - Method in class org.jmol.script.ScriptManager
checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
checkHKL(T3) - Method in class org.jmol.script.ScriptParam
  Note - this check does not allow a 0 for h, k, or l.
checkHover() - Method in class org.jmol.viewer.ActionManager
checkInheritedShapes() - Method in class org.jmol.viewer.ShapeManager
  starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms.
checkInMotion(int) - Method in class org.jmol.viewer.Viewer
checkIntegral(Parameters, String) - Method in class jspecview.common.PanelData
checkInterrupted(JmolThread) - Method in class org.jmol.thread.JmolThread
checkJDXRequiredTokens() - Method in class jspecview.source.JDXDataObject
  for JDXReader only
checkKeyControl(int, boolean) - Method in class jspecview.common.PanelData
checkLast(int) - Method in class org.jmol.script.ScriptParam
checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  sets continuing and doProcessLines
checkLength(int) - Method in class org.jmol.script.ScriptParam
checkLength(int) - Method in class org.jmol.scriptext.ScriptExt
checkLength23() - Method in class org.jmol.script.ScriptParam
checkLength34() - Method in class org.jmol.script.ScriptParam
checkLengthErrorPt(int, int) - Method in class org.jmol.script.ScriptParam
checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
checkLine() - Method in class org.jmol.adapter.readers.more.AFLOWReader
checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
checkLine() - Method in class org.jmol.adapter.readers.more.JcampdxReader
checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
checkLine() - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Reads a Collection of AtomSets from a BufferedReader.
checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
checkLine() - Method in class org.jmol.adapter.readers.simple.FAHReader
checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
checkLine() - Method in class org.jmol.adapter.readers.simple.InputReader
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
checkLine() - Method in class org.jmol.adapter.readers.simple.OrcaReader
checkLine() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.CgdReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.JanaReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.
checkLine() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkMemory() - Static method in class org.jmol.util.Logger
checkMenuFocus(String, String, boolean) - Method in class jspecview.java.AwtPopup
checkMenuUpdate() - Method in class org.jmol.viewer.Viewer
checkMod(int, int) - Method in class jspecview.common.PanelData
checkMotionRendering(int) - Method in class org.jmol.viewer.Viewer
  check motion for rendering during mouse movement, spin, vibration, and animation
checkMovedAtoms(BS, BS, P3[]) - Method in class org.jmol.modelkit.ModelKit
  Something has changed atom positions.
checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
checkNearAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkNew(float[], float[]) - Method in class org.jmol.symmetry.SpaceGroup.ParamCheck
checkNewModel() - Method in class org.jmol.modelkit.ModelKit
checkNoEmptyModel() - Method in class org.jmol.adapter.smarter.AtomSetCollection
checkObjectClicked(boolean, int, int, BS) - Method in class org.jmol.modelset.Text
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Labels
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Shape
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Sticks
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.TextShape
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Draw
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Ellipsoids
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapesurface.Isosurface
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Labels
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Shape
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shapespecial.Draw
checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Frank
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Shape
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Sticks
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.TextShape
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Draw
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapesurface.Isosurface
checkOption(char, String) - Method in class org.jmol.modelkit.ModelKit
  MODELKIT SET options for syntax checking.
checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
checkOvelayInterface(String) - Method in class jspecview.common.JSViewer
checkOverlay() - Method in class jspecview.common.JSViewer
checkPaused(Viewer) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
checkPeriodic(P3, float, float) - Method in interface org.jmol.api.SymmetryInterface
checkPeriodic(P3, float, float) - Method in class org.jmol.symmetry.Symmetry
checkPointCount() - Method in class jspecview.source.AnIMLReader
checkPointCount() - Method in class jspecview.source.NMRMLReader
checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
  Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
checkPropertyParameter(String) - Method in interface org.jmol.api.JmolPropertyManager
checkPropertyParameter(String) - Method in class org.jmol.viewer.PropertyManager
checkPropertyParameter(String) - Method in class org.jmol.viewer.Viewer
checkRange(int, double) - Method in class jspecview.common.PeakInfo
checkRemark() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
checkRemark() - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkScript(int) - Method in class org.jmol.console.ScriptEditor
checkScript(String) - Method in interface jspecview.api.JSVAppletInterface
checkScript(String) - Method in class jspecview.app.JSVApp
checkScript(String) - Method in class jspecview.appletjs.JSVApplet
checkScript(String) - Method in class jspecview.common.JSViewer
checkScriptSilent(String) - Method in interface org.jmol.api.JmolScriptEvaluator
checkScriptSilent(String) - Method in class org.jmol.script.ScriptEval
  a method for just checking a script
checkSelect(Map, T[]) - Method in interface org.jmol.api.JmolScriptEvaluator
checkSelect(Map, T[]) - Method in class org.jmol.script.ScriptEval
  Check a map for a WHERE phrase
checkSelect(Map, T[]) - Method in class org.jmol.viewer.Viewer
checkStart() - Method in class jspecview.source.AnIMLReader
checkStart() - Method in class jspecview.source.NMRMLReader
checkStereoForAtom(SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesStereo
checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  /////////////////////////////////////////////////////////////
checkSupercell(Viewer, Symmetry, BS, int, P3) - Method in class org.jmol.symmetry.SpaceGroupFinder
  Look for a supercell and adjust lattice down if necessary.
checkTickTemps() - Method in class org.jmol.render.FontLineShapeRenderer
checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
checkToken(int) - Method in class org.jmol.script.ScriptParam
checkTrailingText(String, int, int) - Static method in class javajs.util.PT
checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
checkTypeMatch(PeakInfo) - Method in class jspecview.common.PeakInfo
checkTypeModel(String, String) - Method in class jspecview.common.PeakInfo
checkUndoEnabled() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
checkVisible() - Method in class org.jmol.modelset.Atom
checkWithin(T3, Lst, float, boolean) - Static method in class org.jmol.shape.Mesh
chemFileProperty - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
chemical - Static variable in class org.jmol.script.T
chemicalshift - Static variable in class org.jmol.script.T
CHequation - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
children() - Method in interface jspecview.api.JSVTreeNode
children() - Method in class jspecview.tree.SimpleTreeNode
ChimeMessenger - Class in org.jmol.viewer
  A legacy Chime-compatible messenger.
ChimeMessenger() - Constructor for class org.jmol.viewer.ChimeMessenger
ChiralFlagOFF - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Set chiral flag OFF
ChiralFlagON - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Set chiral flag ON
chirality - Static variable in class org.jmol.script.T
chk - Variable in class org.jmol.script.ScriptError
chk - Variable in class org.jmol.scriptext.ScriptExt
chord - Variable in class org.jmol.util.ContactPair
Cif2DataParser - Class in org.jmol.adapter.readers.cif
  Fully implemented 2016.12.1 see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html Will deliver JSON versions of the data while file reading and Java List/Map structures when called by x = getProperty("cifInfo", filename) Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org) found at https://github.com/COMCIFS/cif_api
Cif2DataParser() - Constructor for class org.jmol.adapter.readers.cif.Cif2DataParser
Cif2Reader - Class in org.jmol.adapter.readers.cif
  Preliminary Cif2 reader.
Cif2Reader() - Constructor for class org.jmol.adapter.readers.cif.Cif2Reader
CifDataParser - Class in javajs.util
  A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
CifDataParser() - Constructor for class javajs.util.CifDataParser
  /////////////////////////////////////////////////////////////
CifReader - Class in org.jmol.adapter.readers.cif
  A true line-free CIF file reader for CIF files.
CifReader() - Constructor for class org.jmol.adapter.readers.cif.CifReader
CIFWriter - Class in org.jmol.adapter.writers
  A basic CIF writer only.
CIFWriter() - Constructor for class org.jmol.adapter.writers.CIFWriter
CIP_CHIRALITY_AXIAL_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_CANTDETERMINE - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_EZ_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_m_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_M_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_NAME_MASK - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_NAME_OFFSET - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_NONE - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_p_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_P_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_PSEUDO_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_r_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_R_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_s_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_S_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqcis_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqCis_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqtrans_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqTrans_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_UNKNOWN - Static variable in class org.jmol.viewer.JC
CIPChirality - Class in org.jmol.symmetry
  A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
CIPChirality() - Constructor for class org.jmol.symmetry.CIPChirality
CIPData - Class in org.jmol.symmetry
  A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.
CIPData() - Constructor for class org.jmol.symmetry.CIPData
CIPDataSmiles - Class in org.jmol.symmetry
  A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
CIPDataSmiles() - Constructor for class org.jmol.symmetry.CIPDataSmiles
CIPDataTracker - Class in org.jmol.symmetry
  An optional class to track digraph paths to decisions.
CIPDataTracker() - Constructor for class org.jmol.symmetry.CIPDataTracker
ciprule - Static variable in class org.jmol.script.T
ciprule6full - Static variable in class org.jmol.script.T
circle - Static variable in class org.jmol.script.T
CIRCLE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
CircleRenderer - Class in org.jmol.g3d
  Implements flat circle drawing/filling routines.
CircleRenderer() - Constructor for class org.jmol.g3d.CircleRenderer
CIRCULARPLANE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
clamp_colors - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
clash - Static variable in class org.jmol.script.T
clean() - Method in class org.jmol.shape.MeshCollection
clean() - Method in class org.jmol.shapecgo.CGO
clean() - Method in class org.jmol.shapespecial.Draw
clean(float) - Method in class org.jmol.adapter.writers.XtlWriter
clean(String) - Static method in class javajs.util.PT
clean_electro_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cleanCleg000(String) - Static method in class org.jmol.symmetry.CLEG
cleanLabel(String) - Static method in class jspecview.source.JDXSourceStreamTokenizer
  Extracts spaces, underscores etc.
cleanSmiles(String) - Method in interface org.jmol.api.SmilesMatcherInterface
cleanSmiles(String) - Method in class org.jmol.smiles.SmilesMatcher
cleanT(float) - Method in class org.jmol.adapter.writers.XtlWriter
  right-zero-trimmed
cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
clear - Static variable in class org.jmol.script.T
clear() - Method in class jme.JME
clear() - Method in class jspecview.app.GenericMouse
clear() - Method in class jspecview.common.IntegralData
clear() - Method in interface org.jmol.api.GenericMouseInterface
clear() - Method in interface org.jmol.api.JmolDataManager
clear() - Method in class org.jmol.awtjs2d.Mouse
clear() - Method in class org.jmol.g3d.Graphics3D
clear() - Method in class org.jmol.jvxl.data.JvxlData
clear() - Method in class org.jmol.minimize.forcefield.ForceField
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
clear() - Method in class org.jmol.multitouch.ActionManagerMT
clear() - Method in class org.jmol.shape.Measures
clear() - Static method in exception class org.jmol.smiles.InvalidSmilesException
clear() - Method in class org.jmol.util.CommandHistory
  clears the history.
clear() - Method in class org.jmol.util.GData
clear() - Method in class org.jmol.util.TempArray
clear() - Method in class org.jmol.viewer.ActionManager
clear() - Method in class org.jmol.viewer.DataManager
clear() - Method in class org.openscience.jmol.app.HistoryFile
clear(boolean) - Method in interface org.jmol.api.JmolScriptManager
clear(boolean) - Method in class org.jmol.script.ScriptManager
clear(double, double) - Method in class jspecview.common.MeasurementData
clear(int) - Method in class javajs.util.BS
  Sets the bit specified by the index to `false`.
clear(int) - Method in interface org.jmol.api.JmolRepaintManager
clear(int) - Method in class org.jmol.render.RepaintManager
  //////// renderer management ///////////
clear(String) - Method in class org.jmol.shape.Mesh
clear(String) - Method in class org.jmol.shapecgo.CGOMesh
clear(String) - Method in class org.jmol.shapespecial.DrawMesh
clear(Map) - Static method in class org.jmol.thread.TimeoutThread
CLEAR - Enum constant in enum class jspecview.common.IntegralData.IntMode
clear33() - Method in class javajs.util.M34
clearAll() - Method in class javajs.util.BS
  Sets all of the bits in this BitSet to `false`.
clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
clearAllView() - Method in class jspecview.common.PanelData
  Clears all views in the zoom list
clearAtomConstraints() - Method in class org.jmol.modelkit.ModelKit
clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
clearBindings() - Method in class org.jmol.viewer.ActionManager
clearBits(int, int) - Method in class javajs.util.BS
  Sets the bits from the specified `fromIndex` (inclusive) to the specified `toIndex` (exclusive) to `false`.
clearCache() - Method in class org.jmol.modelset.ModelSet
clearCache() - Method in class org.jmol.util.ColorEncoder
clearColixList() - Method in class org.jmol.shapecgo.CGOMesh
clearCommandWatcherThread() - Method in class org.jmol.script.ScriptManager
clearConsole() - Method in class org.jmol.viewer.StatusManager
clearConsole(JSAppletObject) - Method in interface javajs.api.js.J2SObjectInterface
clearContent(String) - Method in class org.jmol.console.GenericConsole
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelSet
clearDB(int) - Method in class org.jmol.modelset.ModelSet
clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEval
  /////////////////////// defined atom sets ////////////////////////
clearFontCache() - Method in class org.jmol.g3d.Graphics3D
clearFontCache() - Method in class org.jmol.util.GData
clearFunctions() - Method in class org.jmol.viewer.Viewer
clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
clearInButton - Variable in class org.jmol.console.GenericConsole
clearLastModelSet() - Method in class org.jmol.modelkit.ModelKitPopup
clearLinkViews(GraphSet) - Method in class jspecview.common.PanelData
clearMeasurements() - Method in class org.jmol.api.JmolViewer
clearMeasurements() - Method in class org.jmol.viewer.Viewer
clearMesh(String) - Method in class org.jmol.shape.Mesh
clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
clearMouseSet(GraphSet) - Method in class jspecview.common.PanelData
clearNormixList() - Method in class org.jmol.shapecgo.CGOMesh
clearOrbitals() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
clearOutButton - Variable in class org.jmol.console.GenericConsole
clearQueue() - Method in interface org.jmol.api.JmolScriptManager
clearQueue() - Method in class org.jmol.script.ScriptManager
clearScriptQueue() - Method in class org.jmol.viewer.Viewer
clearSelection() - Method in class org.jmol.api.JmolViewer
clearSelection() - Method in class org.jmol.awtjs.swing.JTable
clearSelection() - Method in class org.jmol.viewer.Viewer
clearSg() - Method in class org.jmol.shapesurface.Isosurface
clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
clearSourceMenu(JDXSource) - Method in class jspecview.application.ApplicationMenu
clearStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
clearThreads() - Method in class org.jmol.viewer.Viewer
clearTimeout(String) - Method in class org.jmol.viewer.Viewer
clearTimeouts() - Method in class org.jmol.viewer.Viewer
clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
clearUnitCell(int) - Method in class org.jmol.modelset.ModelSet
clearVisibleSets() - Method in class org.jmol.modelset.AtomCollection
CLEG - Class in org.jmol.symmetry
  A holding class for ClegData and ClegNode, which are called by org.jmol.modelkit.Modelkit to process CLEG strings.
CLEG() - Constructor for class org.jmol.symmetry.CLEG
CLEG.ClegData - Class in org.jmol.symmetry
  running data items for assignSpaceGroup iteration
CLEG.ClegNode - Class in org.jmol.symmetry
ClegData(SymmetryInterface, String[]) - Constructor for class org.jmol.symmetry.CLEG.ClegData
ClegNode(CLEG.ClegData, int, String) - Constructor for class org.jmol.symmetry.CLEG.ClegNode
click(HTMLElement, HTMLWindowEvent) - Method in interface org.jmol.awtjs.swing.SwingController
  Fired from clicking an element such as a button or check box or table entry, or from entering text in a text box.
CLICK - Enum constant in enum class org.jmol.c.CBK
CLICK - Static variable in class com.sparshui.common.TouchState
CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
CLICK - Static variable in class org.jmol.viewer.binding.Binding
CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
clickabilityFlags - Variable in class org.jmol.modelset.Atom
clickable - Static variable in class org.jmol.script.T
clickAssignAtom(int, String, P3) - Method in class org.jmol.modelkit.ModelKit
  From Mouse or handleAtomOrBondBicked
clicked - Variable in class org.jmol.viewer.ActionManager
clicked(long, int, int, int, int) - Method in class jspecview.app.GenericMouse
CLICKED - Static variable in class org.jmol.awtjs.Event
clickedCount - Variable in class org.jmol.viewer.ActionManager
clickProcessXtal(String, String) - Method in class org.jmol.modelkit.ModelKit
client - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
CLIENT - Static variable in class com.sparshui.common.ConnectionType
CLIENT_PORT - Static variable in class com.sparshui.common.NetworkConfiguration
ClientProtocol - Class in com.sparshui.common
  The abstract class for the client protocol that defines members common to both the server-side and client-side protocols.
ClientProtocol(Socket) - Constructor for class com.sparshui.common.ClientProtocol
  Create a new ClientProtocol object.
ClientProtocol.MessageType - Class in com.sparshui.common
ClientServerConnection - Class in com.sparshui.client
  Represents the connection to the GestureServer.
ClientServerConnection(String, SparshClient) - Constructor for class com.sparshui.client.ClientServerConnection
  Instantiate a Server Connection object.
clientService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ClientToServerProtocol - Class in com.sparshui.client
  ClientToServerProtocol implements the Client side protocol.
ClientToServerProtocol(Socket) - Constructor for class com.sparshui.client.ClientToServerProtocol
  Constructor calls ClientProtocol's constructor and sets up data input and output streams for the specified socket.
clipboard - Static variable in class org.jmol.script.T
clipCode(int) - Method in class org.jmol.util.GData
clipCode(int, int, int) - Method in class org.jmol.export.Export3D
clipCode3(int, int, int) - Method in class org.jmol.util.GData
clipImageOrPasteText(String) - Method in class org.jmol.api.JmolViewer
clipImageOrPasteText(String) - Method in class org.jmol.viewer.Viewer
cList - Variable in class org.jmol.shapecgo.CGOMesh
clone() - Method in class com.sparshui.server.TouchPoint
clone() - Method in class javajs.util.BS
  Cloning this `BitSet` produces a new `BitSet` that is equal to it.
clone() - Method in class javajs.util.Matrix
  Clone the Matrix object.
clone() - Method in class org.jmol.adapter.smarter.Structure
clone() - Method in class org.jmol.util.Vibration
cloneAtomSetWithBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneLastAtomSet(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
cloneLastAtomSetFromPoints(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
close() - Method in class com.sparshui.client.ClientServerConnection
close() - Method in interface javajs.api.GenericBinaryDocument
close() - Method in class javajs.img.GifEncoder
close() - Method in class javajs.img.ImageEncoder
close() - Method in class javajs.util.BinaryDocument
close() - Method in class javajs.util.OC
  Deprecated.
close() - Method in class jspecview.common.JSVZipFileSequentialReader
close() - Method in class org.apache.tools.bzip2.CBZip2InputStream
close() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
close() - Method in class org.openscience.jmol.app.janocchio.NoeTable
close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
close() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
close() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
close(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
close(String) - Method in class jspecview.common.JSViewer
CLOSE - Enum constant in enum class jspecview.common.ScriptToken
closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
closeAllAudio() - Method in class org.jmol.viewer.StatusManager
closeAllDialogsExcept(Annotation.AType) - Method in class jspecview.common.PanelData
closeChannel() - Method in interface javajs.api.GenericOutputChannel
closeChannel() - Method in class javajs.util.OC
closeDocument() - Method in class javajs.export.PDFCreator
closeMe() - Method in interface org.jmol.api.GenericImageDialog
closeMe() - Method in class org.jmol.console.ImageDialog
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
closeReader() - Method in class org.jmol.jvxl.readers.JvxlReader
closeReader() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
closeReader() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
closeReaderSFR() - Method in class org.jmol.jvxl.readers.JvxlReader
closeReaderSFR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
closeReaderSFR() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
closeSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
closeSelected() - Method in class jspecview.dialog.ViewsDialog
closeSource(JDXSource) - Method in class jspecview.common.JSViewer
closeSpectrum() - Method in class jspecview.common.PanelData
closest - Variable in class org.jmol.modelset.ModelSet
closeStream() - Method in class org.jmol.util.JSONWriter
closeTag(SB, String) - Static method in class javajs.util.XmlUtil
closeTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
closeZipEntry(Object) - Method in interface javajs.api.GenericZipTools
closeZipEntry(Object) - Method in class javajs.util.ZipTools
cm - Variable in class org.jmol.viewer.Viewer
cmdAssignAddAtoms(String, P3[], BS, float, String) - Method in class org.jmol.modelkit.ModelKit
  MODELKIT ADD @3 ...
cmdAssignAtom(BS, P3, String, String) - Method in class org.jmol.modelkit.ModelKit
  A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom via MODELKIT ASSIGN ATOM
cmdAssignBond(int, char, String) - Method in class org.jmol.modelkit.ModelKit
cmdAssignConnect(int, int, char, String) - Method in class org.jmol.modelkit.ModelKit
cmdAssignDeleteAtoms(BS) - Method in class org.jmol.modelkit.ModelKit
  Delete all atoms that are equivalent to this atom.
cmdAssignMoveAtoms(BS, int, P3, P3[], boolean, boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
cmdAssignSpaceGroup(String, SB, String, float, boolean) - Method in class org.jmol.modelkit.ModelKit
  MODELKIT SPACEGROUP
CmdExt - Class in org.jmol.scriptext
CmdExt() - Constructor for class org.jmol.scriptext.CmdExt
cmdFillOABC(T3[], float, String) - Method in class org.jmol.modelkit.ModelKit
CmdfReader - Class in org.jmol.adapter.readers.xtal
  A reader for CrystalMaker CMDF binary/text files.
CmdfReader() - Constructor for class org.jmol.adapter.readers.xtal.CmdfReader
cmdLoad() - Method in class org.jmol.script.ScriptEval
cmdMinimize(JmolScriptEvaluator, BS, int, float, float, int) - Method in class org.jmol.modelkit.ModelKit
  Minimize a unit cell with full symmetry constraints.
cmdPackUnitCell(SymmetryInterface, BS, float) - Method in class org.jmol.modelkit.ModelKit
  MODELKIT {1 0 0} PACKED
cmdRotate(boolean, boolean) - Method in class org.jmol.script.ScriptEval
cmdRotateAtoms(BS, P3[], float) - Method in class org.jmol.modelkit.ModelKit
cmds - Variable in class org.jmol.shapecgo.CGOMesh
cmdScript(int, String, String, Lst) - Method in class org.jmol.script.ScriptEval
cmdUndoRedo(int) - Method in class org.jmol.script.ScriptEval
cmi - Variable in class org.jmol.viewer.AnimationManager
  current model index
CML - Enum constant in enum class jspecview.common.ExportType
CML - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CMLExporter - Class in jspecview.export
  class `CMLExporter` contains static methods to export a Graph as as CIML.
CMLExporter() - Constructor for class jspecview.export.CMLExporter
CMLWriter - Class in org.jmol.adapter.writers
  An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
CMLWriter() - Constructor for class org.jmol.adapter.writers.CMLWriter
code - Variable in class org.jmol.i18n.Language
codeBase - Variable in class org.jmol.util.GenericApplet
codePath - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
coef - Variable in class org.jmol.quantum.SlaterData
coeffs - Variable in class org.jmol.quantum.MOCalculation
col - Static variable in class org.jmol.script.T
colix - Variable in class org.jmol.adapter.smarter.Bond
colix - Variable in class org.jmol.modelset.Bond
colix - Variable in class org.jmol.modelset.Measurement
colix - Variable in class org.jmol.modelset.MeasurementData
colix - Variable in class org.jmol.modelset.Text
colix - Variable in class org.jmol.render.ShapeRenderer
colix - Variable in class org.jmol.shape.Measures
colix - Variable in class org.jmol.shape.MeshCollection
colix - Variable in class org.jmol.shapespecial.Dipole
colix - Variable in class org.jmol.shapespecial.Ellipsoid
colix - Variable in class org.jmol.shapespecial.Polyhedron
colix - Variable in class org.jmol.util.MeshSurface
COLIX_CONTRAST - Static variable in class org.jmol.util.C
colixA - Variable in class org.jmol.render.FontLineShapeRenderer
colixAtom - Variable in class org.jmol.modelset.Atom
colixB - Variable in class org.jmol.render.FontLineShapeRenderer
colixBack - Variable in class org.jmol.util.MeshSurface
colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
colixCurrent - Variable in class org.jmol.util.GData
colixEdge - Variable in class org.jmol.shapespecial.Polyhedron
colixes - Variable in class org.jmol.renderbio.BackboneRenderer
colixes - Variable in class org.jmol.renderbio.CartoonRenderer
colixes - Variable in class org.jmol.renderbio.MeshRibbonRenderer
colixes - Variable in class org.jmol.renderbio.RibbonsRenderer
colixes - Variable in class org.jmol.renderbio.RocketsRenderer
colixes - Variable in class org.jmol.renderbio.StrandsRenderer
colixes - Variable in class org.jmol.renderbio.TraceRenderer
colixes - Variable in class org.jmol.shape.AtomShape
colixesBack - Variable in class org.jmol.renderbio.BackboneRenderer
colixesBack - Variable in class org.jmol.renderbio.CartoonRenderer
colixesBack - Variable in class org.jmol.renderbio.MeshRibbonRenderer
colixesBack - Variable in class org.jmol.renderbio.RibbonsRenderer
colixesBack - Variable in class org.jmol.renderbio.RocketsRenderer
colixesBack - Variable in class org.jmol.renderbio.StrandsRenderer
colixesBack - Variable in class org.jmol.renderbio.TraceRenderer
colixesBack - Variable in class org.jmol.shapebio.BioShape
colixHighlight - Variable in class org.jmol.shape.Halos
colixRubberband - Variable in class org.jmol.viewer.ColorManager
colixSelection - Variable in class org.jmol.shape.Halos
collapsed - Static variable in class org.jmol.script.T
collapsed - Variable in class org.jmol.shapespecial.Polyhedron
colon - Static variable in class org.jmol.script.T
color - Variable in class org.jmol.jvxl.data.JvxlData
color - Static variable in class org.jmol.script.T
color - Variable in class org.jmol.shape.Mesh
color - Variable in class org.jmol.shape.MeshCollection
color - Variable in class org.jmol.util.BZone
Color - Class in org.jmol.awtjs.swing
Color() - Constructor for class org.jmol.awtjs.swing.Color
COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
COLOR_CONTRAST - Static variable in class org.jmol.viewer.JC
colorCommand - Variable in class org.jmol.shape.Mesh
colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
colorDensity - Variable in class org.jmol.shape.Mesh
ColoredAnnotation - Class in jspecview.common
  ColoredAnnotation is a label on the spectrum; not an integralRegion
ColoredAnnotation() - Constructor for class jspecview.common.ColoredAnnotation
colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
ColorEncoder - Class in org.jmol.util
ColorEncoder(ColorEncoder, Viewer) - Constructor for class org.jmol.util.ColorEncoder
colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
ColorManager - Class in org.jmol.viewer
colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
ColorParameters - Class in jspecview.common
  This a representation of the Display Scheme for the spectral display.
ColorParameters() - Constructor for class jspecview.common.ColorParameters
colorPos - Variable in class org.jmol.jvxl.readers.Parameters
colorPtFromInt(int, P3) - Static method in class javajs.util.CU
colorPtFromString(String) - Static method in class javajs.util.CU
colorPtToFFRGB(T3) - Static method in class javajs.util.CU
colorrasmol - Static variable in class org.jmol.script.T
colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
colorscheme - Static variable in class org.jmol.script.T
colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
colorsExplicit - Variable in class org.jmol.util.MeshSurface
colorTriadToFFRGB(float, float, float) - Static method in class javajs.util.CU
colorType - Variable in class org.jmol.shape.Mesh
columnCount - Variable in class javajs.util.CifDataParser
columnNames - Variable in class javajs.util.CifDataParser
ColumnSelectionModel - Interface in org.jmol.awtjs.swing
com.sparshui - package com.sparshui
com.sparshui.client - package com.sparshui.client
com.sparshui.common - package com.sparshui.common
com.sparshui.common.messages.events - package com.sparshui.common.messages.events
com.sparshui.common.utils - package com.sparshui.common.utils
com.sparshui.gestures - package com.sparshui.gestures
com.sparshui.inputdevice - package com.sparshui.inputdevice
com.sparshui.server - package com.sparshui.server
combineSelected() - Method in class jspecview.dialog.ViewsDialog
combineSpectra(String) - Method in class jspecview.common.JSViewer
combo1 - Variable in class jspecview.dialog.JSVDialog
comma - Static variable in class org.jmol.script.T
command - Static variable in class org.jmol.script.T
commandExpected() - Method in class org.jmol.script.ScriptCompiler
CommandHistory - Class in jspecview.application
  CommandHistory keeps a command history and responds to key events
CommandHistory - Class in org.jmol.util
  Implements a queue for a bash-like command history.
CommandHistory() - Constructor for class org.jmol.util.CommandHistory
  Creates a new instance using the default size (100)
CommandHistory(JSViewer, JTextField) - Constructor for class jspecview.application.CommandHistory
commandHistoryLevelMax - Static variable in class org.jmol.script.ScriptEval
commandLineOptions - Variable in class org.jmol.export.___Exporter
commands - Static variable in class org.jmol.script.T
commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CommandWatcherThread - Class in org.jmol.script
CommandWatcherThread() - Constructor for class org.jmol.script.CommandWatcherThread
commensurateSection1 - Variable in class org.jmol.adapter.readers.cif.MSRdr
COMMENT - Static variable in class jspecview.source.XMLParser
commentChar - Variable in class org.jmol.export.___Exporter
COMPARABLE_COMAPRATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
comparator - Static variable in class org.jmol.script.T
compare - Static variable in class org.jmol.script.T
compare(JmolTouchSimulator.TouchData, JmolTouchSimulator.TouchData) - Method in class com.sparshui.inputdevice.JmolTouchSimulator.TouchDataComparator
compare(Object[], Object[]) - Method in class org.jmol.shapespecial.Polyhedra
compare(Object, Object) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
compare(String[], String[]) - Method in class org.jmol.modelsetbio.BioResolver
compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
compare(SV, SV) - Method in class org.jmol.script.SV.Sort
compare(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.MeshCapperSorter
compareAngles(double, double, double, double) - Static method in class jme.JMEUtil
compareAtoms(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
compareAtoms(int, int) - Method in interface org.jmol.api.PymolAtomReader
compareFloat(int, float, float) - Method in class org.jmol.script.ScriptEval
compareFloatData(int, float[], int, float) - Method in class org.jmol.script.ScriptEval
compareTo(Measure) - Method in class org.openscience.jmol.app.janocchio.Measure
Comparision to Daylight SMARTS - Section in package org.jmol.smiles
Comparision to Daylight SMILES - Section in package org.jmol.smiles
compile(String, boolean) - Method in class org.jmol.util.PatternMatcher
compile(Viewer, String, char, Map) - Static method in class org.jmol.modelset.LabelToken
  Compiles a set of tokens for each primitive element of a label.
compileExpr(String) - Method in class org.jmol.viewer.Viewer
compileExpression() - Method in class org.jmol.script.ScriptCompiler
compileExpressions() - Method in class org.jmol.script.ScriptCompiler
compiler - Variable in class org.jmol.script.ScriptEval
compiler - Variable in class org.jmol.viewer.Viewer
compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEval
compileScriptString(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEval
compileSearchTarget(Node[], int, BS) - Method in interface org.jmol.api.SmilesMatcherInterface
compileSearchTarget(Node[], int, BS) - Method in class org.jmol.smiles.SmilesMatcher
compileSmartsPattern(String) - Method in interface org.jmol.api.SmilesMatcherInterface
compileSmartsPattern(String) - Method in class org.jmol.smiles.SmilesMatcher
completeCommand(String) - Method in class org.jmol.console.GenericConsole
completeCommand(Map, boolean, boolean, String, int) - Static method in class org.jmol.script.T
completeMolecule() - Method in class jme.JMEmol
Component - Class in org.jmol.awtjs.swing
Component(String) - Constructor for class org.jmol.awtjs.swing.Component
componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
CompoundDocument - Class in javajs.util
CompoundDocument() - Constructor for class javajs.util.CompoundDocument
COMPOUNDMENUON - Enum constant in enum class jspecview.common.ScriptToken
computeAngle(T3, T3, T3, V3, V3, boolean) - Static method in class javajs.util.Measure
computeAngleABC(T3, T3, T3, boolean) - Static method in class javajs.util.Measure
computeHelicalAxis(P3, P3, Quat) - Static method in class javajs.util.Measure
  This method calculates measures relating to two points in space with related quaternion frame difference.
computeTorsion(T3, T3, T3, T3, boolean) - Static method in class javajs.util.Measure
concatList(SV, SV, boolean) - Static method in class org.jmol.script.SV
CONE - Static variable in class org.jmol.shapecgo.CGOMesh
cone_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
configuration - Static variable in class org.jmol.script.T
confirm(String, String) - Method in class jspecview.java.AwtPlatform
confirm(String, String) - Method in class jspecview.js2d.JsPlatform
confirm(String, String) - Method in interface org.jmol.api.GenericPlatform
confirm(String, String) - Method in class org.jmol.awt.Platform
confirm(String, String) - Method in class org.jmol.awtjs2d.Platform
confirm(String, String) - Method in class org.jmol.viewer.Viewer
connect - Static variable in class org.jmol.script.T
connect() - Method in class javajs.util.AjaxURLConnection
connect(float[][]) - Method in class org.jmol.modelset.ModelSet
connect_bonded - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
connect_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
connect_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
connected - Static variable in class org.jmol.script.T
connectedAtoms - Variable in class org.jmol.shape.Mesh
connections - Variable in class org.jmol.shape.MeshCollection
ConnectionType - Class in com.sparshui.common
ConnectionType() - Constructor for class com.sparshui.common.ConnectionType
connectNBO(int, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
connectNBO(String) - Method in class org.jmol.viewer.Viewer
console - Static variable in class org.jmol.script.T
console - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
consoleGetImageDialog(Viewer, String, Map) - Method in interface org.jmol.api.js.JmolToJSmolInterface
ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel.console
ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
constraint - Static variable in class org.jmol.script.T
constraints - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
constraints - Variable in class org.jmol.minimize.Minimizer
contact - Static variable in class org.jmol.script.T
Contact - Class in org.jmol.shapesurface
Contact() - Constructor for class org.jmol.shapesurface.Contact
contactPair - Variable in class org.jmol.jvxl.readers.Parameters
ContactPair - Class in org.jmol.util
ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
ContactRenderer - Class in org.jmol.rendersurface
ContactRenderer() - Constructor for class org.jmol.rendersurface.ContactRenderer
contactType - Variable in class org.jmol.util.ContactPair
Container - Class in org.jmol.awtjs.swing
Container(String) - Constructor for class org.jmol.awtjs.swing.Container
contains(int[], int) - Static method in class jme.JMEUtil
contains(int, int) - Method in class org.jmol.util.Rectangle
contentDisabled - Variable in class org.molecularplayground.MPJmolApp
context - Static variable in class org.jmol.script.T
CONTEXT_DELAY - Static variable in class org.jmol.script.ScriptEval
CONTEXT_HOLD_QUEUE - Static variable in class org.jmol.script.ScriptEval
contextdepthmax - Static variable in class org.jmol.script.T
contextFunctions - Variable in class org.jmol.script.ScriptParam
contextPath - Variable in class org.jmol.script.ScriptContext
contextVariables - Variable in class org.jmol.script.ScriptParam
continuecmd - Static variable in class org.jmol.script.T
continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
continuous - Variable in class jspecview.export.AMLExporter
continuous - Variable in class jspecview.export.CMLExporter
continuous - Variable in class jspecview.source.AnIMLReader
continuous - Variable in class jspecview.source.NMRMLReader
contour - Static variable in class org.jmol.script.T
CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
contourColors - Variable in class org.jmol.jvxl.data.JvxlData
contourlines - Static variable in class org.jmol.script.T
contours - Static variable in class org.jmol.script.T
contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourType - Variable in class org.jmol.jvxl.readers.Parameters
contourValues - Variable in class org.jmol.jvxl.data.JvxlData
contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
contrastColix - Variable in class org.jmol.util.GData
  WHITE or BLACK
controlPoints - Variable in class org.jmol.modelsetbio.BioPolymer
controlPoints - Variable in class org.jmol.renderbio.BackboneRenderer
controlPoints - Variable in class org.jmol.renderbio.CartoonRenderer
controlPoints - Variable in class org.jmol.renderbio.MeshRibbonRenderer
controlPoints - Variable in class org.jmol.renderbio.RibbonsRenderer
controlPoints - Variable in class org.jmol.renderbio.RocketsRenderer
controlPoints - Variable in class org.jmol.renderbio.StrandsRenderer
controlPoints - Variable in class org.jmol.renderbio.TraceRenderer
controlPointScreens - Variable in class org.jmol.renderbio.BackboneRenderer
controlPointScreens - Variable in class org.jmol.renderbio.CartoonRenderer
controlPointScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
controlPointScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
controlPointScreens - Variable in class org.jmol.renderbio.RocketsRenderer
controlPointScreens - Variable in class org.jmol.renderbio.StrandsRenderer
controlPointScreens - Variable in class org.jmol.renderbio.TraceRenderer
Converter - Class in com.sparshui.common.utils
  Contains conversion methods that are needed by several elements of the Gesture Server.
Converter() - Constructor for class com.sparshui.common.utils.Converter
convertPointFromScreen(Object, P3) - Method in class jspecview.java.AwtPlatform
  // Display
convertPointFromScreen(Object, P3) - Method in class jspecview.js2d.JsPlatform
convertPointFromScreen(Object, P3) - Method in interface org.jmol.api.GenericPlatform
convertPointFromScreen(Object, P3) - Method in class org.jmol.awt.Platform
  // Display
convertPointFromScreen(Object, P3) - Method in class org.jmol.awtjs2d.Platform
convertToMegabytes(long) - Static method in class org.jmol.popup.GenericPopup
convertTransform(String, M4) - Method in interface org.jmol.api.SymmetryInterface
convertTransform(String, M4) - Method in class org.jmol.symmetry.Symmetry
  A general method to handle converstions between string-based and matrix-based representations of transformations.
convertValue(Map, String) - Static method in class org.qcschema.QCSchemaUnits
  Read a {value:xxxx, units:["name",toAU]} map, converting it to the desired units.
coord - Variable in class org.jmol.minimize.MinAtom
coord - Static variable in class org.jmol.script.T
COORDCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
coordClicked - Variable in class jspecview.common.PanelData
Coordinate - Class in jspecview.common
  The `Coordinate` class stores the x and y values of a coordinate.
Coordinate() - Constructor for class jspecview.common.Coordinate
  Constructor
coordinateInRange(int, int, T3, int, P3i) - Method in class org.jmol.shape.Shape
coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
coordinatesAreFractional - Variable in class org.jmol.script.ScriptParam
  set in getPointOrPlane
coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
  Get the boolean whether coordinates are fractional.
coordinatesColor - Variable in class jspecview.common.PanelData
COORDINATESCOLOR - Enum constant in enum class jspecview.common.ScriptToken
COORDINATESON - Enum constant in enum class jspecview.common.ScriptToken
coordsClicked - Variable in class jspecview.common.PanelData
coordStr - Variable in class jspecview.common.PanelData
copy() - Method in class javajs.util.Matrix
  Make a deep copy of a matrix
copy() - Method in class jspecview.common.ColorParameters
  Returns a copy of this `DisplayScheme`
copy() - Method in class jspecview.common.Coordinate
  Returns a new coordinate that has the same x and y values of this coordinate
copy() - Method in class jspecview.common.Spectrum
  specifically for Abs/Trans conversion.
copy() - Method in class org.jmol.util.Point3fi
copy(String) - Method in class jspecview.common.ColorParameters
  Returns a copy of this `DisplayScheme` with a new name
copy(String) - Method in class jspecview.java.AwtParameters
copy(String) - Method in class jspecview.js2d.JsParameters
copy(BS) - Static method in class javajs.util.BS
  fast copy
copy(BS) - Static method in class org.jmol.util.BSUtil
copy2(BS, BS) - Static method in class org.jmol.util.BSUtil
copyArray(double[]) - Static method in class jme.JMEUtil
copyArray(int[]) - Static method in class jme.JMEUtil
copyArray(int[], int) - Static method in class jme.JMEUtil
copyArray(String[]) - Static method in class jme.JMEUtil
copyColixTranslucency(short, short) - Static method in class org.jmol.util.C
copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
copyInvert(BS, int) - Static method in class org.jmol.util.BSUtil
copyM() - Method in class jspecview.common.Measurement
copyOf(T[], int) - Static method in class jme.JMEUtil
  Copies the specified array, truncating or padding with nulls (if necessary) so the copy has the specified length.
copyOf(U[], int, Class) - Static method in class jme.JMEUtil
  Copies the specified array, truncating or padding with nulls (if necessary) so the copy has the specified length.
copyright - Static variable in class org.jmol.viewer.JC
copySafely(SV) - Static method in class org.jmol.script.SV
  Make a copy if this is a variable -- if it has myName != null.
copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
copyTensor() - Method in class org.jmol.util.Tensor
copyTo(P3, AtomSetCollection) - Method in class org.jmol.adapter.smarter.Atom
copyTo(JDXDataObject) - Method in class jspecview.source.JDXDataObject
copyVertexColorMap() - Method in class org.jmol.shapesurface.IsosurfaceMesh
cordMidPoints - Variable in class org.jmol.renderbio.RocketsRenderer
corners - Static variable in class org.jmol.script.T
cos - Static variable in class org.jmol.script.T
cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
cosBeta - Variable in class org.jmol.util.SimpleUnitCell
cosGamma - Variable in class org.jmol.util.SimpleUnitCell
coulomb_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
coulomb_dielectric - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
coulomb_units_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
count - Variable in class org.jmol.modelset.Measurement
count - Static variable in class org.jmol.script.T
COUNT_MASK - Static variable in class org.jmol.viewer.binding.Binding
countChar(String, char) - Static method in class javajs.util.PT
counter - Variable in class org.jmol.script.ScriptParallelProcessor
countPlusIndices - Variable in class org.jmol.modelset.Measurement
countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
countTokens(String, int) - Static method in class javajs.util.PT
coupleColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
CoupleColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
CoupleColourSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
CoupleParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
CoupleParameterSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
  Creates new form noeParameterSelectionPanel
couples - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
couplesWhole - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
coupleTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
CoupleTable - Class in org.openscience.jmol.app.janocchio
CoupleTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.CoupleTable
  Constructor
covalentradius - Static variable in class org.jmol.script.T
covalentVersion - Static variable in class org.jmol.util.Elements
CPK - Enum constant in enum class org.jmol.c.PAL
cr - Variable in class org.jmol.adapter.readers.cif.MSRdr
create - Static variable in class org.jmol.script.T
create(BZone) - Method in class org.jmol.util.BZone
createAndShowGUI(Viewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
createArray(int) - Static method in class jme.JMEUtil
createArray(int, int) - Static method in class jme.JMEUtil
createArrayOfArrayList(int) - Static method in class javajs.util.AU
  Helper method for creating a List<Tx>[] without warnings.
createArrayOfHashtable(int) - Static method in class javajs.util.AU
  Helper method for creating a Mapinvalid input: '<'K, V>[] without warnings.
createAtomDataSet(Viewer, ModelSet, int, Object, BS) - Static method in class org.jmol.modelset.ModelLoader
createBArray(int) - Static method in class jme.JMEUtil
createBZ(Viewer, int, Object[], boolean, String, float, float, P3) - Method in class org.jmol.util.BZone
  Create a Brillouin zone.
createColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
createCompatibleUnitCell(float[], float[], boolean) - Method in class org.jmol.symmetry.SpaceGroup
  Create a unit cell compatible with
createCube() - Method in class org.jmol.quantum.MepCalculation
createCube() - Method in class org.jmol.quantum.MOCalculation
createCube() - Method in class org.jmol.quantum.NciCalculation
createCube() - Method in class org.jmol.quantum.QuantumCalculation
CREATED - Enum constant in enum class org.jmol.c.FIL
createDArray(int) - Static method in class jme.JMEUtil
createDFMap(int[], String, String, int) - Static method in class org.jmol.quantum.QS
createDialog(Component) - Method in class org.jmol.dialog.FileChooser
createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
createEllipsoidShades() - Method in class org.jmol.util.Shader
createFileData(String) - Method in interface org.jmol.api.JmolDataManager
createFileData(String) - Method in class org.jmol.viewer.DataManager
createFont3D(int, int, float, float, float, FontManager, Object) - Static method in class org.jmol.util.Font
createGeodesic(int) - Static method in class org.jmol.util.Geodesic
  /////////// private methods ///////////////
createGuiMap() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
createGuiMap() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
createImage(Object) - Method in class jspecview.java.AwtPlatform
  could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in class jspecview.js2d.JsPlatform
  could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in interface org.jmol.api.GenericPlatform
  can be ignored (return null) if platform cannot save images
createImage(Object) - Method in class org.jmol.awt.Platform
  could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in class org.jmol.awtjs2d.Platform
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
  Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
createImage(String, String, Object, int) - Method in class org.jmol.util.GenericApplet
createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.status.StatusListener
createImage(String, OC, Map) - Method in interface javajs.api.GenericImageEncoder
createImage(String, OC, Map) - Method in class javajs.img.ImageEncoder
createItemKeys(JmolPanel) - Method in class org.jmol.console.KeyJMenu
createJDXSource(GenericFileInterface, Object, String, boolean, boolean, int, int, float) - Static method in class jspecview.source.JDXReader
  general entrance method
createJDXSourceFromStream(InputStream, boolean, boolean, float) - Static method in class jspecview.source.JDXReader
  used only for preferences display and Android
createLArray(int) - Static method in class jme.JMEUtil
createMainPanel(JSViewer) - Method in interface jspecview.api.AppletFrame
createMainPanel(JSViewer) - Method in class jspecview.appletjs.JSVApplet
createMatrix(Viewer, BS, String[], NMRNoeMatrix.NOEParams) - Static method in class org.jmol.quantum.NMRNoeMatrix
createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create a menu for the app.
createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create the menubar for the app.
createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  This is the hook through which all menu items are created.
createModels(int) - Method in class org.jmol.modelset.ModelSet
createMolecule() - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
  create a movie from a set of image files
createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.image.AviCreator
createPdfDocument(OC, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
createPdfDocument(JSVPanel, PrintLayout, OutputStream) - Method in interface jspecview.api.JSVPdfWriter
createPdfDocument(JSVPanel, PrintLayout, OutputStream) - Method in class jspecview.common.PDFWriter
createSArray(int) - Static method in class jme.JMEUtil
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerAwt
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerJS
createSpaceGroup(int, String, Object, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
createSpaceGroup(int, String, Object, int) - Static method in class org.jmol.symmetry.SpaceGroup
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.CsfReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createStatusBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
createStatusBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
createTable(Object[][], String[], int[]) - Method in interface jspecview.api.PlatformDialog
createTable(Object[][], String[], int[]) - Method in class jspecview.java.AwtDialog
createTable(Object[][], String[], int[]) - Method in class jspecview.js2d.JsDialog
createToolBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
createToolBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create the toolbar.
createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create a button to go inside of the toolbar.
createTree(int, JDXSource, JSVPanel[]) - Method in interface jspecview.api.JSVTree
createTree(int, JDXSource, JSVPanel[]) - Method in class jspecview.application.AwtTree
createTree(int, JDXSource, JSVPanel[]) - Method in class jspecview.tree.SimpleTree
createURLStreamHandler(String) - Method in class javajs.util.AjaxURLStreamHandlerFactory
createView(Lst) - Static method in class jspecview.source.JDXSource
createZip(String, String, Map) - Method in class org.jmol.viewer.Viewer
CREATING_MODELSET - Enum constant in enum class org.jmol.c.FIL
creatingImage - Variable in class org.jmol.viewer.Viewer
CREDITS - Static variable in class jspecview.app.JSVApp
creditsAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CreditsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
CreditsDialog - Class in org.openscience.jmol.app.jmolpanel
CreditsDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.CreditsDialog
criterion - Static variable in class org.jmol.script.T
cross - Static variable in class org.jmol.script.T
cross(T3, T3) - Method in class javajs.util.T3
  Sets this tuple to be the vector cross product of vectors v1 and v2.
cross(V3d, V3d) - Method in class javajs.util.V3d
  Sets this vector to be the vector cross product of vectors v1 and v2.
crossed - Static variable in class org.jmol.script.T
CRYSTAL - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CRYSTAL_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CRYSTAL_SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CRYSTAL_SYMMETRY_TRANSFORM3 - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CrystalReader - Class in org.jmol.adapter.readers.xtal
  A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
crystalReaderLatticeOpsOnly - Variable in class org.jmol.adapter.smarter.AtomSetCollection
CsfReader - Class in org.jmol.adapter.readers.quantum
  CSF file reader based on CIF idea -- fluid property fields.
CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
cterm - Variable in class javajs.util.CifDataParser
  optional token terminator; in CIF 2.0 could be } or ]
CTRL - Static variable in class org.jmol.viewer.binding.Binding
CTRL_ALT - Static variable in class org.jmol.awtjs.Event
CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
CTRL_MASK - Static variable in class org.jmol.awtjs.Event
CTRL_SHIFT - Static variable in class org.jmol.awtjs.Event
CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
ctrlPressed - Variable in class jspecview.common.PanelData
CU - Class in javajs.util
  ColorUtility
CU() - Constructor for class javajs.util.CU
cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
CubeIterator - Class in org.jmol.bspt
  Iterator used for finding all points within a box or a hemi-box
CubeReader - Class in org.jmol.adapter.readers.simple
  Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
cull_spheres - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
current - Variable in class org.jmol.viewer.ActionManager
currentCursor - Variable in class org.jmol.viewer.Viewer
currentDir - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
currentFont - Variable in class org.jmol.util.GData
currentFrameIs(int) - Method in class org.jmol.viewer.AnimationManager
currentIsLast() - Method in class org.jmol.viewer.AnimationManager
currentlocalpath - Static variable in class org.jmol.script.T
currentlyRendering - Variable in class org.jmol.util.GData
currentMenuItemId - Variable in class org.jmol.popup.GenericPopup
currentMesh - Variable in class org.jmol.shape.MeshCollection
currentPalette - Variable in class org.jmol.util.ColorEncoder
currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
currentSource - Variable in class jspecview.common.JSViewer
currentSplitFrame - Variable in class org.jmol.viewer.AnimationManager
currentSplitPoint - Variable in class jspecview.common.PanelData
currentTime - Variable in class org.jmol.thread.JmolThread
CURSOR_CROSSHAIR - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_DEFAULT - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_HAND - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_MOVE - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_WAIT - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_ZOOM - Static variable in interface org.jmol.api.GenericPlatform
curve - Static variable in class org.jmol.script.T
CURVE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
CUSTOM - Enum constant in enum class org.jmol.c.STER
CUSTOM - Static variable in class org.jmol.util.ColorEncoder
CUSTOM_CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
cutoff - Variable in class org.jmol.jvxl.data.JvxlData
cutoff - Variable in class org.jmol.jvxl.readers.Parameters
cutoff - Static variable in class org.jmol.script.T
cutoffRange - Variable in class org.jmol.jvxl.data.JvxlData
cutoffRange - Variable in class org.jmol.jvxl.readers.Parameters
CYAN - Static variable in class org.jmol.util.C
cyclicFlag - Variable in class org.jmol.modelsetbio.BioPolymer
cylinder - Static variable in class org.jmol.script.T
CYLINDER - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
cylinder_shader_ff_workaround - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
cylinders_shader_filter_faces - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings

## D

d - Variable in class org.jmol.util.ContactPair
DARK_GRAY - Static variable in class jspecview.common.ColorParameters
dash_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_gap - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_length - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_round_ends - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dash_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dashDots - Variable in class org.jmol.render.FontLineShapeRenderer
dashes - Static variable in class org.jmol.render.FontLineShapeRenderer
data - Variable in class javajs.util.BArray
data - Variable in class org.jmol.adapter.writers.CIFWriter
data - Variable in class org.jmol.minimize.MinObject
data - Static variable in class org.jmol.script.T
DATA_ATOM_PROP_ENTRY - Static variable in interface org.jmol.api.JmolDataManager
DATA_LABEL - Static variable in interface org.jmol.api.JmolDataManager
DATA_SAVE_IN_STATE - Static variable in interface org.jmol.api.JmolDataManager
DATA_SELECTION - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_AF - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_AFF - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_AFFF - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_LAST - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_STRING - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_UNKNOWN - Static variable in interface org.jmol.api.JmolDataManager
DATA_VALUE - Static variable in interface org.jmol.api.JmolDataManager
DataAdder - Interface in org.jmol.quantum.mo
DataAdder11H - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributions
DataAdder11H() - Constructor for class org.jmol.quantum.mo.DataAdder11H
DataAdder13I - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributions
DataAdder13I() - Constructor for class org.jmol.quantum.mo.DataAdder13I
DataAdder7F - Class in org.jmol.quantum.mo
  adds 7 spherical F orbital contributions
DataAdder7F() - Constructor for class org.jmol.quantum.mo.DataAdder7F
DataAdder9G - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributions
DataAdder9G() - Constructor for class org.jmol.quantum.mo.DataAdder9G
DataAdderF - Class in org.jmol.quantum.mo
  adds 10 cartesian F orbital contributions
DataAdderF() - Constructor for class org.jmol.quantum.mo.DataAdderF
DataAdderG - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributions
DataAdderG() - Constructor for class org.jmol.quantum.mo.DataAdderG
DataAdderH - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributions
DataAdderH() - Constructor for class org.jmol.quantum.mo.DataAdderH
DataAdderI - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributions
DataAdderI() - Constructor for class org.jmol.quantum.mo.DataAdderI
dataClass - Variable in class jspecview.source.JDXHeader
dataFrames - Variable in class org.jmol.modelset.Model
DataLDRTable() - Constructor for class jspecview.source.JDXHeader.DataLDRTable
dataLen - Variable in class javajs.img.PngEncoder
DataManager - Class in org.jmol.viewer
DataManager() - Constructor for class org.jmol.viewer.DataManager
dataMax - Variable in class org.jmol.jvxl.data.JvxlData
dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
dataMin - Variable in class org.jmol.jvxl.data.JvxlData
dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
dataOnly - Variable in class org.jmol.util.MeshSurface
DataReader - Class in javajs.util
  Just a simple abstract class to join a String reader and a String[] reader under the same BufferedReader umbrella.
DataReader() - Constructor for class javajs.util.DataReader
DataReader(Reader) - Constructor for class javajs.util.DataReader
dataseparator - Static variable in class org.jmol.script.T
dataSourceFrame - Variable in class org.jmol.modelset.Model
datatype - Variable in class jspecview.export.AMLExporter
datatype - Variable in class jspecview.export.CMLExporter
dataType - Variable in class jspecview.source.JDXHeader
dataType - Variable in class org.jmol.jvxl.readers.Parameters
dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
date - Variable in class javajs.img.ImageEncoder
date - Static variable in class jspecview.common.JSVersion
date - Variable in class jspecview.common.PrintLayout
date - Variable in class jspecview.export.AMLExporter
date - Variable in class jspecview.export.CMLExporter
date - Variable in class jspecview.source.JDXHeader
date - Static variable in class org.jmol.viewer.JC
dBb(BS, boolean) - Method in class org.jmol.modelset.BondCollection
  Delete bonds, but don't shift arrays, just set bond to null, in order to allow for state.
DBLCLK_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
DBLCLK_EVENT - Static variable in class com.sparshui.GestureType
DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
DBLCLK_GESTURE - Static variable in class com.sparshui.GestureType
DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
DC - Static variable in class org.jmol.quantum.QS
dclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
ddata - Variable in class org.jmol.minimize.MinObject
DEATH - Static variable in class com.sparshui.common.TouchState
DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
debug - Static variable in class org.jmol.script.T
debug(String) - Method in class org.jmol.util.DefaultLogger
debug(String) - Static method in class org.jmol.util.Logger
  Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at DEBUG level.
DEBUG - Enum constant in enum class jspecview.common.ScriptToken
debug_pick - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
debugging - Variable in class javajs.util.CifDataParser
  debugging flag passed from reader; unused
debugging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
debugging - Static variable in class org.jmol.util.Logger
debuggingHigh - Static variable in class org.jmol.util.Logger
debughigh - Static variable in class org.jmol.script.T
debugHigh - Variable in class org.jmol.script.ScriptEval
DebugJS - Class in javajs.util
  A class to insert a JavaScript debug statement for Firefox or Chrome debugger
DebugJS() - Constructor for class javajs.util.DebugJS
debugPrint(String) - Method in class org.jmol.export._ObjExporter
  Debug print utility.
debugscript - Static variable in class org.jmol.script.T
decimal - Static variable in class org.jmol.script.T
decimalScale - Static variable in class javajs.util.PT
decode(byte[]) - Static method in class javajs.util.MessagePackReader
  This single method takes care of all MMTF needs.
decodeBase64(String) - Static method in class javajs.util.Base64
decodeKey(Integer) - Static method in class org.jmol.minimize.MinObject
decodeWindowsBMP(byte[]) - Method in class javajs.img.BMPDecoder
  original comment: loadbitmap() method converted from Windows C code.
decompressData(SB) - Method in class jspecview.source.JDXDecompressor
  Determines the type of compression, decompresses the data and stores coordinates in an array to be returned
deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
  The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
deepCopy(Object, boolean, boolean) - Static method in class org.jmol.script.SV
  Copies a hash or array deeply; invoked by Jmol script x = @a where a.type == "hash" or a.type == "varray"
DEFAULT - Static variable in class org.jmol.smiles.SmilesStereo
default_2fofc_map_rep - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JC
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JC
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JC
default_buster_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
DEFAULT_DRAG_DROP_SCRIPT - Static variable in class org.jmol.viewer.JC
DEFAULT_DRAW_SYM_ID - Static variable in class org.jmol.viewer.JC
default_fofc_map_rep - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JC
  /////////////////////////////////////////////////////////////
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JC
DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
DEFAULT_HEIGHT - Static variable in class jspecview.common.JSViewer
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JC
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JC
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
DEFAULT_MINY - Static variable in class jspecview.common.IntegralData
DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
DEFAULT_OFFSET - Static variable in class jspecview.common.IntegralData
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JC
default_phenix_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
default_phenix_no_fill_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
DEFAULT_RANGE - Static variable in class jspecview.common.IntegralData
default_refmac_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JC
DEFAULT_VISUAL_RANGE - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_WIDTH - Static variable in class jspecview.common.JSViewer
defaultAlignment - Variable in class org.jmol.shape.Labels
defaultanglelabel - Static variable in class org.jmol.script.T
defaultBgcolix - Variable in class org.jmol.shape.Labels
defaultBondingMars - Static variable in class org.jmol.util.Elements
  Default table of bonding radii stored as a short mar ...
defaultcmd - Static variable in class org.jmol.script.T
defaultColix - Variable in class org.jmol.shape.Labels
defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultcolorscheme - Static variable in class org.jmol.script.T
defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
defaultdirectory - Static variable in class org.jmol.script.T
defaultDisplaySchemeName - Variable in class jspecview.application.JSpecView
defaultdistancelabel - Static variable in class org.jmol.script.T
defaultdrawarrowscale - Static variable in class org.jmol.script.T
defaultdropscript - Static variable in class org.jmol.script.T
defaultDropScript - Variable in class org.jmol.viewer.GlobalSettings
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
  /////// character - fraction encoding and decoding
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultFontId - Variable in class org.jmol.shape.Labels
defaultFontId - Variable in class org.jmol.shapespecial.Draw
defaultFontId0 - Variable in class org.jmol.shapespecial.Draw
defaultHeight - Variable in class org.jmol.awtjs.swing.JDialog
defaultlabelpdb - Static variable in class org.jmol.script.T
defaultLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
defaultlabelxyz - Static variable in class org.jmol.script.T
defaultlattice - Static variable in class org.jmol.script.T
defaultloadfilter - Static variable in class org.jmol.script.T
defaultLoadFilter - Variable in class org.jmol.viewer.GlobalSettings
defaultloadscript - Static variable in class org.jmol.script.T
defaultLoadScript - Variable in class org.jmol.viewer.GlobalSettings
DEFAULTLOADSCRIPT - Enum constant in enum class jspecview.common.ScriptToken
DefaultLogger - Class in org.jmol.util
  Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
defaultMacroDirectory - Static variable in class org.jmol.viewer.JC
defaultMessage - Variable in class org.jmol.console.GenericConsole
defaultMode - Variable in class org.jmol.viewer.TransformManager
DEFAULTNMRNORMALIZATION - Enum constant in enum class jspecview.common.ScriptToken
defaultOffset - Variable in class org.jmol.shape.Labels
defaultON - Static variable in class org.jmol.script.T
defaultPaletteID - Variable in class org.jmol.shape.Labels
defaultPlotColorNames - Static variable in class jspecview.common.ColorParameters
defaultPlotColors - Static variable in class jspecview.common.ColorParameters
defaultPointer - Variable in class org.jmol.shape.Labels
defaultPrintHeight - Static variable in class jspecview.common.PanelData
defaultPrintWidth - Static variable in class jspecview.common.PanelData
defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
defaultQuality - Variable in class javajs.img.JpgEncoder
defaults - Static variable in class org.jmol.script.T
defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
defaultstructuredssp - Static variable in class org.jmol.script.T
defaultTickInfo - Variable in class org.jmol.shape.Measures
defaulttorsionlabel - Static variable in class org.jmol.script.T
defaulttranslucent - Static variable in class org.jmol.script.T
defaultvdw - Static variable in class org.jmol.script.T
defaultZPos - Variable in class org.jmol.shape.Labels
defer_builds_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
defer_updates - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
deferred - Variable in class org.jmol.awt.AwtSwingComponent
define - Static variable in class org.jmol.script.T
define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
  called by the client to generate a set of measurements
defineAtomSets(Map) - Method in class org.jmol.viewer.Viewer
defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
definedAtomSets - Variable in class org.jmol.viewer.Viewer
definesStereo() - Method in class org.jmol.smiles.SmilesAtom
  for InChI or any other system that self-defines stereochemistry.
DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
degreesPerRadian - Static variable in class org.jmol.export.___Exporter
degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
delay - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
delay - Static variable in class org.jmol.script.T
delaymaximumms - Static variable in class org.jmol.script.T
delayScript(int) - Method in class org.jmol.script.ScriptEval
delete - Static variable in class org.jmol.script.T
delete(BS) - Method in class org.jmol.modelset.Atom
deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
deleteAllBonds2() - Method in class org.jmol.modelset.BondCollection
deleteAtom(Atom) - Method in class org.jmol.adapter.readers.molxyz.MolReader
deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
deleteAtoms(int, BS, BS) - Method in class org.jmol.modelset.StateScript
deleteAtoms(BS) - Method in class org.jmol.modelset.ModelSet
deleteAtoms(BS, boolean) - Method in class org.jmol.viewer.Viewer
deleteAtomsInVariables(BS) - Method in interface org.jmol.api.JmolScriptEvaluator
deleteAtomsInVariables(BS) - Method in class org.jmol.script.ScriptEval
deleteBits(BS, BS) - Static method in class org.jmol.util.BSUtil
  this one slides deleted bits out of a pattern.
deleteBonds(BS) - Method in class org.jmol.viewer.Viewer
deleteBonds(BS, boolean) - Method in class org.jmol.modelset.ModelSet
deleteConnections(float, float, int, BS, BS, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
DELETED - Enum constant in enum class org.jmol.c.FIL
deleteElements(Object, int, int) - Static method in class javajs.util.AU
deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
deleteMeshI(int) - Method in class org.jmol.shape.MeshCollection
deleteMeshKey(String) - Method in class org.jmol.shape.MeshCollection
deleteModelAtoms(int, int, int, BS) - Method in class org.jmol.viewer.Viewer
deleteModelAtoms(int, int, BS) - Method in interface org.jmol.api.JmolDataManager
deleteModelAtoms(int, int, BS) - Method in class org.jmol.modelset.AtomCollection
deleteModelAtoms(int, int, BS) - Method in class org.jmol.viewer.DataManager
deleteModelBonds(int) - Method in class org.jmol.modelset.ModelSet
deleteModels(int) - Method in class org.jmol.shapecgo.CGO
deleteModels(int, BS) - Method in class org.jmol.viewer.Viewer
  called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
deleteModels(BS) - Method in class org.jmol.modelset.ModelSet
deleteNodes(Lst) - Method in interface jspecview.api.JSVTree
deleteNodes(Lst) - Method in class jspecview.application.AwtTree
deleteNodes(Lst) - Method in class jspecview.tree.SimpleTree
deleteSaved(String) - Method in class org.jmol.viewer.StateManager
deleteShapeAtoms(Object[], BS) - Method in class org.jmol.viewer.ShapeManager
deltaX - Variable in class jspecview.export.AMLExporter
deltaX - Variable in class jspecview.export.CMLExporter
deltaX - Variable in class jspecview.source.AnIMLReader
deltaX - Variable in class jspecview.source.NMRMLReader
deltaX(double, double, int) - Static method in class jspecview.common.Coordinate
  Returns the Delta X value
density - Static variable in class org.jmol.script.T
depict - Variable in class jme.JME
depictBorder - Variable in class jme.JME
deprecatedparam - Static variable in class org.jmol.script.T
depth - Static variable in class org.jmol.script.T
depth - Variable in class org.jmol.util.GData
depth_cue - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
depthValue - Variable in class org.jmol.viewer.TransformManager
depthZ - Variable in class org.jmol.export.___Exporter
DESCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
descent - Variable in class org.jmol.modelset.Text
descent - Variable in class org.jmol.render.LabelsRenderer
desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
destroy() - Method in interface javajs.api.JSInterface
destroy() - Method in class jspecview.appletjs.JSVApplet
destroy() - Method in interface org.jmol.api.JmolAppletInterface
destroy() - Method in class org.jmol.g3d.Graphics3D
destroy() - Method in class org.jmol.util.GData
destroy() - Method in class org.jmol.util.GenericApplet
destroy() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
destroy() - Method in interface org.openscience.jmol.app.JmolPlugin
destroyConsole() - Method in class org.jmol.console.GenericConsole
DetachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
Detailed Jmol SMARTS/Jmol bioSMARTS Specification - Section in package org.jmol.smiles
Detailed Jmol SMILES/bioSMILES Specification - Section in package org.jmol.smiles
detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
determinant3() - Method in class javajs.util.M34
determinant4() - Method in class javajs.util.M4
  Computes the determinant of this matrix.
determineAtomSetCollectionReader(Object, Map) - Static method in class org.jmol.adapter.smarter.Resolver
  the main resolver method.
determineSpaceGroupNA(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
determineSpaceGroupNS(String, SpaceGroup) - Static method in class org.jmol.symmetry.SpaceGroup
determineSurfaceFileType(BufferedReader) - Static method in class org.jmol.viewer.FileManager
  Try to determine a surface file type based on its header.
DEVICE_PORT - Static variable in class com.sparshui.common.NetworkConfiguration
DF - Class in javajs.util
  created to remove ambiguities and make a simpler DecimalFormat
DF() - Constructor for class javajs.util.DF
dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
DgridReader - Class in org.jmol.adapter.readers.quantum
  A reader for Dgrid BASISFILE data.
DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
dialog - Variable in class jspecview.dialog.JSVDialog
Dialog - Class in org.jmol.dialog
Dialog() - Constructor for class org.jmol.dialog.Dialog
Dialog.ExportChoiceListener - Class in org.jmol.dialog
Dialog.QualityListener - Class in org.jmol.dialog
Dialog.TypeFilter - Class in org.jmol.dialog
dialogAsk(String, String, Map) - Method in class org.jmol.viewer.Viewer
  Ask for new file name when saving or opening a file in Java and saving a file in JavaScript.
DialogManager - Class in jspecview.dialog
  Dialogs include Integration, PeakListing, Views, OverlayLegend, and Measurements These dialogs have been generalized for platform independence.' This manager is subclassed as AwtDialogManager and JsDialogManager, which apply their own interpretation of how to create the dialog and get its event callbacks.
DialogManager() - Constructor for class jspecview.dialog.DialogManager
DialogParams - Class in jspecview.dialog
  DialogParams handles all the platform-independent needs of AwtAnnotationDialog and subclasses of it.
DialogParams() - Constructor for class jspecview.dialog.DialogParams
dialogsToFront(Spectrum) - Method in class jspecview.common.PanelData
dialogType - Variable in class org.jmol.dialog.Dialog
diameter - Variable in class org.jmol.jvxl.data.JvxlData
diameter - Variable in class org.jmol.render.MeshRenderer
diameter - Static variable in class org.jmol.script.T
diameter - Variable in class org.jmol.shape.Mesh
DIF - Enum constant in enum class jspecview.common.ExportType
DIFDUP - Enum constant in enum class jspecview.common.ExportType
diff - Variable in class org.openscience.jmol.app.janocchio.Measure
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
diffusepercent - Static variable in class org.jmol.script.T
dihedral_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dihedral_label_position - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dihedral_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dimension - Variable in class org.jmol.util.SimpleUnitCell
Dimension - Class in org.jmol.awtjs.swing
Dimension(int, int) - Constructor for class org.jmol.awtjs.swing.Dimension
DIMENSION_TYPE_ALL - Static variable in class org.jmol.util.SimpleUnitCell
dimensionType - Variable in class org.jmol.util.SimpleUnitCell
  0x07 : z,y,x periodic
dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
dipole - Static variable in class org.jmol.script.T
Dipole - Class in org.jmol.shapespecial
Dipole() - Constructor for class org.jmol.shapespecial.Dipole
dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
dipoles - Variable in class org.jmol.shapespecial.Dipoles
Dipoles - Class in org.jmol.shapespecial
Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
dipolescale - Static variable in class org.jmol.script.T
DipolesRenderer - Class in org.jmol.renderspecial
DipolesRenderer() - Constructor for class org.jmol.renderspecial.DipolesRenderer
dipoleValue - Variable in class org.jmol.shapespecial.Dipole
direct - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
directedDistanceToPlane(P3, P4, P3) - Static method in class javajs.util.Measure
direction - Static variable in class org.jmol.script.T
dirLastExported - Variable in class jspecview.java.AwtFileHelper
dirLastOpened - Variable in class jspecview.java.AwtFileHelper
disable() - Method in class org.jmol.symmetry.CLEG.ClegNode
DISABLE - Static variable in class org.jmol.shapecgo.CGOMesh
disablepopupmenu - Static variable in class org.jmol.script.T
discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilContains(String) - Method in class jspecview.source.JDXReader
discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilContains(String) - Method in interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilContains2(String, String) - Method in class jspecview.source.JDXReader
discardLinesUntilContains2(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilContains2(String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilNonBlank() - Method in class jspecview.source.JDXReader
discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilNonBlank() - Method in interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardPreviousAtoms() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
discardTempDataSR(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
discrete - Static variable in class org.jmol.script.T
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.CmdExt
  The command dispatcher for the set of commands extended by this class.
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.IsoExt
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.ScriptExt
dispatchCommands(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
dispatchTouchEvent(JmolTouchSimulator.TouchData) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
  protocol modified by Bob Hanson for Jmol to demonstrate extended SparshUI protocol to include a return from the server indicating whether or not to consume this event.
displacement - Static variable in class org.jmol.script.T
display - Variable in class jspecview.common.JSViewer
display - Variable in class org.jmol.i18n.Language
display - Static variable in class org.jmol.script.T
display - Variable in class org.jmol.viewer.Viewer
display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
DISPLAY1D - Enum constant in enum class jspecview.common.ScriptToken
DISPLAY2D - Enum constant in enum class jspecview.common.ScriptToken
displayAtoms(BS, boolean, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
displayBonds(BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
displaycellparameters - Static variable in class org.jmol.script.T
displayConsole() - Method in class org.jmol.console.GenericConsole
displayed - Static variable in class org.jmol.script.T
displayFontName - Variable in class jspecview.common.ColorParameters
DISPLAYFONTNAME - Enum constant in enum class jspecview.common.ScriptToken
displayLoadErrors - Variable in class org.jmol.viewer.Viewer
displayMaxX - Variable in class org.jmol.util.GData
displayMaxX2 - Variable in class org.jmol.util.GData
displayMaxY - Variable in class org.jmol.util.GData
displayMaxY2 - Variable in class org.jmol.util.GData
displayMinX - Variable in class org.jmol.util.GData
displayMinX2 - Variable in class org.jmol.util.GData
displayMinY - Variable in class org.jmol.util.GData
displayMinY2 - Variable in class org.jmol.util.GData
displayName - Variable in class org.jmol.symmetry.SpaceGroup
DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
  Action calling evalStringQuiet(<action> + CheckBoxState)
DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
  Action calling moveTo()
DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
  Action calling setStatus()
DisplaySchemesProcessor - Class in jspecview.application
  `DisplaySchemesProcessor` loads and saves the display schemes of Jspecview.
DisplaySchemesProcessor() - Constructor for class jspecview.application.DisplaySchemesProcessor
  Initialises the `DisplaySchemesProcessor`
displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
displayType - Variable in class org.jmol.shapesurface.Contact
displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
dispose() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
dispose() - Method in class com.sparshui.server.GestureServer
dispose() - Method in interface jspecview.api.JSVViewPanel
dispose() - Method in interface jspecview.api.PlatformDialog
dispose() - Method in class jspecview.app.GenericMouse
dispose() - Method in class jspecview.app.JSVApp
dispose() - Method in class jspecview.common.IntegralData
dispose() - Method in class jspecview.common.JSViewer
dispose() - Method in class jspecview.common.PanelData
dispose() - Method in class jspecview.common.PanelNode
dispose() - Method in class jspecview.common.Spectrum
dispose() - Method in class jspecview.dialog.JSVDialog
dispose() - Method in class jspecview.java.AwtDialog
dispose() - Method in class jspecview.java.AwtMainPanel
dispose() - Method in class jspecview.java.AwtPanel
dispose() - Method in class jspecview.java.FileDropperJmol
dispose() - Method in class jspecview.js2d.JsDialog
dispose() - Method in class jspecview.js2d.JsMainPanel
dispose() - Method in class jspecview.js2d.JsPanel
dispose() - Method in class jspecview.source.JDXSource
dispose() - Method in interface org.jmol.api.GenericMouseInterface
dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
dispose() - Method in class org.jmol.api.JmolViewer
dispose() - Method in class org.jmol.awt.FileDropper
dispose() - Method in class org.jmol.awtjs.swing.JDialog
dispose() - Method in class org.jmol.awtjs2d.Mouse
dispose() - Method in class org.jmol.console.GenericConsole
dispose() - Method in class org.jmol.console.JmolConsole
dispose() - Method in class org.jmol.console.ScriptEditor
dispose() - Method in class org.jmol.consolejs.AppletConsole
dispose() - Method in class org.jmol.modelkit.ModelKit
dispose() - Method in class org.jmol.multitouch.ActionManagerMT
dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
dispose() - Method in class org.jmol.viewer.ActionManager
dispose() - Method in class org.jmol.viewer.Viewer
  end of life for this viewer
dispose() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
dispose() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
dispose(SC) - Method in class org.jmol.awt.AwtPopupHelper
dispose(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
dispose(SC) - Method in interface org.jmol.popup.PopupHelper
dispose(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Remove this component's HTML5 equivalent and clear references to it.
disposeGraphics(Object) - Method in class jspecview.java.AwtPlatform
disposeGraphics(Object) - Method in class jspecview.js2d.JsPlatform
disposeGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
disposeGraphics(Object) - Method in class org.jmol.awt.Platform
disposeGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
disposeMenu() - Method in class org.jmol.awtjs.swing.JPopupMenu
dist_counter - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
distance - Variable in class org.jmol.adapter.smarter.Bond
distance - Static variable in class org.jmol.script.T
distance(T3) - Method in class javajs.util.T3
  Returns the distance between this point and point p1.
distance_exclusion - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
distance2V(V3d, V3d) - Static method in class org.jmol.minimize.Util
distance4(P4) - Method in class javajs.util.P4
  Returns the distance between this point and point p1.
distancefactor - Static variable in class org.jmol.script.T
distanceMode - Variable in class org.jmol.quantum.MepCalculation
distancePointToPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
distances - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
distanceSquared(T3) - Method in class javajs.util.T3
  Computes the square of the distance between this point and point p1.
distanceToMappingPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
distanceToPlane(P4, T3) - Static method in class javajs.util.Measure
distanceToPlaneD(P4, float, P3) - Static method in class javajs.util.Measure
distanceToPlaneV(V3, float, P3) - Static method in class javajs.util.Measure
distinguishAndPropagateGroup(Chain, String, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.BioResolver
div - Static variable in class org.jmol.script.T
div(Quat) - Method in class javajs.util.Quat
divide - Static variable in class org.jmol.script.T
divLeft(Quat) - Method in class javajs.util.Quat
dmesh - Variable in class org.jmol.renderspecial.DrawRenderer
DmolReader - Class in org.jmol.adapter.readers.xtal
DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
dna - Static variable in class org.jmol.script.T
DNA - Enum constant in enum class org.jmol.c.STR
DNA_MASK - Static variable in class org.jmol.viewer.JC
doAction() - Method in class jme.JME
doAction(Object) - Method in class org.jmol.console.GenericConsole
doAdvanced(String) - Method in class jspecview.app.JSVApp
  called by Pro's popup window Advanced...
doAjax(Object, String, Object, boolean) - Method in interface javajs.api.js.J2SObjectInterface
doAjax(String, String, Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCapture() - Method in class org.jmol.viewer.Viewer
doCentralize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCircle(int, int, int, boolean) - Method in class javajs.export.PDFCreator
doClose - Variable in class javajs.img.ImageEncoder
doClose(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
doClose(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
Document - Interface in org.jmol.awtjs.swing
documentBase - Variable in class org.jmol.util.GenericApplet
doDebug - Variable in class org.jmol.quantum.QuantumCalculation
doDrop(PropertyChangeEvent) - Method in class jspecview.java.FileDropperJmol
doDrop(PropertyChangeEvent) - Method in class org.jmol.awt.FileDropper
doEval(String) - Method in class org.jmol.util.GenericApplet
  return RAW JAVASCRIPT OBJECT, NOT A STRING
doExitJmol() - Method in interface jspecview.api.AppletFrame
doExitJmol() - Method in class jspecview.appletjs.JSVApplet
doExitJmol() - Method in class jspecview.appletjs.JSVAppletPro
doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
doFormatText - Variable in class org.jmol.modelset.Text
doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
doGetModel(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
doGetSmiles - Variable in class org.jmol.inchi.InchiJmol
doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
doIterate - Variable in class org.jmol.jvxl.data.VolumeData
dollarsign - Static variable in class org.jmol.script.T
doLogLevel(boolean) - Static method in class org.jmol.util.Logger
  Indicates if the level is logged.
domains - Static variable in class org.jmol.script.T
doMenu - Variable in class jme.JME
doMenuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
doMenuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
doMenuSelected() - Method in class jspecview.application.ApplicationMenu
doMouseAtomAction() - Method in class jme.JME
doMouseBondAction() - Method in class jme.JME
doMouseClicked(int, int, boolean) - Method in class jspecview.common.PanelData
doMouseDragged(int, int) - Method in class jspecview.common.PanelData
doMouseMoved(int, int) - Method in class jspecview.common.PanelData
doMousePressed(int, int) - Method in class jspecview.common.PanelData
doMouseReleased(int, int, boolean) - Method in class jspecview.common.PanelData
DOMReader - Class in org.jmol.io
DOMReader() - Constructor for class org.jmol.io.DOMReader
DOMResolve(Map) - Static method in class org.jmol.adapter.smarter.Resolver
  a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
done - Variable in class org.jmol.adapter.readers.cif.MMCifReader
done() - Method in class jspecview.dialog.JSVDialog
doNewMoleculeAction(int, int) - Method in class jme.JME
DONOR - Enum constant in enum class org.jmol.c.HB
DoNotAddH - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  All hydrogens in input structure are explicit [compatible with standard InChI]
doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doPolygon(int[], int[], int, boolean) - Method in class javajs.export.PDFCreator
doPreSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
doPreSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.FSGOutputReader
doPreSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
doPreSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
doPreviewAction(boolean) - Method in class org.jmol.dialog.FilePreview
doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doReadMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doRect(int, int, int, int, boolean) - Method in class javajs.export.PDFCreator
doRepaint(boolean) - Method in interface jspecview.api.JSVPanel
doRepaint(boolean) - Method in class jspecview.java.AwtPanel
doRepaint(boolean) - Method in class jspecview.js2d.JsPanel
doReport() - Method in class org.jmol.script.ScriptEval
doResume() - Method in class org.jmol.console.ScriptEditor
doSendCallback(CBK, Object, Object[], String) - Method in class org.jmol.util.GenericApplet
doShowDocument(URL) - Method in class org.jmol.util.GenericApplet
doShowStatus(String) - Method in class org.jmol.util.GenericApplet
doSort - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
doStep() - Method in class org.jmol.console.ScriptEditor
doStroke(Object, boolean) - Method in class jspecview.common.PDFWriter
doStroke(Object, boolean) - Method in class jspecview.java.AwtG2D
doStroke(Object, boolean) - Method in class jspecview.js2d.JsG2D
doStroke(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
doStroke(Object, boolean) - Method in class org.jmol.awt.AwtG2D
doStroke(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
dot - Static variable in class org.jmol.script.T
dot(Quat) - Method in class javajs.util.Quat
dot(T3) - Method in class javajs.util.T3
  Vector dot product.
dot(V3d) - Method in class javajs.util.V3d
  Computes the dot product of the this vector and vector v.
dot_as_spheres - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_density - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_hydrogens - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_lighting - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_normals - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_solvent - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dot_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
doTags - Variable in class jme.JME
dotdensity - Static variable in class org.jmol.script.T
dotProduct(double, double, double, double) - Static method in class jme.JMEUtil
doTransform - Variable in class org.jmol.adapter.writers.CMLWriter
doTransform4D - Variable in class org.jmol.viewer.TransformManager
doTranslate - Variable in class org.jmol.util.GenericApplet
dots - Static variable in class org.jmol.script.T
Dots - Class in org.jmol.shapespecial
Dots() - Constructor for class org.jmol.shapespecial.Dots
dotscale - Static variable in class org.jmol.script.T
dotsOrDashes - Variable in class org.jmol.render.FontLineShapeRenderer
DotsRenderer - Class in org.jmol.renderspecial
DotsRenderer() - Constructor for class org.jmol.renderspecial.DotsRenderer
dotsselectedonly - Static variable in class org.jmol.script.T
dotsurface - Static variable in class org.jmol.script.T
dotted - Static variable in class org.jmol.script.T
DOTWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
DOUBLE - Enum constant in enum class org.jmol.c.STER
DOUBLE - Static variable in class org.jmol.viewer.binding.Binding
doubleLength(Object) - Static method in class javajs.util.AU
  Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
doubleLengthBool(boolean[]) - Static method in class javajs.util.AU
doubleLengthByte(byte[]) - Static method in class javajs.util.AU
doubleLengthF(float[]) - Static method in class javajs.util.AU
doubleLengthI(int[]) - Static method in class javajs.util.AU
doubleLengthS(String[]) - Static method in class javajs.util.AU
doubleLengthShort(short[]) - Static method in class javajs.util.AU
doubleprecision - Static variable in class org.jmol.script.T
DOWN - Static variable in class org.jmol.viewer.binding.Binding
downsample - Static variable in class org.jmol.script.T
downsample2d(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
downsampleFactor - Variable in class org.jmol.jvxl.readers.JvxlReader
downsampleFactor - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
downsampleFactor - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
downsampleRemainders - Variable in class org.jmol.jvxl.readers.JvxlReader
downsampleRemainders - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
downsampleRemainders - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
doZoomLinked(GraphSet, double, double, boolean, boolean, boolean) - Method in class jspecview.common.PanelData
dpi - Variable in class javajs.img.ImageEncoder
DRAG - Static variable in class org.jmol.viewer.binding.Binding
DRAG_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
DRAG_EVENT - Static variable in class com.sparshui.GestureType
DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
DRAG_GESTURE - Static variable in class com.sparshui.GestureType
DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
DragBinding - Class in org.jmol.viewer.binding
DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
DRAGDROP - Enum constant in enum class org.jmol.c.CBK
dragEnter(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
dragEnter(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
dragEnter(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
DragEvent - Class in com.sparshui.common.messages.events
DragEvent() - Constructor for class com.sparshui.common.messages.events.DragEvent
DragEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.DragEvent
  Constructs a dragEvent from a complete serialized version of the drag event.
DragEvent(float, float, int, long) - Constructor for class com.sparshui.common.messages.events.DragEvent
dragExit(DropTargetEvent) - Method in class jspecview.java.AwtFileDropper
dragExit(DropTargetEvent) - Method in class jspecview.java.FileDropperJmol
dragExit(DropTargetEvent) - Method in class org.jmol.awt.FileDropper
dragged - Variable in class org.jmol.viewer.ActionManager
dragged(long, int, int, int) - Method in class jspecview.app.GenericMouse
DRAGGED - Static variable in class org.jmol.awtjs.Event
dragOver(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
dragOver(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
dragOver(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
dragselected - Static variable in class org.jmol.script.T
draw - Static variable in class org.jmol.script.T
draw(Graphics) - Method in class jme.AtomDisplayLabel
draw(Graphics) - Method in class jme.JMEmol
Draw - Class in org.jmol.shapespecial
Draw() - Constructor for class org.jmol.shapespecial.Draw
DRAW_ARRAYS - Static variable in class org.jmol.shapecgo.CGOMesh
DRAW_BUFFERS - Static variable in class org.jmol.shapecgo.CGOMesh
DRAW_BUFFERS_INDEXED - Static variable in class org.jmol.shapecgo.CGOMesh
DRAW_BUFFERS_NOT_INDEXED - Static variable in class org.jmol.shapecgo.CGOMesh
DRAW_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
draw_frames - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
draw_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
Draw.EnumDrawType - Enum Class in org.jmol.shapespecial
draw000 - Variable in class org.jmol.render.FontLineShapeRenderer
drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
drawAtom(Atom, float) - Method in interface org.jmol.api.JmolRendererInterface
drawAtom(Atom, float) - Method in class org.jmol.export.Export3D
drawAtom(Atom, float) - Method in class org.jmol.g3d.Graphics3D
drawAxes(P3[], String, String) - Method in class org.jmol.modelkit.ModelKit
drawBond(P3, P3, short, short, byte, short, int) - Method in interface org.jmol.api.JmolRendererInterface
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.export.Export3D
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
  draws a simple circle (draw circle)
drawCircle(Object, int, int, int) - Method in class jspecview.common.PDFWriter
drawCircle(Object, int, int, int) - Method in class jspecview.java.AwtG2D
drawCircle(Object, int, int, int) - Method in class jspecview.js2d.JsG2D
drawCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawCoordinates(Object, int, int, int) - Method in class jspecview.common.PanelData
drawDashedCylinder(JmolRendererInterface, int, int, int, int, int, int, int[], int, short, short, int, boolean, P3i) - Static method in class org.jmol.render.FontLineShapeRenderer
drawDashedLineBits(int, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.export.Export3D
drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawEdge(int, int, boolean, T3, T3, P3i, P3i) - Method in class org.jmol.render.MeshRenderer
drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
drawEllipse(P3, P3, P3, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.export.Export3D
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  draws a ring and filled circle (halos, draw CIRCLE, draw handles)
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
  draws a screened circle ...
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawfontsize - Static variable in class org.jmol.script.T
drawGraph(Object, Object, Object, int, int, boolean, boolean) - Method in class jspecview.common.PanelData
  Draws the Spectrum to the panel
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.common.PDFWriter
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.java.AwtG2D
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.js2d.JsG2D
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawHermite4(int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in interface org.jmol.api.JmolRendererInterface
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.export.Export3D
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.g3d.Graphics3D
drawHKL(Viewer, String, P4, P3[]) - Method in class org.jmol.util.BZone
drawhover - Static variable in class org.jmol.script.T
drawImage(Object, int, int, int, int, int, int, int, int) - Method in class javajs.export.PDFCreator
drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
drawImage(Object, Object, int, int, int, int, boolean) - Method in class jspecview.java.AwtPlatform
drawImage(Object, Object, int, int, int, int, boolean) - Method in class jspecview.js2d.JsPlatform
drawImage(Object, Object, int, int, int, int, boolean) - Method in interface org.jmol.api.GenericPlatform
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awt.Platform
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs.Platform
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Platform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class jspecview.java.AwtPlatform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class jspecview.js2d.JsPlatform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
drawing - Static variable in class org.jmol.script.T
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.MeasuresRenderer
drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawLine(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
drawLine(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
drawLine(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
drawLine(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawLine(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawLine(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawLine2(JmolRendererInterface, int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
drawLineAB(P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawLineAB(P3, P3) - Method in class org.jmol.export.Export3D
drawLineAB(P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawLineABBits(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
drawLineBits(short, short, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawLineBits(short, short, P3, P3) - Method in class org.jmol.export.Export3D
drawLineBits(short, short, P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawLineBits(P3, P3, short, short) - Method in class org.jmol.export.Export3D
drawLinePixels(P3i, P3i, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.export.Export3D
drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.g3d.Graphics3D
drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.util.GData
drawLineXYZ(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
DrawMesh - Class in org.jmol.shapespecial
DrawMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
drawpicking - Static variable in class org.jmol.script.T
drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
drawPolygon(Object, int[], int[], int) - Method in class jspecview.common.PDFWriter
drawPolygon(Object, int[], int[], int) - Method in class jspecview.java.AwtG2D
drawPolygon(Object, int[], int[], int) - Method in class jspecview.js2d.JsG2D
drawPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
drawQuadrilateralBits(JmolRendererInterface, short, P3, P3, P3, P3) - Method in class org.jmol.util.GData
drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.util.Escape
drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
  draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
  draws a rectangle
drawRect(Graphics) - Method in class jme.AtomDisplayLabel
drawRect(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
drawRect(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
drawRect(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
drawRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
DrawRenderer - Class in org.jmol.renderspecial
DrawRenderer() - Constructor for class org.jmol.renderspecial.DrawRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.BackboneRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.CartoonRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.RibbonsRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.RocketsRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.StrandsRenderer
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.TraceRenderer
drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.render.FontLineShapeRenderer
drawString(Object, String, int, int) - Method in class jspecview.common.PDFWriter
drawString(Object, String, int, int) - Method in class jspecview.java.AwtG2D
drawString(Object, String, int, int) - Method in class jspecview.js2d.JsG2D
drawString(Object, String, int, int) - Method in interface org.jmol.api.GenericGraphics
drawString(Object, String, int, int) - Method in class org.jmol.awt.AwtG2D
drawString(Object, String, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawString(String, Font, int, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
  draws the specified string in the current font.
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.export.Export3D
  draws the specified string in the current font.
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
  draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
  draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.export.Export3D
  draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
  draws the specified string in the current font.
drawStringRotated(Object, String, int, int, double) - Method in class jspecview.common.PDFWriter
drawStringRotated(Object, String, int, int, double) - Method in class jspecview.java.AwtG2D
drawStringRotated(Object, String, int, int, double) - Method in class jspecview.js2d.JsG2D
drawStringRotated(Object, String, int, int, double) - Method in interface org.jmol.api.GenericGraphics
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awt.AwtG2D
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awtjs2d.JsG2D
drawStringRotated(String, int, int, int) - Method in class javajs.export.PDFCreator
drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
drawSymmetry(String, boolean, int, String, int, P3, P3, P3, int, int, int, int[], boolean) - Method in class org.jmol.modelkit.ModelKit
drawSymop(int, int) - Method in class org.jmol.modelkit.ModelKit
  from set picking symop
drawTicks(int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
drawTitle(Object, int, int, String) - Method in class jspecview.common.PanelData
  Draws Title
drawTriangle(P3i, short, P3i, short, P3i, short, int, int) - Method in class org.jmol.render.MeshRenderer
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.export.Export3D
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.g3d.Graphics3D
drawTriangleBits(JmolRendererInterface, P3, short, P3, short, P3, short, int) - Method in class org.jmol.util.GData
drawTriangles - Variable in class org.jmol.shape.Mesh
drawType - Variable in class org.jmol.shapespecial.DrawMesh
drawUnitCell(String, T3, String) - Method in class org.jmol.modelkit.ModelKit
drawXAxisLeftToRight - Variable in class jspecview.common.PanelData
DRIVER_NONE - Static variable in class com.sparshui.common.messages.events.EventType
DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
drop(DropTargetDropEvent) - Method in class jspecview.java.AwtFileDropper
drop(DropTargetDropEvent) - Method in class jspecview.java.FileDropperJmol
drop(DropTargetDropEvent) - Method in class org.jmol.awt.FileDropper
dropActionChanged(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
dropActionChanged(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
DS - Static variable in class org.jmol.quantum.QS
dslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
dssp - Static variable in class org.jmol.script.T
DSSP - Class in org.jmol.dssx
DSSP() - Constructor for class org.jmol.dssx.DSSP
  /////////////////// DSSP /////////////////////
dsspcalchydrogen - Static variable in class org.jmol.script.T
dssr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
dssr - Static variable in class org.jmol.script.T
DSSR0 - Class in org.jmol.dssx
  The original non-JSON parser for output from 3DNA web service.
DSSR0() - Constructor for class org.jmol.dssx.DSSR0
DSSR1 - Class in org.jmol.dssx
  A parser for output from 3DNA web service.
DSSR1() - Constructor for class org.jmol.dssx.DSSR1
dssrBox - Variable in class org.jmol.modelsetbio.NucleicMonomer
dssrBoxHeight - Variable in class org.jmol.modelsetbio.NucleicMonomer
dssrCache - Variable in class org.jmol.modelset.Model
dssrFrame - Variable in class org.jmol.modelsetbio.NucleicMonomer
dssrNT - Variable in class org.jmol.modelset.Group
DTI - Enum constant in enum class org.jmol.c.STER
dump_binary - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dumpArray(String, float[][], int, int, int, int) - Static method in class javajs.util.AU
dumpContainer(Container, String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
dumpInfo() - Method in class org.jmol.symmetry.SpaceGroup
dumpIntArray(int[], int) - Static method in class javajs.util.AU
dumpList - Static variable in class jspecview.popup.JSVGenericPopup
dVal(String) - Static method in class javajs.util.PT
dyMode - Variable in class jme.JME
dynamic_measures - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dynamic_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dynamic_width_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dynamic_width_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dynamic_width_min - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
dynamicmeasurements - Static variable in class org.jmol.script.T

## E

e - Variable in class org.jmol.scriptext.ScriptExt
e(Object) - Static method in class org.jmol.util.Escape
E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
eAD(double[]) - Static method in class org.jmol.util.Escape
eAF(float[]) - Static method in class org.jmol.util.Escape
eAI(int[]) - Static method in class org.jmol.util.Escape
eAP(T3[]) - Static method in class org.jmol.util.Escape
eAS(String[], boolean) - Static method in class org.jmol.util.Escape
EAST - Static variable in class org.jmol.awtjs.swing.BorderLayout
EAST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
eBond(BS) - Static method in class org.jmol.util.Escape
eBS(BS) - Static method in class org.jmol.util.Escape
ec - Variable in class org.jmol.shapespecial.Dots
eccentricity - Static variable in class org.jmol.script.T
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
echo - Static variable in class org.jmol.script.T
Echo - Class in org.jmol.shape
Echo() - Constructor for class org.jmol.shape.Echo
ECHO - Enum constant in enum class org.jmol.c.CBK
ECHO_BOTTOM - Static variable in class org.jmol.viewer.JC
ECHO_MIDDLE - Static variable in class org.jmol.viewer.JC
ECHO_TOP - Static variable in class org.jmol.viewer.JC
ECHO_XY - Static variable in class org.jmol.viewer.JC
ECHO_XYZ - Static variable in class org.jmol.viewer.JC
EchoRenderer - Class in org.jmol.render
EchoRenderer() - Constructor for class org.jmol.render.EchoRenderer
ed - Static variable in class org.jmol.script.T
Edge - Class in org.jmol.util
Edge() - Constructor for class org.jmol.util.Edge
EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
edgeA - Static variable in class org.jmol.util.Triangulator
edgeB - Static variable in class org.jmol.util.Triangulator
edgeC - Static variable in class org.jmol.util.Triangulator
edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
edges - Static variable in class org.jmol.script.T
edges - Static variable in class org.jmol.util.BoxInfo
EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
EDGES_ONLY - Static variable in class org.jmol.shapespecial.Polyhedra
edgesonly - Static variable in class org.jmol.script.T
edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexes - Static variable in class org.jmol.util.TriangleData
edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edit_light - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
editButton - Variable in class org.jmol.console.GenericConsole
editor - Variable in class org.jmol.console.ScriptEditor
editor_auto_dihedral - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
editor_auto_origin - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
editor_bond_cycle_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
editor_label_fragments - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
editPane - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
eds - Static variable in class org.jmol.script.T
edsdiff - Static variable in class org.jmol.script.T
Eigen - Class in javajs.util
  Eigenvalues and eigenvectors of a real matrix.
Eigen() - Constructor for class javajs.util.Eigen
EigenInterface - Interface in javajs.api
eigenSignMask - Variable in class org.jmol.util.Tensor
eigenValues - Variable in class org.jmol.util.Tensor
eigenVectors - Variable in class org.jmol.util.Tensor
element - Static variable in class org.jmol.script.T
ELEMENT_NUMBER_MASK - Static variable in class org.jmol.util.Elements
elementColors - Variable in class jspecview.common.ColorParameters
elementCounts - Variable in class org.jmol.util.JmolMolecule
elementkey - Static variable in class org.jmol.script.T
elementLabel - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
elementNames - Static variable in class org.jmol.util.Elements
elementNumber - Variable in class org.jmol.adapter.smarter.Atom
elementNumberFromName(String) - Static method in class org.jmol.util.Elements
elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
elementNumberMax - Static variable in class org.jmol.util.Elements
  one larger than the last elementNumber, same as elementSymbols.length
elementNumberMax - Variable in class org.jmol.util.JmolMolecule
Elements - Class in org.jmol.util
Elements() - Constructor for class org.jmol.util.Elements
elementsPresent - Variable in class org.jmol.modelset.ModelSet
elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
elementSymbols - Static variable in class org.jmol.util.Elements
  The default elementSymbols.
elemisono - Static variable in class org.jmol.script.T
elemno - Static variable in class org.jmol.script.T
elemNo - Variable in class org.jmol.quantum.SlaterData
ellipsoid - Static variable in class org.jmol.script.T
Ellipsoid - Class in org.jmol.shapespecial
ELLIPSOID - Static variable in class org.jmol.shapecgo.CGOMesh
ellipsoid_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ellipsoid_probability - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ellipsoid_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ellipsoid_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ellipsoid_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ellipsoidarcs - Static variable in class org.jmol.script.T
ellipsoidarrows - Static variable in class org.jmol.script.T
ellipsoidaxes - Static variable in class org.jmol.script.T
ellipsoidaxisdiameter - Static variable in class org.jmol.script.T
ellipsoidball - Static variable in class org.jmol.script.T
ellipsoiddotcount - Static variable in class org.jmol.script.T
ellipsoiddots - Static variable in class org.jmol.script.T
ellipsoidfill - Static variable in class org.jmol.script.T
Ellipsoids - Class in org.jmol.shapespecial
Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
ellipsoidShades - Variable in class org.jmol.util.Shader
EllipsoidsRenderer - Class in org.jmol.renderspecial
EllipsoidsRenderer() - Constructor for class org.jmol.renderspecial.EllipsoidsRenderer
elsecmd - Static variable in class org.jmol.script.T
elseif - Static variable in class org.jmol.script.T
embedded - Variable in class jme.JME
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JC
embeddingSymmetry - Variable in class org.jmol.symmetry.SpecialGroup
  the space group and unit cell that this group relates to; may be null
embedScript(String) - Static method in class org.jmol.viewer.JC
EMPTY - Static variable in interface javajs.api.GenericCifDataParser
EMPTY - Static variable in class org.jmol.adapter.readers.cif.CifReader
  /////////////////////////////////////////////////////////////
emptySet - Static variable in class org.jmol.util.BSUtil
ENABLE - Static variable in class org.jmol.shapecgo.CGOMesh
enabled - Variable in class org.jmol.awtjs.swing.Component
enableShell(int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...
ENABLEZOOM - Enum constant in enum class jspecview.common.ScriptToken
ENC_CALC_MAX_DIST - Static variable in class org.jmol.viewer.JC
encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
encodeColor(short) - Static method in class org.jmol.shape.Shape
encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
Encoding - Enum Class in javajs.util
end - Static variable in class org.jmol.script.T
end() - Method in class org.jmol.util.PatternMatcher.JSPattern
END - Static variable in class org.jmol.shapecgo.CGOMesh
END_ELEMENT - Static variable in class jspecview.source.XMLParser
endAssignment() - Method in class org.jmol.script.ScriptMathProcessor
endcap - Variable in class org.jmol.render.FontLineShapeRenderer
ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
ENDCAPS_FLAT_TO_SPHERICAL - Static variable in class org.jmol.util.GData
ENDCAPS_HIDDEN - Static variable in class org.jmol.util.GData
ENDCAPS_NONE - Static variable in class org.jmol.util.GData
ENDCAPS_OPEN_TO_SPHERICAL - Static variable in class org.jmol.util.GData
ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
endChainID - Variable in class org.jmol.adapter.smarter.Structure
ENDCOM - Static variable in class javajs.api.GenericZipInputStream
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
ENDHDR - Static variable in class javajs.api.GenericZipInputStream
endifcmd - Static variable in class org.jmol.script.T
endIndex - Variable in class jspecview.export.AMLExporter
endIndex - Variable in class jspecview.export.CMLExporter
ENDINDEX - Enum constant in enum class jspecview.common.ScriptToken
endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
endLayout() - Method in interface jspecview.api.PlatformDialog
endLayout() - Method in class jspecview.java.AwtDialog
endLayout() - Method in class jspecview.js2d.JsDialog
endMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
endOfData - Variable in class org.jmol.jvxl.readers.JvxlReader
endOfData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
endOfData - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
ENDOFF - Static variable in class javajs.api.GenericZipInputStream
endRecording() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
endRendering() - Method in class org.jmol.g3d.Graphics3D
endRendering() - Method in class org.jmol.util.GData
endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
ENDSIG - Static variable in class javajs.api.GenericZipInputStream
ENDSIZ - Static variable in class javajs.api.GenericZipInputStream
ENDSUB - Static variable in class javajs.api.GenericZipInputStream
ENDTOT - Static variable in class javajs.api.GenericZipInputStream
energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
energy - Static variable in class org.jmol.script.T
ENERGY - Enum constant in enum class org.jmol.c.PAL
energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyunits - Static variable in class org.jmol.script.T
energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
energyUnits - Variable in class org.jmol.viewer.GlobalSettings
ensureLength(Object, int) - Static method in class javajs.util.AU
  Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
ensureLengthA(float[], int) - Static method in class javajs.util.AU
ensureLengthByte(byte[], int) - Static method in class javajs.util.AU
ensureLengthI(int[], int) - Static method in class javajs.util.AU
ensureLengthS(String[], int) - Static method in class javajs.util.AU
ensureLengthShort(short[], int) - Static method in class javajs.util.AU
ensureSignedBytes(byte[]) - Static method in class javajs.util.AU
  Ensure that we have signed and not unsigned bytes coming out of any process, but particularly out of file reading.
entered(long, int, int) - Method in class jspecview.app.GenericMouse
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
ENV_CALC_MAX_LEVEL - Static variable in class org.jmol.viewer.JC
EnvelopeCalculation - Class in org.jmol.geodesic
EnvelopeCalculation() - Constructor for class org.jmol.geodesic.EnvelopeCalculation
EOF - Static variable in class jspecview.source.XMLParser
eP(T3) - Static method in class org.jmol.util.Escape
  must be its own, because of the possibility of being null
eP4(P4) - Static method in class org.jmol.util.Escape
equals(int[], int[]) - Static method in class jme.JMEUtil
equals(Object) - Method in class javajs.util.A4
  Returns true if the Object o is of type AxisAngle4f and all of the data members of o1 are equal to the corresponding data members in this AxisAngle4f.
equals(Object) - Method in class javajs.util.BArray
equals(Object) - Method in class javajs.util.BS
  Compares this object against the specified object.
equals(Object) - Method in class javajs.util.M3
  Returns true if the Object o is of type Matrix3f and all of the data members of t1 are equal to the corresponding data members in this Matrix3f.
equals(Object) - Method in class javajs.util.M4
  Returns true if the Object o is of type Matrix4f and all of the data members of t1 are equal to the corresponding data members in this Matrix4f.
equals(Object) - Method in class javajs.util.T3
  Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this
equals(Object) - Method in class javajs.util.T3d
  Returns true if all of the data members of Tuple3d t1 are equal to the corresponding data members in this
equals(Object) - Method in class javajs.util.T3i
  Returns true if the Object o is of type Tuple3i and all of the data members of t are equal to the corresponding data members in this Tuple3i.
equals(Object) - Method in class javajs.util.T4
  Returns true if all of the data members of Object are equal to the corresponding data members in this
equals(Object) - Method in class org.jmol.modelset.Atom
equals(Object) - Method in class org.jmol.script.T
equals(Object) - Method in class org.jmol.smiles.SmilesSearch
equals(Coordinate) - Method in class jspecview.common.Coordinate
  Indicates whether some other Coordinate is equal to this one
err() - Method in class javajs.util.M34
error - Variable in class org.jmol.script.ScriptError
error - Variable in class org.jmol.script.ScriptParallelProcessor
error - Static variable in class org.jmol.script.T
error - Variable in class org.jmol.shapespecial.Dipole
error(int) - Method in class org.jmol.script.ScriptError
error(int) - Method in class org.jmol.script.ScriptCompiler
error(int) - Method in class org.jmol.scriptext.ScriptExt
error(String) - Method in class org.jmol.util.DefaultLogger
error(String) - Static method in class org.jmol.util.Logger
  Writes a log at ERROR level.
error(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at ERROR level.
error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
ERROR - Enum constant in enum class org.jmol.c.CBK
ERROR - Static variable in class jspecview.source.JDXDataObject
  Error number that is returned when a min value is undefined
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptError
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptCompiler
ERROR_badContext - Static variable in class org.jmol.script.ScriptCompiler
ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptError
ERROR_cannotSet - Static variable in class org.jmol.script.ScriptError
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptCompiler
ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptCompiler
ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptError
ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptError
ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptError
ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptError
ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptError
ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptError
ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptError
ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptCompiler
ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptError
ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptError
ERROR_MESSAGE - Static variable in class jspecview.dialog.DialogManager
ERROR_missingEnd - Static variable in class org.jmol.script.ScriptCompiler
ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptError
ERROR_moIndex - Static variable in class org.jmol.script.ScriptError
ERROR_moModelError - Static variable in class org.jmol.script.ScriptError
ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptError
ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptError
ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptError
ERROR_noData - Static variable in class org.jmol.script.ScriptError
ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptError
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptError
ERROR_operationCanceled - Static variable in class org.jmol.script.ScriptError
ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptCompiler
ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptCompiler
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptCompiler
ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptCompiler
ERROR_what - Static variable in class org.jmol.script.ScriptError
ERROR_writeWhat - Static variable in class org.jmol.script.ScriptError
errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
errorEx(String, Throwable) - Static method in class org.jmol.util.Logger
  Writes a log at ERROR level with detail on exception.
errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at ERROR level with detail on exception.
errorIntStr2(int, String, String) - Method in class org.jmol.script.ScriptCompiler
errorLine - Variable in class org.jmol.script.ScriptCompiler
errorLog - Variable in class jspecview.source.AnIMLReader
errorLog - Variable in class jspecview.source.NMRMLReader
errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
errorMessage - Variable in class org.jmol.script.ScriptContext
errorMessage - Variable in class org.jmol.script.ScriptError
errorMessage - Variable in class org.jmol.script.ScriptCompiler
errorMessageUntranslated - Variable in class org.jmol.script.ScriptError
errorMessageUntranslated - Variable in class org.jmol.script.ScriptCompiler
errorStr(int, String) - Method in class org.jmol.script.ScriptError
errorStr(int, String) - Method in class org.jmol.script.ScriptCompiler
errorStr2(int, String, String) - Method in class org.jmol.script.ScriptError
errorStr2(String, String) - Method in class org.jmol.script.ScriptCompiler
errorType - Variable in class org.jmol.script.ScriptContext
errorType - Variable in class org.jmol.script.ScriptError
errorType - Variable in class org.jmol.script.ScriptCompiler
errString - Variable in class org.jmol.symmetry.CLEG.ClegData
esc(String) - Static method in class javajs.util.PT
escape() - Method in class org.jmol.script.SV
escape(BS, char, char) - Static method in class javajs.util.BS
Escape - Class in org.jmol.util
Escape() - Constructor for class org.jmol.util.Escape
escapeColor(int) - Static method in class org.jmol.util.Escape
escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
escapeHelical(String, int, P3, P3, T3[]) - Static method in class org.jmol.util.Escape
  Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxis
escapeHTML(String) - Static method in class org.jmol.i18n.GT
escapeKeyPressed(boolean) - Method in class jspecview.common.PanelData
escapeMap(Map) - Static method in class org.jmol.util.Escape
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
escapeMultiplier(T3) - Static method in class org.jmol.util.SimpleUnitCell
  Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
escapeUrl(String) - Static method in class javajs.util.PT
escF(float) - Static method in class javajs.util.PT
  ensures that a float turned to string has a decimal point
escUnicode(String) - Static method in class javajs.util.PT
EspressoReader - Class in org.jmol.adapter.readers.xtal
EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
eta - Static variable in class org.jmol.script.T
eV(Lst) - Static method in class org.jmol.util.Escape
eval - Static variable in class org.jmol.script.T
eval - Variable in class org.jmol.thread.JmolThread
eval - Variable in class org.jmol.viewer.Viewer
eval(String) - Method in interface org.jmol.api.JmolStatusListener
eval(String) - Method in class org.jmol.util.GenericApplet
eval(String) - Method in class org.openscience.jmol.app.status.StatusListener
EVAL - Enum constant in enum class org.jmol.c.CBK
evalCallback(String, Object[], boolean) - Method in interface org.jmol.api.JmolScriptManager
evalCallback(String, Object[], boolean) - Method in class org.jmol.script.ScriptManager
evalCallback(String, Object[], boolean) - Method in class org.jmol.viewer.Viewer
evalError(String, String) - Method in class org.jmol.script.ScriptError
evalFile(String) - Method in interface org.jmol.api.JmolScriptManager
evalFile(String) - Method in class org.jmol.api.JmolViewer
evalFile(String) - Method in class org.jmol.script.ScriptManager
evalFile(String) - Method in class org.jmol.viewer.Viewer
evalFileArgs(String, String) - Method in interface org.jmol.api.JmolScriptManager
evalFileArgs(String, String) - Method in class org.jmol.api.JmolViewer
evalFileArgs(String, String) - Method in class org.jmol.script.ScriptManager
evalFileArgs(String, String) - Method in class org.jmol.viewer.Viewer
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.api.JmolScriptEvaluator
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEval
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.api.JmolScriptEvaluator
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptEval
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.scriptext.CmdExt
  used for TRY command
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
evalString(String) - Method in class org.jmol.api.JmolViewer
evalString(String) - Method in class org.jmol.viewer.Viewer
evalStringGUI(String) - Method in class org.jmol.viewer.Viewer
  Run a script asynchronously, adding the GUI flag to indicate that we should fire the SELECT callback at the end if there is one.
evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
evalStringQuietSync(String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
evaluate(ScriptMathProcessor, T, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateCompiledScript(Object[], boolean, boolean, boolean, boolean, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
evaluateCompiledScript(Object[], boolean, boolean, boolean, boolean, SB, boolean) - Method in class org.jmol.script.ScriptEval
evaluateExpression(Object) - Method in class org.jmol.api.JmolViewer
evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
  synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
evaluateExpression(Object, boolean, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
evaluateExpression(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
  a general-use method to evaluate a "SET" type expression.
evaluateExpressionAsVariable(Object) - Method in class org.jmol.api.JmolViewer
evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
Event - Class in org.jmol.awtjs
Event - Interface in com.sparshui.common
  This interface must be implemented by all user-defined events.
Event() - Constructor for class org.jmol.awtjs.Event
EVENT - Static variable in class com.sparshui.common.ClientProtocol.MessageType
eventApply() - Method in class jspecview.dialog.JSVDialog
eventFocus() - Method in class jspecview.dialog.JSVDialog
EventManager - Interface in org.jmol.api
EventType - Class in com.sparshui.common.messages.events
  This is an enumeration of all event types currently available.
EventType() - Constructor for class com.sparshui.common.messages.events.EventType
evspoints - Variable in class jspecview.source.AnIMLReader
evspoints - Variable in class jspecview.source.NMRMLReader
EX - Variable in class org.jmol.quantum.MOCalculation
excl_display_lists_shaders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
excludeAtoms(BS, boolean) - Method in class org.jmol.viewer.SelectionManager
excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
execLoad(String, String) - Method in class jspecview.common.JSViewer
execute(String) - Method in class org.jmol.console.AppletConsole
execute(String) - Method in class org.jmol.console.GenericConsole
execute(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
executionPaused - Variable in class org.jmol.script.ScriptContext
executionStepping - Variable in class org.jmol.script.ScriptContext
executor - Variable in class org.jmol.viewer.Viewer
execView(String, boolean) - Method in class jspecview.common.JSViewer
exit - Static variable in class org.jmol.script.T
exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
exitBondRotation() - Method in class org.jmol.awt.AwtModelKitPopup
exitBondRotation() - Method in class org.jmol.modelkit.ModelKitPopup
exitBondRotation(String) - Method in class org.jmol.modelkit.ModelKit
exited(long, int, int) - Method in class jspecview.app.GenericMouse
exitjmol - Static variable in class org.jmol.script.T
exitJmol() - Method in class org.jmol.viewer.Viewer
exitJSpecView(boolean, Object) - Method in class jspecview.app.JSVAppPro
exitJSpecView(boolean, Object) - Method in class jspecview.application.JSpecView
  StatusListener (Jmol will not actually close; we will here if stand-alone)
exitJSpecView(boolean, Object) - Method in interface org.jmol.api.JSVInterface
exitJSpecView(boolean, Object) - Method in class org.openscience.jmol.app.status.StatusListener
exitMeasurementMode(String) - Method in class org.jmol.viewer.ActionManager
expandFloatArray(float[], int, boolean) - Method in class org.jmol.script.ScriptEval
  Accepts a float array and expands [1 -3] to [1 2 3], for example.
explicitID - Variable in class org.jmol.shape.MeshCollection
export(String, int) - Method in class jspecview.appletjs.JSVApplet
  Deprecated.
export(String, int) - Method in class jspecview.common.JSViewer
EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JC
EXPORT_NOT - Static variable in class org.jmol.util.GData
EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
export3D - Variable in class org.jmol.export.___Exporter
Export3D - Class in org.jmol.export
Export3D() - Constructor for class org.jmol.export.Export3D
exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExportChoiceListener() - Constructor for class org.jmol.dialog.Dialog.ExportChoiceListener
exportCmd(JSVPanel, Lst, boolean) - Method in interface jspecview.export.ExportInterface
  from EXPORT command
exporter - Variable in class org.jmol.export.Export3D
Exporter - Class in jspecview.export
Exporter() - Constructor for class jspecview.export.Exporter
ExportInterface - Interface in jspecview.api
ExportInterface - Interface in jspecview.export
exportPass - Variable in class org.jmol.render.MeshRenderer
exportPrecision - Variable in class jspecview.common.ScaleData
exportscale - Static variable in class org.jmol.script.T
exportScale - Variable in class org.jmol.export.___Exporter
exportSpectrum(String, int) - Method in interface jspecview.api.JSVAppletInterface
  Delivers spectrum coded as desired: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML, PDF(base64-encoded)
exportSpectrum(String, int) - Method in class jspecview.app.JSVApp
  Delivers spectrum coded as desired: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML
exportSpectrum(String, int) - Method in class jspecview.appletjs.JSVApplet
exportSpectrum(JSViewer, String) - Method in interface jspecview.export.ExportInterface
exportSurface(short) - Method in class org.jmol.render.MeshRenderer
exportTheSpectrum(String, String, Spectrum, int, int) - Method in interface jspecview.export.ExportInterface
  returns message if path is not null, otherwise full string of text (unsigned applet)
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in interface jspecview.api.JSVExporter
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.AMLExporter
  Exports the Spectrum that is displayed by JSVPanel to a file given by fileName If display is zoomed then export the current view
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.CMLExporter
  Exports the Spectrum that is displayed by JSVPanel to a file given by fileName If display is zoomed then export the current view
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.Exporter
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.JDXExporter
  Exports spectrum in one of several formats
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.SVGExporter
  Export a Graph as SVG to a file given by fileName
exportType - Variable in class org.jmol.render.ShapeRenderer
ExportType - Enum Class in jspecview.common
expressionBegin - Static variable in class org.jmol.script.T
expressionEnd - Static variable in class org.jmol.script.T
EXTCRC - Static variable in class javajs.api.GenericZipInputStream
extendGrid - Variable in class org.jmol.jvxl.readers.Parameters
externalContainer - Variable in class org.jmol.console.JmolConsole
EXTHDR - Static variable in class javajs.api.GenericZipInputStream
EXTLEN - Static variable in class javajs.api.GenericZipInputStream
extractMolData(String) - Method in class org.jmol.api.JmolViewer
extractMolData(String) - Method in class org.jmol.viewer.Viewer
extractProperty(Object, Object, int) - Method in class org.jmol.viewer.Viewer
extractProperty(Object, Object, int, Lst, boolean) - Method in interface org.jmol.api.JmolPropertyManager
extractProperty(Object, Object, int, Lst, boolean) - Method in class org.jmol.viewer.PropertyManager
extractTagOnly(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
EXTSIG - Static variable in class javajs.api.GenericZipInputStream
EXTSIZ - Static variable in class javajs.api.GenericZipInputStream
EY - Variable in class org.jmol.quantum.MOCalculation
EZ - Variable in class org.jmol.quantum.MOCalculation

## F

facecenteroffset - Static variable in class org.jmol.script.T
faceMap - Variable in class org.jmol.renderspecial.DotsRenderer
faceOrder - Static variable in class org.jmol.util.BoxInfo
facePoints - Static variable in class org.jmol.util.BoxInfo
faces - Variable in class org.jmol.shapespecial.Polyhedron
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.AdfReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.AmsReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.DgridReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.AdfReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.AmsReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.DgridReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
FACTOR - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
factorType - Variable in class org.jmol.atomdata.RadiusData
FAHReader - Class in org.jmol.adapter.readers.simple
  FoldingAtHome json reader.
FAHReader() - Constructor for class org.jmol.adapter.readers.simple.FAHReader
falsifyMesh() - Method in class org.jmol.shapebio.BioShape
fast_idle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fatal(String) - Method in class org.jmol.util.DefaultLogger
fatal(String) - Static method in class org.jmol.util.Logger
  Writes a log at FATAL level.
fatal(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at FATAL level.
fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger
  Writes a log at FATAL level with detail on exception.
fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at ERROR level with detail on exception.
FC - Static variable in class org.jmol.quantum.QS
fclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
fcoord(T3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
fcoord(T3, String) - Static method in class org.jmol.symmetry.SymmetryOperation
  Get string version of fraction
FD_PROPERTY_INLINE - Static variable in class jspecview.java.FileDropperJmol
fdup(String, int, int) - Static method in class javajs.util.PT
  fdup duplicates p or q formats for formatCheck and the format() function.
fetch_host - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fetch_path - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ffAtomType - Variable in class org.jmol.minimize.MinAtom
fflistValue(T, int) - Static method in class org.jmol.script.SV
fformat(double, int, int) - Static method in class jme.JMEUtil
  Truncate to dec digits after the decimal place and left-pad to length len.
FFParam - Class in org.jmol.minimize.forcefield
FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
ffParams - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
ffType - Variable in class org.jmol.minimize.MinAtom
fid - Variable in class org.jmol.util.Font
fids - Variable in class org.jmol.shape.Labels
field_of_view - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fieldProperty(int) - Method in class org.jmol.adapter.readers.cif.CifReader
FIL - Enum Class in org.jmol.c
file - Static variable in class org.jmol.script.T
FILE_DATA - Static variable in class org.jmol.viewer.JC
FILE_DROPPED - Static variable in class org.jmol.viewer.FileManager
FILE_OPEN_ALREADY - Static variable in class jspecview.common.JSViewer
FILE_OPEN_ERROR - Static variable in class jspecview.common.JSViewer
FILE_OPEN_NO_DATA - Static variable in class jspecview.common.JSViewer
FILE_OPEN_OK - Static variable in class jspecview.common.JSViewer
FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
fileAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
filecachedirectory - Static variable in class org.jmol.script.T
filecaching - Static variable in class org.jmol.script.T
FileChooser - Class in org.jmol.dialog
  JFileChooser with possibility to fix size and location
FileChooser() - Constructor for class org.jmol.dialog.FileChooser
FileDropper - Class in org.jmol.awt
  A simple Dropping class to allow files to be dragged onto a target.
FileDropper(JmolStatusListener, Viewer, JmolDropEditor) - Constructor for class org.jmol.awt.FileDropper
FileDropperJmol - Class in jspecview.java
  A simple Dropping class to allow files to be dragged onto a target.
FileDropperJmol(PlatformViewer) - Constructor for class jspecview.java.FileDropperJmol
fileFirstX - Variable in class jspecview.source.JDXDataObject
  JDXReader only
fileHelper - Variable in class jspecview.common.JSViewer
fileLastX - Variable in class jspecview.source.JDXDataObject
  JDXReader only
FileManager - Class in org.jmol.viewer
filename - Variable in class org.jmol.console.ScriptEditor
fileName - Variable in class jspecview.common.PanelNode
fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fileName - Variable in class org.jmol.atomdata.AtomData
fileName - Variable in class org.jmol.export.___Exporter
fileName - Variable in class org.jmol.jvxl.readers.Parameters
fileNPoints - Variable in class jspecview.source.JDXDataObject
  JDXReader only
fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filePath - Variable in class jspecview.source.AnIMLReader
filePath - Variable in class jspecview.source.NMRMLReader
filePath - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
FilePreview - Class in org.jmol.dialog
  File previsualisation before opening
FilePreview(Viewer, JFileChooser, boolean, Map) - Constructor for class org.jmol.dialog.FilePreview
  Constructor
FileReader - Class in org.jmol.io
FileReader(Viewer, String, String, String, String, Object, Map, boolean) - Constructor for class org.jmol.io.FileReader
fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filesData - Variable in class org.jmol.jvxl.readers.Parameters
FilesReader - Class in org.jmol.io
  open a set of models residing in different files
FilesReader() - Constructor for class org.jmol.io.FilesReader
FileSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
fill - Variable in class org.jmol.awtjs.swing.GridBagConstraints
fill - Static variable in class org.jmol.script.T
fill() - Method in class javajs.export.PDFCreator
fill3x3(String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  fills a double[3][3]
fillADa(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
fillBackground(Object, GenericColor) - Method in class jspecview.common.PDFWriter
fillBackground(Object, GenericColor) - Method in class jspecview.java.AwtG2D
fillBackground(Object, GenericColor) - Method in class jspecview.js2d.JsG2D
fillBackground(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
fillBackground(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
fillBackground(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
fillCircle(Object, int, int, int) - Method in class jspecview.common.PDFWriter
fillCircle(Object, int, int, int) - Method in class jspecview.java.AwtG2D
fillCircle(Object, int, int, int) - Method in class jspecview.js2d.JsG2D
fillCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
fillCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
fillCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.export.Export3D
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._PovrayExporter
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._TachyonExporter
fillCylinder(byte, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.export.Export3D
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
fillCylinder(JmolRendererInterface, short, short, byte, int, int, int, int, int, int, int, boolean) - Static method in class org.jmol.render.FontLineShapeRenderer
fillCylinderBits(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.export.Export3D
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.Export3D
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.g3d.Graphics3D
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
fillDataBlockFixed(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format.
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in interface org.jmol.api.JmolRendererInterface
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.export.Export3D
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.Graphics3D
fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  fills a float array with string data from a file
fillFloatArrays(V3[], float[]) - Method in interface javajs.api.EigenInterface
fillFloatArrays(V3[], float[]) - Method in class javajs.util.Eigen
  Specifically for 3x3 systems, returns eigenVectors as V3[3] and values as float[3]; sorted from smallest to largest value.
fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int, String[][]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  Extracts a block of frequency data from a file.
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
fillParams(V3, V3, V3, float[]) - Static method in class org.jmol.util.SimpleUnitCell
fillPolygon(Object, int[], int[], int) - Method in class jspecview.common.PDFWriter
fillPolygon(Object, int[], int[], int) - Method in class jspecview.java.AwtG2D
fillPolygon(Object, int[], int[], int) - Method in class jspecview.js2d.JsG2D
fillPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fillRect(Graphics) - Method in class jme.AtomDisplayLabel
fillRect(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
fillRect(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
fillRect(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
fillRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
fillRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
fillRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
fillSphereBits(int, P3) - Method in interface org.jmol.api.JmolRendererInterface
  fills a solid sphere
fillSphereBits(int, P3) - Method in class org.jmol.export.Export3D
  fills a solid sphere
fillSphereBits(int, P3) - Method in class org.jmol.g3d.Graphics3D
  fills a solid sphere
fillSphereI(int, P3i) - Method in interface org.jmol.api.JmolRendererInterface
  fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.export.Export3D
  fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.g3d.Graphics3D
  fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.export.Export3D
  fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
  fills a solid sphere
fillTextRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  fills background rectangle for label
fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
  fills background rectangle for label
fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
  fills background rectangle for label
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.___Exporter
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__CartesianExporter
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export._PovrayExporter
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export._TachyonExporter
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.export.Export3D
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.export.Export3D
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3f(P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.export.Export3D
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangles - Variable in class org.jmol.shape.Mesh
fillTriangleTwoSided(short, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.export.Export3D
fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filter - Static variable in class org.jmol.script.T
FILTER_LAST - Static variable in class javajs.img.PngEncoder
FILTER_NONE - Static variable in class javajs.img.PngEncoder
  Constants for filters
FILTER_SUB - Static variable in class javajs.img.PngEncoder
FILTER_UP - Static variable in class javajs.img.PngEncoder
filterAllHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterCased - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterCIFAtom(Atom, String) - Method in class org.jmol.adapter.readers.cif.CifReader
filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
filteredPrecision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  check line for filter options
filterPDBAtom(Atom, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalize() - Method in class com.sparshui.server.GestureServer
finalize() - Method in class org.jmol.viewer.Viewer
finalizeAromatic(Lst) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
finalizeAtoms(BS, boolean) - Method in class org.jmol.viewer.ShapeManager
finalizeHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
finalizeMOData(Map) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeModelSet() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
finalizeModelSet() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeModulation() - Method in class org.jmol.adapter.readers.cif.MSRdr
  Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.
finalizeModulation() - Method in interface org.jmol.adapter.smarter.MSInterface
finalizeMoments(String, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
  from XtalSymmetry.applySymmetryFromReader via CifReader and JanaReader doPreSymmetry
finalizeObject(int, int, float, int, boolean, Object, int, BS) - Method in class org.jmol.scriptext.ScriptExt
finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
finalizeOutput() - Method in class org.jmol.export.___Exporter
finalizeOutput() - Method in class org.jmol.export._IdtfExporter
finalizeOutput() - Method in class org.jmol.export._ObjExporter
finalizeOutput() - Method in class org.jmol.export._PovrayExporter
finalizeOutput() - Method in class org.jmol.export._StlExporter
finalizeOutput() - Method in class org.jmol.export.Export3D
finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
finalizeOutput2() - Method in class org.jmol.export.___Exporter
finalizeOutput2() - Method in class org.jmol.export._PovrayExporter
finalizeOutput2() - Method in class org.jmol.export._TachyonExporter
finalizeParsing() - Method in class org.jmol.adapter.readers.xml.CDXMLParser
finalizeReader() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  PRIOR to symmetry application, process all internal symop/translation aspects.
finalizeReaderASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeReaderMR() - Method in class org.jmol.adapter.readers.molxyz.MolReader
finalizeReaderPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
finalizeRingData() - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
finalizeRna3d(Map) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
finalizeStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.BCIFReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.CifReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.P2nReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.InputReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
  Fix connections to Fragments and Nicknames, adjust stereochemistry for wavy displays, flag invalid atoms, and adjust the scale to something more molecular.
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.FSGOutputReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  Set final auxiliary info and symmetry, including "fileHeader", "magresUnits", and "interactionTensors"; note that print getProperty("auxiliaryInfo.models[1].magresUnits") should return a catalog of tensor types.
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
finalizeSubclassReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  Symmetry has been applied.
finalizeTrajectoryAs(Lst, Lst) - Method in class org.jmol.adapter.smarter.AtomSetCollection
finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
finalizeValidations(Viewer, Map) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
  Create property_xxxx for each validation category.
find - Static variable in class org.jmol.script.T
find() - Method in class org.jmol.util.PatternMatcher.JSPattern
find(double) - Method in class jspecview.common.MeasurementData
find(Object, Object, int) - Method in interface org.jmol.api.SmilesMatcherInterface
find(Object, Object, int) - Method in class org.jmol.smiles.SmilesMatcher
  Searches for all matches of a pattern within a SMILES string.
find(String, int) - Method in class org.jmol.util.CommandHistory
find(Lst, Measurement) - Static method in class org.jmol.modelset.Measurement
find(ModelSet, BS, Vibration) - Static method in class org.jmol.util.Vibration
findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
findAtomsInRectangle(Rectangle) - Method in class org.jmol.modelset.ModelSet
findAtomsLike(String) - Method in class org.jmol.modelset.Atom
findAtomsLike(String) - Method in class org.jmol.smiles.SmilesAtom
findAtomsLike(String) - Method in interface org.jmol.util.Node
findAxis(P3[], int, P3, V3, V3) - Static method in class javajs.util.Measure
findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Have the vwr show a particular frame with frequencies if it can be found.
findLineSeparator(String) - Static method in class jme.JMEUtil
findMatchingPeakInfo(PeakInfo) - Method in class jspecview.common.PanelData
findMatchingPeakInfo(PeakInfo) - Method in class jspecview.common.Spectrum
findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
findMonomer(BS, boolean) - Method in class org.jmol.modelsetbio.ProteinStructure
findNearest2(int, int, Atom[], BS, int) - Method in class org.jmol.modelset.AtomCollection
  ////////////////////////////////////////
findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
findNearestAtomIndex(int, int, BS, int) - Method in class org.jmol.modelset.ModelSet
findNearestAtomIndex(int, int, Atom[], short[], int, BS) - Method in class org.jmol.modelsetbio.BioPolymer
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
  /////////////////////////////////////////////////////////////
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shape.Shape
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShape
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShapeCollection
findNearestAtomIndexMovable(int, int, boolean) - Method in class org.jmol.viewer.Viewer
findNearestShapeAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.viewer.ShapeManager
findNode(String, int, P3) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  Called from TLink and TAtom to find a node with the given symmetry.
findNode(JSVPanel, Lst) - Static method in class jspecview.common.PanelNode
  Returns the tree node that is associated with a panel
findNodeById(String, Lst) - Static method in class jspecview.common.PanelNode
findPeakByCoord(int, Coordinate) - Method in class jspecview.common.Spectrum
findSeparator(String) - Static method in class jme.JMEmol
findSourceByNameOrId(String, Lst) - Static method in class jspecview.common.PanelNode
findSpaceGroup(BS, String, float[], T3, T3[], int) - Method in interface org.jmol.api.SymmetryInterface
findSpaceGroup(BS, String, float[], T3, T3[], int) - Method in class org.jmol.symmetry.Symmetry
findSpaceGroup(SymmetryInterface, BS, String, float[], T3, T3[], int) - Method in class org.jmol.viewer.Viewer
findSpaceGroupFromXYZ(String) - Static method in class org.jmol.symmetry.SpaceGroup
findX(Spectrum, double) - Method in class jspecview.common.PanelData
FINDX - Enum constant in enum class jspecview.common.ScriptToken
findXForPeakNearest(double) - Method in class jspecview.common.Spectrum
findXForPeakNearest(Coordinate[], double, boolean) - Static method in class jspecview.common.Coordinate
finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
finish(Object) - Method in class org.jmol.api.JmolAdapter
FINISH - Static variable in class org.jmol.thread.JmolThread
first - Variable in class org.jmol.modelset.TickInfo
first - Static variable in class org.jmol.script.T
firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
  to be filled:
firstAtomIndex - Variable in class org.jmol.modelset.Group
firstAtomIndex - Variable in class org.jmol.modelset.Model
firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
firstAtomToBond - Variable in class org.jmol.adapter.smarter.AtomSetCollection
firstChar - Variable in class org.jmol.adapter.readers.cif.CifReader
firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
firstIsotope - Static variable in class org.jmol.util.Elements
  first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstModelIndex - Variable in class org.jmol.atomdata.AtomData
firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
firstX - Variable in class jspecview.export.AMLExporter
firstX - Variable in class jspecview.export.CMLExporter
firstX - Variable in class jspecview.source.AnIMLReader
firstX - Variable in class jspecview.source.NMRMLReader
firstY - Variable in class jspecview.source.AnIMLReader
firstY - Variable in class jspecview.source.NMRMLReader
fit_iterations - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fit_kabsch - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fit_tolerance - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
FIX - Enum constant in enum class jspecview.common.ExportType
fix2Stereo() - Method in class org.jmol.adapter.smarter.AtomSetCollection
fixAtoms(int, SV, BS, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
fixAtoms(int, SV, BS, int, int) - Method in class org.jmol.dssx.AnnotationParser
  Adjusts _atoms bitset to account for added hydrogen atoms.
fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
fixD(float, boolean) - Method in class org.jmol.modelset.BondCollection
fixDataString(String) - Static method in class org.jmol.util.Parser
fixDeletedBonds(BS) - Method in class org.jmol.modelset.ModelSet
fixDOSName(String) - Static method in class org.jmol.adapter.smarter.Resolver
fixDOSName(String) - Static method in class org.jmol.viewer.FileManager
  Switch \ for / only for DOS names such as C:\temp\t.xyz, not names like http://cactus.nci.nih.gov/chemical/structure/CC/C=C\CC
fixDouble(double, double) - Static method in class javajs.util.PT
fixDoubleA(double[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fixDSSRJSONMap(Map) - Method in interface org.jmol.api.JmolAnnotationParser
fixDSSRJSONMap(Map) - Method in class org.jmol.dssx.AnnotationParser
fixDSSRJSONMap(Map) - Method in class org.jmol.dssx.DSSR1
  kissingLoops and coaxStacks use index arrays instead of duplication;
fixed - Static variable in class org.jmol.script.T
FixedH - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Include Fixed H layer
fixedLattice - Variable in class org.jmol.jvxl.data.JvxlData
fixedOrigin - Variable in class org.jmol.shape.Axes
fixedOriginUC - Variable in class org.jmol.shape.Axes
fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
fixedRotationCenter - Variable in class org.jmol.export.___Exporter
fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
fixedtemp - Static variable in class org.jmol.script.T
FIXEDTEMP - Enum constant in enum class org.jmol.c.PAL
fixedTranslation - Variable in class org.jmol.viewer.TransformManager
fixedValue - Variable in class org.jmol.modelset.Measurement
fixedValue - Variable in class org.jmol.modelset.MeasurementData
fixFloat(float, double) - Static method in class javajs.util.PT
fixFloatA(float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fixFloatPt(P3, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fixFormalCharges(BS) - Method in class org.jmol.modelset.AtomCollection
fixIndices(int, int, BS) - Method in class org.jmol.modelset.Model
fixIndices(int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
fixIndices(int, BS) - Method in class org.jmol.modelset.Group
fixIndicesM(int, int, BS) - Method in class org.jmol.modelset.Model
fixInlineString(String, char) - Static method in class org.jmol.viewer.Viewer
fixJMEFormalCharges(BS, String) - Method in interface org.jmol.api.JmolPropertyManager
fixJMEFormalCharges(BS, String) - Method in class org.jmol.viewer.PropertyManager
  Fix a JME string returned from NCI CIR to have the proper formal charges.
fixKey(String) - Method in interface javajs.api.GenericCifDataParser
fixKey(String) - Method in class javajs.util.CifDataParser
  Switch '." to "_" in a key, and also make any quirky key name changes that need to be done
fixPropertyValue(BS, Object, boolean) - Method in class org.jmol.modelsetbio.BioResolver
fixPtFloats(T3, float) - Static method in class javajs.util.PT
fixRadius(float) - Static method in class org.jmol.adapter.readers.pdb.PdbReader
fixScreenZ(int) - Method in class org.jmol.export.___Exporter
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  Only for 5D, 10F, 15G designations.
fixTextImageRGB(int) - Static method in class org.jmol.g3d.Graphics3D
fixTitle(String) - Static method in class jspecview.dialog.DialogManager
fixUnitCell(float[]) - Method in interface org.jmol.api.SymmetryInterface
fixUnitCell(float[]) - Method in class org.jmol.symmetry.Symmetry
fixUnits(String) - Static method in class org.jmol.modelset.Measurement
fixUTF(byte[]) - Static method in class javajs.util.Rdr
  ////////
fixUTF(byte[]) - Static method in class jspecview.common.JSVFileManager
fixValue(String, boolean) - Method in class org.jmol.modelset.Measurement
fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
FLAG_STRUTS_ONLY - Static variable in class org.jmol.render.SticksRenderer
flags - Variable in class org.jmol.render.ShapeRenderer
flat - Static variable in class org.jmol.script.T
FLICK_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
FLICK_EVENT - Static variable in class com.sparshui.GestureType
FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
FLICK_GESTURE - Static variable in class com.sparshui.GestureType
FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
FlickEvent - Class in com.sparshui.common.messages.events
FlickEvent() - Constructor for class com.sparshui.common.messages.events.FlickEvent
FlickEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.FlickEvent
  Constructs a flickEvent from a complete serialized version of the drag event.
FlickEvent(float, float) - Constructor for class com.sparshui.common.messages.events.FlickEvent
FlickEvent(int, int, int) - Constructor for class com.sparshui.common.messages.events.FlickEvent
flistValue(T, int) - Static method in class org.jmol.script.SV
float_labels - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
FLOAT_MIN_SAFE - Static variable in class org.jmol.viewer.JC
floatifyJavaDouble - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
floatparam - Static variable in class org.jmol.script.T
floatParameter(int) - Method in class org.jmol.script.ScriptParam
floatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
floatParameterRange(int, float, float) - Method in class org.jmol.script.ScriptParam
floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptParam
  process a general string or set of parameters as an array of floats, allowing for relatively free form input
floatproperty - Static variable in class org.jmol.script.T
floatToByteArray(byte[], int, float) - Static method in class com.sparshui.common.utils.Converter
floatToIntBits(float) - Static method in class javajs.util.T3
flowCommand - Static variable in class org.jmol.script.T
FlowLayout - Class in org.jmol.awtjs.swing
FlowLayout() - Constructor for class org.jmol.awtjs.swing.FlowLayout
flushBytes() - Method in class javajs.img.GifEncoder
flushImage(Object) - Method in class jspecview.java.AwtPlatform
flushImage(Object) - Method in class jspecview.js2d.JsPlatform
flushImage(Object) - Method in interface org.jmol.api.GenericPlatform
flushImage(Object) - Method in class org.jmol.awt.Platform
flushImage(Object) - Method in class org.jmol.awtjs2d.Platform
fm - Variable in class org.jmol.adapter.readers.spartan.SpartanUtil
fm - Variable in class org.jmol.viewer.Viewer
fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
foccupancy - Variable in class org.jmol.adapter.smarter.Atom
focusGained(FocusEvent) - Method in class jspecview.java.AwtDialogManager
focusLost(FocusEvent) - Method in class jspecview.java.AwtDialogManager
fog - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fog_start - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
FoldCRU - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Remove repeats within constitutional repeating units (CRU/SRU)
FoldingXyzReader - Class in org.jmol.adapter.readers.simple
  This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
font - Variable in class jspecview.common.PrintLayout
  The font of the elements
font - Variable in class org.jmol.modelset.Text
font - Static variable in class org.jmol.script.T
font - Variable in class org.jmol.util.Font
Font - Class in org.jmol.util
  Provides font support using a int fid (Font ID) as an index into font table.
FONT - Static variable in class org.jmol.shapecgo.CGOMesh
FONT_AXES - Static variable in class org.jmol.shapecgo.CGOMesh
FONT_FACE_MONO - Static variable in class org.jmol.util.Font
FONT_FACE_SANS - Static variable in class org.jmol.util.Font
FONT_FACE_SERIF - Static variable in class org.jmol.util.Font
FONT_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
FONT_STYLE_BOLD - Static variable in class org.jmol.util.Font
FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.util.Font
FONT_STYLE_ITALIC - Static variable in class org.jmol.util.Font
FONT_STYLE_PLAIN - Static variable in class org.jmol.util.Font
FONT_VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
font3d - Variable in class org.jmol.render.FontLineShapeRenderer
font3d - Variable in class org.jmol.shape.FontLineShape
font3d - Variable in class org.jmol.shape.Frank
font3d - Variable in class org.jmol.shape.Measures
fontcaching - Static variable in class org.jmol.script.T
fontChild - Variable in class org.jmol.export._VrmlExporter
fontFace - Variable in class org.jmol.export._VrmlExporter
fontFace - Variable in class org.jmol.util.Font
fontID - Variable in class org.jmol.shapespecial.DrawMesh
FontLineShape - Class in org.jmol.shape
FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
FontLineShapeRenderer - Class in org.jmol.render
FontLineShapeRenderer() - Constructor for class org.jmol.render.FontLineShapeRenderer
FontManager - Interface in org.jmol.api
  A generic interface for font queries.
fontScale - Variable in class org.jmol.modelset.Text
fontscaling - Static variable in class org.jmol.script.T
fontsize - Static variable in class org.jmol.script.T
fontSize - Variable in class org.jmol.export._VrmlExporter
fontSize - Variable in class org.jmol.util.Font
fontSizeAngstroms - Variable in class org.jmol.util.Font
fontSizeNominal - Variable in class org.jmol.util.Font
fontStringWidth(Font, String) - Method in class jspecview.java.AwtPlatform
  // FONT
fontStringWidth(Font, String) - Method in class jspecview.js2d.JsPlatform
fontStringWidth(Font, String) - Method in interface org.jmol.api.FontManager
fontStringWidth(Font, String) - Method in class org.jmol.awt.Platform
  // FONT
fontStringWidth(Font, String) - Method in class org.jmol.awtjs2d.Platform
fontStyle - Variable in class org.jmol.export._VrmlExporter
fontStyle - Variable in class org.jmol.util.Font
force - Variable in class org.jmol.minimize.MinAtom
forceAsyncLoad(String) - Method in class jspecview.java.AwtPlatform
forceAsyncLoad(String) - Method in class jspecview.js2d.JsPlatform
forceAsyncLoad(String) - Method in interface org.jmol.api.GenericPlatform
forceAsyncLoad(String) - Method in class org.jmol.awt.Platform
forceAsyncLoad(String) - Method in class org.jmol.awtjs2d.Platform
forceautobond - Static variable in class org.jmol.script.T
forcefield - Static variable in class org.jmol.script.T
ForceField - Class in org.jmol.minimize.forcefield
ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
ForceFieldMMFF - Class in org.jmol.minimize.forcefield
  MMFF94 implementation 5/14/2012 - fully validated for atom types and charges - reasonably well validated for energies (see below) - TODO: add UFF for preliminary/backup calculation
ForceFieldMMFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldMMFF
ForceFieldReader - Class in org.jmol.adapter.readers.more
ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
ForceFieldUFF - Class in org.jmol.minimize.forcefield
ForceFieldUFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
forceMOPAC - Variable in class org.jmol.adapter.readers.quantum.MOReader
forcePacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
forceShowTriangles - Variable in class org.jmol.render.MeshRenderer
forceSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
forcmd - Static variable in class org.jmol.script.T
FORMAL_CHARGE - Enum constant in enum class org.jmol.c.PAL
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
  ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber invalid input: '<'invalid input: '<' 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
formalcharge - Static variable in class org.jmol.script.T
formalCharge - Variable in class org.jmol.adapter.smarter.Atom
format - Static variable in class org.jmol.script.T
format(SV[], int) - Static method in class org.jmol.script.SV
  Accepts arguments from the format() function First argument is a format string.
FORMAT_ABC - Static variable in class org.jmol.script.SV
FORMAT_ARRAY - Static variable in class org.jmol.script.SV
FORMAT_BASE64 - Static variable in class org.jmol.script.SV
FORMAT_BYTEARRAY - Static variable in class org.jmol.script.SV
FORMAT_JSON - Static variable in class org.jmol.script.SV
FORMAT_RXYZ - Static variable in class org.jmol.script.SV
FORMAT_STRING - Static variable in class org.jmol.script.SV
FORMAT_UVW - Static variable in class org.jmol.script.SV
FORMAT_XYZ - Static variable in class org.jmol.script.SV
formatCheck(String) - Static method in class javajs.util.PT
  formatCheck checks p and q formats and duplicates if necessary "%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
formatD(double, int, int, boolean, boolean) - Static method in class javajs.util.PT
formatDecimal(double, int) - Static method in class javajs.util.DF
  a simple alternative to DecimalFormat (which Java2Script does not have and which is quite too complex for our use here.)
formatDecimalDbl(double, int) - Static method in class javajs.util.DF
formatDecimalTrimmed(double, int) - Static method in class javajs.util.DF
  an alternative to DecimalFormat "0.#"
formatDecimalTrimmed0(double, int) - Static method in class javajs.util.DF
  an alternative to DecimalFormat "0.0"
formatDistance(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
formatExpNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
formatF(float, int, int, boolean, boolean) - Static method in class javajs.util.PT
formatJ(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
formatLabel(Viewer, Atom, String, P3) - Method in class org.jmol.modelset.LabelToken
  ///////// label formatting for atoms, bonds, and measurements ///////////
formatLabelAtomArray(Viewer, Atom, LabelToken[], char, int[], P3) - Static method in class org.jmol.modelset.LabelToken
  returns a formatted string based on the precompiled label tokens
formatLabelBond(Viewer, Bond, LabelToken[], Map, int[], P3) - Static method in class org.jmol.modelset.LabelToken
formatLabelMeasure(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
formatMeasurementAs(String, String, boolean) - Method in class org.jmol.modelset.Measurement
formatNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
formats - Variable in class org.jmol.shape.Labels
formatS(String, int, int, boolean, boolean) - Static method in class javajs.util.PT
formatStringF(String, String, float) - Static method in class javajs.util.PT
formatStringI(String, String, int) - Static method in class javajs.util.PT
formatStringS(String, String, String) - Static method in class javajs.util.PT
formatText(String) - Method in class org.jmol.viewer.Viewer
forThermalEllipsoid - Variable in class org.jmol.util.Tensor
foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
foundDistance2() - Method in class org.jmol.bspt.CubeIterator
  After calling nextElement(), allows one to find out the value of the distance squared.
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
foundDistance2() - Method in class org.jmol.symmetry.UnitCellIterator
fourdots - Static variable in class org.jmol.render.FontLineShapeRenderer
fps - Static variable in class org.jmol.script.T
FRACTIONAL_PRECISION - Static variable in class javajs.util.PT
fractionalizeCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fractionalPoint - Variable in class org.jmol.script.ScriptParam
  set in getPointOrPlane
fractionalrelative - Static variable in class org.jmol.script.T
fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
fracx - Static variable in class org.jmol.script.T
fracxyz - Static variable in class org.jmol.script.T
fracy - Static variable in class org.jmol.script.T
fracz - Static variable in class org.jmol.script.T
frame - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
frame - Static variable in class org.jmol.script.T
frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
frameCounter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
FrameCounter - Class in org.openscience.jmol.app.janocchio
FrameCounter(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameCounter
  Constructor
frameDelay - Variable in class org.jmol.modelset.Model
frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
FrameDeltaDisplay - Class in org.openscience.jmol.app.janocchio
FrameDeltaDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
  Constructor
frameTitle - Variable in class jspecview.common.PanelNode
frameTitles - Variable in class org.jmol.modelset.ModelSet
frank - Static variable in class org.jmol.script.T
Frank - Class in org.jmol.shape
Frank() - Constructor for class org.jmol.shape.Frank
frankAscent - Variable in class org.jmol.shape.Frank
frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
frankDescent - Variable in class org.jmol.shape.Frank
frankMargin - Static variable in class org.jmol.shape.Frank
frankOn - Variable in class org.jmol.viewer.Viewer
frankPopup - Variable in class org.jmol.popup.JmolGenericPopup
FrankRenderer - Class in org.jmol.render
FrankRenderer() - Constructor for class org.jmol.render.FrankRenderer
frankString - Static variable in class org.jmol.shape.Frank
frankWidth - Variable in class org.jmol.shape.Frank
freeBonds - Variable in class org.jmol.modelset.BondCollection
freeTempEnum(STR[]) - Method in class org.jmol.util.TempArray
freeTempEnum(STR[]) - Method in class org.jmol.viewer.Viewer
freeTempPoints(P3[]) - Method in class org.jmol.util.TempArray
freeTempPoints(P3[]) - Method in class org.jmol.viewer.Viewer
freeTempScreens(P3i[]) - Method in class org.jmol.util.TempArray
freeTempScreens(P3i[]) - Method in class org.jmol.viewer.Viewer
freeze() - Method in class org.jmol.modelset.Model
freeze() - Method in class org.jmol.modelsetbio.BioModel
freezeM() - Method in class org.jmol.modelset.Model
freq2dX - Variable in class jspecview.source.JDXDataObject
freq2dY - Variable in class jspecview.source.JDXDataObject
fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
FRIENDLY - Static variable in class org.jmol.util.ColorEncoder
from - Static variable in class org.jmol.script.T
from3D() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
fromASC(AtomSetCollection) - Static method in class org.jmol.adapter.writers.CDXMLWriter
fromCDX(GenericBinaryDocumentReader) - Static method in class org.jmol.adapter.writers.CDXMLWriter
fromOABC(T3[], boolean) - Static method in class org.jmol.symmetry.UnitCell
  A special constructor for spacially defined unit cells.
fromParams(float[], boolean, float) - Static method in class org.jmol.symmetry.UnitCell
fromString(Viewer, String, String) - Static method in class org.jmol.adapter.writers.CDXMLWriter
fromUnits(float, String) - Static method in class org.jmol.modelset.Measurement
front - Static variable in class org.jmol.script.T
frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
frontedges - Static variable in class org.jmol.script.T
frontlit - Static variable in class org.jmol.script.T
frontonly - Static variable in class org.jmol.script.T
frontOnly - Variable in class org.jmol.render.MeshRenderer
frontOnly - Variable in class org.jmol.shape.Mesh
FS - Static variable in class org.jmol.quantum.QS
fScrPtSafe - Variable in class org.jmol.viewer.TransformManager
FSG2SCIFConverter - Class in org.jmol.adapter.writers
  This class, a subclass of CIFWriter, should only be initialized dynamically and by CIFWriter.
FSG2SCIFConverter() - Constructor for class org.jmol.adapter.writers.FSG2SCIFConverter
FSGOutputReader - Class in org.jmol.adapter.readers.xtal
  A reader for JSON output from the FINDSPINGROUP program.
FSGOutputReader() - Constructor for class org.jmol.adapter.readers.xtal.FSGOutputReader
fslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
full - Static variable in class org.jmol.script.T
full_screen - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
fullAtomWidthLabel - Variable in class jme.AtomDisplayLabel
fullCommand - Variable in class org.jmol.script.ScriptEval
fullCubeCorners - Static variable in class org.jmol.util.Triangulator
  For each corner 0-7: {c c c t} where c c c are the connected corners, arranged clockwise and t is the bitset of triangles associated with faces intersecting at this corner.
fullCubePolygon - Static variable in class org.jmol.util.Triangulator
fullName - Variable in class jspecview.common.JSViewer
fullName - Variable in class org.jmol.util.GenericApplet
fullName - Variable in class org.jmol.viewer.Viewer
fullplane - Static variable in class org.jmol.script.T
fullTrim(Object) - Static method in class org.jmol.adapter.readers.cif.CifReader
fullylit - Static variable in class org.jmol.script.T
fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
func - Variable in class org.jmol.jvxl.readers.Parameters
function - Static variable in class org.jmol.script.T
functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
functionName - Variable in class org.jmol.script.ScriptContext
functionName - Variable in class org.jmol.script.ScriptEval
functionxy - Static variable in class org.jmol.script.T
functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
  for isosurface FUNCTIONXY
functionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
  fills an array with data -- if nX invalid input: '<' 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
functionXY(String, int, int) - Method in class org.openscience.jmol.app.status.StatusListener
  this is just a test method for isosurface FUNCTIONXY
functionxyz - Static variable in class org.jmol.script.T
functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
  for isosurface FUNCTIONXYZ
functionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.status.StatusListener
fux - Static variable in class org.jmol.script.T
fuxyz - Static variable in class org.jmol.script.T
fuy - Static variable in class org.jmol.script.T
fuz - Static variable in class org.jmol.script.T
fVal(String) - Static method in class javajs.util.PT
fValue(T) - Static method in class org.jmol.script.SV

## G

g - Variable in class org.jmol.util.Rgb16
g - Variable in class org.jmol.viewer.Viewer
g(String) - Method in class javajs.export.PDFCreator
G_SIZE - Static variable in interface org.apache.tools.bzip2.BZip2Constants
g2d - Variable in class jspecview.common.JSViewer
g2d - Variable in class jspecview.common.PanelData
g2d0 - Variable in class jspecview.common.PanelData
g3d - Variable in class org.jmol.modelset.AtomCollection
g3d - Variable in class org.jmol.render.ShapeRenderer
  could be vwr.gdata or an exporter
G3DRenderer - Interface in org.jmol.g3d
GamessReader - Class in org.jmol.adapter.readers.quantum
GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
GamessUKReader - Class in org.jmol.adapter.readers.quantum
GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
GamessUSReader - Class in org.jmol.adapter.readers.quantum
GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
gamma - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gamma - Variable in class org.jmol.util.SimpleUnitCell
gaussian_b_adjust - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gaussian_b_floor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gaussian_resolution - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
GaussianDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
GaussianFchkReader - Class in org.jmol.adapter.readers.quantum
  Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
GaussianFchkReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianFchkReader
gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
GaussianReader - Class in org.jmol.adapter.readers.quantum
  Reader for Gaussian 94/98/03/09 output files.
GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
gaussians - Variable in class org.jmol.quantum.MOCalculation
GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
  Reader for Gaussian Wfn files -- not implemented yet
GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
GC - Static variable in class org.jmol.quantum.QS
gdata - Variable in class org.jmol.export.___Exporter
gdata - Variable in class org.jmol.viewer.Viewer
GData - Class in org.jmol.util
GData() - Constructor for class org.jmol.util.GData
  It is possible to instantiate this class with no Graphics3D.
geCIFWriterValue(String) - Method in interface org.jmol.api.SymmetryInterface
geCIFWriterValue(String) - Method in class org.jmol.symmetry.Symmetry
generate() - Method in class javajs.img.GifEncoder
generate() - Method in class javajs.img.ImageEncoder
generate() - Method in class javajs.img.Jpg64Encoder
generate() - Method in class javajs.img.JpgEncoder
generate() - Method in class javajs.img.PdfEncoder
generate() - Method in class javajs.img.PngEncoder
generate() - Method in class javajs.img.PpmEncoder
generateAllOperators(HallInfo.HallReceiver) - Method in class org.jmol.symmetry.HallInfo
generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
generateCrystalClass(int, P3) - Method in class org.jmol.modelset.AtomCollection
generateCrystalClass(P3) - Method in interface org.jmol.api.SymmetryInterface
generateCrystalClass(P3) - Method in class org.jmol.symmetry.Symmetry
generateOutputForExport(Map) - Method in class org.jmol.api.JmolViewer
  for POV-Ray
generateOutputForExport(Map) - Method in class org.jmol.viewer.Viewer
generatePrimes(int) - Static method in class jme.JMEUtil
generateScene(Map) - Method in interface org.jmol.api.JmolSceneGenerator
GenericApplet - Class in org.jmol.util
  A collection of all methods necessary for initialization of and communication with the applet.
GenericApplet() - Constructor for class org.jmol.util.GenericApplet
GenericBinaryDocument - Interface in javajs.api
GenericBinaryDocumentReader - Interface in javajs.api
GenericCifDataParser - Interface in javajs.api
GenericColor - Interface in javajs.api
  GenericColor allows both java.awt.Color and javajs.awt.Color to be handled by methods that need not distinguish between them.
GenericConsole - Class in org.jmol.console
GenericConsole() - Constructor for class org.jmol.console.GenericConsole
GenericConsoleTextArea - Interface in org.jmol.api.js
GenericFileInterface - Interface in org.jmol.api
GenericGraphics - Interface in org.jmol.api
GenericImageDialog - Interface in org.jmol.api
GenericImageEncoder - Interface in javajs.api
GenericLineReader - Interface in javajs.api
GenericMenuInterface - Interface in org.jmol.api
GenericMouse - Class in jspecview.app
GenericMouse(JSVPanel) - Constructor for class jspecview.app.GenericMouse
GenericMouseInterface - Interface in org.jmol.api
GenericOutputChannel - Interface in javajs.api
GenericPlatform - Interface in org.jmol.api
GenericPopup - Class in org.jmol.popup
  The overall parent of all popup classes in Jmol and JSmol.
GenericPopup() - Constructor for class org.jmol.popup.GenericPopup
GenericTextArea - Interface in org.jmol.console
GenericZipInputStream - Class in javajs.api
GenericZipInputStream(InputStream) - Constructor for class javajs.api.GenericZipInputStream
GenericZipTools - Interface in javajs.api
  Class abandoned as unnecessary in SwingJS
GenNBOReader - Class in org.jmol.adapter.readers.quantum
  NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure
GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
Geodesic - Class in org.jmol.util
  J2SRequireImport is needed because we use ArrayUtil in a static method
Geodesic() - Constructor for class org.jmol.util.Geodesic
geometry_export_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
geosurface - Static variable in class org.jmol.script.T
GeoSurface - Class in org.jmol.shapespecial
GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
GeoSurfaceRenderer - Class in org.jmol.renderspecial
GeoSurfaceRenderer() - Constructor for class org.jmol.renderspecial.GeoSurfaceRenderer
Gesture - Interface in com.sparshui.gestures
  Defines the interface that all user-defined gestures must implement.
GestureServer - Class in com.sparshui.server
  The main gesture server class.
GestureServer() - Constructor for class com.sparshui.server.GestureServer
GestureServer(int, GestureServer) - Constructor for class com.sparshui.server.GestureServer
gestureswipefactor - Static variable in class org.jmol.script.T
GestureType - Class in com.sparshui
  This class is a place for the enum GestureType to stand.
GestureType(int) - Constructor for class com.sparshui.GestureType
GestureType(String) - Constructor for class com.sparshui.GestureType
get(int) - Method in class javajs.util.BS
  Returns the value of the bit with the specified index.
get(int) - Method in class org.jmol.util.Int2IntHash
get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
GET_ALLOWED_GESTURES - Static variable in class com.sparshui.common.ClientProtocol.MessageType
GET_GROUP_ID - Static variable in class com.sparshui.common.ClientProtocol.MessageType
get1(int) - Static method in class org.jmol.awtjs.swing.Color
get2SidedNormix(V3, BS) - Static method in class org.jmol.util.Normix
get3(int, int, int) - Static method in class org.jmol.awtjs.swing.Color
get33(int, int) - Method in class javajs.util.M34
get3dProjection(V3) - Method in class javajs.util.Quat
get4(int, int, int, int) - Static method in class org.jmol.awtjs.swing.Color
getAbbrSimulationFileName(String) - Static method in class jspecview.common.JSVFileManager
  In the case of applet-based simulations with file names that involve mol=..., we want to abbreviate those names for display
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Fetch the action that was created for the given command.
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
getActionCommand() - Method in interface org.jmol.api.SC
getActionCommand() - Method in class org.jmol.awt.AwtSwingComponent
getActionCommand() - Method in class org.jmol.awtjs.swing.JComponent
getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
getActionName(int) - Static method in class org.jmol.viewer.ActionManager
getActiveMenu() - Method in class org.jmol.modelkit.ModelKit
  for the thin box on the top left of the window
getActualMass(String, int) - Static method in class org.iupac.InchiUtils
getAdditionalHydrogens(BS, Lst, int) - Method in class org.jmol.viewer.Viewer
getAdditionalOperations() - Method in interface org.jmol.api.SymmetryInterface
getAdditionalOperations() - Method in class org.jmol.symmetry.Symmetry
getAdditionalOperations(SymmetryOperation[], int) - Static method in class org.jmol.symmetry.SymmetryOperation
getAdditionalOperationsCount() - Method in interface org.jmol.api.SymmetryInterface
getAdditionalOperationsCount() - Method in class org.jmol.symmetry.Symmetry
getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
getAlignment(int) - Static method in class org.jmol.viewer.JC
getAllAtomInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getAllAtoms() - Method in class org.jmol.viewer.Viewer
getAllAtomTensors(String) - Method in class org.jmol.modelset.AtomCollection
getAllBondInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getAllChainInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getAllChimeInfo(SB) - Method in class org.jmol.viewer.ChimeMessenger
getAllChimeInfo(SB) - Method in interface org.jmol.viewer.JmolChimeMessenger
getAllCifData() - Method in interface javajs.api.GenericCifDataParser
getAllCifData() - Method in class javajs.util.CifDataParser
  Parses all CIF data for a reader defined in the constructor into a standard Map structure and close the BufferedReader if it exists.
getAllCifDataType(String...) - Method in interface javajs.api.GenericCifDataParser
getAllCifDataType(String...) - Method in class javajs.util.CifDataParser
getAllData() - Method in class javajs.util.CompoundDocument
getAllDataFiles(String, String) - Method in interface javajs.api.GenericBinaryDocument
getAllDataFiles(String, String) - Method in class javajs.util.BinaryDocument
getAllDataFiles(String, String) - Method in class javajs.util.CompoundDocument
getAllDataMapped(String, String, Map) - Method in interface javajs.api.GenericBinaryDocument
getAllDataMapped(String, String, Map) - Method in class javajs.util.BinaryDocument
getAllDataMapped(String, String, Map) - Method in class javajs.util.CompoundDocument
  reads a compound document directory and saves all data in a Hashtable so that the files may be organized later in a different order.
getAllDefaultStructures(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAlleneAtoms(boolean, SmilesAtom, SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
getAllHeteroList(int) - Method in class org.jmol.modelsetbio.BioModelSet
getAllOperators() - Method in class org.jmol.modelkit.ModelKit
getAllowedGestures(int) - Method in interface com.sparshui.client.SparshClient
  This method must return the allowed Gestures for the specified group.
getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
getAllowJSThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
getAllowJSThreads() - Method in class org.jmol.script.ScriptEval
getAllPoints(int, int) - Method in class org.jmol.scriptext.ScriptExt
getAllPolymerInfo(BS, Map) - Method in class org.jmol.modelsetbio.BioModelSet
getAllPolymerPointsAndVectors(BS, Lst, boolean, float) - Method in class org.jmol.modelsetbio.BioModelSet
getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
getAllSequenceBits(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAllSettings(String) - Method in class org.jmol.viewer.Viewer
getAllStructures(String, Lst) - Method in class org.jmol.adapter.readers.quantum.NBOParser
getAllZipData(InputStream, String[], String, String, String, Map) - Method in interface javajs.api.GenericZipTools
getAllZipData(InputStream, String[], String, String, String, Map) - Method in class javajs.util.ZipTools
  Deprecated.
getAltLoc() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelSet
  /////////// individual models ////////////////
getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelSet
getAmbientPercent() - Method in class org.jmol.util.GData
getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioModelSet
getAndCheckValue(Map, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
getAndCheckValue(Map, String) - Method in class org.jmol.util.JSONWriter
getAndRegisterPlugin(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getAndSetNewVariable(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
getAngles() - Method in class org.jmol.minimize.Minimizer
getAnnotationInfo(SV, String, int) - Method in class org.jmol.viewer.Viewer
getAnnotationInfo(Viewer, SV, String, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
getAnnotationInfo(Viewer, SV, String, int, int) - Method in class org.jmol.dssx.AnnotationParser
  Get a string report of annotation data
getAnnotationParser(boolean) - Method in class org.jmol.viewer.Viewer
getApiPlatform() - Method in interface jspecview.api.JSVPanel
getApiPlatform() - Method in class jspecview.java.AwtPanel
getApiPlatform() - Method in class jspecview.js2d.JsPanel
getApp() - Method in interface jspecview.api.AppletFrame
getApp() - Method in class jspecview.appletjs.JSVApplet
getApplet() - Method in class jspecview.common.JSViewer
getAppletFrame() - Method in class jspecview.app.JSVApp
getAppletInfo() - Method in interface jspecview.api.AppletFrame
getAppletInfo() - Static method in class jspecview.app.JSVApp
getAppletInfo() - Method in class jspecview.appletjs.JSVApplet
  Get Applet information
getAppletInfo() - Method in class jspecview.appletjs.JSVAppletPro
getAppletInfo() - Method in interface org.jmol.api.JmolAppletInterface
getAppletInfo() - Method in class org.jmol.util.GenericApplet
getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
getApproxString100() - Method in class org.jmol.util.Vibration
getArgb() - Method in class org.jmol.util.Rgb16
getArgb(float) - Method in class org.jmol.util.ColorEncoder
getArgb(short) - Static method in class org.jmol.util.C
getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
getArgbFromString(String) - Static method in class javajs.util.CU
  accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or [red,green,blue] or a valid JavaScript color
getArgbGreyscale(short) - Static method in class org.jmol.util.C
getArgbHbondType(int) - Static method in class org.jmol.util.Edge
getArgbMinMax(float, float, float) - Method in class org.jmol.util.ColorEncoder
getArgbParam(int) - Method in class org.jmol.script.ScriptParam
getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptParam
getArgbParamOrNone(int, boolean) - Method in class org.jmol.script.ScriptParam
getArgbs(int) - Method in class org.jmol.modelsetbio.BioResolver
getArray() - Method in class javajs.util.Matrix
  Access the internal two-dimensional array.
getArrayCopy() - Method in class javajs.util.Matrix
  Copy the internal two-dimensional array.
getArrayDepth(T) - Static method in class org.jmol.script.SV
getArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
  turn "[1,2,3]" into [1.0,2.0,3.0] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
getAscent() - Method in class org.jmol.util.Font
getAsciiFileOrNull(String) - Method in class org.jmol.viewer.Viewer
getAssocArray(int) - Method in class org.jmol.script.ScriptEval
getAssociatedAtoms(ModelSet) - Method in class org.jmol.modelset.BondSet
getAssociatedPeakInfo(int, Coordinate) - Method in class jspecview.common.Spectrum
getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
getAtom(int) - Method in class org.jmol.modelset.AtomCollection
getAtom(int) - Method in class org.jmol.modelset.Bond
getAtom(int) - Method in class org.jmol.modelset.Measurement
getAtom(int) - Method in class org.jmol.smiles.SmilesBond
getAtom(int) - Method in interface org.jmol.util.SimpleEdge
  Get the respective atom, 0 or 1
getAtom1() - Method in class org.jmol.smiles.SmilesBond
getAtomAt(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getAtomBits(int, Object) - Method in class org.jmol.script.ScriptEval
getAtomBits(Viewer, String, Object, Map, int, int, BS) - Method in interface org.jmol.api.JmolAnnotationParser
getAtomBits(Viewer, String, Object, Map, int, int, BS) - Method in class org.jmol.dssx.AnnotationParser
  ////////////////// general post-load processing ////////////////
getAtomBits(Viewer, String, Object, Map, int, int, BS) - Method in class org.jmol.dssx.DSSR1
getAtomBitsBS(int, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAtomBitSet(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
getAtomBitSet(Object) - Method in class org.jmol.script.ScriptEval
  A general method to evaluate a string representing an atom set.
getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in interface org.jmol.api.JmolScriptManager
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.script.ScriptManager
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelSet
getAtomBitsMDa(int, Object, BS) - Method in class org.jmol.modelset.AtomCollection
  general unqualified lookup of atom set type
getAtomBitsMDb(int, Object) - Method in class org.jmol.modelset.BondCollection
getAtomBitsStr(int, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAtomCIPChiralityCode(Atom) - Method in class org.jmol.modelset.ModelSet
  Determine the Cahn-Ingold-Prelog R/S chirality of an atom
getAtomCount() - Method in class jme.JMEmol
getAtomCount() - Method in class org.jmol.modelset.ModelLoader
getAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getAtomCount(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomCount(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the number of atoms contained in the file.
getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getAtomData(String, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getAtomData(String, String, boolean) - Method in class org.jmol.viewer.PropertyManager
  use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.
getAtomDefs(Map) - Method in class org.jmol.viewer.Viewer
getAtomFromName(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
getAtomFromName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
getAtomGroupQuaternions(BS, int) - Method in class org.jmol.viewer.Viewer
getAtomGroupQuaternions(BS, int, char) - Method in class org.jmol.modelset.ModelSet
getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.Node
getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
getAtomicDSSRData(float[], String) - Method in class org.jmol.modelsetbio.BioModel
getAtomicDSSRData(int) - Method in class org.jmol.modelset.ModelSet
getAtomicDSSRData(ModelSet, int, float[], String) - Method in interface org.jmol.api.JmolAnnotationParser
getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.AnnotationParser
getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.DSSR1
getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
  Returns the atomic mass of the atom.
getAtomicMass(int) - Static method in class org.jmol.util.Elements
getAtomicNumber(String) - Static method in class org.iupac.InchiUtils
getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
getAtomIdentityInfo(int, Map, P3) - Method in class org.jmol.modelset.AtomCollection
getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
getAtomIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomIndex(String, int) - Method in class org.jmol.modelset.Group
getAtomIndex(String, int) - Method in class org.jmol.modelsetbio.Monomer
getAtomIndex1() - Method in class org.jmol.modelset.Bond
getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
getAtomIndex1() - Method in class org.jmol.util.Edge
getAtomIndex2() - Method in class org.jmol.modelset.Bond
getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
getAtomIndex2() - Method in class org.jmol.util.Edge
getAtomIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
getAtomIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
getAtomIndices(BS) - Method in class org.jmol.modelset.AtomCollection
getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
getAtomInfo(int, String, P3) - Method in class org.jmol.modelset.AtomCollection
getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  /////////////////////////////////////////////////////////////
getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
  Get an AtomIterator for retrieval of all atoms in the file.
getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
getAtomName() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAtomName() - Method in class org.jmol.modelset.Atom
getAtomName() - Method in class org.jmol.smiles.SmilesAtom
getAtomName() - Method in interface org.jmol.util.Node
getAtomName() - Method in interface org.jmol.util.SimpleNode
getAtomName(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getAtomNumber() - Method in class org.jmol.modelset.Atom
getAtomNumber() - Method in class org.jmol.smiles.SmilesAtom
  Returns the Jmol atom number
getAtomNumber() - Method in interface org.jmol.util.Node
getAtomNumber(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
getAtomPointVector(BS) - Method in class org.jmol.modelset.AtomCollection
getAtomPropertiesLike(String) - Static method in class org.jmol.script.T
getAtoms() - Method in class jspecview.common.PeakInfo
getAtoms(int, Object) - Method in class org.jmol.modelset.ModelSet
  general lookup for integer type -- from Eval
getAtoms(Object) - Method in interface org.jmol.api.SmilesMatcherInterface
getAtoms(Object) - Method in class org.jmol.smiles.SmilesMatcher
getAtomsConnected(float, float, int, BS) - Method in class org.jmol.modelset.BondCollection
getAtomSetAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetAtomIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the auxiliary information for a particular atomSet.
getAtomSetAuxiliaryInfoValue(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetBondCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetCenter(BS) - Method in class org.jmol.modelset.ModelSet
getAtomSetCollection() - Method in interface org.jmol.api.JmolFilesReaderInterface
getAtomSetCollection() - Method in class org.jmol.io.FileReader
getAtomSetCollection() - Method in class org.jmol.io.FilesReader
getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  Create the AtomSetCollection and return it
getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
  Get the auxiliary information for this atomSetCollection.
getAtomSetCollectionFromDOM(Object, Map) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  Direct DOM HTML4 page reading; Egon was interested in this at one point.
getAtomSetCollectionFromDOM(Object, Map) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionFromReader(String, Object, Map) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionFromReader(String, Object, Map) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionFromReaderType(String, String, Object, Map) - Method in class org.jmol.api.JmolAdapter
  all in one -- for TestSmarterJmolAdapter
getAtomSetCollectionFromSet(Object, Object, Map) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
getAtomSetCollectionFromSet(Object, Object, Map) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionInline(Object, Map) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionInline(Object, Map) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  /////////////////////// post processing ////////////////////////////
getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
  Get the name of the atom set collection, if known.
getAtomSetCollectionOrBufferedReaderFromZip(Viewer, InputStream, String, String[], Map, int, boolean) - Method in class org.jmol.io.JmolUtil
  A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
getAtomSetCollectionReader(String, String, Object, Map) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionReader(String, String, Object, Map) - Method in class org.jmol.api.JmolAdapter
  Read an atomSetCollection object from a bufferedReader and close the reader.
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map, boolean) - Method in class org.jmol.api.JmolAdapter
  Associate an atomSetCollection object with an array of BufferedReader.
getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
  Get number of atomSets in the file or specific model index in file
getAtomSetIndex() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the name of an atomSet.
getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the number identifying each atomSet.
getAtomsFromAtomNumberInFrame(int) - Method in class org.jmol.modelset.AtomCollection
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.JmolStateCreator
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.StateCreator
getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
getAtomsInFrame(BS) - Method in class org.jmol.modelset.AtomCollection
getAtomSite() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAtomSite() - Method in class org.jmol.modelset.Atom
getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
getAtomSite() - Method in interface org.jmol.util.Node
getAtomsNearPlane(float, P4) - Method in class org.jmol.modelset.AtomCollection
getAtomsNearPt(float, P3, BS) - Method in class org.jmol.viewer.Viewer
getAtomsStartingAt(int) - Method in class org.jmol.script.ScriptParam
getAtomsWithin(float, T3, BS, int) - Method in class org.jmol.modelset.ModelSet
getAtomsWithinRadius(float, BS, boolean, RadiusData, BS) - Method in class org.jmol.modelset.ModelSet
  Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
getAtomSymmetry(Atom, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.readers.cif.MSRdr
  When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.
getAtomSymmetry(Atom, XtalSymmetry.FileSymmetry) - Method in interface org.jmol.adapter.smarter.MSInterface
getAtomTensor(int, String) - Method in class org.jmol.modelset.AtomCollection
getAtomTensorList(int) - Method in class org.jmol.modelset.AtomCollection
getAtomType() - Method in class org.jmol.modelset.Atom
getAtomType() - Method in class org.jmol.smiles.SmilesAtom
getAtomType() - Method in interface org.jmol.util.Node
getAtomTypeDescriptions() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getAtomTypeDescs(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapterBondIterator
getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapterBondIterator
getAtomValidation(String, Atom) - Method in class org.jmol.viewer.Viewer
getAtomValidation(Viewer, String, Atom) - Method in interface org.jmol.api.JmolAnnotationParser
getAtomValidation(Viewer, String, Atom) - Method in class org.jmol.dssx.AnnotationParser
  Get all validation values corresponding to a specific validation type.
getAtropicStereoFlag(Node[]) - Static method in class org.jmol.smiles.SmilesStereo
getAtropismNode(int, Node, boolean) - Static method in class org.jmol.util.Edge
getAtropismOrder(int, int) - Static method in class org.jmol.util.Edge
getAtropismOrder12(int) - Static method in class org.jmol.util.Edge
getAtropisomerKeys(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  called by SmilesParser to get nn in ^nn- base on match to actual structure
getAttachedAtomForPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
  Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
getAttribute(String, String) - Method in interface org.jmol.api.JmolJDXMOLParser
getAttribute(String, String) - Method in class org.jmol.jsv.JDXMOLParser
getAttributeList() - Method in class jspecview.source.XMLParser
getAttrValue(String) - Method in class jspecview.source.XMLParser
getAttrValueLC(String) - Method in class jspecview.source.XMLParser
getAType() - Method in interface jspecview.api.AnnotationData
getAType() - Method in class jspecview.common.MeasurementData
getAType() - Method in class jspecview.dialog.JSVDialog
getAverageAtomPoint() - Method in class org.jmol.modelset.ModelSet
getAxesState(SB) - Method in class org.jmol.shape.Axes
getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
getAxisLabel(boolean) - Method in class jspecview.common.Spectrum
  checks in order: (1) Peaks tag attribute xUnits/yUnits, then (2) ##XLABEL/##YLABEL, then (3) ##XUNITS/##YUNITS
getAxisPoint(int, boolean, P3) - Method in class org.jmol.shape.Axes
  axisPoints are offset cartesian values.
getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
getBackgroundColor() - Method in class jspecview.java.AwtPanel
getBase64() - Method in class javajs.util.OC
getBase64(byte[]) - Static method in class javajs.util.Base64
getBaseModelBitSet() - Method in class org.jmol.viewer.Viewer
getBaseModelIndex(int) - Method in interface org.jmol.api.JmolJSpecView
getBaseModelIndex(int) - Method in class org.jmol.jsv.JSV
getBasePairs() - Method in class org.jmol.modelsetbio.NucleicMonomer
getBasePairs(Viewer, int) - Method in interface org.jmol.api.JmolAnnotationParser
getBasePairs(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
getBasePairs(Viewer, int) - Method in class org.jmol.dssx.DSSR1
getBasePeakInfo() - Method in class jspecview.common.Spectrum
getBaseRing6Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getBaseSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
  Get the symmetry that was in place prior to any supercell business.
getBasisAtom(int) - Method in class org.jmol.modelkit.ModelKit
getBasisAtom(int, boolean) - Method in class org.jmol.modelset.ModelSet
getBBoxVertices() - Method in class org.jmol.modelset.ModelSet
getBestLineThroughPoints(P3[], int) - Static method in class javajs.util.Measure
  Get the endpoints of the best line through N points, where N >= 2
getBfactor() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getBfactor100() - Method in class org.jmol.modelset.Atom
getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
getBFactors() - Method in class org.jmol.modelset.AtomCollection
getBgContrast(int) - Static method in class org.jmol.util.C
getBinaryType(InputStream) - Static method in class org.jmol.adapter.smarter.Resolver
getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
getBindingInfo(String[], String[], String) - Method in class org.jmol.viewer.binding.Binding
getBindings() - Method in class org.jmol.viewer.binding.Binding
getBioBranches(Lst) - Method in class org.jmol.modelsetbio.BioModel
getBioModel(int, int, Map, Properties, Map) - Method in class org.jmol.modelsetbio.BioResolver
getBioModelSet(ModelSet) - Method in class org.jmol.modelsetbio.BioResolver
getBioPolymerCount() - Method in class org.jmol.modelsetbio.BioModel
getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getBioPolymerCountInModel(int) - Method in class org.jmol.modelsetbio.BioModelSet
getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
getBioPolymerLength() - Method in class org.jmol.modelset.Group
getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
getBioSmiles(BS) - Method in class org.jmol.viewer.Viewer
getBioSmilesType() - Method in class org.jmol.modelset.Atom
getBioSmilesType() - Method in class org.jmol.smiles.SmilesAtom
getBioSmilesType() - Method in interface org.jmol.util.Node
getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
getBioStructureTypeName() - Method in interface org.jmol.util.Node
getBioStructureTypeName(boolean) - Method in enum class org.jmol.c.STR
getBIS(byte[]) - Static method in class javajs.util.Rdr
  /////// stream/byte methods ///////////
getBisectingPlane(P3, V3, T3, V3, P4) - Static method in class javajs.util.Measure
getBitSet() - Method in class jspecview.common.IntegralData
getBitSet(SV, boolean) - Static method in class org.jmol.script.SV
getBitSetForMF(Atom[], BS, String) - Static method in class org.jmol.util.JmolMolecule
getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in class org.jmol.scriptext.CmdExt
getBitsetIdentFull(BS, String, boolean, int, boolean, String[]) - Method in class org.jmol.scriptext.CmdExt
getBitsetProperty(BS, Lst, int, P3, P4, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEval
getBitsetPropertyFloat(BS, int, String, float, float) - Method in class org.jmol.script.ScriptEval
getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
getBond(int) - Method in class org.jmol.smiles.SmilesAtom
  Returns the bond at index `number`.
getBond(CDXMLParser.CDNode, CDXMLParser.CDNode) - Method in class org.jmol.adapter.readers.xml.CDXMLParser
getBond(Atom) - Method in class org.jmol.modelset.Atom
getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
getBondCount() - Method in class jme.JMEmol
getBondCount() - Method in class org.jmol.modelset.Atom
getBondCount() - Method in class org.jmol.modelset.Model
getBondCount() - Method in class org.jmol.smiles.SmilesAtom
getBondCount() - Method in interface org.jmol.util.SimpleNode
  Get the total number of bonds, including hydrogen bonds.
getBondCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
  for general use
getBondCountInModel(int) - Method in class org.jmol.modelset.ModelSet
  /////// bonds /////////
getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
getBondedAtomIndex(int) - Method in interface org.jmol.util.Node
getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
getBondIndex(int) - Method in class org.jmol.minimize.MinAtom
getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
getBondingRadii() - Method in class org.jmol.modelset.AtomCollection
getBondingRadius() - Method in class org.jmol.modelset.Atom
getBondingRadius(int, int) - Static method in class org.jmol.api.JmolAdapter
getBondingRadius(int, int) - Static method in class org.jmol.util.Elements
  This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.
getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
  Get a BondIterator for retrieval of all bonds in the file.
getBondIterator(BS) - Method in class org.jmol.modelset.BondCollection
getBondIteratorForType(int, BS) - Method in class org.jmol.modelset.BondCollection
getBondKey(int, int) - Static method in class org.jmol.adapter.readers.xml.CDXMLParser
getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getBondList(Object) - Method in class org.jmol.api.JmolAdapter
getBondOrder(String) - Method in class org.jmol.adapter.readers.cif.CifReader
getBondOrder(String) - Method in interface org.jmol.adapter.readers.xml.CDXMLParser.CDXReaderI
getBondOrder(String) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
getBondOrderFromFloat(float) - Static method in class org.jmol.util.Edge
getBondOrderFromString(String) - Static method in class org.jmol.util.Edge
  Encode name such as 1 2 3 2.1 3.1 single double triple atropisomer_12 or "partial 1.3"
getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.Edge
getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.Edge
  used for formatting labels and in the connect PARTIAL command
getBondPickingMode() - Method in class org.jmol.viewer.ActionManager
getBondProperties(int) - Method in class jme.JMEmol
getBondRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getBondsForSelectedAtoms(BS) - Method in class org.jmol.viewer.Viewer
getBondsForSelectedAtoms(BS, boolean) - Method in class org.jmol.modelset.BondCollection
getBondTo(int) - Method in class org.jmol.minimize.MinAtom
getBondType() - Method in class org.jmol.util.Edge
getBondType() - Method in interface org.jmol.util.SimpleEdge
  Get the order of the bond.
getBoolean(boolean) - Static method in class org.jmol.script.SV
getBoolean(int) - Method in class org.jmol.api.JmolViewer
getBoolean(int) - Method in class org.jmol.viewer.Viewer
getBoolean(ScriptToken) - Method in class jspecview.common.PanelData
getBoolean(ScriptToken) - Method in class jspecview.common.Parameters
getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
getBooleans() - Method in class jspecview.common.Parameters
getBooleanValue(String, boolean) - Method in class org.jmol.util.GenericApplet
getBoolName(int) - Static method in class org.jmol.viewer.JC
getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelSet
getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelSet
getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelSet
getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
getBoundBoxOrientation(int, BS, P3[]) - Method in class org.jmol.modelset.ModelSet
getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
  Return basic info on boundbox in the form of an array.
getBoundBoxVertices() - Method in class org.jmol.util.BoxInfo
getBoundingBox() - Method in class org.jmol.shape.Mesh
getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getBox(int) - Method in class org.jmol.shape.Labels
getBoxFacesFromOABC(P3[]) - Static method in class org.jmol.util.BoxInfo
getBoxInfo() - Method in class org.jmol.modelset.ModelSet
getBoxInfo(BS, float) - Method in class org.jmol.modelset.ModelSet
getBR(String) - Static method in class javajs.util.Rdr
getBranchBitSet(int, int, boolean) - Method in class org.jmol.viewer.Viewer
  given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.
getBranchBitSet(Node[], int, BS, Lst, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
  given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
getBranchesForInversion(Node[], int, BS) - Static method in class org.jmol.util.JmolMolecule
getBSAll() - Method in class org.jmol.adapter.smarter.StructureIterator
getBSAll() - Method in class org.jmol.api.JmolAdapterStructureIterator
getBSAtoms(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Create bsAtoms if it is null, and set bits if desired.
getBsBranches(float[]) - Method in class org.jmol.modelset.ModelSet
getBSSideChain() - Method in class org.jmol.modelset.Group
getBSSideChain() - Method in class org.jmol.modelsetbio.AminoMonomer
getBsSurfaceClone() - Method in interface org.jmol.api.JmolEnvCalc
getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
getBufferData() - Method in class jspecview.source.XMLParser
getBufferedFileInputStream(String) - Method in class jspecview.java.AwtPlatform
getBufferedFileInputStream(String) - Method in class jspecview.js2d.JsPlatform
getBufferedFileInputStream(String) - Method in interface org.jmol.api.GenericPlatform
getBufferedFileInputStream(String) - Method in class org.jmol.awt.Platform
getBufferedFileInputStream(String) - Method in class org.jmol.awtjs2d.Platform
getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
getBufferedInputStreamOrErrorMessageFromName(String, String, boolean, boolean, byte[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
getBufferedReader() - Method in class javajs.util.DataReader
getBufferedReader(BufferedInputStream, String) - Static method in class javajs.util.Rdr
  Read an input stream fully, saving a byte array, then return a buffered reader to those bytes converted to string form.
getBufferedReader(String) - Method in class org.jmol.minimize.forcefield.ForceField
getBufferedReaderForInputStream(InputStream) - Static method in class jspecview.common.JSVFileManager
getBufferedReaderForResource(Viewer, Class, String, String) - Static method in class org.jmol.viewer.FileManager
getBufferedReaderForStringOrBytes(Object) - Static method in class jspecview.common.JSVFileManager
getBufferedReaderFromName(String) - Static method in class jspecview.common.JSVFileManager
getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.io.FilesReader
  called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
getBundle(String) - Method in class org.jmol.modelkit.ModelKitPopup
  ///////////// menu creation and update ///////////////
getBundle(String) - Method in class org.jmol.popup.JmolGenericPopup
getBundle(String) - Method in class org.jmol.popup.JmolPopup
getButtonCount() - Method in class org.jmol.awtjs.swing.ButtonGroup
getButtonGroup() - Method in class org.jmol.awt.AwtPopupHelper
getButtonGroup() - Method in class org.jmol.awtjs2d.JSPopupHelper
getButtonGroup() - Method in interface org.jmol.popup.PopupHelper
getButtonMods(int) - Static method in class org.jmol.viewer.binding.Binding
getByteCount() - Method in class javajs.util.OC
getByteCount() - Method in class org.jmol.export.___Exporter
getBytes() - Method in class javajs.img.PngEncoder
getBytes64(byte[]) - Static method in class javajs.util.Base64
getBytesFromSB(SB) - Static method in class javajs.util.Rdr
  Allow for base64-encoding check.
getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
getCachedPngjBytes(FileManager, String) - Method in class org.jmol.io.JmolUtil
getCalcType(String) - Static method in class org.jmol.symmetry.CLEG
getCalcType(Atom[], String[], int) - Static method in class org.jmol.quantum.NMRCalculation
getCalcValue() - Method in class org.openscience.jmol.app.janocchio.Measure
getCallback(String) - Static method in enum class org.jmol.c.CBK
getCallbackParameter(int) - Method in class org.jmol.script.ScriptParam
getCameraDepth() - Method in class org.jmol.viewer.TransformManager
getCameraFactors() - Method in class org.jmol.viewer.TransformManager
  This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
getCanonicalCopy(float, boolean) - Method in interface org.jmol.api.SymmetryInterface
getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.Symmetry
getCanonicalCopy(P3[], float) - Static method in class org.jmol.util.BoxInfo
  Change points references to canonical form used in Triangulator, while also scaling.
getCanonicalCopyTrimmed(P3, float) - Method in class org.jmol.symmetry.UnitCell
getCanonicalName(String) - Method in class org.jmol.viewer.FileManager
getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getCaretPosition() - Method in interface org.jmol.api.js.GenericConsoleTextArea
getCaretPosition() - Method in interface org.jmol.console.GenericTextArea
getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
getCartoonType(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getCartoonType(int) - Method in interface org.jmol.api.PymolAtomReader
getCel() - Method in class org.jmol.util.GData
getCellRange() - Method in interface org.jmol.api.SymmetryInterface
getCellRange() - Method in class org.jmol.symmetry.Symmetry
getCellRange(T3, P3[]) - Static method in class org.jmol.util.SimpleUnitCell
getCellStyle(int, int, GridBagConstraints) - Method in interface org.jmol.awtjs.swing.TableCellRenderer
getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
  Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
getCellWeight(P3) - Method in interface org.jmol.api.SymmetryInterface
getCellWeight(P3) - Method in class org.jmol.symmetry.Symmetry
getCellWeights(BS) - Method in class org.jmol.modelset.ModelSet
getCelPower() - Method in class org.jmol.util.GData
getCenter() - Method in class com.sparshui.common.messages.events.RotateEvent
getCenter() - Method in class com.sparshui.common.messages.events.ZoomEvent
getCenter(int) - Method in class org.jmol.symmetry.UnitCell
  Takes into account subperiodic groups using BoxInfo.unitCubePoints P3.new3(0, 0, 0), // 0 P3.new3(0, 0, 1), // 1 c P3.new3(0, 1, 0), // 2 b P3.new3(0, 1, 1), // 3 bc P3.new3(1, 0, 0), // 4 a P3.new3(1, 0, 1), // 5 ac P3.new3(1, 1, 0), // 6 ab P3.new3(1, 1, 1), // 7 }; abc
getCenter(Location, Location) - Static method in class com.sparshui.common.Location
getCenterAndPoints(Lst, boolean) - Method in class org.jmol.modelset.ModelSet
getCenterAndPoints(Lst, boolean) - Method in class org.jmol.viewer.Viewer
getCenterAndPoints(Lst) - Static method in class javajs.util.Measure
  from a list of points, create an array that includes the center point as the first point.
getCenterAtom() - Method in interface org.iupac.InChIStructureProvider
getCenterAtom() - Method in class org.jmol.inchi.InChIJNA
getCenterAtom() - Method in class org.jmol.inchi.InChIJS
getCenterText() - Method in class org.jmol.modelkit.ModelKit
getCentroid(Location, Location, float) - Static method in class com.sparshui.common.Location
  get weighted average location.
getChainAt(int) - Method in class org.jmol.modelset.Model
getChainBits(int) - Method in class org.jmol.modelset.AtomCollection
getChainCount(boolean) - Method in class org.jmol.modelset.Model
getChainCountInModelWater(int, boolean) - Method in class org.jmol.modelset.ModelSet
getChainID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getChainID() - Method in class org.jmol.modelset.Atom
getChainID() - Method in class org.jmol.smiles.SmilesAtom
getChainID() - Method in interface org.jmol.util.Node
getChainID(String, boolean) - Method in class org.jmol.viewer.Viewer
  Create a unique integer for any chain string.
getChainIDStr() - Method in class org.jmol.modelset.Atom
getChainIDStr() - Method in class org.jmol.smiles.SmilesAtom
getChainIDStr() - Method in interface org.jmol.util.Node
getChainIDStr(int) - Method in class org.jmol.viewer.Viewer
getChangeableColix(int, int) - Method in class org.jmol.util.GData
getChangeableColixIndex(short) - Static method in class org.jmol.util.C
getChangeInX() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
getChangeInY() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
getCharacters() - Method in class jspecview.source.XMLParser
getCharge() - Method in interface org.iupac.InChIStructureProvider
getCharge() - Method in class org.jmol.inchi.InChIJNA
getCharge() - Method in class org.jmol.inchi.InChIJS
getCharge() - Method in class org.jmol.smiles.SmilesAtom
  Returns the charge of the atom.
getCharge(int) - Method in class jme.JMEmol
getCheckBox(String) - Method in class org.jmol.awt.AwtPopupHelper
getCheckBox(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getCheckBox(String) - Method in interface org.jmol.popup.PopupHelper
getChemicalInfo(String, String, BS) - Method in class org.jmol.viewer.Viewer
getChemicalShift(Atom) - Method in interface org.jmol.api.JmolNMRInterface
  If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
getChemicalShift(Atom) - Method in class org.jmol.quantum.NMRCalculation
getChildCount() - Method in interface jspecview.api.JSVTreeNode
getChildCount() - Method in class jspecview.tree.SimpleTreeNode
getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
getChimeInfo(int, BS) - Method in interface org.jmol.api.JmolPropertyManager
getChimeInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
getChimeMessenger() - Method in class org.jmol.viewer.Viewer
getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
getChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
getChiralityForAtoms(CIPData) - Method in class org.jmol.symmetry.CIPChirality
  A general determination of chirality that involves ultimately all of Rules 1-6.
getCifData(int) - Method in class org.jmol.viewer.Viewer
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.BCIFReader
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.Cif2Reader
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.CifReader
getCIPChirality(boolean) - Method in class org.jmol.modelset.Atom
  Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
getCIPChirality(boolean) - Method in class org.jmol.modelset.Bond
  Not implemented.
getCIPChirality(boolean) - Method in class org.jmol.smiles.SmilesAtom
getCIPChirality(boolean) - Method in class org.jmol.util.Edge
getCIPChirality(boolean) - Method in interface org.jmol.util.Node
getCIPChiralityCode() - Method in class org.jmol.modelset.Atom
getCIPChiralityCode() - Method in class org.jmol.smiles.SmilesAtom
getCIPChiralityCode() - Method in interface org.jmol.util.Node
getCIPChiralityCode(char) - Static method in class org.jmol.viewer.JC
getCIPChiralityName(int) - Static method in class org.jmol.viewer.JC
getCIPChiralityRule() - Method in class org.jmol.modelset.Atom
getCIPRuleName(int) - Static method in class org.jmol.viewer.JC
getCleanITAName() - Method in class org.jmol.symmetry.CLEG.ClegNode
getClegId() - Method in class org.jmol.symmetry.SpaceGroup
getClickableSet(boolean) - Method in class org.jmol.modelset.AtomCollection
getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
getClickedCoordinate() - Method in class jspecview.common.PanelData
  Returns the spectrum coordinate of the point on the display that was clicked
getClipboardText() - Static method in class jspecview.java.AwtClipboard
  Get the String residing on the clipboard.
getClipboardText() - Method in class org.jmol.api.JmolViewer
getClipboardText() - Static method in class org.jmol.awt.AwtClipboard
  Get the String residing on the clipboard.
getClipboardText() - Method in class org.jmol.viewer.Viewer
getClone() - Method in class org.jmol.adapter.smarter.Atom
getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
getCmdExt() - Method in class org.jmol.script.ScriptEval
getCmlBondOrder(int) - Static method in class org.jmol.util.Edge
getCode() - Method in enum class org.jmol.c.FIL
getCode() - Method in class org.jmol.symmetry.SymmetryOperation
getColix() - Method in class org.jmol.api.JmolAdapterBondIterator
getColix(int) - Static method in class org.jmol.util.C
getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
getColix2(int, Atom, boolean) - Method in class org.jmol.shape.Labels
getColixA(short, byte, Atom) - Method in class org.jmol.shape.Shape
getColixArray(String) - Static method in class org.jmol.util.C
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
getColixB(short, int, Bond) - Method in class org.jmol.shape.Shape
getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
getColixI(short, byte, int) - Method in class org.jmol.shape.Shape
getColixInherited(short, short) - Static method in class org.jmol.util.C
getColixO(Object) - Static method in class org.jmol.util.C
getColixS(String) - Static method in class org.jmol.util.C
getColixTranslucencyFractional(short) - Static method in class org.jmol.util.C
getColixTranslucencyLabel(short) - Static method in class org.jmol.util.C
getColixTranslucencyLevel(short) - Static method in class org.jmol.util.C
getColixTranslucent(int) - Static method in class org.jmol.util.C
getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.C
getColor() - Method in class jme.JME
getColor() - Method in class jspecview.common.ColoredAnnotation
getColor() - Method in enum class org.jmol.c.STR
getColor(ScriptToken) - Method in class jspecview.common.PanelData
getColor1(int) - Method in class jspecview.common.ColorParameters
getColor1(int) - Method in class jspecview.common.PDFWriter
getColor1(int) - Method in class jspecview.java.AwtG2D
getColor1(int) - Method in class jspecview.java.AwtParameters
getColor1(int) - Method in class jspecview.js2d.JsG2D
getColor1(int) - Method in class jspecview.js2d.JsParameters
getColor1(int) - Method in interface org.jmol.api.GenericGraphics
getColor1(int) - Method in class org.jmol.awt.AwtG2D
getColor1(int) - Method in class org.jmol.awtjs2d.JsG2D
getColor3(int, int, int) - Method in class jspecview.common.ColorParameters
getColor3(int, int, int) - Method in class jspecview.common.PDFWriter
getColor3(int, int, int) - Method in class jspecview.java.AwtG2D
getColor3(int, int, int) - Method in class jspecview.java.AwtParameters
getColor3(int, int, int) - Method in class jspecview.js2d.JsG2D
getColor3(int, int, int) - Method in class jspecview.js2d.JsParameters
getColor3(int, int, int) - Method in interface org.jmol.api.GenericGraphics
getColor3(int, int, int) - Method in class org.jmol.awt.AwtG2D
getColor3(int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
getColor4(int, int, int, int) - Method in class jspecview.common.PDFWriter
getColor4(int, int, int, int) - Method in class jspecview.java.AwtG2D
getColor4(int, int, int, int) - Method in class jspecview.js2d.JsG2D
getColor4(int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
getColor4(int, int, int, int) - Method in class org.jmol.awt.AwtG2D
getColor4(int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
getColorArgbOrGray(short) - Method in class org.jmol.util.GData
getColorCommand(String, byte, short, boolean) - Static method in class org.jmol.shape.Shape
getColorCommandUnk(String, short, boolean) - Static method in class org.jmol.shape.Shape
getColoredAnnotation(GenericGraphics, Spectrum, Lst, Annotation) - Static method in class jspecview.common.Annotation
getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
getColorFromString(String) - Method in class jspecview.common.ColorParameters
getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
getColorKey() - Method in class org.jmol.util.ColorEncoder
getColorList(int, short[], int, BS, Map) - Method in class org.jmol.export.___Exporter
  input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
getColorRange(int) - Method in class org.jmol.script.ScriptEval
getColorScheme() - Method in class org.jmol.util.ColorEncoder
getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
getColorTrans(ScriptEval, int, boolean, int[]) - Method in class org.jmol.scriptext.ScriptExt
  Checks color, translucent, opaque parameters.
getColour(Spectrum, boolean) - Method in interface jspecview.api.VisibleInterface
getColour(Spectrum, boolean) - Method in class jspecview.common.Visible
  Returns the integer color of a solution based on its visible spectrum.
getColumn(int) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
getColumn(int) - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
getColumn(int) - Method in class org.jmol.awtjs.swing.JTable
getColumn(int, float[]) - Method in class javajs.util.M3
  Copies the matrix values in the specified column into the array parameter.
getColumn(int, float[]) - Method in class javajs.util.M4
  Copies the matrix values in the specified column into the array parameter.
getColumn33(int, float[]) - Method in class javajs.util.M34
getColumnCentering(int) - Method in class jspecview.java.AwtDialog
getColumnCentering(int) - Method in class jspecview.js2d.JsDialog
getColumnClass(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
getColumnCount() - Method in interface javajs.api.GenericCifDataParser
getColumnCount() - Method in class javajs.util.CifDataParser
getColumnCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
getColumnData(int) - Method in interface javajs.api.GenericCifDataParser
getColumnData(int) - Method in class javajs.util.CifDataParser
  Column i in the current row
getColumnDimension() - Method in class javajs.util.Matrix
  Get column dimension.
getColumnModel() - Method in class org.jmol.awtjs.swing.JTable
getColumnName(int) - Method in interface javajs.api.GenericCifDataParser
getColumnName(int) - Method in class javajs.util.CifDataParser
getColumnName(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
getColumnV(int, T3) - Method in class javajs.util.M3
  Copies the matrix values in the specified column into the vector parameter.
getCommand(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
getCommandDown() - Method in class org.jmol.util.CommandHistory
  Retrieves the following command from the top of the list, updates list position.
getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Generates a commandline from the options set for povray path etc and sets in the textField.
getCommands(Map, Map, String) - Method in class org.jmol.viewer.Viewer
getCommandSet(String) - Static method in class org.jmol.script.T
  retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCommandString() - Method in class org.jmol.console.GenericConsole
getCommandUp() - Method in class org.jmol.util.CommandHistory
  Retrieves the following command from the bottom of the list, updates list position.
getCommonNMRIsotope(String) - Static method in class org.jmol.util.Elements
getComparator(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
getComponent(int) - Method in interface org.jmol.api.SC
getComponent(int) - Method in class org.jmol.awt.AwtSwingComponent
getComponent(int) - Method in class org.jmol.awtjs.swing.Container
getComponentCount() - Method in interface org.jmol.api.SC
getComponentCount() - Method in class org.jmol.awt.AwtSwingComponent
getComponentCount() - Method in class org.jmol.awtjs.swing.Container
getComponents() - Method in interface org.jmol.api.SC
getComponents() - Method in class org.jmol.awt.AwtSwingComponent
getComponents() - Method in class org.jmol.awtjs.swing.Container
getConeMesh(P3, M3, short) - Static method in class org.jmol.export.___Exporter
getConformation(int, boolean, BS, BS) - Method in class org.jmol.modelsetbio.BioModel
getConformation(int, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
getConnectingAtoms(BS, BS) - Method in class org.jmol.modelset.ModelSet
getConsole() - Method in class org.jmol.viewer.Viewer
getConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getConsoleFontScale() - Method in class org.jmol.viewer.Viewer
getConstrainableEquivAtom(Atom) - Method in interface org.jmol.api.SymmetryInterface
getConstrainableEquivAtom(Atom) - Method in class org.jmol.symmetry.Symmetry
  This atom is usually the atom being moved, but in some cases we need to switch to a different atom in order to avoid the special case where a screw axis (SG 224 Wyckoff i) or glide (plane group 12 Wyckoff c) creates a stationary point.
getContentPane() - Method in class org.jmol.awtjs.swing.JDialog
getContents() - Method in class javajs.util.AjaxURLConnection
getContext(String) - Method in class org.jmol.viewer.StateManager
getContextVariableAsVariable(String, boolean) - Method in class org.jmol.script.ScriptParam
getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
  create a set of contour data.
getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
  NWCHEM only
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.AlphaPolymer
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.BioPolymer
getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.UnitCell
  return a conventional lattice from a primitive
getConversionFactor(Map, String, String) - Static method in class org.qcschema.QCSchemaUnits
  Get the necessary conversion factor to the desired units from a key_units or atomic units
getConversionFactorTo(ArrayList, String) - Static method in class org.qcschema.QCSchemaUnits
  For a reader, use the JSON [units, factor] along with a desired unit to get the conversion factor from file values to desired units.
getConvertedSpectrum() - Method in class jspecview.common.Spectrum
getCoord() - Method in class jspecview.common.PeakPickEvent
getCoordinate() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript to return the coordinate of clicked point in the plot area of the `JSVPanel`
getCoordinate() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript to return the coordinate of clicked point in the plot area of the `JSVPanel`
getCoordinate() - Method in class jspecview.appletjs.JSVApplet
getCoordinate() - Method in class jspecview.common.JSViewer
getCoordinateMap(T3[], int[], BS) - Method in class org.jmol.export.__CartesianExporter
getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
getCoordinateState(BS) - Method in class org.jmol.viewer.Viewer
getCorrelationMaps(Object, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getCorrelationMaps(Object, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
getCorrelationTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
  get the correlation time in seconds
getCorrelationTimeTauPS() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  get the correlation time in picoseconds
getCouples() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
getCoupleWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
getCovalentBondCount() - Method in class org.jmol.modelset.Atom
getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
  Returns the number of bonds of this atom.
getCovalentBondCount() - Method in interface org.jmol.util.Node
getCovalentBondCount() - Method in interface org.jmol.util.SimpleNode
  Get the total number of covalent bonds, thus not including hydrogen bonds.
getCovalentBondCountPlusMissingH() - Method in class org.jmol.modelset.Atom
getCovalentBondCountPlusMissingH() - Method in class org.jmol.smiles.SmilesAtom
getCovalentBondCountPlusMissingH() - Method in interface org.jmol.util.Node
  includes actual + missing
getCovalentBondOrder(int) - Static method in class org.jmol.util.Edge
getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getCovalentHydrogenCount() - Method in interface org.jmol.util.Node
getCovalentOrder() - Method in class org.jmol.modelset.Bond
getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
getCovalentOrder() - Method in class org.jmol.util.Edge
getCovalentOrder() - Method in interface org.jmol.util.SimpleEdge
getCovalentOrPartialBondCount() - Method in class org.jmol.modelset.Atom
getCovalentRadius(int) - Static method in class org.jmol.util.Elements
  Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR
getCrcValue(byte[]) - Method in interface javajs.api.GenericZipTools
getCrcValue(byte[]) - Method in class javajs.util.ZipTools
getCrossLinkGroup(int, Lst, Group, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
getCrossLinkVector(Lst, boolean, boolean) - Method in class org.jmol.modelset.Atom
  Used by SMILES to get vector of cross-links
getCrossLinkVector(Lst, boolean, boolean) - Method in class org.jmol.modelset.Group
getCrossLinkVector(Lst, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
getCrossLinkVector(Lst, boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
getCrossLinkVector(Lst, boolean, boolean) - Method in class org.jmol.smiles.SmilesAtom
getCrossLinkVector(Lst, boolean, boolean) - Method in interface org.jmol.util.Node
getCSSstyle(int, int) - Method in class org.jmol.awtjs.swing.Component
getCSVString(String, int[]) - Static method in class javajs.util.PT
  CSV format -- escaped quote is "" WITHIN "..."
getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
getCurrentColorSchemeName() - Method in class org.jmol.util.ColorEncoder
getCurrentFileAsString(String) - Method in class org.jmol.viewer.Viewer
  /////// File-related methods ////////////
getCurrentGraphSet() - Method in class jspecview.common.PanelData
getCurrentModelAuxInfo() - Method in class org.jmol.viewer.Viewer
getCurrentModelFileAsString(String) - Method in class org.jmol.script.ScriptEval
getCurrentModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getCurrentPanelIndex() - Method in interface jspecview.api.JSVMainPanel
getCurrentPanelIndex() - Method in class jspecview.java.AwtMainPanel
getCurrentPanelIndex() - Method in class jspecview.js2d.JsMainPanel
getCurrentPlotColor(int) - Method in class jspecview.common.PanelData
getCurrentSpectrumIndex() - Method in class jspecview.common.PanelData
getCurrentSpinAtoms() - Method in class org.jmol.modelset.ModelSet
  include this frame and all related frames
getCurrentSplitModelIndex() - Method in class org.jmol.viewer.AnimationManager
getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
getCurrentStructureFile() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getCurrentSubSpectrum() - Method in class jspecview.common.Spectrum
getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
getCursorX() - Method in class org.jmol.viewer.Viewer
getCursorY() - Method in class org.jmol.viewer.Viewer
getCutoff() - Method in class org.openscience.jmol.app.janocchio.NoeTable
  get the cutoff distance
getCutoffAng() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  get the cutoff distance
getCutoffField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
getData() - Method in interface javajs.api.GenericCifDataParser
getData() - Method in class javajs.util.CifDataParser
  The work horse; a general reader for loop data.
getData() - Method in interface jspecview.api.AnnotationData
getData() - Method in class jspecview.common.MeasurementData
getData() - Method in class jspecview.dialog.JSVDialog
getData(InputStream, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  called by SmarterJmolAdapter via JmolUtil to open a Spartan directory and get all the needed data as a string.
getData(String, String) - Method in class org.jmol.api.JmolViewer
getData(String, String) - Method in class org.jmol.viewer.Viewer
getData(String, BS, int) - Method in interface org.jmol.api.JmolDataManager
getData(String, BS, int) - Method in class org.jmol.viewer.DataManager
getDataClass() - Method in class jspecview.source.JDXHeader
  Returns the data class spectrum only
getDataHeader() - Method in class jspecview.common.IntegralData
getDataHeader() - Method in class jspecview.common.MeasurementData
getDataHeader() - Method in class jspecview.common.PeakData
getDataObj(String, BS, int) - Method in class org.jmol.viewer.Viewer
  Retrieve a data object
getDataState(JmolStateCreator, SB) - Method in interface org.jmol.api.JmolDataManager
getDataState(JmolStateCreator, SB) - Method in class org.jmol.viewer.DataManager
getDataType() - Method in class jspecview.source.JDXHeader
  Getter for property dataType.
getDate() - Method in class jspecview.source.JDXHeader
  Getter for property date.
getDateFormat(String) - Method in class jspecview.java.AwtPlatform
getDateFormat(String) - Method in class jspecview.js2d.JsPlatform
getDateFormat(String) - Method in interface org.jmol.api.GenericPlatform
getDateFormat(String) - Method in class org.jmol.awt.Platform
getDateFormat(String) - Method in class org.jmol.awtjs2d.Platform
getDef(String) - Method in class org.jmol.export._VrmlExporter
getDefaultAnnotationInfo(Annotation.AType) - Method in class jspecview.source.JDXDataObject
getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelsetbio.BioModel
getDefaultLattice() - Method in class org.jmol.viewer.Viewer
getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
  When creating a new bond, determine bond diameter from order
getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
getDefaultModel() - Method in class org.jmol.modelkit.ModelKit
getDefaultPropertyParam(int) - Method in interface org.jmol.api.JmolPropertyManager
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.PropertyManager
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.Viewer
getDefaultScheme() - Method in class jspecview.application.DisplaySchemesProcessor
getDefaultStructure(BS, BS) - Method in class org.jmol.modelset.ModelSet
getDefaultUnitPrecision() - Method in class jspecview.source.JDXDataObject
getDefaultVdwNameOrData(int, VDW, BS) - Method in class org.jmol.viewer.Viewer
getDefaultVdwNameOrData(VDW, BS) - Method in interface org.jmol.api.JmolDataManager
getDefaultVdwNameOrData(VDW, BS) - Method in class org.jmol.viewer.DataManager
getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelSet
getDefinedAtomSet(String) - Method in class org.jmol.viewer.Viewer
getDegrees(float, boolean) - Method in class org.jmol.multitouch.ActionManagerMT
getDegrees(float, boolean) - Method in class org.jmol.viewer.ActionManager
  Transform a screen pixel change to an angular change such that a full sweep of the dimension (up to 500 pixels) corresponds to 180 degrees of rotation.
getDelayMaximumMs() - Method in class org.jmol.viewer.Viewer
getDeltaX() - Method in class jspecview.source.JDXDataObject
  Returns the delta X
getDescent() - Method in class org.jmol.util.Font
getDescription() - Method in enum class jspecview.common.ScriptToken
getDescription() - Method in class jspecview.java.AwtDialogFileFilter
  Returns the JSpecViewFileFilter description
getDescription() - Method in class org.jmol.dialog.Dialog.TypeFilter
getDescription() - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getDFMap(String, String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  finds the position in the Jmol-required list of function types.
getDialog() - Method in class org.jmol.dialog.FileChooser
getDialog(Annotation.AType) - Method in class jspecview.common.PanelData
getDialog(Annotation.AType, Spectrum) - Method in class jspecview.common.JSViewer
getDialog(JSVDialog) - Method in class jspecview.dialog.DialogManager
getDialog(JSVDialog) - Method in class jspecview.java.AwtDialogManager
getDialog(JSVDialog) - Method in class jspecview.js2d.JsDialogManager
getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.dialog.DialogManager
getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.java.AwtDialogManager
getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.js2d.JsDialogManager
getDialogManager() - Method in class jspecview.common.JSViewer
getDialogs() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getDiameter(int, int) - Method in class org.jmol.render.FontLineShapeRenderer
getDiff() - Method in class org.openscience.jmol.app.janocchio.Measure
getDiffusePercent() - Method in class org.jmol.util.GData
getDihedralCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
getDihedralMap(int[]) - Method in class org.jmol.modelset.ModelSet
getDimensionality() - Method in interface org.jmol.api.SymmetryInterface
getDimensionality() - Method in class org.jmol.symmetry.Symmetry
  plane 2 freize 2 layer 3 rod 3
getDimensionFromParams(float[]) - Static method in class org.jmol.util.SimpleUnitCell
  Allows for abc, ab, or a
getDimensionValue(int) - Method in class org.jmol.modelset.Atom
getDipolarConstantHz(Atom, Atom) - Method in interface org.jmol.api.JmolNMRInterface
getDipolarConstantHz(Atom, Atom) - Method in class org.jmol.quantum.NMRCalculation
getDipolarCouplingHz(Atom, Atom, V3) - Method in interface org.jmol.api.JmolNMRInterface
getDipolarCouplingHz(Atom, Atom, V3) - Method in class org.jmol.quantum.NMRCalculation
getDirectedNormalThroughPoints(T3, T3, T3, T3, V3, V3) - Static method in class javajs.util.Measure
getDirectory() - Method in class javajs.util.CompoundDocument
getDirectoryListing(String) - Method in class javajs.util.CompoundDocument
getDisplay1D() - Method in class jspecview.common.PanelData
getDisplayModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getDisplayName() - Method in class org.jmol.symmetry.SpaceGroup
getDisplaySchemes() - Method in class jspecview.application.DisplaySchemesProcessor
  Returns the list of `DisplayScheme`s that were loaded
getDisplaySchemesProcessor(JSVInterface) - Method in class jspecview.application.JSpecView
getDistance(Location) - Method in class com.sparshui.common.Location
getDistanceFormatForState() - Method in class org.jmol.modelset.Measurement
getDistances() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
getDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
getDocument() - Method in class org.jmol.awtjs.swing.JTextPane
getDocumentBase() - Method in interface jspecview.api.AppletFrame
getDocumentBase() - Method in class jspecview.appletjs.JSVApplet
getDoTranslate() - Static method in class org.jmol.i18n.GT
getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
getDouble(Map, String) - Method in class org.molecularplayground.MPJmolApp
getDouble(Map, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getDouble(Map, String, String) - Static method in class org.qcschema.QCSchemaUnits
  Reads a value from an associative array, converting it to the desired units.
getDoubleArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
  Retrieve a double array, possibly unpacking it if it is run-length encoded.
getDrawArrayParams(int, int[]) - Method in class org.jmol.shapecgo.CGOMesh
getDrawHover() - Method in class org.jmol.viewer.Viewer
getDrawTitle(boolean, int) - Method in class jspecview.common.PanelData
getDSSRFrame(Map) - Method in interface org.jmol.api.JmolAnnotationParser
getDSSRFrame(Map) - Method in class org.jmol.dssx.AnnotationParser
getDSSRFrame(Map) - Method in class org.jmol.dssx.DSSR1
getDSSRFrame(Viewer) - Method in class org.jmol.modelsetbio.NucleicMonomer
getDx() - Method in class com.sparshui.common.messages.events.DragEvent
getDy() - Method in class com.sparshui.common.messages.events.DragEvent
getEchoName(int) - Static method in class org.jmol.viewer.JC
getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
getEdgePoints(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getEdges() - Method in class org.jmol.modelset.Atom
getEdges() - Method in class org.jmol.smiles.SmilesAtom
getEdges() - Method in interface org.jmol.util.Node
getEdges() - Method in interface org.jmol.util.SimpleNode
  Get the bond array, including hydrogen bonds.
getEigenvalues() - Method in interface javajs.api.EigenInterface
getEigenvalues() - Method in class javajs.util.Eigen
  return values sorted from smallest to largest value.
getEigenvectorsFloatTransposed() - Method in interface javajs.api.EigenInterface
getEigenvectorsFloatTransposed() - Method in class javajs.util.Eigen
  Transpose V and turn into floats; sorted from smallest to largest value.
getElement() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getElement(int, int) - Method in class javajs.util.M3
  Retrieves the value at the specified row and column of this matrix.
getElement(int, int) - Method in class javajs.util.M4
  Retrieves the value at the specified row and column of this matrix.
getElement(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
  allow for any number of characters, for which the first one or two are an element symbol.
getElementColix(int) - Method in class org.jmol.viewer.ColorManager
getElementColor(ScriptToken) - Method in class jspecview.common.ColorParameters
  Gets the color of an element in the scheme
getElementFromUser() - Method in class org.jmol.modelkit.ModelKit
getElementName(int) - Method in class org.jmol.modelset.AtomCollection
getElementNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getElementNumber() - Method in class org.jmol.modelset.Atom
getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
  Returns the atomic number of the element or 0
getElementNumber() - Method in interface org.jmol.util.Node
getElementNumber() - Method in interface org.jmol.util.SimpleNode
getElementNumber(int) - Static method in class org.jmol.util.Elements
getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelSet
getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
getElementSymbol() - Method in class org.jmol.modelset.Atom
getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
getElementSymbolIso(boolean) - Method in class org.jmol.modelset.Atom
getElementType() - Method in interface org.iupac.InChIStructureProvider
getElementType() - Method in class org.jmol.inchi.InChIJNA
getElementType() - Method in class org.jmol.inchi.InChIJS
getElemNos(boolean) - Method in class org.jmol.shapespecial.Polyhedron
getEllipsoidForAtomTensor(Tensor, Atom) - Static method in class org.jmol.shapespecial.Ellipsoid
getEllipsoidShade(float, float, float, int, M4) - Method in class org.jmol.util.Shader
getEmbeddedFileState(String, boolean, String) - Method in class org.jmol.viewer.FileManager
  Get the specified SPT file of a Jmol zip collection or the embedded script for any other file that is embeddable.
getEmbeddedScript(String) - Static method in class org.jmol.viewer.FileManager
  Extract a Jmol script embedded using JC.EMBEDDED_SCRIPT_TAG.
getEmptyEllipsoid(String, int) - Static method in class org.jmol.shapespecial.Ellipsoid
getEmptyPanel(JSViewer) - Static method in class jspecview.java.AwtPanel
  Constructs a new JSVPanel
getEmptyPanel(JSViewer) - Static method in class jspecview.js2d.JsPanel
  Constructs a new JSVPanel
getEncodedOrder() - Method in class org.jmol.api.JmolAdapterBondIterator
getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within <jvxlSurfaceData> element
getEndChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
getEndChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getEndingPointIndex(int) - Method in class jspecview.common.PanelData
getEndingPointIndex(int) - Method in class jspecview.common.ViewData
  in some cases, there is only one scaleData, but there are more than that number of spectra this is no problem -- we just use mod to set this to 0
getEndInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
getEndInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
getEndTag() - Method in class jspecview.source.XMLParser
getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
getEnergy() - Method in class org.jmol.modelset.Bond
getEnergy() - Method in class org.jmol.modelset.HBond
getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
getEntryIcon(String[]) - Method in class org.jmol.popup.GenericPopup
getEquationForQuadricWithCenter(float, float, float, M3, V3, M3, double[], M4) - Static method in class org.jmol.shapespecial.Ellipsoid
getEquivalentAtoms(int) - Method in class org.jmol.modelset.ModelSet
getEquivPointList(int, String, M4[], float, Lst, SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
getEquivPointList(int, String, M4[], float, Lst, SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
  Load a list of initial current points, and one or more starting points with equivalent points.
getEquivPoints(Point3fi, String, float) - Method in interface org.jmol.api.SymmetryInterface
getEquivPoints(Point3fi, String, float) - Method in class org.jmol.symmetry.Symmetry
getErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptError
getErrorLineMessage2() - Method in class org.jmol.script.ScriptEval
getErrorLog() - Method in class jspecview.source.JDXSource
  Returns the error log for this source
getErrorMessage() - Method in interface org.jmol.api.JmolScriptEvaluator
getErrorMessage() - Method in class org.jmol.api.JmolViewer
getErrorMessage() - Method in class org.jmol.script.ScriptError
getErrorMessage() - Method in class org.jmol.viewer.Viewer
getErrorMessageUn() - Method in class org.jmol.api.JmolViewer
getErrorMessageUn() - Method in class org.jmol.viewer.Viewer
getErrorMessageUntranslated() - Method in interface org.jmol.api.JmolScriptEvaluator
getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptError
getErrorMessageUntranslated() - Method in exception class org.jmol.script.ScriptException
getEulerZXZ() - Method in class javajs.util.Quat
getEulerZYZ() - Method in class javajs.util.Quat
getEvalContextAndHoldQueue(JmolScriptEvaluator) - Method in class org.jmol.viewer.Viewer
getEventType() - Method in interface com.sparshui.common.Event
  Returns the integer value of this event type.
getEventType() - Method in class com.sparshui.common.messages.events.DragEvent
getEventType() - Method in class com.sparshui.common.messages.events.FlickEvent
getEventType() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
getEventType() - Method in class com.sparshui.common.messages.events.RotateEvent
getEventType() - Method in class com.sparshui.common.messages.events.SpinEvent
getEventType() - Method in class com.sparshui.common.messages.events.TouchEvent
getEventType() - Method in class com.sparshui.common.messages.events.ZoomEvent
getExecutor() - Method in interface org.jmol.api.JmolParallelProcessor
getExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
getExpCouple(int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
getExpDist(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
getExplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getExplicitHydrogenCount() - Method in interface org.jmol.util.Node
  [CH2] for example
getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
getExplicitSpecialGroupType(String) - Static method in class org.jmol.symmetry.SpaceGroup
getExpNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
getExportDate() - Method in class org.jmol.export.___Exporter
getExportDriverList() - Method in class org.jmol.viewer.Viewer
getExportName() - Method in interface org.jmol.api.JmolRendererInterface
getExportName() - Method in class org.jmol.export.Export3D
getExportName() - Method in class org.jmol.g3d.Graphics3D
getExportType() - Method in interface org.jmol.api.JmolRendererInterface
getExportType() - Method in class org.jmol.export.Export3D
getExportType() - Method in class org.jmol.g3d.Graphics3D
getExpValue() - Method in class org.openscience.jmol.app.janocchio.Measure
getExtension(File) - Method in class jspecview.java.AwtDialogFileFilter
  Returns the extension of a file
getF2C() - Method in class org.jmol.symmetry.UnitCell
getFaces() - Method in class org.jmol.util.MeshSurface
getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
getFactoredValue(int) - Method in class org.jmol.util.Tensor
  Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor
getFactorToAU(String) - Static method in class org.qcschema.QCSchemaUnits
  Get the standard conversion factor to atomic units for this unit.
getFieldString(byte) - Method in class org.jmol.adapter.readers.cif.CifReader
getFile() - Method in class org.openscience.jmol.app.HistoryFile
getFile(String, Object, boolean) - Method in interface jspecview.api.JSVFileHelper
getFile(String, Object, boolean) - Method in class jspecview.java.AwtFileHelper
getFile(String, Object, boolean) - Method in class jspecview.js2d.JsFileHelper
getFileAsBytes(String, OC) - Method in class org.jmol.viewer.FileManager
getFileAsMap(String, String, boolean) - Method in class org.jmol.viewer.FileManager
  create a PNG or ZIP file and return it as a map or, optionally, as a byte[]
getFileAsString(String) - Method in class javajs.util.CompoundDocument
getFileAsString(String) - Static method in class jspecview.common.JSVFileManager
getFileAsString(String) - Method in class org.jmol.viewer.Viewer
getFileAsString3(String, boolean, String) - Method in class org.jmol.viewer.Viewer
getFileAsString4(String, int, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
getFileData(int) - Method in class org.jmol.modelset.ModelSet
getFileDataAsString(String[], int, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
getFileHeader() - Method in interface javajs.api.GenericCifDataParser
getFileHeader() - Method in class javajs.util.CifDataParser
getFileHeader(int) - Method in class org.jmol.modelset.ModelSet
getFileInfo() - Method in class org.jmol.viewer.FileManager
getFileList(String, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  get a complete critical file list for a spartan file Mac directory based on file extension ".spardir.zip" or ".spardir"
getFileName() - Method in class javajs.util.OC
getFileName() - Method in class org.jmol.viewer.FileManager
getFileName() - Method in exception class org.jmol.viewer.JmolAsyncException
getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
getFilePath() - Method in class jspecview.common.PeakInfo
getFilePath() - Method in class jspecview.source.JDXDataObject
  The path to the file
getFilePath() - Method in class jspecview.source.JDXSource
getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
getFilePathForwardSlash() - Method in class jspecview.source.JDXDataObject
getFileReferences(String, Lst, Lst) - Static method in class org.jmol.viewer.FileManager
getFileType() - Method in class org.jmol.viewer.FileManager
getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
  From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
getFileTypefromFilter(String) - Static method in class org.jmol.adapter.smarter.Resolver
getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  Just get the resolved file type; if a file, does NOT close the reader
getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
  Get the type of this file or molecular model, if known.
getFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getFilterWithCase(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getFinalOperationCount() - Method in interface org.jmol.api.SymmetryInterface
getFinalOperationCount() - Method in class org.jmol.symmetry.Symmetry
getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
getFirstAtomIndexFromAtomNumber(int, BS) - Method in class org.jmol.modelset.AtomCollection
getFirstModelWithPeaks() - Method in interface org.jmol.api.JmolJDXMOLParser
getFirstModelWithPeaks() - Method in class org.jmol.jsv.JDXMOLParser
getFirstX() - Method in class jspecview.source.JDXDataObject
  Returns the first X value
getFirstY() - Method in class jspecview.source.JDXDataObject
  Returns the first Y value
getFlagFromName(String) - Static method in enum class io.github.dan2097.jnainchi.InchiFlag
getFlexFitList(BS, BS, String, boolean) - Method in class org.jmol.scriptext.SmilesExt
getFloat(int) - Method in class org.jmol.api.JmolViewer
getFloat(int) - Method in class org.jmol.shapecgo.CGOMesh
getFloat(int) - Method in class org.jmol.viewer.Viewer
getFloatColumnData(int) - Method in class org.jmol.adapter.readers.cif.BCIFReader
  Called by processAtomSites to retrieve individual matrix elements and set them by name.
getFloatColumnData(int) - Method in class org.jmol.adapter.readers.cif.CifReader
getFloatEncodedInt(String) - Static method in class org.jmol.util.Edge
  Encodes a string such as "2.10" as an integer instead of a double so as to distinguish "2.1" from "2.10".
getFloatProperty(String) - Method in class org.jmol.modelset.Atom
getFloatProperty(String) - Method in class org.jmol.smiles.SmilesAtom
getFloatProperty(String) - Method in interface org.jmol.util.Node
getFloats(byte[], int, float) - Static method in class javajs.util.MessagePackReader
  mmtf type 1 and 11 byte[4] to float32
getFocusNow(boolean) - Method in interface jspecview.api.JSVPanel
getFocusNow(boolean) - Method in class jspecview.java.AwtPanel
  // threading and focus
getFocusNow(boolean) - Method in class jspecview.js2d.JsPanel
getFont(float) - Method in class org.jmol.shape.Frank
getFont3D(float) - Method in class org.jmol.util.GData
getFont3D(int) - Static method in class org.jmol.util.Font
getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
getFont3DCurrent() - Method in class org.jmol.util.GData
getFont3DFS(String, float) - Method in class org.jmol.util.GData
getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
getFont3DScaled(Font, float) - Method in class org.jmol.util.GData
getFontAscent(Object) - Method in class jspecview.java.AwtPlatform
getFontAscent(Object) - Method in class jspecview.js2d.JsPlatform
getFontAscent(Object) - Method in interface org.jmol.api.FontManager
getFontAscent(Object) - Method in class org.jmol.awt.Platform
getFontAscent(Object) - Method in class org.jmol.awtjs2d.Platform
getFontCommand(String, Font) - Static method in class org.jmol.shape.Shape
getFontDescent(Object) - Method in class jspecview.java.AwtPlatform
getFontDescent(Object) - Method in class jspecview.js2d.JsPlatform
getFontDescent(Object) - Method in interface org.jmol.api.FontManager
getFontDescent(Object) - Method in class org.jmol.awt.Platform
getFontDescent(Object) - Method in class org.jmol.awtjs2d.Platform
getFontFaceID(String) - Method in interface jspecview.api.JSVPanel
getFontFaceID(String) - Method in class jspecview.java.AwtPanel
getFontFaceID(String) - Method in class jspecview.js2d.JsPanel
getFontFaceID(String) - Static method in class org.jmol.util.Font
getFontFidFS(String, float) - Method in class org.jmol.util.GData
getFontFidI(float) - Method in class org.jmol.util.GData
getFontMetrics() - Method in class org.jmol.util.Font
getFontMetrics(Font, Object) - Method in class jspecview.java.AwtPlatform
getFontMetrics(Font, Object) - Method in class jspecview.js2d.JsPlatform
getFontMetrics(Font, Object) - Method in interface org.jmol.api.FontManager
getFontMetrics(Font, Object) - Method in class org.jmol.awt.Platform
getFontMetrics(Font, Object) - Method in class org.jmol.awtjs2d.Platform
getFontName(ScriptToken, String) - Method in class jspecview.common.ColorParameters
getFontStyleID(String) - Static method in class org.jmol.util.Font
getForceField(String) - Method in class org.jmol.minimize.Minimizer
  ////////////////////////// minimize //////////////////////
getForceFieldUsed() - Method in class org.jmol.minimize.Minimizer
getFormalCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getFormalCharge() - Method in class org.jmol.modelset.Atom
getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
getFormalCharge() - Method in interface org.jmol.util.Node
getFormalCharge() - Method in interface org.jmol.util.SimpleNode
getFormat(SV, int) - Static method in class org.jmol.script.SV
getFormatType(String) - Static method in class org.jmol.script.SV
getFormulaForAtoms(BS, String, boolean) - Method in class org.jmol.viewer.Viewer
  Get formula -- MF or CELLFORMULA, possibly empirical
getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  get all integers after letters negative entries are spaces (1Xn)
getFractional(Atom, P3) - Method in class org.jmol.modelset.Trajectory
getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
getFractionalCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
getFractionalOffset(boolean) - Method in interface org.jmol.api.SymmetryInterface
getFractionalOffset(boolean) - Method in class org.jmol.symmetry.Symmetry
  determine if an offset cell is a unit translation, so that the space group can be continued
getFractionalOrigin() - Method in interface org.jmol.api.SymmetryInterface
getFractionalOrigin() - Method in class org.jmol.symmetry.Symmetry
getFractionalOrigin() - Method in class org.jmol.util.SimpleUnitCell
  Get the fractional origin for the UccageRenderer.
getFractionalPoint(int) - Method in class org.jmol.script.ScriptParam
  Could return a P4 for large 1100100100 type indicators
getFrame() - Method in interface jspecview.java.JmolFrame
getFrame() - Method in interface org.jmol.awt.JmolFrame
getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
getFrameActions() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getFrameActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getFrameAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getFrameAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getFrameAtoms() - Method in class org.jmol.viewer.Viewer
getFrameBase(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getFrameCount() - Method in class org.jmol.viewer.AnimationManager
getFrameDelayMs(int) - Method in class org.jmol.modelset.ModelSet
getFrameModelInfo(String) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.FrameCounter
getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
getFrameOffsets(BS, boolean) - Method in class org.jmol.modelset.ModelSet
getFrameTitle() - Method in class org.jmol.viewer.Viewer
getFrameTitle(int) - Method in class org.jmol.modelset.ModelSet
getFreqField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
getFullMap() - Method in class org.jmol.script.ScriptContext
getFullName() - Method in interface javajs.api.JSInterface
getFullName() - Method in class jspecview.appletjs.JSVApplet
getFullName() - Method in class org.jmol.util.GenericApplet
getFullPath() - Method in interface org.jmol.api.GenericFileInterface
getFullPathName(boolean) - Method in class org.jmol.script.ScriptEval
getFullPathName(boolean) - Method in class org.jmol.viewer.FileManager
getFullPathName(String) - Static method in class jspecview.common.JSVFileManager
  FileManager.classifyName follow this with .replace('\\','/') and Escape.escape() to match Jmol's file name in
getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
getFullPDBHeader() - Method in class org.jmol.modelsetbio.BioModel
getFullProteinStructureState(BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
getFullScreenDimensions(Object, int[]) - Method in class jspecview.java.AwtPlatform
getFullScreenDimensions(Object, int[]) - Method in class jspecview.js2d.JsPlatform
getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.GenericPlatform
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awtjs2d.Platform
getFunction(String) - Method in class org.jmol.script.ScriptEval
getFunction(String) - Method in class org.jmol.viewer.Viewer
getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
getFunctions(boolean) - Method in class org.jmol.viewer.Viewer
getGestures(int) - Method in class com.sparshui.server.ServerToClientProtocol
  Retrieve a list of allowed gestures for the provided group id.
getGestureType() - Method in interface com.sparshui.gestures.Gesture
  Get the integer value of this gesture type.
getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
getGlideFromTrans(T3, T3) - Static method in class org.jmol.symmetry.SymmetryOperation
  note = this method will return 'n' for SG 161 do an operator's odd 1/2 -1/2 1/2 glide (but only for additional operations, not the basic set but ITA says "tetragonal and cubic only" in Table ITA1969 4.1.6
getGLmolView() - Method in class org.jmol.util.GenericApplet
  This method is only called by JmolGLmol applet._refresh();
getGLmolView() - Method in class org.jmol.viewer.Viewer
  This method is only called by JmolGLmol applet._refresh();
getGraphics(Object) - Method in class jspecview.java.AwtPlatform
getGraphics(Object) - Method in class jspecview.js2d.JsPlatform
getGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
getGraphics(Object) - Method in class org.jmol.awt.Platform
getGraphics(Object) - Method in class org.jmol.awtjs.Platform
getGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
getGraphSetKey() - Method in interface jspecview.api.AnnotationData
getGraphSetKey() - Method in class jspecview.common.MeasurementData
getGraphSetKey() - Method in class jspecview.dialog.JSVDialog
getGroup1() - Method in class org.jmol.modelset.Group
getGroup1() - Method in class org.jmol.modelsetbio.Monomer
getGroup1(char) - Method in class org.jmol.modelset.Atom
getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
getGroup1(char) - Method in interface org.jmol.util.Node
getGroup1b() - Method in class org.jmol.modelsetbio.Monomer
getGroup1b() - Method in class org.jmol.modelsetbio.NucleicMonomer
getGroup3() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getGroup3() - Method in class org.jmol.modelset.Group
getGroup3(boolean) - Method in class org.jmol.modelset.Atom
getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
getGroup3(boolean) - Method in interface org.jmol.util.Node
getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
getGroupBits(BS) - Method in class org.jmol.modelset.Atom
getGroupBits(BS) - Method in class org.jmol.smiles.SmilesAtom
getGroupBits(BS) - Method in interface org.jmol.util.Node
getGroupCount() - Method in class org.jmol.modelset.Model
getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
getGroupID(Location) - Method in interface com.sparshui.client.SparshClient
  This method must return an ID for a group of points that should be processed together.
getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
getGroupID(TouchPoint) - Method in class com.sparshui.server.ServerToClientProtocol
  Retrieve a list of allowed gestures for the provided group id.
getGroupID(String) - Method in class org.jmol.modelsetbio.BioResolver
getGroupInfo(int, P3) - Method in class org.jmol.modelset.Group
getGroupParameter(int) - Method in class org.jmol.modelset.Group
  Monomers only
getGroupParameter(int) - Method in class org.jmol.modelsetbio.Monomer
getGroups() - Method in class org.jmol.modelset.ModelSet
  In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
getGroupsWithin(int, BS) - Method in class org.jmol.modelset.ModelSet
getGroupsWithin(int, BS) - Method in class org.jmol.viewer.Viewer
getGroupsWithinAll(int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getGroupType() - Method in interface org.jmol.api.SymmetryInterface
getGroupType() - Method in class org.jmol.symmetry.Symmetry
getGroupTypePrefix(int) - Static method in class org.jmol.symmetry.SpaceGroup
getGyromagneticRatio(String) - Static method in class jspecview.source.JDXDataObject
getHallSymbol() - Method in class org.jmol.symmetry.HallInfo
getHBonds(ModelSet, int, Lst, boolean) - Method in interface org.jmol.api.JmolAnnotationParser
getHBonds(ModelSet, int, Lst, boolean) - Method in class org.jmol.dssx.AnnotationParser
getHBonds(ModelSet, int, Lst, boolean) - Method in class org.jmol.dssx.DSSR1
getHCount() - Method in class org.jmol.minimize.MinAtom
getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
getHeader(int) - Method in class javajs.util.LimitedLineReader
getHeaderMap(InputStream, Map) - Static method in class jspecview.source.JDXReader
getHeaderMapS(InputStream, Map, int, String) - Static method in class jspecview.source.JDXReader
getHeaderRendererIcon(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
getHeaderRowDataAsArray() - Method in class jspecview.source.JDXDataObject
getHeaderRowDataAsArray(boolean, int) - Method in class jspecview.source.JDXHeader
getHeaderRowDataAsArray(boolean, String[][]) - Method in class jspecview.source.JDXSource
getHeaderTable() - Method in class jspecview.source.JDXHeader
  Returns the table of headers
getHeight() - Method in interface jspecview.api.JSVViewPanel
getHeight() - Method in class jspecview.common.JSViewer
getHeight() - Method in class jspecview.js2d.JsMainPanel
getHeight() - Method in class jspecview.js2d.JsPanel
getHeight() - Method in class org.jmol.awtjs.swing.Component
getHeight() - Method in class org.jmol.util.Font
getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
getHelp(String) - Method in class org.jmol.viewer.Viewer
getHermiteLevel() - Method in class org.jmol.viewer.Viewer
getHermiteList(int, T3, T3, T3, T3, T3, T3[], int, int, boolean) - Static method in class org.jmol.util.GData
  Used by Navigator, BioShapeRenderer, and DrawRenderer
getHeteroList(int) - Method in class org.jmol.modelset.ModelSet
getHexCode(short) - Static method in class org.jmol.util.C
getHexCodes(short[]) - Static method in class org.jmol.util.C
getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
getHexitValue(char) - Static method in class org.jmol.util.Escape
getHiddenCanvas(JSAppletObject, String, int, int) - Method in interface javajs.api.js.J2SObjectInterface
getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
getHistoryWindowPosition(String) - Method in interface org.jmol.api.JmolAppAPI
getHistoryWindowPosition(String) - Method in class org.openscience.jmol.app.JmolApp
getHistoryWindowSize(String) - Method in interface org.jmol.api.JmolAppAPI
getHistoryWindowSize(String) - Method in class org.openscience.jmol.app.JmolApp
getHklPlane(T3, float, Lst) - Method in class org.jmol.script.ScriptParam
getHMName() - Method in class org.jmol.symmetry.SpaceGroup
getHMNameShort() - Method in class org.jmol.symmetry.SpaceGroup
getHorizAlignmentName(int) - Static method in class org.jmol.viewer.JC
getHoverDelay() - Method in class org.jmol.viewer.Viewer
getHtmlDisabled() - Method in class org.jmol.awtjs.swing.AbstractButton
getHtmlDisabled() - Method in class org.jmol.awtjs.swing.JMenuItem
getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getHybridizationAndAxes(int, int, V3, V3, String, boolean, boolean, boolean, T3) - Method in class org.jmol.modelset.AtomCollection
getHybridizationAndAxes(int, V3, V3, String) - Method in class org.jmol.viewer.Viewer
getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
  Get the hydrogen atom count -- for ligand files
getHydrogenCount() - Method in class jspecview.source.JDXDataObject
getHydrogenCount(int) - Method in class jme.JMEmol
getHydrophobicity() - Method in class org.jmol.modelset.Atom
getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
getHydrophobicity(int) - Static method in class org.jmol.util.Elements
getIcon() - Method in interface org.jmol.api.SC
getIcon() - Method in class org.jmol.awt.AwtSwingComponent
getIcon() - Method in class org.jmol.awtjs.swing.AbstractButton
getIconX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getIconX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
getIconX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getId() - Method in enum class org.jmol.c.STR
getID() - Method in class com.sparshui.server.Group
getID() - Method in class com.sparshui.server.TouchPoint
  Get the touch point ID.
getIdentifierOrNull(String) - Method in class org.jmol.modelsetbio.BioModelSet
getIdentity() - Method in class org.jmol.minimize.MinAtom
getIdentity() - Method in class org.jmol.modelset.Bond
getIdentityXYZ(P3, int) - Method in class org.jmol.modelset.Atom
getIDStr() - Method in class org.jmol.modelset.Chain
getImage(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
getImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
getImage(Viewer, Object, String, boolean) - Method in class org.jmol.io.JmolUtil
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.api.JmolViewer
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
getImageDialog(String, Map) - Method in class jspecview.java.AwtPlatform
getImageDialog(String, Map) - Method in class jspecview.js2d.JsPlatform
getImageDialog(String, Map) - Method in interface org.jmol.api.GenericPlatform
getImageDialog(String, Map) - Method in class org.jmol.awt.Platform
getImageDialog(String, Map) - Method in class org.jmol.awtjs2d.Platform
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in class org.jmol.dialog.Dialog
getImageHeight(Object) - Method in class jspecview.java.AwtPlatform
getImageHeight(Object) - Method in class jspecview.js2d.JsPlatform
getImageHeight(Object) - Method in interface org.jmol.api.GenericPlatform
getImageHeight(Object) - Method in class org.jmol.awt.Platform
getImageHeight(Object) - Method in class org.jmol.awtjs2d.Platform
getImageIcon(String) - Method in class jspecview.java.AwtPopup
getImageIcon(String) - Method in class jspecview.js2d.JsPopup
getImageIcon(String) - Method in class org.jmol.awt.AwtJmolPopup
getImageIcon(String) - Method in class org.jmol.awt.AwtModelKitPopup
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSJmolPopup
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
getImageIcon(String) - Method in class org.jmol.popup.GenericPopup
getImagEigenvalues() - Method in class javajs.util.Eigen
  Return the imaginary parts of the eigenvalues
getImageURL(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getImageWidth(Object) - Method in class jspecview.java.AwtPlatform
getImageWidth(Object) - Method in class jspecview.js2d.JsPlatform
getImageWidth(Object) - Method in interface org.jmol.api.GenericPlatform
getImageWidth(Object) - Method in class org.jmol.awt.Platform
getImageWidth(Object) - Method in class org.jmol.awtjs2d.Platform
getImplicitH() - Method in interface org.iupac.InChIStructureProvider
getImplicitH() - Method in class org.jmol.inchi.InChIJNA
getImplicitH() - Method in class org.jmol.inchi.InChIJS
getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getImplicitHydrogenCount() - Method in interface org.jmol.util.Node
  can be > 0 for PDB model with no H atoms or for SMILES string CCC
getImplicitSpecialGroupType(int) - Static method in class org.jmol.symmetry.SpaceGroup
getInchi(BS, Object, String) - Method in class org.jmol.viewer.Viewer
  Get an InChI or InChIKey for a set of atoms or MOL data.
getInchi(Viewer, BS, Object, String) - Method in interface org.jmol.api.JmolInChI
getInchi(Viewer, BS, Object, String) - Method in class org.jmol.inchi.InChIJNA
getInchi(Viewer, BS, Object, String) - Method in class org.jmol.inchi.InChIJS
getInChI() - Method in class jspecview.java.AwtPlatform
getInChI() - Method in class jspecview.js2d.JsPlatform
getInChI() - Method in interface org.jmol.api.GenericPlatform
getInChI() - Method in class org.jmol.awt.Platform
getInChI() - Method in class org.jmol.awtjs2d.Platform
getInchiBondType() - Method in interface org.iupac.InChIStructureProvider
getInchiBondType() - Method in class org.jmol.inchi.InChIJNA
getInchiBondType() - Method in class org.jmol.inchi.InChIJS
getInchiModel - Variable in class org.jmol.inchi.InchiJmol
getIndex() - Method in interface jspecview.api.JSVTreeNode
getIndex() - Method in class jspecview.application.AwtTreeNode
getIndex() - Method in class jspecview.common.PeakInfo
getIndex() - Method in class jspecview.tree.SimpleTreeNode
getIndex() - Method in class org.jmol.modelset.Atom
getIndex() - Method in class org.jmol.smiles.SmilesAtom
  Returns the atom index of the atom.
getIndex() - Method in class org.jmol.symmetry.SpaceGroup
getIndex() - Method in interface org.jmol.util.Node
getIndex() - Method in interface org.jmol.util.SimpleNode
getIndex(int, int, int, int) - Method in class org.jmol.modelsetbio.BioPolymer
getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
getIndexFromName(String) - Method in class org.jmol.shape.Shape
getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
getIndexFromName(String) - Method in class org.jmol.shapespecial.Polyhedra
getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
getIndexOriginAtom() - Method in interface org.iupac.InChIStructureProvider
getIndexOriginAtom() - Method in class org.jmol.inchi.InChIJNA
getIndexOriginAtom() - Method in class org.jmol.inchi.InChIJS
getIndexTargetAtom() - Method in interface org.iupac.InChIStructureProvider
getIndexTargetAtom() - Method in class org.jmol.inchi.InChIJNA
getIndexTargetAtom() - Method in class org.jmol.inchi.InChIJS
getInfo() - Method in class org.jmol.modelset.Atom
getInfo() - Method in class org.jmol.symmetry.SymmetryOperation
getInfo() - Method in class org.jmol.util.Font
getInfo() - Method in class org.jmol.util.Modulation
getInfo(boolean) - Method in class org.jmol.shape.Mesh
getInfo(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
getInfo(int, String) - Method in class org.jmol.modelset.ModelSet
getInfo(String) - Method in class jspecview.common.Spectrum
getInfo(String) - Method in interface org.jmol.api.JmolNMRInterface
getInfo(String) - Method in class org.jmol.quantum.NMRCalculation
getInfo(String) - Method in class org.jmol.util.BoxInfo
  for {*}.boundbox("info"|"volume"|"center"|null)
getInfo(String) - Method in class org.jmol.util.Tensor
  returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
getInfo(Map) - Method in class jspecview.common.IntegralData
getInfo(Map) - Method in class jspecview.common.PeakData
getInfo(Map) - Method in class org.jmol.util.ModulationSet
getInfo(Map) - Method in class org.jmol.util.Vibration
getInfoAsString(int) - Method in class org.jmol.shape.Measures
getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
getInfoB(int, String) - Method in class org.jmol.modelset.ModelSet
getInfoI(int, String) - Method in class org.jmol.modelset.ModelSet
getInfoM(String) - Method in class org.jmol.modelset.ModelSet
getInfoStr(String) - Method in class org.jmol.util.SimpleUnitCell
getInfoXYZ(Atom) - Method in class org.jmol.viewer.ChimeMessenger
  called when an atom is picked
getInfoXYZ(Atom) - Method in interface org.jmol.viewer.JmolChimeMessenger
getInlineChar() - Method in class org.jmol.viewer.Viewer
getInlineData() - Method in class jspecview.source.JDXDataObject
getInlineData(int) - Method in class org.jmol.modelset.ModelSet
getInlineData(SB, String, boolean, Integer, String) - Method in class org.jmol.viewer.StateCreator
getInMotion(boolean) - Method in class org.jmol.viewer.Viewer
getInnerXML() - Method in class jspecview.source.XMLParser
getInput(String, String, String) - Method in interface jspecview.api.JSVPanel
getInput(String, String, String) - Method in class jspecview.java.AwtPanel
getInput(String, String, String) - Method in class jspecview.js2d.JsPanel
  // threading and focus
getInputStream() - Method in interface javajs.api.GenericBinaryDocument
getInputStream() - Method in class javajs.util.AjaxURLConnection
getInputStream() - Method in class javajs.util.BinaryDocument
getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
getInputStream(String, boolean, byte[]) - Static method in class jspecview.common.JSVFileManager
getInsCode() - Method in class org.jmol.modelset.Group
getInsertedCommand() - Method in class org.jmol.viewer.Viewer
getInsertionCode() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getInsertionCode() - Method in class org.jmol.modelset.Atom
getInsertionCode() - Method in class org.jmol.modelset.Group
getInsertionCode() - Method in class org.jmol.smiles.SmilesAtom
getInsertionCode() - Method in interface org.jmol.util.Node
getInsertionCodeChar(int) - Static method in class org.jmol.modelset.Group
getInsertionCodeFor(int) - Static method in class org.jmol.modelset.Group
getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getInstance() - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
getInstanceWithParams(String, Class[], Object...) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getInt(int) - Method in class org.jmol.api.JmolViewer
getInt(int) - Method in class org.jmol.shapecgo.CGOMesh
getInt(int) - Method in class org.jmol.viewer.Viewer
getInt(Map, String) - Method in class org.molecularplayground.MPJmolApp
getInt(Map, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getInt4(int, byte[]) - Static method in class javajs.img.PngEncoder
getIntArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
  Retrieve an int array, possibly unpacking it if it is run-length encoded.
getIntArray2(int) - Method in class org.jmol.scriptext.ScriptExt
getIntArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
  turn "[1,2,3]" into [1,2,3] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
getIntegralFactor() - Method in class jspecview.common.IntegralData
getIntegration() - Method in class org.jmol.quantum.QuantumCalculation
getIntegrationRatiosFromString(Spectrum, String) - Static method in class jspecview.common.IntegralData
  Parses x-coordinates and values from a string and returns them as `IntegrationRatio` objects
getInterface(String) - Static method in class javajs.api.Interface
getInterface(String) - Static method in class jspecview.common.JSViewer
getInterface(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getInterface(String, Viewer, String) - Static method in class org.jmol.api.Interface
getInternalInchiVersion() - Static method in class org.jmol.inchi.InChIJNA
  Get the InChI version directly from the inchi code without an API.
getIntersection(float, P4, P3[], Lst, float[], BS, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSlicer
getIntersection(P3, V3, P4, P3, V3, V3) - Static method in class javajs.util.Measure
  Calculate the intersection of a line with a plane.
getIntersectionPP(P4, P4) - Static method in class javajs.util.Measure
  Calculate the line that is the intersection of two planes.
getInts(byte[], int) - Static method in class javajs.util.MessagePackReader
  mmtf types 2-4 Decode a byte array into a byte, short, or int array.
getIntTableIndex() - Method in interface org.jmol.api.SymmetryInterface
getIntTableIndex() - Method in class org.jmol.symmetry.Symmetry
getIntTableNumber() - Method in interface org.jmol.api.SymmetryInterface
getIntTableNumber() - Method in class org.jmol.symmetry.Symmetry
getIntTableTransform() - Method in interface org.jmol.api.SymmetryInterface
getIntTableTransform() - Method in class org.jmol.symmetry.Symmetry
getInvariantSymops(P3, int[]) - Method in interface org.jmol.api.SymmetryInterface
getInvariantSymops(P3, int[]) - Method in class org.jmol.symmetry.Symmetry
getInverseNormix(short) - Static method in class org.jmol.util.Normix
getIsHetero() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getIsoExt() - Method in class org.jmol.script.ScriptEval
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in interface org.jmol.api.JmolNMRInterface
  If t is null, then a1, a2, and type are used to find the appropriate tensor.
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
getIsotope() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getIsotopeNumber() - Method in class org.jmol.modelset.Atom
getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
getIsotopeNumber() - Method in interface org.jmol.util.Node
getIsotopeNumber() - Method in interface org.jmol.util.SimpleNode
getIsotopeNumber(int) - Static method in class org.jmol.util.Elements
getIsotopicMass() - Method in interface org.iupac.InChIStructureProvider
  from inchi_api.h #define ISOTOPIC_SHIFT_FLAG 10000 add to isotopic mass if isotopic_mass = (isotopic mass - average atomic mass) AT_NUM isotopic_mass; 0 => non-isotopic; isotopic mass or ISOTOPIC_SHIFT_FLAG + mass - (average atomic mass)
getIsotopicMass() - Method in class org.jmol.inchi.InChIJNA
getIsotopicMass() - Method in class org.jmol.inchi.InChIJS
getItaIndex() - Method in class org.jmol.symmetry.SpaceGroup
getItaNumberFor(String) - Method in class org.jmol.viewer.Viewer
getItem(int) - Method in class org.jmol.awtjs.swing.JMenu
getItem(int) - Static method in class org.jmol.quantum.QS
getItemCount() - Method in class org.jmol.awtjs.swing.JMenu
getItemType(SC) - Method in class org.jmol.awt.AwtPopupHelper
getItemType(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
getItemType(SC) - Method in interface org.jmol.popup.PopupHelper
getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelSet
  only some models can be iterated through.
getIterator(Viewer, Atom, BS, float) - Method in interface org.jmol.api.SymmetryInterface
getIterator(Viewer, Atom, BS, float) - Method in class org.jmol.symmetry.Symmetry
getITNo(String, int) - Static method in class org.jmol.symmetry.SpaceGroup
getJavaConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getJavaConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Deprecated.
getJBR() - Method in class org.jmol.viewer.Viewer
getJcampdx() - Method in class jspecview.source.JDXHeader
  Getter for property jcampdx.
getJCouplingHz(Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
getJDXBaseModelIndex(int) - Method in class org.jmol.viewer.Viewer
  get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
getJDXSpectrum(int) - Method in class jspecview.source.JDXSource
  Returns the Spectrum at a given index in the list
getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
getJmol(JFrame, int, int, Map) - Static method in class org.openscience.jmol.app.Jmol
getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.Jmol
getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelSet
getJmolDataFrameInt(int, int) - Method in class org.jmol.modelset.ModelSet
getJmolDataFrameProperties(ScriptEval, int, int[], String[], BS, P3, P3, String, boolean) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
getJmolDataFrameScripts(Viewer, int, int, int, String, String, String[], boolean) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
getJmolDataFrameTypeInt() - Method in class org.jmol.viewer.Viewer
getJmolDataReader() - Method in class org.jmol.viewer.FileManager
getJmolDataSourceFrame() - Method in class org.jmol.viewer.Viewer
getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelSet
getJmolDistance(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
getJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
  Calc using Jmol atom index
getJmolFilePath(String) - Static method in class jspecview.common.JSVFileManager
getJmolFrameType(int) - Method in class org.jmol.modelset.ModelSet
getJmolFrameTypeInt(int) - Method in class org.jmol.modelset.ModelSet
getJmolNoe(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
getJmolNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
getJmolParameter(String) - Method in class org.jmol.util.GenericApplet
getJmolPerspective() - Method in class org.jmol.export.___Exporter
getJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJmolValueAsString(Viewer, String) - Static method in class org.molecularplayground.MPJmolApp
getJmolVersion() - Static method in class org.jmol.api.JmolViewer
getJmolVersion() - Static method in class org.jmol.viewer.Viewer
getJmolVersionNoDate() - Static method in class org.jmol.api.JmolViewer
getJsObjectInfo(Object[], String, Object[]) - Method in class jspecview.java.AwtPlatform
  misc
getJsObjectInfo(Object[], String, Object[]) - Method in class jspecview.js2d.JsPlatform
getJsObjectInfo(Object[], String, Object[]) - Method in interface org.jmol.api.GenericPlatform
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awt.Platform
  misc
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awtjs2d.Platform
getJsonNioServer() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJspecViewProperties(Object) - Method in class org.jmol.viewer.Viewer
getJSpecViewProperty(String) - Method in class jspecview.application.JSpecView
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolStatusListener
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolSyncInterface
getJSpecViewProperty(String) - Method in class org.jmol.util.GenericApplet
  JSpecView shares the JmolSyncInterface; used to get JSpecView
getJSpecViewProperty(String) - Method in class org.openscience.jmol.app.status.StatusListener
getJSVPanel(JSViewer, Lst) - Method in interface jspecview.api.AppletFrame
getJSVPanel(JSViewer, Lst) - Method in class jspecview.appletjs.JSVApplet
getJVXLCutoff() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getJVXLCutoff() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getJzt() - Method in class org.jmol.viewer.Viewer
getJzu() - Method in class org.jmol.viewer.FileManager
getKey - Variable in class org.jmol.inchi.InchiJmol
getKey() - Method in interface org.jmol.api.JmolAbstractButton
getKey() - Method in class org.jmol.console.JmolButton
getKey() - Method in class org.jmol.console.JmolLabel
getKey() - Method in class org.jmol.console.JmolToggleButton
getKey() - Method in class org.jmol.console.KeyJCheckBox
getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
getKey() - Method in class org.jmol.console.KeyJMenu
getKey() - Method in class org.jmol.console.KeyJMenuItem
getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
getKey(int, char) - Static method in class org.jmol.modelkit.ModelKit
getKey(int, int, int, int, int) - Static method in class org.jmol.minimize.MinObject
getKey(ScriptTokenizer) - Static method in enum class jspecview.common.ScriptToken
getKeyMap() - Static method in class org.jmol.shapecgo.CGOMesh
getKeys(boolean) - Method in class org.jmol.script.SV
getLabel(int) - Method in class org.jmol.shape.Labels
getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
getLabel(String) - Static method in class org.jmol.console.GenericConsole
getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
getLabel1() - Method in class org.jmol.console.AppletConsole
getLabel1() - Method in class org.jmol.console.GenericConsole
getLabelArray() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
getLabeler() - Method in class org.jmol.modelset.AtomCollection
  ///////// atoms //////////////
getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.GenericConsole
getLanguage() - Static method in class org.jmol.i18n.GT
getLanguageList() - Static method in class org.jmol.i18n.Language
  This is the place to put the list of supported languages.
getLanguageList(GT) - Static method in class org.jmol.i18n.GT
getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getLastError() - Static method in exception class org.jmol.smiles.InvalidSmilesException
getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
getLastException() - Method in class org.jmol.smiles.SmilesMatcher
getLastFileFirstNode(Lst) - Static method in class jspecview.common.PanelNode
getLastIndex() - Method in class org.jmol.modelset.Measurement
getLastPathComponent() - Method in interface jspecview.api.JSVTreePath
getLastPathComponent() - Method in class jspecview.tree.SimpleTreePath
getLastVibrationVector(int, int) - Method in class org.jmol.modelset.ModelSet
getLastX() - Method in class jspecview.source.JDXDataObject
  Returns the last X value
getLastY() - Method in class jspecview.source.JDXDataObject
  Returns the last Y value
getLatticeCentering() - Method in interface org.jmol.api.SymmetryInterface
getLatticeCentering() - Method in class org.jmol.symmetry.Symmetry
getLatticeCentering(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
getLatticeCenteringStrings(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
getLatticeCode() - Method in class org.jmol.symmetry.HallInfo
getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
getLatticeIndex(char) - Static method in class org.jmol.symmetry.HallInfo
getLatticeIndexFromCode(int) - Static method in class org.jmol.symmetry.HallInfo
getLatticeOp() - Method in interface org.jmol.api.SymmetryInterface
getLatticeOp() - Method in class org.jmol.symmetry.Symmetry
getLatticePoints(Lst, int, int, int) - Static method in class javajs.util.Measure
  Based on a set of centering points, creates a list of lattice points in place.
getLatticeType() - Method in interface org.jmol.api.SymmetryInterface
getLatticeType() - Method in class org.jmol.symmetry.Symmetry
getLeadAtom() - Method in class org.jmol.modelset.Group
getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
getLeadAtomOr(Atom) - Method in class org.jmol.modelset.Group
getLeadColix(int) - Method in class org.jmol.renderbio.BackboneRenderer
getLeadColix(int) - Method in class org.jmol.renderbio.CartoonRenderer
getLeadColix(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
getLeadColix(int) - Method in class org.jmol.renderbio.RibbonsRenderer
getLeadColix(int) - Method in class org.jmol.renderbio.RocketsRenderer
getLeadColix(int) - Method in class org.jmol.renderbio.StrandsRenderer
getLeadColix(int) - Method in class org.jmol.renderbio.TraceRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.BackboneRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.CartoonRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.RibbonsRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.RocketsRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.StrandsRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.TraceRenderer
getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
getLength(int) - Method in class org.jmol.shapespecial.Ellipsoid
getLength(Object) - Static method in class javajs.util.AU
getLevel(int) - Static method in class org.jmol.util.Logger
  Returns the text corresponding to a level.
getlexpNoes() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getLigandInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
getLigandInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getLigandModel(String, String, String, String) - Method in class org.jmol.viewer.Viewer
  obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state
getLightingState() - Method in class org.jmol.viewer.Viewer
getLightSource() - Method in class org.jmol.util.GData
getLimitedStreamBytes(InputStream, long) - Static method in class javajs.util.Rdr
  Read a possibly limited number of bytes (when n > 0) from a stream, leaving the stream open.
getLine() - Method in class org.jmol.jvxl.readers.XmlReader
getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEval
getList() - Method in class org.jmol.script.SV
getList(Object, String) - Static method in class org.qcschema.QCSchemaUnits
  Retrieve an array of any sort as a list of objects, possibly unpacking it if it is run-length encoded.
getList(String) - Method in class org.jmol.symmetry.CIPData
  Retrieve an array of bit sets that match a given SMARTS
getList(String) - Method in class org.jmol.symmetry.CIPDataSmiles
getLoadSymmetryParams(int, SB, Map) - Method in class org.jmol.scriptext.CmdExt
getLocalDirectory(Viewer, boolean) - Static method in class org.jmol.viewer.FileManager
getLocalPathForWritingFile(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
getLocalUrl(String) - Method in class jspecview.java.AwtPlatform
getLocalUrl(String) - Method in class jspecview.js2d.JsPlatform
getLocalUrl(String) - Method in interface org.jmol.api.GenericPlatform
getLocalUrl(String) - Method in class org.jmol.awt.Platform
getLocalUrl(String) - Method in class org.jmol.awtjs2d.Platform
getLocalUrl(String) - Method in class org.jmol.viewer.Viewer
getLocation() - Method in class com.sparshui.server.TouchPoint
  Get the touch point location.
getLocationOnScreen(Object) - Method in class jspecview.dialog.DialogManager
getLocationOnScreen(Object) - Method in class jspecview.java.AwtDialogManager
getLocationOnScreen(Object) - Method in class jspecview.js2d.JsDialogManager
getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
getLogFileName() - Method in class org.jmol.viewer.Viewer
getLogLevel() - Static method in class org.jmol.util.Logger
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerAwt
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerJS
getLong(Map, String) - Method in class org.molecularplayground.MPJmolApp
getLong(Map, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getLongDate() - Method in class jspecview.source.JDXHeader
  Getter for property longDate.
getMacro(String) - Method in class org.jmol.viewer.Viewer
  retrieve macros.json from the directory
getMadBond() - Method in class org.jmol.api.JmolViewer
getMadBond() - Method in class org.jmol.viewer.Viewer
getMadParameter() - Method in class org.jmol.script.ScriptParam
getMagic(InputStream, int) - Static method in class javajs.util.Rdr
getMagneticShielding(Atom) - Method in interface org.jmol.api.JmolNMRInterface
getMagneticShielding(Atom) - Method in class org.jmol.quantum.NMRCalculation
getManifestScriptPath(String) - Static method in class org.jmol.viewer.FileManager
  check a JmolManifest for a reference to a script file (.spt)
getMap() - Method in class org.jmol.script.SV
getMapForJME(String, Atom[], BS) - Method in interface org.jmol.api.SmilesMatcherInterface
getMapForJME(String, Atom[], BS) - Method in class org.jmol.smiles.SmilesMatcher
getMapForStream(BufferedInputStream) - Method in class javajs.util.MessagePackReader
getMapKeys(int, boolean) - Method in class org.jmol.script.SV
getMapValueNoCase(Map, String) - Static method in class javajs.util.PT
getMass() - Method in class org.jmol.modelset.Atom
getMass() - Method in class org.jmol.smiles.SmilesAtom
getMass() - Method in interface org.jmol.util.Node
getMass() - Method in interface org.jmol.util.SimpleNode
getMatch() - Method in class jspecview.common.PeakInfo
getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
  Returns the matching atom or null.
getMatchingAtomIndex() - Method in class org.jmol.smiles.SmilesAtom
  Returns the number of a matching atom in a molecule.
getMatchingBond() - Method in class org.jmol.smiles.SmilesBond
getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
getMathExt() - Method in class org.jmol.script.ScriptEval
getMatrix() - Method in class javajs.util.Quat
getMatrix4f(M3, T3) - Static method in class org.jmol.script.ScriptMathProcessor
getMatrixAndUnitCell(Viewer, SimpleUnitCell, Object, M4) - Static method in class org.jmol.symmetry.UnitCell
getMatrixFromXYZ(String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getMatrixFromXYZScaled(String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getMatrixOperation(int) - Method in interface org.jmol.symmetry.HallInfo.HallReceiver
  Get the 4x4 matrix for the kth operation.
getMatrixOperation(int) - Method in class org.jmol.symmetry.SpaceGroup
getMatrixOperationCount() - Method in interface org.jmol.symmetry.HallInfo.HallReceiver
  Get the receiver's current operation count.
getMatrixOperationCount() - Method in class org.jmol.symmetry.SpaceGroup
getMatrixParam(int, int, boolean) - Method in class org.jmol.script.ScriptParam
getMatrixSelected(int[], int) - Method in class javajs.util.Matrix
  Get a submatrix for a give number of columns and selected row set.
getMax(int) - Static method in class org.jmol.symmetry.SpaceGroup
getMaxDim() - Method in class org.jmol.util.BoxInfo
getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
getMaxX() - Method in class jspecview.source.JDXDataObject
  Calculates and returns the maximum x value in the list of coordinates Fairly expensive operation
getMaxX(Lst, ViewData) - Static method in class jspecview.common.Coordinate
  Returns the maximum x value value from an array of arrays of `Coordinate`s.
getMaxX(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
  Returns the minimum x value of an array of `Coordinate`s
getMaxY() - Method in class jspecview.source.JDXDataObject
  Calculates and returns the maximum y value in the list of coordinates Fairly expensive operation
getMaxY() - Method in class jspecview.source.JDXDecompressor
getMaxY(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
  Returns the maximum y value of an array of `Coordinate`s
getMaxYUser(Lst, ViewData) - Static method in class jspecview.common.Coordinate
  Returns the maximum y value value from an array of arrays of `Coordinate`s.
getMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
getMeasurementCount() - Method in class org.jmol.api.JmolViewer
getMeasurementCount() - Method in class org.jmol.viewer.Viewer
getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
getMeasurementListArray(String) - Method in class jspecview.common.IntegralData
getMeasurementListArray(String) - Method in class jspecview.common.MeasurementData
getMeasurementListArray(String) - Method in class jspecview.common.PeakData
getMeasurementListArrayReal(String) - Method in class jspecview.common.IntegralData
getMeasurementListArrayReal(String) - Method in class jspecview.common.PeakData
getMeasurements(boolean, boolean) - Method in class org.jmol.modelset.MeasurementData
  if this is the client, then this method can be called to get the result vector, either as a string or as an array.
getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
  Used by MouseManager and Picking Manager to build the script
getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
getMeasurementTable() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getMenu(String) - Method in class org.jmol.awt.AwtPopupHelper
getMenu(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getMenu(String) - Method in interface org.jmol.popup.PopupHelper
getMenu(String) - Method in class org.jmol.viewer.Viewer
getMenuAsText(String) - Method in class jspecview.popup.JSVPopupResourceBundle
getMenuAsText(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
getMenuAsText(String) - Method in class org.jmol.popup.MainPopupResourceBundle
getMenuAsText(String) - Method in class org.jmol.popup.PopupResource
getMenuHTML() - Method in class org.jmol.awtjs.swing.AbstractButton
getMenuIcon() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
getMenuIcon() - Method in interface org.openscience.jmol.app.JmolPlugin
getMenuItem(String) - Method in class org.jmol.awt.AwtPopupHelper
getMenuItem(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getMenuItem(String) - Method in interface org.jmol.popup.PopupHelper
getMenuItem(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Fetch the menu item that was created for the given command.
getMenuName() - Method in class jspecview.popup.JSVPopupResourceBundle
getMenuName() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
getMenuName() - Method in class org.jmol.popup.MainPopupResourceBundle
getMenuName() - Method in class org.jmol.popup.PopupResource
getMenuPopup(String, char) - Method in class jspecview.java.AwtPlatform
getMenuPopup(String, char) - Method in class jspecview.js2d.JsPlatform
getMenuPopup(String, char) - Method in interface org.jmol.api.GenericPlatform
getMenuPopup(String, char) - Method in class org.jmol.awt.Platform
getMenuPopup(String, char) - Method in class org.jmol.awtjs2d.Platform
getMenuScript(String) - Static method in class org.jmol.viewer.JC
getMenuText() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
getMenuText() - Method in interface org.openscience.jmol.app.JmolPlugin
getMesh(String) - Method in class org.jmol.shape.MeshCollection
getMeshList(String, boolean) - Method in class org.jmol.shape.MeshCollection
  Get matching list of meshes, order reversed
getMeshSlicer() - Method in class org.jmol.util.MeshSurface
getMessage() - Method in exception class org.jmol.script.ScriptException
getMessage() - Method in exception class org.jmol.smiles.InvalidSmilesException
getMFArray(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shape.Mesh
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getMinDistances(MeasurementData) - Method in interface org.jmol.api.JmolNMRInterface
getMinDistances(MeasurementData) - Method in class org.jmol.quantum.NMRCalculation
getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
getMinindex() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
getMinindex() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getMinMax() - Method in class jme.JMEmol
getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
getMinMax(Object, int, boolean) - Method in class org.jmol.scriptext.MathExt
getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
getMinX() - Method in class jspecview.source.JDXDataObject
  Calculates and returns the minimum x value in the list of coordinates Fairly expensive operation
getMinX(Lst, ViewData) - Static method in class jspecview.common.Coordinate
  Returns the minimum x value value from an array of arrays of `Coordinate`s.
getMinX(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
  Returns the minimum x value of an array of `Coordinate`s
getMinY() - Method in class jspecview.source.JDXDataObject
  Calculates and returns the minimum y value in the list of coordinates Fairly expensive operation
getMinY() - Method in class jspecview.source.JDXDecompressor
getMinY(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
  Returns the minimum y value of an array of `Coordinate`s
getMinYUser(Lst, ViewData) - Static method in class jspecview.common.Coordinate
  Returns the minimum y value value from an array of arrays of `Coordinate`s.
getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
getMissingHydrogenCount(Atom, boolean) - Method in class org.jmol.modelset.AtomCollection
getMixingTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
  get the mixing time
getMixingTimeSec() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  get the mixing time
getMKState() - Method in class org.jmol.modelkit.ModelKit
getMMFF94AtomTypes(String[], Node[], int, BS, Lst, Lst[]) - Method in interface org.jmol.api.SmilesMatcherInterface
getMMFF94AtomTypes(String[], Node[], int, BS, Lst, Lst[]) - Method in class org.jmol.smiles.SmilesMatcher
  called by ForceFieldMMFF.setAtomTypes only
getMod(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.
getMod(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getMode(String) - Static method in enum class jspecview.common.PanelData.LinkMode
getMode(String) - Static method in enum class jspecview.common.Spectrum.IRMode
getModel() - Method in class jspecview.common.PeakInfo
getModel() - Method in class org.jmol.modelset.Group
  BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelAdapter() - Method in class org.jmol.api.JmolViewer
getModelAdapter() - Method in class org.jmol.viewer.Viewer
getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelSet
  Note that this method returns all atoms, included deleted ones.
getModelAtomBitSetIncludingDeletedBs(BS) - Method in class org.jmol.modelset.ModelSet
  note -- this method returns ALL atoms, including deleted.
getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelSet
getModelBS(int, BS) - Method in class org.jmol.modelset.Trajectory
  set bits for all trajectories associated with this model
getModelBS(BS, boolean) - Method in class org.jmol.modelset.ModelSet
  Get the set of models associated with a set of atoms.
getModelCellRange(int) - Method in class org.jmol.modelset.ModelSet
getModelCenter() - Method in class org.jmol.export.__CartesianExporter
getModelCml(BS, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
getModelCml(BS, int, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getModelCml(BS, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
getModelCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getModelDataBaseName(BS) - Method in class org.jmol.modelset.ModelSet
getModelDipole() - Method in class org.jmol.viewer.Viewer
getModelDipole(int) - Method in class org.jmol.modelset.ModelSet
getModelExtract(Object, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
  V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
getModelExtract(BS, boolean, boolean, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getModelExtract(BS, boolean, boolean, String, boolean) - Method in class org.jmol.viewer.PropertyManager
  V3000, SDF, MOL, JSON, CD (ChemDoodle), XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON, PWMAT, XSF MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)
getModelFileData(String, String, boolean) - Method in class org.jmol.viewer.Viewer
getModelFileInfo() - Method in class org.jmol.viewer.Viewer
getModelFileInfo(BS) - Method in interface org.jmol.api.JmolPropertyManager
getModelFileInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
getModelFileName(int) - Method in class org.jmol.modelset.ModelSet
getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
getModelFileType(int) - Method in class org.jmol.modelset.ModelSet
getModelForAtomIndex(int) - Method in class org.jmol.viewer.Viewer
getModelIndex() - Method in class org.jmol.modelset.Atom
getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
getModelIndex() - Method in interface org.jmol.util.Node
getModelIndexForAtom(int) - Method in class org.jmol.viewer.Viewer
getModelIndexFromId(String) - Method in interface org.jmol.api.JmolAppletInterface
getModelIndexFromId(String) - Method in class org.jmol.api.JmolViewer
getModelIndexFromId(String) - Method in class org.jmol.modelset.ModelSet
getModelIndexFromId(String) - Method in class org.jmol.util.GenericApplet
getModelIndexFromId(String) - Method in class org.jmol.viewer.Viewer
getModelIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
getModelIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
getModelInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
getModelInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getModelInfo(String) - Method in class org.jmol.viewer.Viewer
  get a value from the current model's Model.auxiliaryInfo
getModelInfoAsString() - Method in class org.jmol.modelset.ModelSet
getModelkit(boolean) - Method in class org.jmol.viewer.Viewer
getModelkitPropertySafely(String) - Method in class org.jmol.viewer.Viewer
  Get a ModelKit property, but only if the modelkit exists already.
getModelName(int) - Method in class org.jmol.api.JmolViewer
getModelName(int) - Method in class org.jmol.modelset.ModelSet
getModelName(int) - Method in class org.jmol.viewer.Viewer
getModelNumber() - Method in class org.jmol.modelset.Atom
getModelNumber(int) - Method in class org.jmol.api.JmolViewer
getModelNumber(int) - Method in class org.jmol.modelset.ModelSet
getModelNumber(int) - Method in class org.jmol.viewer.Viewer
getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelSet
getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
getModelOrientation(int) - Method in class org.jmol.modelset.ModelSet
getModelPeakInfoForAutoSelectOnLoad() - Method in class jspecview.common.Spectrum
getModelProperties(int) - Method in class org.jmol.api.JmolViewer
getModelProperties(int) - Method in class org.jmol.viewer.Viewer
getModelProperty(int, String) - Method in class org.jmol.modelset.ModelSet
getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
getModelSetAuxiliaryInfo(BS) - Method in class org.jmol.modelset.ModelSet
  Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.
getModelSetAuxiliaryInfoForAtoms(Object) - Method in class org.jmol.viewer.Viewer
getModelSetFileName() - Method in class org.jmol.api.JmolViewer
getModelSetFileName() - Method in class org.jmol.viewer.Viewer
getModelSetPathName() - Method in class org.jmol.api.JmolViewer
getModelSetPathName() - Method in class org.jmol.viewer.Viewer
getModelSetProperties() - Method in class org.jmol.api.JmolViewer
getModelSetProperties() - Method in class org.jmol.viewer.Viewer
getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelSet
getModelTitle(int) - Method in class org.jmol.modelset.ModelSet
getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
getModelUndeletedAtomsBitSetBs(BS) - Method in class org.jmol.viewer.Viewer
getModPoint(boolean) - Method in interface org.jmol.api.JmolModulationSet
getModPoint(boolean) - Method in class org.jmol.util.ModulationSet
getModType(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
getModType(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getModulation() - Method in class org.jmol.modelset.Atom
getModulation(char, T3, boolean) - Method in interface org.jmol.api.JmolModulationSet
getModulation(char, T3, boolean) - Method in class org.jmol.util.ModulationSet
getModulation(int) - Method in class org.jmol.modelset.AtomCollection
getModulationList(BS, char, P3) - Method in class org.jmol.modelset.ModelSet
getModulationMap() - Method in class org.jmol.adapter.readers.cif.MSRdr
getModulationMap() - Method in interface org.jmol.adapter.smarter.MSInterface
getMOHeader(int, String[], Map[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
getMoInfo(int) - Method in class org.jmol.shapesurface.MolecularOrbital
getMolecularFormula(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
getMolecularFormula(Object, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
getMolecularFormula(Object, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
getMolecularFormulaAtoms(Node[], BS, float[], boolean) - Static method in class org.jmol.util.JmolMolecule
getMoleculeBitSet(BS) - Method in class org.jmol.modelset.ModelSet
  return cumulative sum of all atoms in molecules containing these atoms
getMoleculeBitSetForAtom(int) - Method in class org.jmol.modelset.ModelSet
getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelSet
  ////// molecules /////////
getMoleculeInfo(Object) - Method in class org.jmol.viewer.PropertyManager
  info ///
getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
getMoleculeNumber(boolean) - Method in class org.jmol.smiles.SmilesAtom
getMoleculeNumber(boolean) - Method in interface org.jmol.util.Node
getMolecules() - Method in class org.jmol.modelset.ModelSet
getMolecules(Node[], BS[], Lst, BS) - Static method in class org.jmol.util.JmolMolecule
  Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
getMonomerIndex() - Method in class org.jmol.modelset.Group
getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMoreInfo() - Method in interface org.jmol.api.SymmetryInterface
getMoreInfo() - Method in class org.jmol.symmetry.Symmetry
getMOString(float[]) - Static method in class org.jmol.quantum.QS
getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
getMotionFixedAtoms(SymmetryInterface, BS) - Method in class org.jmol.viewer.Viewer
  For the current SINGLE model only.
getMouseAction(int, int, int) - Static method in class org.jmol.viewer.binding.Binding
getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
getMouseActionStr(String) - Static method in class org.jmol.viewer.binding.Binding
  create an action code from a string such as "CTRL-LEFT-double click"
getMouseEnabled() - Method in class org.jmol.viewer.Viewer
getMouseManager(double, Object) - Method in class jspecview.java.AwtPlatform
  /// Mouse
getMouseManager(double, Object) - Method in class jspecview.js2d.JsPlatform
getMouseManager(double, Object) - Method in interface org.jmol.api.GenericPlatform
  / Mouse
getMouseManager(double, Object) - Method in class org.jmol.awt.Platform
  /// Mouse
getMouseManager(double, Object) - Method in class org.jmol.awtjs2d.Platform
getMoveToText(boolean) - Method in class org.jmol.modelset.Orientation
getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
getMSInfoB(String) - Method in class org.jmol.modelset.ModelSet
getMult() - Method in class org.jmol.adapter.smarter.Atom
getMyInfo(P3) - Method in class org.jmol.modelsetbio.Monomer
getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
getName() - Method in interface com.sparshui.gestures.Gesture
  Get the name of this gesture.
getName() - Method in class javajs.util.OC
getName() - Method in interface org.jmol.api.GenericFileInterface
getName() - Method in interface org.jmol.api.JmolAbstractButton
getName() - Method in interface org.jmol.api.JmolScriptFunction
getName() - Method in interface org.jmol.api.SC
getName() - Method in class org.jmol.awt.AwtSwingComponent
getName() - Method in class org.jmol.awtjs.swing.Component
getName() - Method in enum class org.jmol.c.STER
getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
getName() - Method in class org.jmol.script.ScriptFunction
getName() - Method in class org.jmol.symmetry.CLEG.ClegNode
getName() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
getName() - Method in interface org.openscience.jmol.app.JmolPlugin
getName(int) - Static method in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
getNameList() - Static method in enum class org.jmol.c.CBK
getNameList(Lst) - Static method in enum class jspecview.common.ScriptToken
getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
getNavigationState() - Method in interface org.jmol.api.JmolNavigatorInterface
getNavigationState() - Method in class org.jmol.navigate.Navigator
getNavigationState() - Method in class org.jmol.viewer.TransformManager
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
getNavPtHeight() - Method in class org.jmol.viewer.TransformManager
getNBOAtomLabel(Atom) - Method in class org.jmol.adapter.readers.quantum.NBOParser
  get the
getNBOAtomLabel(Atom) - Method in class org.jmol.viewer.Viewer
getNBOTypeFromName(String) - Static method in class org.jmol.viewer.JC
getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
getNearestIndexForX(Coordinate[], double) - Static method in class jspecview.common.Coordinate
getNearestXWithYAbove(Coordinate[], double, double, boolean, boolean) - Static method in class jspecview.common.Coordinate
  discovers nearest peak left or right of x that is above threshold y
getNeighbors() - Method in interface org.iupac.InChIStructureProvider
getNeighbors() - Method in class org.jmol.inchi.InChIJNA
getNeighbors() - Method in class org.jmol.inchi.InChIJS
getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
getNetByID(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  Find or create a net with this netID, giving it a default name "Net"+id
getNetFor(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  Find or create a TNet for this id and label.
getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
getNewDfCoefMap() - Static method in class org.jmol.quantum.QS
getNewScales(int, boolean, double, double) - Method in class jspecview.common.ViewData
getNext(Object, int) - Method in class javajs.util.MessagePackReader
getNextDataToken() - Method in interface javajs.api.GenericCifDataParser
getNextDataToken() - Method in class javajs.util.CifDataParser
  first checks to see if the next token is an unquoted control code, and if so, returns null
getNextStatement() - Method in interface org.jmol.api.JmolScriptEvaluator
getNextStatement() - Method in class org.jmol.script.ScriptEval
  when paused, indicates what statement will be next
getNextToken() - Method in interface javajs.api.GenericCifDataParser
getNextToken() - Method in class javajs.util.CifDataParser
  Get a token as a String value (for the reader)
getNextTokenObject() - Method in class javajs.util.CifDataParser
  Get the token as a Java Object
getNextTokenProtected() - Method in class javajs.util.CifDataParser
  Just makes sure
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.JvxlReader
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getNHPoint(P3, V3, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
getNitrogenAtom() - Method in class org.jmol.modelset.Group
getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
  /////////////////////////////////////////////////////////////
getNMRCalculation() - Method in class org.jmol.viewer.Viewer
getNmrDataJSON() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
getNMRfreq() - Method in class org.openscience.jmol.app.janocchio.NoeTable
  gets the NMR frequency
getNMRfreqMHz() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  gets the NMR frequency
getNmrNucleusFromName(String) - Static method in class org.jmol.util.Elements
getNMRPredict(String) - Method in class org.jmol.viewer.Viewer
getNoeExprefValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getnoeNPrefIndices() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getNOEorJHH(Atom[], int) - Method in interface org.jmol.api.JmolNMRInterface
getNOEorJHH(Atom[], int) - Method in class org.jmol.quantum.NMRCalculation
getNoesy() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  get if NOESY or ROESY was used for simulation
getNoesy() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getNoeWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
getNominalMass() - Method in class org.jmol.modelset.Atom
getNominalSpecFreq(String, double) - Static method in class jspecview.source.JDXDataObject
getNormal() - Method in class javajs.util.Quat
getNormalDirected(V3) - Method in class javajs.util.Quat
getNormalFromCenter(P3, P3, P3, P3, boolean, V3, V3) - Static method in class javajs.util.Measure
getNormalMap(T3[], int, BS, Lst) - Method in class org.jmol.export.__CartesianExporter
getNormals(T3[], P4) - Method in class org.jmol.shape.Mesh
getNormalsTemp() - Method in class org.jmol.shape.Mesh
getNormalThroughPoints(T3, T3, T3, T3, T3) - Static method in class javajs.util.Measure
getNormalToLine(P3, P3, V3) - Static method in class javajs.util.Measure
getNormixCount() - Static method in class org.jmol.util.Normix
getNormixes() - Method in class org.jmol.shapespecial.Polyhedron
getNormixV(V3, BS) - Static method in class org.jmol.util.Normix
getNoValue() - Method in class org.jmol.quantum.NciCalculation
getNoValue() - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
getNPoints() - Method in class com.sparshui.common.messages.events.DragEvent
getNPointsFound() - Method in class jspecview.source.JDXDecompressor
  Report out the number of points found (for error reporting)
getNull(boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
getNumAtoms() - Method in interface org.iupac.InChIStructureProvider
getNumAtoms() - Method in class org.jmol.inchi.InChIJNA
  atoms ///
getNumAtoms() - Method in class org.jmol.inchi.InChIJS
  Atoms ///
getNumberOfGraphSets() - Method in class jspecview.common.PanelData
  Returns the Number of Graph sets
getNumberOfSpectra() - Method in class jspecview.source.JDXSource
  Returns the number of Spectra in this Source
getNumberOfSpectraInCurrentSet() - Method in class jspecview.common.PanelData
getNumBonds() - Method in interface org.iupac.InChIStructureProvider
getNumBonds() - Method in class org.jmol.inchi.InChIJNA
  bonds ///
getNumBonds() - Method in class org.jmol.inchi.InChIJS
  Bonds ///
getNumDim() - Method in class jspecview.source.JDXDataObject
getNumStereo0D() - Method in interface org.iupac.InChIStructureProvider
getNumStereo0D() - Method in class org.jmol.inchi.InChIJNA
  Stereo ///
getNumStereo0D() - Method in class org.jmol.inchi.InChIJS
  Stereo ///
getObjectBoundingBox(String) - Method in class org.jmol.script.ScriptEval
getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEval
getObjectColix(int) - Method in class org.jmol.viewer.Viewer
getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
getObjectMad10(int) - Method in class org.jmol.viewer.Viewer
getObjectMap(Map, char) - Method in class org.jmol.viewer.Viewer
  used in autocompletion in console using TAB
getObservedFreq() - Method in class jspecview.source.JDXDataObject
  Returns the observed frequency (for NMR Spectra)
getObservedNucleus() - Method in class jspecview.source.JDXDataObject
  ^1H, ^13C, for example
getOccupancy() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getOccupancy100() - Method in class org.jmol.modelset.Atom
getOccupancy100(boolean) - Method in class org.jmol.util.ModulationSet
getOccupancy100(boolean) - Method in class org.jmol.util.Vibration
getOccupancyFloat(int) - Method in class org.jmol.modelset.AtomCollection
getOffset(int, int, boolean) - Static method in class org.jmol.viewer.JC
  Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered".
getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.Node
getOffsetVertices(P4) - Method in class org.jmol.shape.Mesh
geTokens() - Method in interface org.jmol.api.JmolScriptFunction
geTokens() - Method in class org.jmol.script.ScriptFunction
getOpacity255() - Method in interface javajs.api.GenericColor
getOpacity255() - Method in class jspecview.java.AwtColor
getOpacity255() - Method in class org.jmol.awt.AwtColor
getOpacity255() - Method in class org.jmol.awtjs.swing.Color
getOpAxis() - Method in class org.jmol.symmetry.SymmetryOperation
getOpDesc() - Method in class org.jmol.symmetry.SymmetryOperation
getOpenFileNameFromDialog(Map, Viewer, String, JmolAppAPI, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
getOpenFileNameFromDialog(Map, Viewer, String, JmolAppAPI, String, boolean) - Method in class org.jmol.dialog.Dialog
getOpenSmiles(BS) - Method in class org.jmol.api.JmolViewer
getOpenSmiles(BS) - Method in class org.jmol.viewer.Viewer
getOperationRsVs(int) - Method in interface org.jmol.api.SymmetryInterface
getOperationRsVs(int) - Method in class org.jmol.symmetry.Symmetry
getOperativeSymmetry() - Method in class org.jmol.viewer.Viewer
  Only return symmetry that has operators.
getOpIsCCW() - Method in class org.jmol.symmetry.SymmetryOperation
getOpOrder() - Method in class org.jmol.symmetry.SymmetryOperation
getOpPoint() - Method in class org.jmol.symmetry.SymmetryOperation
getOpPoint2() - Method in class org.jmol.symmetry.SymmetryOperation
getOption(String[], String, String) - Method in interface jspecview.api.js.JSVAppletObject
getOption(String, Viewer, String) - Static method in class org.jmol.api.Interface
  Note! Do not use this method with "viewer." or "util." because when the JavaScript is built, "org.jmol.util" and "org.jmol.viewer" are condensed to "JU" and "JV" (javajs.util is also JU)
getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.dialog.DialogManager
getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.java.AwtDialogManager
getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.js2d.JsDialogManager
getOptionFromDialog(String[], String, String) - Method in class jspecview.common.JSViewer
getOpTrans() - Method in class org.jmol.symmetry.SymmetryOperation
getOpType() - Method in class org.jmol.symmetry.SymmetryOperation
getOrAddBond(Atom, Atom, int, short, BS, float, boolean) - Method in class org.jmol.modelset.BondCollection
getOrCalcPartialCharges(BS, BS) - Method in class org.jmol.viewer.Viewer
getOrientation(int, String, BS, P3[]) - Method in class org.jmol.viewer.Viewer
getOrigin() - Method in class jspecview.source.JDXHeader
  Getter for property origin.
getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
getOriginVaVbVc() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
getOtherNode(SimpleNode) - Method in class org.jmol.modelset.Bond
getOtherNode(SimpleNode) - Method in class org.jmol.smiles.SmilesBond
getOtherNode(SimpleNode) - Method in interface org.jmol.util.SimpleEdge
getOuterXML() - Method in class jspecview.source.XMLParser
getOutputChannel(String, boolean) - Method in class jspecview.common.JSViewer
getOutputChannel(String, String[]) - Method in class org.jmol.viewer.Viewer
getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
getOverallSpan() - Method in class org.jmol.adapter.smarter.XtalSymmetry
getOverlayLegendData() - Method in class jspecview.common.PanelData
getOwner() - Method in class jspecview.source.JDXHeader
  Getter for property owner.
getP(String) - Method in class org.jmol.viewer.Viewer
getPackingRangeValue(float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getPalette(String) - Static method in enum class org.jmol.c.PAL
getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
getPaletteID(String) - Static method in enum class org.jmol.c.PAL
getPaletteName(byte) - Static method in enum class org.jmol.c.PAL
getPane() - Method in class org.jmol.console.JmolConsole
getPanelData() - Method in interface jspecview.api.JSVPanel
getPanelData() - Method in class jspecview.java.AwtPanel
getPanelData() - Method in class jspecview.js2d.JsPanel
getPanelMany(JSViewer, Lst) - Static method in class jspecview.java.AwtPanel
  Constructs a `JSVPanel` with List of spectra and corresponding start and end indices of data points that should be displayed
getPanelMany(JSViewer, Lst) - Static method in class jspecview.js2d.JsPanel
  Constructs a `JSVPanel` with List of spectra and corresponding start and end indices of data points that should be displayed
getPanelNode() - Method in interface jspecview.api.JSVTreeNode
getPanelNode() - Method in class jspecview.application.AwtTreeNode
getPanelNode() - Method in class jspecview.tree.SimpleTreeNode
getPanelOne(JSViewer, Spectrum) - Static method in class jspecview.java.AwtPanel
  Constructs a new JSVPanel
getParameter(String) - Method in interface jspecview.api.AppletFrame
getParameter(String) - Method in class jspecview.appletjs.JSVApplet
getParameter(String) - Method in class org.jmol.api.JmolViewer
getParameter(String) - Method in class org.jmol.viewer.Viewer
getParameter(String, int, boolean) - Method in class org.jmol.script.ScriptParam
getParameter(String, String) - Method in class jspecview.appletjs.JSVApplet
getParameters() - Method in interface jspecview.api.AnnotationData
getParameters() - Method in class jspecview.common.MeasurementData
getParameters() - Method in class jspecview.dialog.JSVDialog
getParameters(boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getParams() - Method in class org.jmol.quantum.NMRNoeMatrix
getParamType(int) - Static method in class org.jmol.script.T
getParent() - Method in interface org.jmol.api.SC
getParent() - Method in class org.jmol.awt.AwtSwingComponent
getParent() - Method in class org.jmol.awtjs.swing.Component
getParentAsFile() - Method in interface org.jmol.api.GenericFileInterface
getParity() - Method in interface org.iupac.InChIStructureProvider
getParity() - Method in class org.jmol.inchi.InChIJNA
getParity() - Method in class org.jmol.inchi.InChIJS
getPart() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getPartialBondDotted(int) - Static method in class org.jmol.util.Edge
getPartialBondOrder(int) - Static method in class org.jmol.util.Edge
getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.util.Edge
  reads standard n.m double-as-integer (n*1000000 + m) and returns partial bond order as (n % 7) invalid input: '<'invalid input: '<' 5 + (m % 0x1F)
getPartialCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getPartialCharge() - Method in class org.jmol.modelset.Atom
getPartialCharges() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
getPartialCharges(BS) - Method in class org.jmol.script.ScriptEval
getPartnerAtom(NucleicMonomer) - Method in class org.jmol.modelsetbio.BasePair
getPath() - Method in interface jspecview.api.JSVTreeNode
getPath() - Method in class jspecview.tree.SimpleTreeNode
getPathForAllFiles() - Method in class org.jmol.viewer.FileManager
getPatternIndex() - Method in class org.jmol.smiles.SmilesAtom
getPdbAtomData(BS, OC, boolean, boolean) - Method in class org.jmol.viewer.Viewer
getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
  PDB or PQR only
getPdbData(int, String, BS, Object[], OC, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.PropertyManager
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.Viewer
getPdbData(String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioModel
getPDBHeader(int) - Method in class org.jmol.modelset.ModelSet
getPdbID() - Method in class org.jmol.viewer.Viewer
getPeakInfo() - Method in class jspecview.common.PeakPickEvent
getPeakList() - Method in class jspecview.common.Spectrum
getPeakListArray(Measurement, double[], double) - Method in class jspecview.source.JDXDataObject
getPeakListing(Parameters, Boolean) - Method in class jspecview.common.PanelData
getPeakTitle() - Method in class jspecview.common.Spectrum
getPeakWidth() - Method in class jspecview.common.Spectrum
getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
getPercentMinimumY() - Method in class jspecview.common.IntegralData
getPercentOffset() - Method in class jspecview.common.IntegralData
getPercentYValueAt(double) - Method in class jspecview.common.IntegralData
getPercentYValueAt(double) - Method in class jspecview.common.Spectrum
getPeriodicity() - Method in interface org.jmol.api.SymmetryInterface
getPeriodicity() - Method in class org.jmol.symmetry.Symmetry
  0x1 a only frieze, rod-a 0x2 b only rod-b 0x4 c only rod-c 0x3 ab only plane, layer 0x5 ac only n/a 0x6 bc only n/a 0x7 abc all space
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
  calculate the perspective factor based on z
getPhiPsiForHelixType(String) - Method in class org.jmol.modelsetbio.BioExt
getPhongExponent() - Method in class org.jmol.util.GData
getPickedCoordinates(Coordinate, Coordinate) - Method in class jspecview.common.PanelData
  click event processing
getPickedPoint(T3, int) - Method in class org.jmol.shape.MeshCollection
getPickingMode() - Method in class org.jmol.viewer.Viewer
getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
getPickingState() - Method in class org.jmol.viewer.ActionManager
getPickingStyleIndex(String) - Static method in class org.jmol.viewer.ActionManager
getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getPlane(int) - Method in class org.jmol.jvxl.readers.JvxlReader
getPlane(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getPlane(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
getPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptEval
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.JvxlReader
  Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
  Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneProjection(T3, P4, T3, V3) - Static method in class javajs.util.Measure
  Project a point onto a plane, also returning the normal vector and the directed distance to the plane.
getPlaneSR(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getPlaneThroughPoint(T3, V3, P4) - Static method in class javajs.util.Measure
getPlaneThroughPoints(T3, T3, T3, V3, V3, P4) - Static method in class javajs.util.Measure
getPlatformInterface(String) - Method in class jspecview.common.JSViewer
getPlotColors(String) - Method in class jspecview.common.ColorParameters
getPlotSpinSet(Viewer, BS, int, P3, P3) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
  remove non-spin atoms and atoms with duplicated spin and set min/max XYZ for the plot
getPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getPLYData(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getPmeshData(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getPngZipStream(BufferedInputStream, boolean) - Static method in class javajs.util.Rdr
  Either advance a PNGJ stream to its zip file data or pull out the ZIP data bytes and create a new stream for them from which a ZIP utility can start extracting files.
getPoint(int, P3) - Method in class org.jmol.jvxl.data.VolumeData
getPoint(int, T3) - Method in class org.jmol.shapecgo.CGOMesh
getPoint3f(int, boolean) - Method in class org.jmol.scriptext.ScriptExt
getPoint3f(int, boolean, boolean) - Method in class org.jmol.script.ScriptParam
  Get an {x,y,z} value, possibly fractional, with option to throw an error.
getPoint4f(int) - Method in class org.jmol.script.ScriptParam
getPoint4fNoError(int) - Method in class org.jmol.script.ScriptParam
getPointArray(int, int, boolean, boolean) - Method in class org.jmol.script.ScriptParam
  may return null values in some cases
getPointer(int) - Static method in class org.jmol.viewer.JC
getPointerName(int) - Static method in class org.jmol.viewer.JC
getPointGroupAsString(BS, String, int, float, P3[], P3, String) - Method in class org.jmol.modelset.ModelSet
getPointGroupInfo(int, String, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
getPointGroupInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
getPointGroupInfo(BS, String) - Method in class org.jmol.modelset.ModelSet
getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
getPointOrCenterVector(T) - Method in class org.jmol.script.ScriptParam
getPointOrPlane(int, int) - Method in class org.jmol.script.ScriptParam
  Get the point or plane at an index
getPoints() - Method in interface org.jmol.api.JmolEnvCalc
getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
getPointsOnPlane(P3[], P4) - Static method in class javajs.util.Measure
  Based on a set of centering points, returns the list of points on a given plane.
getPointTransf(int, Atom, Quat, P3) - Method in class org.jmol.modelset.ModelSet
  pick up the appropriate value for this atom
getPointVector(T, int) - Method in class org.jmol.script.ScriptParam
getPolygonColorData(int, short[], int[][], BS) - Static method in class org.jmol.shapesurface.Isosurface
getPolymerPointsAndVectors(int, BS, Lst, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
getPolymerPointsAndVectors(BS, Lst) - Method in class org.jmol.viewer.Viewer
getPolymerPointsAndVectors(BS, Lst, boolean, float) - Method in class org.jmol.modelset.ModelSet
getPolymerSequenceAtoms(int, int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
getPopulation() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
getPopupMenu() - Method in interface org.jmol.api.SC
getPopupMenu() - Method in class org.jmol.awt.AwtSwingComponent
getPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
getPopupMenu() - Method in class org.jmol.awtjs.swing.JMenu
getPOrNull(String) - Method in class org.jmol.viewer.Viewer
getPort() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
getPort() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getPosition() - Method in interface javajs.api.GenericBinaryDocumentReader
getPosition() - Method in class javajs.util.BinaryDocument
getPosition() - Method in interface org.jmol.api.AtomIndexIterator
getPosition() - Method in class org.jmol.modelset.AtomIteratorWithinModel
getPosition() - Method in class org.jmol.symmetry.UnitCellIterator
getPosXY() - Method in class jspecview.dialog.IntegrationDialog
getPosXY() - Method in class jspecview.dialog.JSVDialog
getPosXY() - Method in class jspecview.dialog.MeasurementsDialog
getPosXY() - Method in class jspecview.dialog.OverlayLegendDialog
getPosXY() - Method in class jspecview.dialog.PeakListDialog
getPosXY() - Method in class jspecview.dialog.ViewsDialog
getPrecision() - Method in interface org.jmol.api.SymmetryInterface
getPrecision() - Method in class org.jmol.symmetry.Symmetry
getPrecision() - Method in class org.jmol.util.SimpleUnitCell
getPreference(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getPreferences() - Method in class jspecview.application.PreferencesDialog
  Returns the preferences (`Properties` Object)
getPreserveState() - Method in class org.jmol.viewer.Viewer
  This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
getPreviousMolecule() - Method in class jme.JME
getPrevNode() - Method in class org.jmol.symmetry.CLEG.ClegData
getPrintLayout() - Method in interface jspecview.api.JSVPrintDialog
getPrintLayout() - Method in class jspecview.java.AwtPrintDialog
  Returns the PrintLayout object
getPrintLayout(boolean) - Method in class jspecview.common.JSViewer
getPrivateKey() - Method in class org.jmol.export.Export3D
getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
getProjectedLineSegment(P3[], int, P3, V3, V3) - Static method in class javajs.util.Measure
getPropC(String, int) - Method in class org.jmol.shapesurface.Contact
getPropDataMC(String, Object[]) - Method in class org.jmol.shape.MeshCollection
getProperties() - Method in class org.openscience.jmol.app.HistoryFile
getproperty - Static variable in class org.jmol.script.T
getProperty(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
getProperty(String) - Method in class org.jmol.modelkit.ModelKit
  Get a property of the modelkit.
getProperty(String) - Method in class org.jmol.util.GenericApplet
getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
  only called from org.openscience.jvxl.Jvxl.main
getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
getProperty(String, int) - Method in class org.jmol.shape.Axes
getProperty(String, int) - Method in class org.jmol.shape.Labels
getProperty(String, int) - Method in class org.jmol.shape.Measures
getProperty(String, int) - Method in class org.jmol.shape.Shape
getProperty(String, int) - Method in class org.jmol.shape.Sticks
getProperty(String, int) - Method in class org.jmol.shapecgo.CGO
getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
getProperty(String, int) - Method in class org.jmol.shapespecial.Polyhedra
getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
getProperty(String, int) - Method in class org.jmol.shapesurface.Contact
getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
getProperty(String, int) - Method in class org.jmol.shapesurface.Pmesh
getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
getProperty(String, String) - Method in class org.jmol.util.GenericApplet
  @XXXj2sOverride
getProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
  Get the value of a property
getProperty(String, String, Object) - Method in interface org.jmol.api.JmolPropertyManager
getProperty(String, String, Object) - Method in class org.jmol.api.JmolViewer
getProperty(String, String, Object) - Method in class org.jmol.viewer.PropertyManager
  / static methods used by Eval and Viewer ////
getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
GETPROPERTY - Enum constant in enum class jspecview.common.ScriptToken
getPropertyAsJavaObject(String) - Method in interface jspecview.api.JSVAppletInterface
getPropertyAsJavaObject(String) - Method in class jspecview.app.JSVApp
getPropertyAsJavaObject(String) - Method in class jspecview.appletjs.JSVApplet
getPropertyAsJavaObject(String) - Method in class jspecview.common.JSViewer
getPropertyAsJSON(String) - Method in interface jspecview.api.JSVAppletInterface
getPropertyAsJSON(String) - Method in class jspecview.app.JSVApp
getPropertyAsJSON(String) - Method in class jspecview.appletjs.JSVApplet
getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsJSON(String) - Method in class org.jmol.util.GenericApplet
getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsJSON(String, String) - Method in class org.jmol.util.GenericApplet
  @XXXj2sOverride
getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsString(String) - Method in class org.jmol.util.GenericApplet
getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsString(String, String) - Method in class org.jmol.util.GenericApplet
  @XXXj2sOverride
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Echo
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Shape
getPropertyData(String, Object[]) - Method in class org.jmol.shapecgo.CGO
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Draw
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
getPropertyData(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
getPropertyNumber(String) - Method in interface org.jmol.api.JmolPropertyManager
getPropertyNumber(String) - Method in class org.jmol.viewer.PropertyManager
getPropertyNumber(String) - Method in class org.jmol.viewer.Viewer
getPropI(String, int) - Method in class org.jmol.shapesurface.Isosurface
getPropMC(String, int) - Method in class org.jmol.shape.MeshCollection
getPropMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
getPropShape(String, Object[]) - Method in class org.jmol.shape.Shape
getProteinStructure(int) - Method in class org.jmol.modelsetbio.AlphaPolymer
getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
getProteinStructureState(BS, int) - Method in class org.jmol.modelset.ModelSet
getProteinStructureSubType() - Method in class org.jmol.modelset.Group
getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
getProteinStructureTag() - Method in class org.jmol.modelset.Group
getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
getProteinStructureType() - Method in class org.jmol.modelset.Group
getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
  /////////////////////////////////////////////////////////////
getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getProteinStructureType(String) - Static method in enum class org.jmol.c.STR
  In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
getPymolRadius() - Method in class org.jmol.api.JmolAdapterBondIterator
getPymolScreenOffset(P3, P3i, int, P3, float) - Method in class org.jmol.modelset.Text
  PyMOL will use 1 here for pymolOffset[0] for relative, 0 or absolute.
getQCoefs(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
getQCoefs(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getQuadrupolarConstant(Tensor) - Method in interface org.jmol.api.JmolNMRInterface
  Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
getQuadrupolarConstant(Tensor) - Method in class org.jmol.quantum.NMRCalculation
getQualifiedDataType() - Method in class jspecview.source.JDXHeader
getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
getQuality(String) - Method in class org.jmol.dialog.Dialog
getQuantumShellTag(int) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getQuantumShellTag(int) - Static method in class org.jmol.quantum.QS
getQuantumShellTagID(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getQuantumShellTagID(String) - Static method in class org.jmol.quantum.QS
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.quantum.QS
getQuaternion(char) - Method in class org.jmol.modelset.Group
getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
getQuaternionAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternionArray(Object, int) - Method in class org.jmol.script.ScriptEval
getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
getQuaternionFrame(P3, T3, T3) - Static method in class javajs.util.Quat
  returns a quaternion frame based on three points (center, x, and any point in xy plane) or two vectors (vA, vB).
getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
getQuaternionFrameCenterAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternionFrameV(V3, V3, V3, boolean) - Static method in class javajs.util.Quat
  Create a quaternion based on a frame
getQuaternionP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternionParameter(int, BS, boolean) - Method in class org.jmol.script.ScriptParam
getQuaternionRotation(String) - Method in interface org.jmol.api.SymmetryInterface
getQuaternionRotation(String) - Method in class org.jmol.symmetry.Symmetry
getQuotedAttribute(String, String) - Static method in class javajs.util.PT
getQuotedOrUnquotedAttribute(String, String) - Static method in class javajs.util.PT
  single- or double-quoted string or up to the first space -- like HTML5 not case-sensitive
getQuotedStringAt(String, int) - Static method in class javajs.util.PT
  general static string-parsing class ///
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.JvxlReader
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getQuotedStringNext(String, int[]) - Static method in class javajs.util.PT
getQuotedStringOrObject(char) - Method in class javajs.util.CifDataParser
  CIF 1.0 only.
getQuotedStringOrObject(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  final get for quoted object
getRadio(String) - Method in class org.jmol.awt.AwtPopupHelper
getRadio(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getRadio(String) - Method in interface org.jmol.popup.PopupHelper
getRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getRadius() - Method in class org.jmol.modelset.Atom
getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
getRange(BS, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
getRangeGroups(int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
getRasMolRadius() - Method in class org.jmol.modelset.Atom
getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
getReader(String, Map) - Static method in class org.jmol.adapter.smarter.Resolver
  Get a reader based on its name.
getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
getRealCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
getRealEigenvalues() - Method in class javajs.util.Eigen
  Return the real parts of the eigenvalues
getReciprocal(T3[], T3[], float) - Static method in class org.jmol.util.SimpleUnitCell
  Generate the reciprocal unit cell, scaled as desired
getRecord(String) - Method in interface org.jmol.api.JmolJDXMOLParser
getRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
getRedField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
getRedField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
getRedValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
getRedValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getRefreshing() - Method in class org.jmol.viewer.Viewer
getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
getRegistryInfo() - Method in class org.jmol.util.GenericApplet
getRegistryInfo() - Method in class org.openscience.jmol.app.status.StatusListener
getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
getRemainingScript() - Method in class jspecview.common.ScriptTokenizer
getRendering() - Method in class org.jmol.shape.Mesh
getResno() - Method in class org.jmol.modelset.Atom
getResno() - Method in class org.jmol.modelset.Group
  /////////////////////////////////////////////////////////////
getResno() - Method in class org.jmol.smiles.SmilesAtom
getResno() - Method in interface org.jmol.util.Node
getResolution() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getResolution() - Method in class org.jmol.util.MeshSurface
getResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getResourceString(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getResourceString(Object, String, String[]) - Static method in class jspecview.common.JSVFileManager
getRGB() - Method in interface javajs.api.GenericColor
getRGB() - Method in class org.jmol.awtjs.swing.Color
getRhoStar() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getRhoStarField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
getRiboseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
getRmsd(P3[][], Quat) - Static method in class javajs.util.Measure
getRootNode() - Method in interface jspecview.api.JSVTree
getRootNode() - Method in class jspecview.application.AwtTree
getRootNode() - Method in class jspecview.tree.SimpleTree
getRotateBondIndex() - Method in class org.jmol.modelkit.ModelKit
getRotation() - Method in class com.sparshui.common.messages.events.RotateEvent
getRotation() - Method in class javajs.util.Matrix
  similarly to M3/M4 standard rotation/translation matrix we set a rotationTranslation matrix to be: [ nxn rot nx1 trans 1xn 0 1x1 1 ]
getRotation(int) - Method in class javajs.export.PDFCreator
getRotation(M3) - Method in class org.jmol.viewer.TransformManager
getRotationCount() - Method in class org.jmol.symmetry.HallInfo
getRotationMatrix(P3, P3, float) - Method in class org.jmol.export.___Exporter
getRotationMatrix(P3, P3, float, P3, P3) - Method in class org.jmol.export.___Exporter
getRotationQ() - Method in class org.jmol.viewer.TransformManager
getRotationScale(M3) - Method in class javajs.util.M4
  Gets the upper 3x3 values of this matrix and places them into the matrix m1.
getRotationX() - Method in class com.sparshui.common.messages.events.SpinEvent
getRotationY() - Method in class com.sparshui.common.messages.events.SpinEvent
getRotationZ() - Method in class com.sparshui.common.messages.events.SpinEvent
getRotTransArrayAndXYZ(String, float[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
  MMCifReader only
getRotTransArrayAndXYZ(SymmetryOperation, String, float[], boolean, boolean, boolean, String) - Static method in class org.jmol.symmetry.SymmetryOperation
  Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format
getRow(int, float[]) - Method in class javajs.util.M3
  Copies the matrix values in the specified row into the array parameter.
getRow(int, float[]) - Method in class javajs.util.M34
getRow(int, float[]) - Method in class javajs.util.M4
  Copies the matrix values in the specified row into the array parameter.
getRow33(int, float[]) - Method in class javajs.util.M34
getRowCount() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
getRowCount() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getRowCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
getRowDimension() - Method in class javajs.util.Matrix
  Get row dimension.
getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
getRuleName(int) - Method in class org.jmol.symmetry.CIPChirality
getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
getSavedState(String) - Method in class org.jmol.viewer.StateManager
getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
getSavedUnitCell(String) - Method in class org.jmol.viewer.StateManager
getSaveFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
getSaveFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
getScale() - Method in class com.sparshui.common.messages.events.ZoomEvent
getScale() - Method in class jspecview.common.ViewData
getScale() - Method in interface org.jmol.api.JmolModulationSet
getScale() - Method in class org.jmol.util.ModulationSet
getScaleData() - Method in class jspecview.common.ViewData
getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
getScaleText(String, boolean, float, float[]) - Method in class org.jmol.viewer.Viewer
  Depending upon the measure text, we need to indicate |-------| 1 A or 0.1 A for example.
getScreenDim() - Method in class org.jmol.viewer.Viewer
getScreenDimensions(Dimension) - Method in interface org.jmol.awtjs.swing.SwingController
  Return the width and height of the window in d.
getScreenHeight() - Method in class org.jmol.api.JmolViewer
getScreenHeight() - Method in class org.jmol.viewer.Viewer
getScreenImage() - Method in class org.jmol.viewer.Viewer
getScreenImage() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
getScreenImage(boolean) - Method in class org.jmol.g3d.Graphics3D
getScreenImage(boolean) - Method in class org.jmol.util.GData
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.api.JmolViewer
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.viewer.Viewer
  Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
getScreenNormal(T3, T3, float) - Method in class org.jmol.export._PovrayExporter
getScreenNormal(T3, T3, float) - Method in class org.jmol.export._TachyonExporter
getScreenTemp(T3, P3) - Method in class org.jmol.viewer.TransformManager
getScreenTemp(T3, P3) - Method in class org.jmol.viewer.TransformManager4D
getScreenWidth() - Method in class org.jmol.api.JmolViewer
getScreenWidth() - Method in class org.jmol.viewer.Viewer
getScript() - Method in interface org.jmol.api.JmolScriptEvaluator
getScript() - Method in class org.jmol.script.ScriptEval
getScriptContext(String) - Method in interface org.jmol.api.JmolScriptEvaluator
getScriptContext(String) - Method in class org.jmol.script.ScriptEval
getScriptContext(String) - Method in class org.jmol.viewer.Viewer
getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
getScriptEditor() - Method in class org.jmol.console.GenericConsole
getScriptEditor() - Method in class org.jmol.console.JmolConsole
getScriptEditor() - Method in class org.jmol.consolejs.AppletConsole
getScriptForCallback(SC, String, String) - Method in class jspecview.popup.JSVGenericPopup
getScriptForCallback(SC, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
  Secondary processing of menu item click
getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.GenericPopup
getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.JmolPopup
getScriptItem(boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
getScriptItem(boolean, boolean) - Method in class org.jmol.script.ScriptManager
getScriptQueue() - Method in interface jspecview.api.JSVAppInterface
getScriptQueue() - Method in class jspecview.app.JSVApp
getScriptQueue() - Method in interface org.jmol.api.JmolScriptManager
getScriptQueue() - Method in class org.jmol.script.ScriptManager
getScriptQueueInfo() - Method in class org.jmol.viewer.Viewer
getScriptToken(String) - Static method in enum class jspecview.common.ScriptToken
getScriptTokenList(String, boolean) - Static method in enum class jspecview.common.ScriptToken
getSDFDateLine(String) - Static method in class jme.JMEUtil
  See CTFile -- this line is NOT optional.
getSDFDateLine(String, boolean) - Static method in class org.jmol.viewer.PropertyManager
getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
getSelected() - Method in class org.jmol.shape.Measures
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
getSelectedAtomIterator(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
getSelectedDisplayScheme() - Method in class jspecview.application.PreferencesDialog
  Retruns the current Display Scheme
getSelectedIndex() - Method in class org.jmol.awtjs.swing.JComboBox
getSelectedIndex(Object) - Method in interface jspecview.api.PlatformDialog
getSelectedIndex(Object) - Method in class jspecview.java.AwtDialog
getSelectedIndex(Object) - Method in class jspecview.js2d.JsDialog
getSelectedIntegral() - Method in class jspecview.common.PanelData
getSelectedItem() - Method in class org.jmol.awtjs.swing.JComboBox
getSelectedItem(Object) - Method in interface jspecview.api.PlatformDialog
getSelectedItem(Object) - Method in class jspecview.java.AwtDialog
getSelectedItem(Object) - Method in class jspecview.js2d.JsDialog
getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
getSelectedPeak() - Method in class jspecview.common.Spectrum
getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
getSelectionHalosEnabled() - Method in class org.jmol.viewer.Viewer
getSelectionModel() - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
getSelectionModel() - Method in class org.jmol.awtjs.swing.JTable
getSelectorName(Object) - Method in class jspecview.dialog.DialogManager
getSeqCode(T) - Static method in class org.jmol.script.ScriptEval
getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
getSeqcodeFor(int, char) - Static method in class org.jmol.modelset.Group
getSeqcodeString() - Method in class org.jmol.modelset.Group
getSeqcodeStringFor(int) - Static method in class org.jmol.modelset.Group
getSeqID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSeqID() - Method in class org.jmol.modelset.Atom
getSeqNumberFor(int) - Static method in class org.jmol.modelset.Group
getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
getSequenceBits(String, BS, BS) - Method in class org.jmol.modelset.ModelSet
  // bio-only methods /////
getSequenceNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSequenceNumber(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getSequenceNumber(int) - Method in interface org.jmol.api.PymolAtomReader
getSerial() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getServiceCommand(String) - Static method in class org.jmol.viewer.JC
getSetAxesTypeMad10(int) - Method in class org.jmol.script.ScriptEval
getSetHistory(int) - Method in class org.jmol.api.JmolViewer
getSetHistory(int) - Method in class org.jmol.util.CommandHistory
  Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n invalid input: '<'= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
getSetHistory(int) - Method in class org.jmol.viewer.Viewer
  Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n invalid input: '<'= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
getSettableTokFromString(String) - Static method in class org.jmol.script.T
getShadeB(float, float, float) - Method in class org.jmol.util.Shader
getShadeFp8(float, float, float) - Method in class org.jmol.util.Shader
getShadeIndex(float, float, float) - Method in class org.jmol.util.Shader
getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
getShadeN(float, float, float, float) - Method in class org.jmol.util.Shader
getShades(short) - Method in class org.jmol.util.GData
getShape(int) - Method in class org.jmol.viewer.ShapeManager
getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JC
getShapeDetail() - Method in class org.jmol.shape.Echo
getShapeDetail() - Method in class org.jmol.shape.Shape
getShapeDetail() - Method in class org.jmol.shapecgo.CGO
getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
getShapeDetail() - Method in class org.jmol.shapespecial.Draw
getShapeDetail() - Method in class org.jmol.shapespecial.Polyhedra
getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
getShapeErrorState() - Method in class org.jmol.viewer.Viewer
getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
  Returns the shape type index for a shape object given the object name.
getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEval
getShapeProperty(int, String) - Method in class org.jmol.scriptext.ScriptExt
getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.script.ScriptEval
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
getShapePropertyIndex(int, String, int) - Method in class org.jmol.viewer.ShapeManager
getShapeState() - Method in class org.jmol.shape.AtomShape
getShapeState() - Method in class org.jmol.shape.FontLineShape
getShapeState() - Method in class org.jmol.shape.Frank
getShapeState() - Method in class org.jmol.shape.Shape
getShapeState() - Method in class org.jmol.shape.Sticks
getShapeState() - Method in class org.jmol.shape.TextShape
getShapeState() - Method in class org.jmol.shapebio.BioShape
getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
getShapeState() - Method in class org.jmol.shapecgo.CGO
getShapeState() - Method in class org.jmol.shapespecial.Dipole
getShapeState() - Method in class org.jmol.shapespecial.Dipoles
getShapeState() - Method in class org.jmol.shapespecial.Dots
getShapeState() - Method in class org.jmol.shapespecial.Draw
getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
getShapeState() - Method in class org.jmol.shapesurface.Isosurface
getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JC
getShowAnnotation(Annotation.AType) - Method in class jspecview.common.PanelData
getShowAxes() - Method in class org.jmol.viewer.Viewer
getShowBbcage() - Method in class org.jmol.viewer.Viewer
getShowFrank() - Method in class org.jmol.viewer.Viewer
getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
getShowSelectedOnce() - Method in class org.jmol.viewer.Viewer
getShowUnitCell() - Method in class org.jmol.viewer.Viewer
getSignature() - Method in interface org.jmol.api.JmolScriptFunction
getSignature() - Method in class org.jmol.script.ScriptFunction
getSimpleXmlReader(BufferedReader) - Method in class jspecview.source.AnIMLReader
getSimpleXmlReader(BufferedReader) - Method in class jspecview.source.NMRMLReader
getSimulationFileData(String, String) - Static method in class jspecview.common.JSVFileManager
getSimulationType(String) - Static method in class jspecview.common.JSVFileManager
getSiteMultiplicity(P3) - Method in interface org.jmol.api.SymmetryInterface
getSiteMultiplicity(P3) - Method in class org.jmol.symmetry.Symmetry
getSize(int) - Method in class org.jmol.shape.AtomShape
getSize(int) - Method in class org.jmol.shape.Shape
  overridden in Dots, CGOMesh, and AtomShape
getSize(int) - Method in class org.jmol.shapespecial.Dots
getSize(int, boolean) - Static method in class org.jmol.shapecgo.CGOMesh
getSizeG(Group) - Method in class org.jmol.shape.Shape
getSizeG(Group) - Method in class org.jmol.shapebio.BioShapeCollection
getSlabColor() - Method in class org.jmol.util.MeshSurface
getSlabObjectType(int, Object, boolean, Object) - Static method in class org.jmol.util.TempArray
getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
getSlabType() - Method in class org.jmol.util.MeshSurface
getSlabWithinRange(float, float) - Static method in class org.jmol.util.TempArray
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.AdfReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.AmsReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.DgridReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaters() - Method in class org.jmol.adapter.readers.quantum.AdfReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.AmsReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.CsfReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.DgridReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
getSlaters() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
getSmartsMap(String, BS, int) - Method in class org.jmol.viewer.Viewer
getSmartsMatch(String, BS) - Method in class org.jmol.api.JmolViewer
getSmartsMatch(String, BS) - Method in class org.jmol.viewer.Viewer
getSmartsMatchForNodes(String, Node[]) - Method in class org.jmol.viewer.Viewer
getSmiles(BS) - Method in class org.jmol.api.JmolViewer
getSmiles(BS) - Method in class org.jmol.viewer.Viewer
  NOT getting aromatic smiles
getSmiles(Node[], int, BS, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getSmiles(Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesMatcher
  internal to Jmol -- called by org.jmol.Viewer.getSmiles
getSmiles(Viewer, String) - Method in class org.jmol.inchi.InchiJmol
getSmilesAtoms(String) - Method in class org.jmol.viewer.Viewer
getSmilesChiralityArray() - Method in class org.jmol.symmetry.CIPDataSmiles
getSmilesCorrelation(BS, BS, String, Lst, Lst, M4, Lst, boolean, int[][], P3, boolean, int) - Method in class org.jmol.scriptext.SmilesExt
  The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
getSmilesExt() - Method in class org.jmol.script.ScriptEval
getSmilesFromJME(String) - Method in interface org.jmol.api.SmilesMatcherInterface
getSmilesFromJME(String) - Method in class org.jmol.smiles.SmilesMatcher
getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
getSmilesMatches(Object, Object, BS, BS, int, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
getSmilesOpt(BS, int, int, int, String) - Method in class org.jmol.viewer.Viewer
  returns the SMILES string for a sequence or atom set does not include attached protons on groups
getSolnColour() - Method in interface jspecview.api.JSVAppletInterface
  Returns the calculated colour of a visible spectrum (Transmittance)
getSolnColour() - Method in class jspecview.app.JSVApp
  Returns the calculated colour of a visible spectrum (Transmittance)
getSolnColour() - Method in class jspecview.appletjs.JSVApplet
getSolutionColor(boolean) - Method in class jspecview.common.JSViewer
GETSOLUTIONCOLOR - Enum constant in enum class jspecview.common.ScriptToken
getSolutionColorStr(boolean) - Method in class jspecview.common.JSViewer
getSortingStatus(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
getSource(String, BufferedReader) - Method in interface jspecview.api.SourceReader
getSource(String, BufferedReader) - Method in class jspecview.source.AnIMLReader
getSource(String, BufferedReader) - Method in class jspecview.source.NMRMLReader
getSourceID() - Method in class jspecview.common.PanelData
getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupClegId() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupClegId() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupInfoObj(String, Object, boolean, boolean) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupInfoObj(String, Object, boolean, boolean) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupJmolId() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupJmolId() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupJSON(String, String, int) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupJSON(String, String, int) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupOperationCode(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupTitle() - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
getSpaceGroupXyzOriginal(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupXyzOriginal(int, boolean) - Method in class org.jmol.symmetry.Symmetry
getSpecFreq(String, double) - Static method in class jspecview.source.JDXDataObject
getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
getSpecialGroupName(int) - Static method in class org.jmol.symmetry.SpaceGroup
getSpecialLabel(String, String) - Method in class org.jmol.popup.JmolPopup
  menus or menu items with SPECIAL in their name are sent here for on-the-fly labeling
getSpecialPrefix() - Method in class org.jmol.symmetry.SpaceGroup
getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
getSpectra() - Method in class jspecview.source.JDXSource
  Returns the Vector of Spectra
getSpectraAsArray() - Method in class jspecview.source.JDXSource
  Used in Android
getSpectrum() - Method in interface jspecview.api.AnnotationData
getSpectrum() - Method in class jspecview.common.Measurement
getSpectrum() - Method in class jspecview.common.MeasurementData
getSpectrum() - Method in class jspecview.common.PanelData
getSpectrum() - Method in class jspecview.common.PanelNode
getSpectrum() - Method in class jspecview.dialog.JSVDialog
getSpectrumAt(int) - Method in class jspecview.common.PanelData
getSpectrumListAsString(Lst) - Static method in class jspecview.common.PanelNode
getSpecular() - Method in class org.jmol.util.GData
getSpecularExponent() - Method in class org.jmol.util.GData
getSpecularPercent() - Method in class org.jmol.util.GData
getSpecularPower() - Method in class org.jmol.util.GData
getSpeedLevel() - Method in class com.sparshui.common.messages.events.FlickEvent
getSPF(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlReader
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getSphereData(int) - Static method in class org.jmol.util.MeshSurface
  Calculates the data (faces, vertices, normals) for a sphere.
getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
getSpin(int) - Method in class org.jmol.modelset.ModelSet
getSpinIndex(int) - Method in interface org.jmol.api.SymmetryInterface
getSpinIndex(int) - Method in class org.jmol.symmetry.Symmetry
getSpinOp(int) - Method in interface org.jmol.api.SymmetryInterface
getSpinOp(int) - Method in class org.jmol.symmetry.Symmetry
getSpinState() - Method in class org.jmol.viewer.Viewer
getSpinString(M34, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
  allows for 3x3 rotation-only matrix;
getSpinSym() - Method in interface org.jmol.api.SymmetryInterface
getSpinSym() - Method in class org.jmol.symmetry.Symmetry
getSplitFrameAtoms(boolean) - Method in class org.jmol.viewer.AnimationManager
getSplitFrameModel() - Method in class org.jmol.viewer.AnimationManager
getSplitFrameModels() - Method in class org.jmol.viewer.AnimationManager
getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
getStartChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
getStartChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStartingPointIndex(int) - Method in class jspecview.common.PanelData
getStartingPointIndex(int) - Method in class jspecview.common.ViewData
  in some cases, there is only one scaleData, but there are more than that number of spectra this is no problem -- we just use mod to set this to 0
getStartInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
getStartInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
getState() - Method in class com.sparshui.common.messages.events.TouchEvent
getState() - Method in class com.sparshui.server.GestureServer
getState() - Method in class com.sparshui.server.TouchPoint
  Get the touch point state.
getState() - Method in interface jspecview.api.AnnotationData
getState() - Method in class jspecview.common.MeasurementData
getState() - Method in class jspecview.dialog.JSVDialog
getState() - Method in interface org.jmol.api.JmolGestureServerInterface
getState() - Method in interface org.jmol.api.JmolModulationSet
getState() - Method in class org.jmol.modelset.Trajectory
getState() - Method in class org.jmol.util.ModulationSet
getState(String) - Method in class org.jmol.shape.Mesh
getState(SB) - Method in interface org.jmol.api.JmolNMRInterface
getState(SB) - Method in class org.jmol.quantum.NMRCalculation
getState(ModelSet, int, SB) - Method in interface org.jmol.api.SymmetryInterface
getState(ModelSet, int, SB) - Method in class org.jmol.symmetry.Symmetry
getStateCreator() - Method in class org.jmol.viewer.Viewer
getStateInfo() - Method in class org.jmol.api.JmolViewer
getStateInfo() - Method in class org.jmol.viewer.Viewer
getStateInfo3(String, int, int) - Method in class org.jmol.viewer.Viewer
getStateText() - Method in class org.jmol.modelset.Text
getStaticGraphics(Object, boolean) - Method in class jspecview.java.AwtPlatform
getStaticGraphics(Object, boolean) - Method in class jspecview.js2d.JsPlatform
getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.GenericPlatform
getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs.Platform
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs2d.Platform
getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
getStereo() - Method in class org.jmol.smiles.SmilesAtom
getStereoAtAt(SimpleNode[]) - Method in class org.jmol.smiles.SmilesAtom
getStereoMode(String) - Static method in enum class org.jmol.c.STER
getStereoType() - Method in interface org.iupac.InChIStructureProvider
getStereoType() - Method in class org.jmol.inchi.InChIJNA
getStereoType() - Method in class org.jmol.inchi.InChIJS
getStrandCount() - Method in class org.jmol.adapter.smarter.StructureIterator
getStrandCount() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStrandCount(int) - Method in class org.jmol.viewer.Viewer
getStrandID() - Method in class org.jmol.adapter.smarter.StructureIterator
getStrandID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStream() - Method in class javajs.util.Rdr.StreamReader
getStream(InputStream) - Method in class org.apache.tools.bzip2.CBZip2InputStreamFactory
  jsjava addition for reflection
getStreamAsBytes(BufferedInputStream, OC) - Static method in class javajs.util.Rdr
  Read a an entire BufferedInputStream for its bytes, and either return them or leave them in the designated output channel.
getStreamAsBytes(BufferedInputStream, OC) - Static method in class jspecview.common.JSVFileManager
getStreamAsString(InputStream) - Static method in class javajs.util.ZipTools
getString() - Method in class org.jmol.modelset.Measurement
getString(Map, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getStringArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
  Retrieve a String array, possibly unpacking it if it is run-length encoded.
getStringDetail() - Method in class org.jmol.modelset.Measurement
getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getStringX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getStringX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
getStringX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getStrucNo() - Method in class org.jmol.modelset.Group
getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
getStructure() - Method in class org.jmol.modelset.Group
getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getStructuredModels() - Method in class org.jmol.adapter.smarter.StructureIterator
getStructuredModels() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStructureId() - Method in class org.jmol.modelset.Group
getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
getStructureId() - Method in class org.jmol.modelsetbio.Monomer
getStructureID() - Method in class org.jmol.adapter.smarter.StructureIterator
getStructureID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
  Get a StructureIterator.
getStructureList() - Method in class org.jmol.modelset.ModelSet
getStructureList() - Method in class org.jmol.viewer.GlobalSettings
getStructureList() - Method in class org.jmol.viewer.Viewer
getStructureMap(Lst, String, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
  Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
getStructures(String, String, Lst) - Method in class org.jmol.adapter.readers.quantum.NBOParser
  Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
getStructures46(String[], String, Lst, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
  Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
getStructureState() - Method in class org.jmol.viewer.Viewer
getStructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
getStructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.BackboneRenderer
  Get strut point for trace, rocket, strand
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.CartoonRenderer
  Get strut point for trace, rocket, strand
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.MeshRibbonRenderer
  Get strut point for trace, rocket, strand
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.RibbonsRenderer
  Get strut point for trace, rocket, strand
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.RocketsRenderer
  Get strut point for trace, rocket, strand
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.StrandsRenderer
  Get strut point for trace, rocket, strand
getStrutPointIfNeeded(Atom) - Method in class org.jmol.renderbio.TraceRenderer
  Get strut point for trace, rocket, strand
getStuctureAsText(String, String[][], String[][]) - Method in class org.jmol.popup.PopupResource
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Component
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Container
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.JSplitPane
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Component
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Container
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.JSplitPane
getSubgroupJSON(String, String, int, int, int, Map, Lst) - Method in interface org.jmol.api.SymmetryInterface
getSubgroupJSON(String, String, int, int, int, Map, Lst) - Method in class org.jmol.symmetry.Symmetry
  Retrieve subgroup information for a space group.
getSubIndex() - Method in class jspecview.common.Spectrum
getSubIndex() - Method in class jspecview.common.SubSpecChangeEvent
getSubmatrix(int, int, int, int) - Method in class javajs.util.Matrix
  Get a submatrix.
getSubSpectra() - Method in class jspecview.common.Spectrum
getSubstructureSet(Object, Object, int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getSubstructureSet(Object, Object, int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  Returns a bitset matching the pattern within a set of Jmol atoms.
getSubstructureSetArray(Object, BS, int) - Method in class org.jmol.viewer.Viewer
getSubstructureSetArray(Object, Node[], int, BS, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getSubstructureSetArray(Object, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  Returns a vector of bitsets indicating which atoms match the pattern.
getSubstructureSetArrayForNodes(Object, Node[], int) - Method in class org.jmol.viewer.Viewer
getSubstructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
getSubstructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
getSubSystemUnitCell() - Method in interface org.jmol.api.JmolModulationSet
getSubSystemUnitCell() - Method in class org.jmol.util.ModulationSet
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
  getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
  ////////// VertexDataServer interface methods ////////////////
getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
getSUVW() - Method in class org.jmol.symmetry.SymmetryOperation
getSwingComponent(Object) - Method in class org.jmol.awt.AwtPopupHelper
getSwingComponent(Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
getSwingComponent(Object) - Method in interface org.jmol.popup.PopupHelper
getSym(int) - Method in class org.jmol.modelkit.ModelKit
getSymEditState() - Method in class org.jmol.modelkit.ModelKit
getSymMatrices(int) - Method in class org.jmol.modelset.ModelSet
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
getSymmetry() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSymmetry(Viewer, String) - Static method in class org.jmol.api.Interface
getSymmetryEquivAtoms(BS, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
  Return a bitset of equivalent atoms
getSymmetryEquivAtomsForAtom(int, BS, BS, BS) - Method in class org.jmol.modelset.ModelSet
  Set a bitset of the equivalent atoms of an atom.
getSymmetryEquivPointList(Lst, String) - Method in class org.jmol.viewer.Viewer
getSymmetryEquivPoints(Point3fi, String) - Method in class org.jmol.viewer.Viewer
getSymmetryFromCode(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
getSymmetryFromCode(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getSymmetryInfo(int, String, int, P3, P3, P3, int, String, float, int, int, int[]) - Method in class org.jmol.viewer.Viewer
  A general method for retrieving symmetry information with full capability of the symop() scripting function.
getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelSet
getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int, int[]) - Method in interface org.jmol.api.SymmetryInterface
getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int, int[]) - Method in class org.jmol.symmetry.Symmetry
getSymmetryInfoStr() - Method in interface org.jmol.api.SymmetryInterface
getSymmetryInfoStr() - Method in class org.jmol.symmetry.Symmetry
  When information is desired about the space group, we use SymmetryInfo.
getSymmetryInvariant(int) - Method in class org.jmol.modelset.ModelSet
getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
  Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
getSymopList(boolean) - Method in interface org.jmol.api.SymmetryInterface
getSymopList(boolean) - Method in class org.jmol.symmetry.Symmetry
getSymopText() - Method in class org.jmol.modelkit.ModelKit
getSymStatic() - Method in class org.jmol.viewer.Viewer
  Retrieve the static Symmetry object, which should be used only statically
getSymTemp() - Method in class org.jmol.viewer.Viewer
  Retrieve a new Symmetry object.
getSymViewState() - Method in class org.jmol.modelkit.ModelKit
getSyncMode() - Method in class org.jmol.viewer.StatusManager
getTableHeader() - Method in class org.openscience.jmol.app.janocchio.TableSorter
getTableModel() - Method in class org.openscience.jmol.app.janocchio.TableSorter
getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
getTagName() - Method in class jspecview.source.XMLParser
getTagName(String) - Static method in class jspecview.common.JSVFileManager
  Returns a name that can be used as a tag, possibly abbreviated.
getTagType() - Method in class jspecview.source.XMLParser
getTaintedAtoms(int) - Method in class org.jmol.modelset.AtomCollection
getTauField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
getTensor(Viewer, float[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.UnitCell
getTensorInfo(String, String, BS) - Method in interface org.jmol.api.JmolNMRInterface
getTensorInfo(String, String, BS) - Method in class org.jmol.quantum.NMRCalculation
getTensors() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getTensors() - Method in class org.jmol.modelset.Atom
getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
getText() - Method in interface org.jmol.api.js.GenericConsoleTextArea
getText() - Method in interface org.jmol.api.SC
getText() - Method in class org.jmol.awt.AwtSwingComponent
getText() - Method in class org.jmol.awtjs.swing.Component
getText() - Method in class org.jmol.console.GenericConsole
getText() - Method in interface org.jmol.console.GenericTextArea
getText() - Method in class org.jmol.console.ScriptEditor
getText() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
getText(Object) - Method in interface jspecview.api.PlatformDialog
getText(Object) - Method in class jspecview.java.AwtDialog
getText(Object) - Method in class jspecview.js2d.JsDialog
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class jspecview.java.AwtPlatform
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class jspecview.js2d.JsPlatform
getTextPixels(String, Font, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
getTextPosition() - Method in class org.jmol.util.GData
getTFToggle(String) - Static method in class jspecview.common.Parameters
getThermalRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoid
getTheta() - Method in class javajs.util.Quat
getThetaDirected(P4) - Method in class javajs.util.Quat
getThetaDirectedV(V3) - Method in class javajs.util.Quat
getThetaRadians() - Method in class javajs.util.Quat
getThisContext() - Method in interface org.jmol.api.JmolScriptEvaluator
getThisContext() - Method in class org.jmol.script.ScriptEval
getThisModelAtoms() - Method in class org.jmol.viewer.Viewer
getThread() - Method in class org.jmol.minimize.Minimizer
getThresh() - Method in class jspecview.common.PeakData
getTime() - Method in class com.sparshui.common.messages.events.DragEvent
getTime() - Method in class com.sparshui.common.messages.events.RotateEvent
getTime() - Method in class com.sparshui.common.messages.events.TouchEvent
getTime() - Method in class com.sparshui.common.messages.events.ZoomEvent
getTime() - Method in class com.sparshui.server.TouchPoint
getTime() - Method in class jspecview.source.JDXHeader
  Getter for property time.
getTimerMsg(String, int) - Static method in class org.jmol.util.Logger
getTip() - Method in enum class jspecview.common.ScriptToken
getTitle() - Method in interface jspecview.api.JSVViewPanel
getTitle() - Method in class jspecview.common.PanelData
  Returns the title displayed on the graph
getTitle() - Method in class jspecview.common.PeakInfo
getTitle() - Method in class jspecview.java.AwtMainPanel
getTitle() - Method in class jspecview.java.AwtPanel
getTitle() - Method in class jspecview.js2d.JsMainPanel
getTitle() - Method in class jspecview.js2d.JsPanel
getTitle() - Method in class jspecview.source.JDXHeader
  Getter for property title.
getTitleLabel() - Method in class jspecview.common.Spectrum
gettMixField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
getTok() - Method in interface org.jmol.api.JmolScriptFunction
getTok() - Method in class org.jmol.script.ScriptFunction
getToken(int) - Method in class org.jmol.script.ScriptContext
getToken(int) - Method in class org.jmol.script.ScriptParam
getToken(int) - Method in class org.jmol.scriptext.ScriptExt
getTokenCount() - Method in class org.jmol.script.ScriptContext
getTokenFromName(String) - Static method in class org.jmol.script.T
getTokenPeeked() - Method in interface javajs.api.GenericCifDataParser
getTokenPeeked() - Method in class javajs.util.CifDataParser
getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getTokens() - Method in class org.jmol.jvxl.readers.JvxlReader
getTokens() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getTokens() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getTokens(String) - Static method in class javajs.util.PT
getTokens(String) - Static method in enum class jspecview.common.ScriptToken
  read a string for possibly quoted tokens separated by space until // or # is reached.
getTokensAt(String, int) - Static method in class javajs.util.PT
getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getTokensLike(String) - Static method in class org.jmol.script.T
getTokensType(Map, int) - Static method in class org.jmol.script.T
getTokFromName(String) - Static method in class org.jmol.script.T
getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
getTopPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
getTorsionAngleRadians(double[], double[], double[], double[], V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
getTorsions(boolean) - Method in class org.jmol.minimize.Minimizer
getTotalHydrogenCount() - Method in class org.jmol.modelset.Atom
getTotalHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getTotalHydrogenCount() - Method in interface org.jmol.util.Node
getTotalValence() - Method in class org.jmol.modelset.Atom
getTotalValence() - Method in class org.jmol.smiles.SmilesAtom
getTotalValence() - Method in interface org.jmol.util.Node
getTouchID() - Method in class com.sparshui.common.messages.events.TouchEvent
getTrajectoryState() - Method in class org.jmol.viewer.Viewer
getTransferData(DataFlavor) - Method in class jspecview.java.AwtClipboard
getTransferData(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
getTransferDataFlavors() - Method in class jspecview.java.AwtClipboard
getTransferDataFlavors() - Method in class org.jmol.awt.AwtClipboard
getTransform(P3, P3, boolean) - Method in interface org.jmol.api.SymmetryInterface
getTransform(P3, P3, boolean) - Method in class org.jmol.symmetry.Symmetry
getTransform(UnitCell, SymmetryOperation[], P3, P3, boolean) - Method in class org.jmol.symmetry.SymmetryDesc
getTransformABC(M4, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
  This method properly transposes the matrix for ABC format, converting columns to rows before passing the information to getXYZFromMatrixFrac(...,"ABC").
getTransformABCd(M4, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getTransformedVertexVectors() - Method in class org.jmol.util.GData
getTransformMatrix4(Lst, Lst, M4, P3) - Static method in class javajs.util.Measure
  Fills a 4x4 matrix with rotation-translation of mapped points A to B.
getTransformMatrix4(Lst, Lst, M4, P3) - Static method in class org.jmol.script.ScriptParam
  Fills a 4x4 matrix with rotation-translation of mapped points A to B.
getTransformUVW(M4) - Static method in class org.jmol.symmetry.SymmetryOperation
getTransformXYZ(M4) - Static method in class org.jmol.symmetry.SymmetryOperation
getTranslation() - Method in class javajs.util.Matrix
getTranslation(int) - Method in class org.jmol.modelset.ModelSet
getTranslation(T3) - Method in class javajs.util.M4
  Retrieves the translational components of this matrix.
getTranslationScript() - Method in class org.jmol.viewer.TransformManager
getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEval
getTreeNode() - Method in class jspecview.common.PanelNode
getTriad(T3) - Method in class org.jmol.export.___Exporter
getTriad(T3) - Method in class org.jmol.export._PovrayExporter
getTriadC(T3) - Method in class org.jmol.export.___Exporter
getTriangulator() - Method in class org.jmol.viewer.Viewer
getTrueAtomCount() - Method in class org.jmol.modelset.Model
  not actually accessed -- just pointing out what it is
getType() - Method in class javajs.util.OC
getType() - Method in class jspecview.common.PeakInfo
getType() - Method in interface org.jmol.api.JmolDialogInterface
getType() - Method in class org.jmol.dialog.Dialog
getType() - Method in class org.jmol.modelsetbio.BioPolymer
getType(int) - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
getType(String) - Static method in enum class jspecview.common.ExportType
getType(Atom) - Static method in enum class org.jmol.c.HB
getTypeLabel() - Method in class jspecview.source.JDXDataObject
getUndoInfo() - Method in class org.jmol.viewer.StateManager
getUndoMax() - Method in class org.jmol.viewer.StateManager
getUndoRedoState(int) - Method in class org.jmol.viewer.StateManager
getUnGzippedInputStream(byte[]) - Method in interface javajs.api.GenericZipTools
getUnGzippedInputStream(byte[]) - Method in class javajs.util.ZipTools
getUniqueID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
getUniqueID(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  PymolAtomReader interface
getUniqueID(int) - Method in interface org.jmol.api.PymolAtomReader
getUniqueTensorSet(BS) - Method in interface org.jmol.api.JmolNMRInterface
  An attempt to find unique atoms using tensors.
getUniqueTensorSet(BS) - Method in class org.jmol.quantum.NMRCalculation
getUnitCell() - Method in class org.jmol.shape.Mesh
getUnitCell() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getUnitCell(int) - Method in class org.jmol.modelset.ModelSet
getUnitCell(T3[], boolean, String) - Method in interface org.jmol.api.SymmetryInterface
getUnitCell(T3[], boolean, String) - Method in class org.jmol.symmetry.Symmetry
getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
getUnitCellAtomIndex() - Method in class org.jmol.viewer.AnimationManager
getUnitCellAtomIndex() - Method in class org.jmol.viewer.Viewer
getUnitCellCenter() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellCenter() - Method in class org.jmol.symmetry.Symmetry
getUnitCellCenter() - Method in class org.jmol.viewer.Viewer
getUnitCellDisplayName() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellDisplayName() - Method in class org.jmol.symmetry.Symmetry
getUnitCellForAtom(int) - Method in class org.jmol.modelset.ModelSet
getUnitCellInfo(boolean) - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfo(boolean) - Method in class org.jmol.symmetry.Symmetry
getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
getUnitCellInfoMap() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfoMap() - Method in class org.jmol.symmetry.Symmetry
getUnitCellInfoStr(String) - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfoStr(String) - Method in class org.jmol.symmetry.Symmetry
getUnitCellInfoStr(String) - Method in class org.jmol.viewer.Viewer
getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
getUnitCellInfoType(int) - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfoType(int) - Method in class org.jmol.symmetry.Symmetry
getUnitCellMultiplied() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellMultiplied() - Method in class org.jmol.symmetry.Symmetry
  Note, this has no origin shift.
getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
getUnitCellParams() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellParams() - Method in class org.jmol.symmetry.Symmetry
getUnitCellParams() - Method in class org.jmol.util.SimpleUnitCell
getUnitCellPointsWithin(float, BS, P3, boolean) - Method in class org.jmol.modelset.ModelSet
getUnitCellState() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellState() - Method in class org.jmol.modelkit.ModelKit
getUnitCellState() - Method in class org.jmol.symmetry.Symmetry
getUnitCellVectors() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellVectors() - Method in class org.jmol.symmetry.Symmetry
getUnitCellVerticesNoOffset() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellVerticesNoOffset() - Method in class org.jmol.symmetry.Symmetry
getUnitConversion(String, String) - Static method in class org.qcschema.QCSchemaUnits
  Calculate the unit conversion between two units, using a static unit-to-unit cache for efficiency.
getUnitID(int) - Method in class org.jmol.modelset.Atom
getUnitID(Atom, int) - Method in class org.jmol.modelsetbio.BioModel
  Get a unitID.
getUnitIDFlags(String) - Static method in class org.jmol.viewer.JC
  Get a unitID type
getUnitsJSON(String, boolean) - Static method in class org.qcschema.QCSchemaUnits
  Get the [name, toAU] JSON code or just a new String[] {name, toAU}.
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class jspecview.java.AwtPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
getUnlikely() - Static method in class javajs.util.P3
getUnzippedInputStream(GenericZipTools, BufferedInputStream) - Static method in class javajs.util.Rdr
  Drill down into a GZIP stack until no more layers.
getUnzippedInputStreamBZip2(GenericZipTools, BufferedInputStream) - Static method in class javajs.util.Rdr
getUnzippedReaderOrStreamFromName(String, Object, boolean, boolean, boolean, boolean, Map) - Method in class org.jmol.viewer.FileManager
getURLContents(URL, byte[], String, boolean) - Method in class jspecview.java.AwtPlatform
getURLContents(URL, byte[], String, boolean) - Method in class jspecview.js2d.JsPlatform
getURLContents(URL, byte[], String, boolean) - Method in interface org.jmol.api.GenericPlatform
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awt.Platform
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awtjs2d.Platform
getURLContentsStatic(URL, byte[], String, boolean) - Static method in class org.jmol.awtjs2d.Platform
  In case this needs to be performed directly, without interface
getUrlFromDialog(String, String) - Method in interface jspecview.api.JSVFileHelper
getUrlFromDialog(String, String) - Method in class jspecview.java.AwtFileHelper
getUrlFromDialog(String, String) - Method in class jspecview.js2d.JsFileHelper
getUserDirectory() - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
  Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserFunctionResult(String, Lst, SV) - Method in class org.jmol.script.ScriptEval
getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
  / atom coordinate and property changing //////////
getUserYFactor() - Method in class jspecview.common.Spectrum
getUtil(String, Viewer, String) - Static method in class org.jmol.api.Interface
getUVWMatrix(boolean) - Method in class org.jmol.modelset.Model
getV0abc(int, Object) - Method in class org.jmol.viewer.Viewer
  Convert string abc;offset or M3d or M4d to origin and three vectors -- a, b, c.
getV0abc(Object, M4) - Method in interface org.jmol.api.SymmetryInterface
getV0abc(Object, M4) - Method in class org.jmol.symmetry.Symmetry
getV3() - Method in interface org.jmol.api.JmolModulationSet
getV3() - Method in class org.jmol.util.ModulationSet
getValence() - Method in class org.jmol.modelset.Atom
  return the total bond order for this atom
getValence() - Method in class org.jmol.modelset.Bond
getValence() - Method in class org.jmol.smiles.SmilesAtom
getValence() - Method in class org.jmol.smiles.SmilesBond
getValence() - Method in interface org.jmol.util.Node
getValence() - Method in interface org.jmol.util.SimpleNode
getValidValues(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getValidVertices(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getValue() - Method in class jspecview.common.Measurement
getValue() - Method in class jspecview.source.JDXSourceStreamTokenizer
getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
  for readers only
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
getValue(String, String) - Method in class org.jmol.util.GenericApplet
getValue(ScriptToken, ScriptTokenizer, String) - Static method in enum class jspecview.common.ScriptToken
  tweak command options depending upon special cases
getValue2(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getValueArray(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
getValueAt(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
getValueAtPoint(P3) - Method in class org.jmol.quantum.MepCalculation
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
getValues(Mesh) - Method in class org.jmol.shape.MeshCollection
getValues(Mesh) - Method in class org.jmol.shapesurface.Isosurface
getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
getVanderwaalsMar(int, VDW) - Static method in class org.jmol.util.Elements
getVanderwaalsMarType(int, VDW) - Method in class org.jmol.viewer.Viewer
getVanderwaalsRadiusFloat(Viewer, VDW) - Method in class org.jmol.modelset.Atom
getVariable(Object) - Static method in class org.jmol.script.SV
getVariable(String) - Method in class org.jmol.script.ScriptContext
  Context variables go up the stack until a function is found.
getVariableAD(double[]) - Static method in class org.jmol.script.SV
getVariableList() - Method in class org.jmol.viewer.GlobalSettings
getVariableList(Map, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
getVariableList(Lst) - Static method in class org.jmol.script.SV
getVariableMap(Map) - Static method in class org.jmol.script.SV
getVarList(String) - Static method in class jspecview.source.JDXReader
getVarParameter(String, boolean) - Method in class org.jmol.script.ScriptParam
getVDW(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getVDW(int) - Method in interface org.jmol.api.PymolAtomReader
getVdwLabel() - Method in enum class org.jmol.c.VDW
getVdwType(String) - Static method in enum class org.jmol.c.VDW
getVdwType2(String) - Static method in enum class org.jmol.c.VDW
getVector(int) - Method in class javajs.util.Quat
getVector(Location) - Method in class com.sparshui.common.Location
getVectorScaled(int, float) - Method in class javajs.util.Quat
getVersion() - Method in class javajs.util.CifDataParser
getVersion() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
getVersion() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
getVersion() - Method in interface org.openscience.jmol.app.JmolPlugin
getVertexColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getVertexCount(int) - Static method in class org.jmol.util.Geodesic
getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
getVertexVector(int) - Static method in class org.jmol.util.Geodesic
getVertexVectors() - Static method in class org.jmol.util.Geodesic
getVertexVectors() - Static method in class org.jmol.util.Normix
getVertices() - Method in class org.jmol.util.MeshSurface
getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
getVertices(Mesh) - Method in class org.jmol.shapesurface.Isosurface
getVerticesFromOABC(T3[]) - Static method in class org.jmol.util.BoxInfo
getVib() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getVib(char) - Method in class org.jmol.modelset.Atom
getVibCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
  also handles modulation info
getVibration(boolean) - Method in interface org.jmol.api.JmolModulationSet
getVibration(boolean) - Method in class org.jmol.util.ModulationSet
getVibration(int, boolean) - Method in class org.jmol.modelset.AtomCollection
getVibrationPoint(Vibration, T3, float) - Method in class org.jmol.viewer.TransformManager
  return
getVibrationVector() - Method in class org.jmol.modelset.Atom
getView() - Method in class jspecview.common.PanelData
getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
getViewpoint() - Method in class org.jmol.export._VrmlExporter
getVisibleFrameAtomsNoSplitData() - Method in class org.jmol.viewer.Viewer
getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
getVisibleFramesBitSetNoJmolData() - Method in class org.jmol.viewer.Viewer
getVisibleSet(boolean) - Method in class org.jmol.modelset.AtomCollection
getVisibleVBS() - Method in class org.jmol.shape.Mesh
getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
getVisibleVertexBitSet() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
getVoxelDataAt(int) - Method in class org.jmol.jvxl.data.VolumeData
getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
getWebSite() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
getWebSite() - Method in interface org.openscience.jmol.app.JmolPlugin
getWidth() - Method in interface jspecview.api.JSVViewPanel
getWidth() - Method in class jspecview.common.JSViewer
getWidth() - Method in class jspecview.js2d.JsMainPanel
getWidth() - Method in class jspecview.js2d.JsPanel
getWidth() - Method in class org.jmol.awtjs.swing.Component
getWindow(Container) - Static method in class jspecview.java.AwtPlatform
getWindow(Container) - Static method in class org.jmol.awt.Platform
getWindowBorder(String) - Method in class org.openscience.jmol.app.HistoryFile
getWindowInnerDimension(String) - Method in class org.openscience.jmol.app.HistoryFile
getWindowName() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
getWindowName() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getWindowPosition(String) - Method in class org.openscience.jmol.app.HistoryFile
getWindowSize(String) - Method in class org.openscience.jmol.app.HistoryFile
getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
getWordContents() - Method in class jspecview.popup.JSVPopupResourceBundle
getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
getWordContents() - Method in class org.jmol.popup.PopupResource
getWrappedStateScript() - Method in class org.jmol.viewer.Viewer
getWyckoffPosition(boolean) - Method in class org.jmol.modelset.Atom
getWyckoffPosition(P3, String) - Method in interface org.jmol.api.SymmetryInterface
getWyckoffPosition(P3, String) - Method in class org.jmol.symmetry.Symmetry
getX() - Method in class com.sparshui.common.Location
getX() - Method in class com.sparshui.common.messages.events.RotateEvent
getX() - Method in class com.sparshui.common.messages.events.TouchEvent
getX() - Method in class com.sparshui.common.messages.events.ZoomEvent
getX() - Method in class jspecview.common.PeakInfo
getX() - Method in interface org.iupac.InChIStructureProvider
getX() - Method in class org.jmol.inchi.InChIJNA
getX() - Method in class org.jmol.inchi.InChIJS
getX() - Method in class org.jmol.script.ScriptMathProcessor
getX(int) - Method in class jme.JMEmol
getXdirection() - Method in class com.sparshui.common.messages.events.FlickEvent
getXFactor() - Method in class jspecview.source.JDXDataObject
  Returns the original x factor
getXMax() - Method in class jspecview.common.PeakInfo
getXMin() - Method in class jspecview.common.PeakInfo
getXML(BufferedReader) - Method in class jspecview.source.AnIMLReader
getXML(BufferedReader) - Method in class jspecview.source.NMRMLReader
getXmlAttrib(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
getXmlData(String, String, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
getXmlDataLF(String, String, boolean, boolean, boolean, int[]) - Method in class org.jmol.jvxl.readers.XmlReader
getXmlPoint(String, String) - Method in class org.jmol.jvxl.readers.XmlReader
getXOffset(int) - Static method in class org.jmol.viewer.JC
  X offset in pixels.
getXPixel() - Method in class jspecview.common.PeakInfo
getXSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getXTok() - Method in class org.jmol.script.ScriptMathProcessor
getXUnits() - Method in class jspecview.source.JDXDataObject
  Returns the units for x-axis when spectrum is displayed
getXVal() - Method in class jspecview.common.Coordinate
  Returns the x value of the coordinate
getXVal2() - Method in class jspecview.common.Measurement
getXYCoords() - Method in class jspecview.common.IntegralData
getXYCoords() - Method in class jspecview.common.Spectrum
  Returns the array of coordinates
getXyz(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
getXYZ() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getXYZ() - Method in class org.jmol.modelset.Atom
getXYZ() - Method in class org.jmol.smiles.SmilesAtom
getXYZ() - Method in interface org.jmol.util.Node
getXYZ() - Method in interface org.jmol.util.SimpleNode
getXYZFromMatrix(M4, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getXYZFromRsVs(Matrix, Matrix, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getxyzTrans(T3) - Method in class org.jmol.symmetry.SymmetryOperation
getY() - Method in class com.sparshui.common.Location
getY() - Method in class com.sparshui.common.messages.events.RotateEvent
getY() - Method in class com.sparshui.common.messages.events.TouchEvent
getY() - Method in class com.sparshui.common.messages.events.ZoomEvent
getY() - Method in interface org.iupac.InChIStructureProvider
getY() - Method in class org.jmol.inchi.InChIJNA
getY() - Method in class org.jmol.inchi.InChIJS
getY(int) - Method in class jme.JMEmol
getY2D() - Method in class jspecview.source.JDXDataObject
getY2DPPM() - Method in class jspecview.source.JDXDataObject
getYdirection() - Method in class com.sparshui.common.messages.events.FlickEvent
getYellowField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
getYellowField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
getYellowValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
getYellowValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
getYFactor() - Method in class jspecview.source.JDXDataObject
  Returns the original y factor
getYMax() - Method in class jspecview.common.PeakInfo
getYMin() - Method in class jspecview.common.PeakInfo
getYOffset(int) - Static method in class org.jmol.viewer.JC
  Y offset in pixels; negative of this is the actual screen offset
getYRef() - Method in class jspecview.source.JDXDataObject
getYUnits() - Method in class jspecview.source.JDXDataObject
  Returns the units for y-axis when spectrum is displayed
getYVal() - Method in class jspecview.common.Coordinate
  Returns the y value of the coordinate
getYVal2() - Method in class jspecview.common.Measurement
getYValueAt(double) - Method in class jspecview.common.Spectrum
getYValueAt(Coordinate[], double) - Static method in class jspecview.common.Coordinate
getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
getZ() - Method in interface org.iupac.InChIStructureProvider
getZ() - Method in class org.jmol.inchi.InChIJNA
getZ() - Method in class org.jmol.inchi.InChIJS
getZapName() - Method in class org.jmol.viewer.Viewer
getZCurrent(float, float, int) - Method in class org.jmol.g3d.PrecisionRenderer
getZipDirectory(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
getZipDirectoryAndClose(BufferedInputStream, String) - Method in interface javajs.api.GenericZipTools
getZipDirectoryAndClose(BufferedInputStream, String) - Method in class javajs.util.ZipTools
getZipDirectoryAsString(String) - Method in class org.jmol.viewer.Viewer
getZipDirectoryAsStringAndClose(BufferedInputStream) - Method in interface javajs.api.GenericZipTools
getZipDirectoryAsStringAndClose(BufferedInputStream) - Method in class javajs.util.ZipTools
getZipFileContentsAsBytes(BufferedInputStream, String[], int) - Method in interface javajs.api.GenericZipTools
getZipFileContentsAsBytes(BufferedInputStream, String[], int) - Method in class javajs.util.ZipTools
getZipFileDirectory(BufferedInputStream, String[], int, boolean) - Method in interface javajs.api.GenericZipTools
getZipFileDirectory(BufferedInputStream, String[], int, boolean) - Method in class javajs.util.ZipTools
  iteratively drills into zip files of zip files to extract file content or zip file directory.
getZipOutputStream(Object) - Method in interface javajs.api.GenericZipTools
getZipOutputStream(Object) - Method in class javajs.util.ZipTools
getZipRoot(String) - Static method in class javajs.util.Rdr
  We define a request for zip file extraction by vertical bar: zipName|interiorFileName.
getZoomSetting() - Method in class org.jmol.viewer.TransformManager
GhemicalMMReader - Class in org.jmol.adapter.readers.simple
  Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
GifEncoder - Class in javajs.img
  GifEncoder extensively adapted for Jmol by Bob Hanson Color quantization roughly follows the GIMP method "dither Floyd-Steinberg (normal)" but with some twists.
GifEncoder() - Constructor for class javajs.img.GifEncoder
gl_ambient - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
GL_LINE_LOOP - Static variable in class org.jmol.shapecgo.CGOMesh
GL_LINE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
GL_LINES - Static variable in class org.jmol.shapecgo.CGOMesh
GL_POINTS - Static variable in class org.jmol.shapecgo.CGOMesh
GL_TRIANGLE_FAN - Static variable in class org.jmol.shapecgo.CGOMesh
GL_TRIANGLE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
GL_TRIANGLES - Static variable in class org.jmol.shapecgo.CGOMesh
GLOBAL_AROMATICBONDS - Static variable in class org.jmol.viewer.JC
GLOBAL_CONECT - Static variable in class org.jmol.viewer.JC
GLOBAL_DOMAINS - Static variable in class org.jmol.viewer.JC
GLOBAL_FRACTCOORD - Static variable in class org.jmol.viewer.JC
GLOBAL_ISPDB - Static variable in class org.jmol.viewer.JC
GLOBAL_MODULATED - Static variable in class org.jmol.viewer.JC
GLOBAL_SUPERCELL - Static variable in class org.jmol.viewer.JC
GLOBAL_SYMMETRY - Static variable in class org.jmol.viewer.JC
GLOBAL_UNITCELLS - Static variable in class org.jmol.viewer.JC
GLOBAL_VALIDATIONS - Static variable in class org.jmol.viewer.JC
globalBooleans - Static variable in class org.jmol.viewer.JC
GlobalSettings - Class in org.jmol.viewer
goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
GOLD - Static variable in class org.jmol.util.C
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
gotocmd - Static variable in class org.jmol.script.T
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
gotoTop() - Method in class org.jmol.console.ScriptEditor
grabPixels(Object, int, int, int[]) - Method in class jspecview.java.AwtPlatform
grabPixels(Object, int, int, int[]) - Method in class jspecview.js2d.JsPlatform
grabPixels(Object, int, int, int[]) - Method in interface org.jmol.api.GenericPlatform
grabPixels(Object, int, int, int[]) - Method in class org.jmol.awt.Platform
grabPixels(Object, int, int, int[]) - Method in class org.jmol.awtjs2d.Platform
gradient_max_length - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gradient_min_length - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gradient_min_slope - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gradient_normal_min_dot - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gradient_spacing - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gradient_step_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
gradient_symmetry - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
Graphics3D - Class in org.jmol.g3d
  Provides high-level graphics primitives for 3D visualization for the software renderers.
Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
graphicsForMetrics - Variable in class org.jmol.util.GData
graphSets - Variable in class jspecview.common.PanelData
GRAY - Static variable in class org.jmol.util.C
GREEN - Static variable in class org.jmol.util.C
greyscalerendering - Static variable in class org.jmol.script.T
Grid - Class in org.jmol.awtjs.swing
grid_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
grid_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
grid_slot - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
GridBagConstraints - Class in org.jmol.awtjs.swing
GridBagConstraints(int, int, int, int, double, double, int, int, Insets, int, int) - Constructor for class org.jmol.awtjs.swing.GridBagConstraints
GridBagLayout - Class in org.jmol.awtjs.swing
GridBagLayout() - Constructor for class org.jmol.awtjs.swing.GridBagLayout
gridColor - Variable in class jspecview.common.PanelData
GRIDCOLOR - Enum constant in enum class jspecview.common.ScriptToken
gridheight - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gridOn - Variable in class jspecview.common.PanelData
GRIDON - Enum constant in enum class jspecview.common.ScriptToken
gridpoints - Static variable in class org.jmol.script.T
gridwidth - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gridx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gridy - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gRight - Variable in class org.jmol.util.GenericApplet
GromacsReader - Class in org.jmol.adapter.readers.more
GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PdbReader
group - Variable in class org.jmol.modelset.Atom
group - Static variable in class org.jmol.script.T
group() - Method in class org.jmol.util.PatternMatcher.JSPattern
Group - Class in com.sparshui.server
  Represents a group of touch points for the gesture server.
Group - Class in org.jmol.modelset
  The essential container for every atom.
Group() - Constructor for class org.jmol.modelset.Group
Group(int, Lst, ServerToClientProtocol) - Constructor for class com.sparshui.server.Group
  Construct a new group with the given gesture IDs and the given connection to the client.
GROUP - Enum constant in enum class org.jmol.c.PAL
group_arrow_prefix - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
group_auto_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
group_full_member_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
group1 - Variable in class org.jmol.modelset.Group
group1 - Static variable in class org.jmol.script.T
group3 - Variable in class org.jmol.adapter.smarter.Atom
group3Counts - Variable in class org.jmol.modelset.ModelLoader
group3Lists - Variable in class org.jmol.modelset.ModelLoader
group3NameCount - Static variable in class org.jmol.modelsetbio.BioResolver
group3Names - Static variable in class org.jmol.modelset.Group
groupCount - Variable in class org.jmol.modelset.Chain
groupCount - Variable in class org.jmol.modelset.Model
groupid - Static variable in class org.jmol.script.T
groupID - Variable in class org.jmol.modelset.Group
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JC
GROUPID_ARGININE - Static variable in class org.jmol.viewer.JC
  /////////////////////////////////////////////////////////////
GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JC
GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JC
GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JC
GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JC
GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JC
GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JC
GROUPID_LYSINE - Static variable in class org.jmol.viewer.JC
GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JC
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JC
GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JC
GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JC
GROUPID_WATER - Static variable in class org.jmol.viewer.JC
groupindex - Static variable in class org.jmol.script.T
groupIndex - Variable in class org.jmol.modelset.Group
groups - Variable in class org.jmol.modelset.Chain
  Groups form the essence of what a Chain is.
groups - Variable in class org.jmol.modelset.ModelLoader
groupType - Variable in class org.jmol.symmetry.SpaceGroup
growArray(double[], int) - Static method in class jme.JMEUtil
growArray(int[][], int) - Static method in class jme.JMEUtil
growArray(int[], int) - Static method in class jme.JMEUtil
growArray(String[], int) - Static method in class jme.JMEUtil
growArray(T[], int) - Static method in class jme.JMEUtil
growAtomArrays(int) - Method in class org.jmol.modelset.ModelSet
GS - Static variable in class org.jmol.quantum.QS
GT - Class in org.jmol.i18n
  The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
GT() - Constructor for class org.jmol.i18n.GT
GT(Viewer, String) - Constructor for class org.jmol.i18n.GT
guessMimeTypeForBytes(byte[]) - Static method in class javajs.util.Rdr
guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
GuiMap - Class in org.openscience.jmol.app.jmolpanel
GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
GulpReader - Class in org.jmol.adapter.readers.xtal
  Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
GWT() - Constructor for class jme.JMEUtil.GWT

## H

h_bond_cone - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_cutoff_center - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_cutoff_edge - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_exclusion - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_from_proton - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_max_angle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_power_a - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
h_bond_power_b - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
half_bonds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
HallInfo - Class in org.jmol.symmetry
  Bob Hanson 9/2006 This class could be easily adapted for other use by implementing something like M4 (4x4 matrix), P3i (integer point), and SB (stringBuilder) references: International Tables for Crystallography Vol.
HallInfo.HallReceiver - Interface in org.jmol.symmetry
  An interface to receive the decoded matrices from Hall notation.
halo - Static variable in class org.jmol.script.T
Halos - Class in org.jmol.shape
Halos() - Constructor for class org.jmol.shape.Halos
HalosRenderer - Class in org.jmol.render
HalosRenderer() - Constructor for class org.jmol.render.HalosRenderer
halt - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
haltExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
haltExecution() - Method in class org.jmol.script.ScriptEval
haltScriptExecution() - Method in class org.jmol.api.JmolViewer
haltScriptExecution() - Method in class org.jmol.viewer.Viewer
handleAssignNew(MouseState, MouseState, MeasurementPending, int, int) - Method in class org.jmol.modelkit.ModelKit
  handle a mouse-generated assignNew event
handleCoordinates(Map) - Method in interface org.jmol.adapter.readers.xml.CDXMLParser.CDXReaderI
handleCoordinates(Map) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
handleError(Throwable, boolean) - Method in class org.jmol.viewer.Viewer
handleEvent(Event) - Method in interface org.jmol.api.JmolAppletInterface
handleEvent(Event) - Method in class org.jmol.util.GenericApplet
  /////////// JmolAppletInterface //////////////
handleEvent(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
handleOutputToFile(Map, boolean) - Method in class org.jmol.viewer.OutputManagerAwt
  general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
handleOutputToFile(Map, boolean) - Method in class org.jmol.viewer.OutputManagerJS
  general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
hasConstraint(int, boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
hasContent() - Method in class org.jmol.g3d.Graphics3D
hasCurrentMeasurements(Annotation.AType) - Method in class jspecview.common.PanelData
hasDatabasePrefix(String) - Static method in class org.jmol.viewer.Viewer
hasDisplay - Variable in class jspecview.common.JSViewer
hasFileLoaded(String) - Method in class jspecview.common.PanelData
hasFocus() - Method in interface jspecview.api.JSVPanel
hasFocus() - Method in class jspecview.common.PanelData
hasFocus() - Method in class jspecview.js2d.JsPanel
hasFocus() - Method in class org.jmol.viewer.Viewer
hasFocus(Object) - Method in class jspecview.java.AwtPlatform
hasFocus(Object) - Method in class jspecview.js2d.JsPlatform
hasFocus(Object) - Method in interface org.jmol.api.GenericPlatform
hasFocus(Object) - Method in class org.jmol.awt.Platform
hasFocus(Object) - Method in class org.jmol.awtjs2d.Platform
hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
hash - Static variable in class org.jmol.script.T
hash_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
hashCode() - Method in class javajs.util.A4
  Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.BArray
hashCode() - Method in class javajs.util.BS
  Returns a hash code value for this bit set.
hashCode() - Method in class javajs.util.M3
  Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.M4
  Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T3
  Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T3d
  Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T3i
  Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T4
  Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.modelset.Atom
hashCode() - Method in class org.jmol.script.T
hashCode() - Method in class org.jmol.smiles.SmilesSearch
hasMeasure(int[]) - Method in class org.jmol.modelset.Trajectory
hasMoreElements() - Method in class jspecview.tree.SimpleTreeEnumeration
hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
  normal iterator predicate
hasMoreTokens() - Method in class jspecview.common.ScriptTokenizer
hasNext() - Method in class jspecview.source.JDXDecompressor
hasNext() - Method in class jspecview.source.XMLParser
hasNext() - Method in class org.jmol.adapter.smarter.StructureIterator
hasNext() - Method in interface org.jmol.api.AtomIndexIterator
hasNext() - Method in interface org.jmol.api.JmolAdapterAtomIterator
hasNext() - Method in class org.jmol.api.JmolAdapterBondIterator
hasNext() - Method in class org.jmol.api.JmolAdapterStructureIterator
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
hasNext() - Method in interface org.jmol.modelset.BondIterator
hasNext() - Method in class org.jmol.symmetry.UnitCellIterator
hasNext2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
hasOuputSocket() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
hasOuputSocket() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
hasPrevious() - Method in class jme.JME
hasRasmolHBonds - Variable in class org.jmol.modelset.Model
hasRingData(int) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
hasSelected - Variable in class org.jmol.viewer.Viewer
hasStructure - Variable in class org.jmol.modelsetbio.BioPolymer
hasStructure(Object, Object[], int) - Method in interface org.jmol.api.SmilesMatcherInterface
hasStructure(Object, Object[], int) - Method in class org.jmol.smiles.SmilesMatcher
  Look for pattern in each smilesSet string.
hasStructure(String, String, boolean) - Method in class org.jmol.viewer.Viewer
hasTranslucentVertices - Variable in class org.jmol.shape.Mesh
hasValues() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
hasVibration() - Method in class org.jmol.modelset.Atom
hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
hAtomRadius - Variable in class org.jmol.atomdata.AtomData
hAtoms - Variable in class org.jmol.atomdata.AtomData
have(byte[], byte) - Static method in class org.jmol.modelsetbio.Monomer
haveAccess(Viewer.ACCESS) - Method in class org.jmol.viewer.Viewer
haveAccessInternal(String) - Method in class org.jmol.viewer.Viewer
  Check for allowed access only to the designated path starting with this path.
haveAnisou - Variable in class org.jmol.adapter.smarter.AtomSetCollection
haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
haveAtropicBonds - Variable in class org.jmol.modelset.BondCollection
haveBioModels - Variable in class org.jmol.modelset.ModelSet
haveBorder - Variable in class org.openscience.jmol.app.JmolApp
haveBsDisplay - Variable in class org.jmol.render.MeshRenderer
haveChirality - Variable in class org.jmol.modelset.AtomCollection
haveCoefs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
haveCommon(BS, BS) - Static method in class org.jmol.util.BSUtil
haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
haveCustom - Variable in class org.jmol.adapter.writers.CIFWriter
haveData - Variable in class javajs.util.CifDataParser
haveDisplay - Variable in class org.jmol.viewer.Viewer
haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
haveDocumentAccess - Variable in class org.jmol.util.GenericApplet
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
haveFileSet() - Method in class org.jmol.viewer.Viewer
haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
haveJavaConsole - Variable in class org.openscience.jmol.app.JmolApp
haveJmolDataFrames - Variable in class org.jmol.modelset.ModelSet
haveKeys - Variable in class org.jmol.modelkit.ModelKit
haveMacro - Variable in class org.jmol.script.ScriptCompiler
haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
haveModified - Variable in class org.jmol.modelset.MeasurementPending
haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
haveNotifiedError - Variable in class org.jmol.util.GenericApplet
haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
havePlanarContours - Variable in class org.jmol.shape.Mesh
havePoints - Variable in class org.jmol.quantum.MOCalculation
haveQuads - Variable in class org.jmol.util.MeshSurface
haveReference - Variable in class org.jmol.thread.JmolThread
haveSelectedSpectrum() - Method in class jspecview.common.PanelData
haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
haveStraightness - Variable in class org.jmol.modelset.AtomCollection
haveStrutPoints - Variable in class org.jmol.shape.Sticks
  False here means strut points have not been calculated and need to be reset.
haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
haveTarget - Variable in class org.jmol.modelset.MeasurementPending
haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
haveTranslucentObjects() - Method in class org.jmol.export.Export3D
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
haveUnitCell - Variable in class org.jmol.adapter.writers.XtlWriter
haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
haveUnitCells - Variable in class org.jmol.modelset.ModelSet
haveXyPoints - Variable in class org.jmol.shape.Mesh
HB - Enum Class in org.jmol.c
  Enum for hydrogen bonding donor/acceptor type
hBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
hbond - Static variable in class org.jmol.script.T
HBond - Class in org.jmol.modelset
HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
hbondhxdistancemaximum - Static variable in class org.jmol.script.T
hbondnodistancemaximum - Static variable in class org.jmol.script.T
hbondsangleminimum - Static variable in class org.jmol.script.T
hbondsbackbone - Static variable in class org.jmol.script.T
hbondsrasmol - Static variable in class org.jmol.script.T
hbondssolid - Static variable in class org.jmol.script.T
HC - Static variable in class org.jmol.quantum.QS
hDashes - Static variable in class org.jmol.render.FontLineShapeRenderer
HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
headerTable - Variable in class jspecview.source.JDXHeader
headless - Variable in class org.jmol.viewer.Viewer
  determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN <rate>, ANIMATION ON turns SPIN <rate> <end> into just ROTATE <end>
heavy_neighbor_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
height - Variable in class javajs.img.ImageEncoder
height - Variable in class org.jmol.awtjs.swing.Component
height - Variable in class org.jmol.awtjs.swing.Dimension
height - Variable in class org.jmol.util.GData
height - Variable in class org.jmol.util.Rectangle
height - Variable in class org.jmol.viewer.TransformManager
helix - Static variable in class org.jmol.script.T
Helix - Class in org.jmol.modelsetbio
HELIX - Enum constant in enum class org.jmol.c.STR
helix310 - Static variable in class org.jmol.script.T
HELIX310 - Enum constant in enum class org.jmol.c.STR
helixalpha - Static variable in class org.jmol.script.T
HELIXALPHA - Enum constant in enum class org.jmol.c.STR
helixpi - Static variable in class org.jmol.script.T
HELIXPI - Enum constant in enum class org.jmol.c.STR
helixRockets - Variable in class org.jmol.renderbio.RocketsRenderer
helixstep - Static variable in class org.jmol.script.T
help - Static variable in class org.jmol.script.T
HELP - Enum constant in enum class jspecview.common.ScriptToken
HelpDialog - Class in org.openscience.jmol.app.jmolpanel
HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
HelpDialog(JFrame, String, boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
  If url is null, then the default help url is taken.
helper - Variable in class org.jmol.popup.GenericPopup
helppath - Static variable in class org.jmol.script.T
hermitelevel - Static variable in class org.jmol.script.T
HermiteRenderer - Class in org.jmol.g3d
  Implementation of hermite curves for drawing smoothed curves that pass through specified points.
HermiteRenderer() - Constructor for class org.jmol.g3d.HermiteRenderer
hetero - Static variable in class org.jmol.script.T
HEX_TO_RHOMB - Static variable in class org.jmol.symmetry.CLEG
HEX_TO_RHOMB - Static variable in class org.jmol.util.SimpleUnitCell
hi - Variable in class org.jmol.util.ColorEncoder
hidden - Variable in class org.jmol.modelset.Text
hidden - Static variable in class org.jmol.script.T
HIDDEN - Enum constant in enum class jspecview.common.ScriptToken
hiddenlinesdashed - Static variable in class org.jmol.script.T
hide - Static variable in class org.jmol.script.T
hide_long_bonds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
hide_underscore_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
hidenameinpopup - Static variable in class org.jmol.script.T
hidenavigationpoint - Static variable in class org.jmol.script.T
hidenotselected - Static variable in class org.jmol.script.T
HIGH - Static variable in class org.jmol.util.ColorEncoder
highlight - Static variable in class org.jmol.script.T
highlight(BS) - Method in class org.jmol.viewer.Viewer
HIGHLIGHT - Enum constant in enum class jspecview.common.ScriptToken
highlightBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
  from Sticks
highlightColor - Variable in class jspecview.common.PanelData
HIGHLIGHTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
highresolution - Static variable in class org.jmol.script.T
history - Static variable in class org.jmol.script.T
historyButton - Variable in class org.jmol.console.GenericConsole
historyDisabled - Variable in class org.jmol.script.ScriptEval
historyFile - Variable in class org.openscience.jmol.app.JmolApp
historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
HistoryFile - Class in org.openscience.jmol.app
  The history file contains data from previous uses of Jmol.
HistoryFile(File, String) - Constructor for class org.openscience.jmol.app.HistoryFile
  Creates a history file.
historyFind(String, int) - Method in class org.jmol.viewer.Viewer
historylevel - Static variable in class org.jmol.script.T
hkl - Static variable in class org.jmol.script.T
hklParameter(int, Lst, boolean) - Method in class org.jmol.script.ScriptParam
hmMatches(String, String, int) - Static method in class org.jmol.symmetry.SpaceGroup
  Matches Hermann-Mauguin names for special types by ignoring spaces and some special treatment for plane groups.
holdRepaint - Variable in class org.jmol.render.RepaintManager
  //////// thread management ///////////
homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
homePosition() - Method in class org.jmol.api.JmolViewer
homePosition() - Method in class org.jmol.viewer.Viewer
homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
homo - Static variable in class org.jmol.script.T
HORIZONTAL_SPLIT - Static variable in class org.jmol.awtjs.swing.JSplitPane
HOTPINK - Static variable in class org.jmol.util.C
hover - Static variable in class org.jmol.script.T
Hover - Class in org.jmol.shape
Hover() - Constructor for class org.jmol.shape.Hover
HOVER - Enum constant in enum class org.jmol.c.CBK
hoverdelay - Static variable in class org.jmol.script.T
hoverEnabled - Variable in class org.jmol.thread.JmolThread
hoverlabel - Static variable in class org.jmol.script.T
hoverLabel - Variable in class org.jmol.shape.Mesh
hoverOnPt(int, int, String, String, T3) - Method in class org.jmol.viewer.Viewer
  Hover over an arbitrary point.
HoverRenderer - Class in org.jmol.render
HoverRenderer() - Constructor for class org.jmol.render.HoverRenderer
hoverText - Variable in class org.jmol.shape.Hover
hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
HoverWatcherThread - Class in org.jmol.thread
HoverWatcherThread(ActionManager, MouseState, MouseState, Viewer) - Constructor for class org.jmol.thread.HoverWatcherThread
HS - Static variable in class org.jmol.quantum.QS
hslToRGB(P3) - Static method in class javajs.util.CU
  Convert HSL (hue/saturation/luninance) values to RGB
ht3 - Variable in class org.jmol.util.GData
htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
htBooleans - Variable in class jspecview.common.Parameters
htCheckbox - Variable in class org.jmol.popup.GenericPopup
htDialogs - Variable in class jspecview.dialog.DialogManager
htElementMap - Static variable in class org.jmol.util.Elements
htFields - Static variable in class javajs.util.CifDataParser
  A global, static map that contains field information.
htGroup - Static variable in class org.jmol.modelsetbio.BioResolver
htGroup1 - Variable in class org.jmol.adapter.readers.cif.CifReader
htGroup1 - Static variable in class org.jmol.modelsetbio.NucleicPolymer
htHetero - Variable in class org.jmol.adapter.readers.cif.MMCifReader
htMenus - Variable in class org.jmol.popup.GenericPopup
htMessageCallbacks - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
htMin - Variable in class org.jmol.modelset.MeasurementData
html5Applet - Variable in class jspecview.common.JSViewer
html5Applet - Variable in class org.jmol.viewer.Viewer
HTMLElement - Interface in org.jmol.awtjs.swing
htmlMenuOpener(String) - Method in class org.jmol.awtjs.swing.AbstractButton
htmlName - Variable in class org.jmol.util.GenericApplet
htmlName - Variable in class org.jmol.viewer.Viewer
HTMLWindowEvent - Interface in org.jmol.awtjs.swing
  The window.Event in HTML5 See SwingController.
htModelAtomMap - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
htObjects - Variable in class org.jmol.shape.MeshCollection
htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
htParams - Variable in class org.jmol.util.GenericApplet
htPeaks - Variable in class org.jmol.modelset.ModelSet
htRegistry - Static variable in class org.jmol.util.GenericApplet
htSites - Variable in class org.jmol.adapter.readers.cif.MMCifReader
htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
htTracker - Variable in class org.jmol.symmetry.CIPDataTracker
  a table to track decision making when only one atom is selected for calculation
htUij - Variable in class org.jmol.util.ModulationSet
  current value of anisotropic parameter modulation
htUserFunctions - Variable in class org.jmol.script.ScriptCompiler
HUGE - Static variable in class org.jmol.util.GData
HYDRO - Enum constant in enum class org.jmol.c.VDW
hydrogen - Static variable in class org.jmol.script.T
hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
hydrogenCount - Variable in class org.jmol.modelset.Model
hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
hydrophobicity - Static variable in class org.jmol.script.T
HyperChemReader - Class in org.jmol.adapter.readers.simple
  Support for .hin, HyperChem's native file format.
HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog

## I

i - Variable in class org.jmol.util.Point3fi
  index in full collection
i(int) - Static method in class org.jmol.script.T
i(String, int) - Static method in class org.jmol.i18n.GT
iA - Variable in class org.jmol.util.MeshSurface
iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
iB - Variable in class org.jmol.util.MeshSurface
iC - Variable in class org.jmol.util.MeshSurface
IC - Static variable in class org.jmol.quantum.QS
ich - Variable in class javajs.util.CifDataParser
  pointer to current character on str
ichComment - Variable in class org.jmol.script.ScriptCompiler
ichCurrentCommand - Variable in class org.jmol.script.ScriptCompiler
ichEnd - Variable in class org.jmol.script.ScriptCompiler
ichToken - Variable in class org.jmol.script.ScriptCompiler
iCommand - Variable in class org.jmol.script.ScriptCompiler
iCommandError - Variable in class org.jmol.script.ScriptContext
iCommandError - Variable in class org.jmol.script.ScriptError
id - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
id - Variable in class jspecview.common.PanelNode
id - Variable in class jspecview.common.Spectrum
id - Variable in class org.jmol.awtjs.swing.Component
id - Variable in enum class org.jmol.c.PAL
id - Variable in class org.jmol.minimize.Minimizer
id - Variable in class org.jmol.modelset.TickInfo
id - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
id - Variable in class org.jmol.script.ScriptContext
id - Static variable in class org.jmol.script.T
id - Variable in class org.jmol.shapespecial.Polyhedron
id - Variable in class org.jmol.symmetry.Symmetry
id - Variable in class org.jmol.util.BZone
id - Variable in class org.jmol.util.Tensor
ID_ALL - Static variable in class org.jmol.modelset.Atom
ID_ATOMS - Static variable in class org.jmol.modelset.Atom
ID_CHIME - Static variable in class org.jmol.modelset.Atom
ID_U - Static variable in class org.jmol.modelset.Atom
ID_XTAL - Static variable in class org.jmol.modelset.Atom
ident - Variable in class jspecview.export.AMLExporter
ident - Variable in class jspecview.export.CMLExporter
identifier - Variable in class jspecview.source.AnIMLReader
identifier - Variable in class jspecview.source.NMRMLReader
identifier - Static variable in class org.jmol.script.T
identify - Static variable in class org.jmol.script.T
identity(int, int) - Static method in class javajs.util.Matrix
  Generate identity matrix
idFontFace - Variable in class org.jmol.util.Font
idFontStyle - Variable in class org.jmol.util.Font
idle_delay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
idSpherical - Static variable in class org.jmol.quantum.QS
ifcmd - Static variable in class org.jmol.script.T
iformat(int, int) - Static method in class jme.JMEUtil
  right-justify using spaces
ignore - Static variable in class org.jmol.script.T
ignore_case - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ignore_pdb_segi - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
ignoreError - Variable in class org.jmol.script.ScriptError
ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
ignoreStructure - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
iHaveCoefMaps - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cif.CifReader
iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHideBackground - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
ijkToPoint3f(int, P3, int, int) - Static method in class org.jmol.util.SimpleUnitCell
  Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499 for example, a 3x3x3 block of 27 cells: {444 666 1} or {1494949 1515151 1} or {1499499499 1501501501 1}
image - Variable in class org.jmol.console.ImageDialog
image - Variable in class org.jmol.modelset.Text
image - Static variable in class org.jmol.script.T
IMAGE - Enum constant in enum class org.jmol.c.CBK
image_copy_always - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
image_dots_per_inch - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
IMAGE_OR_SCENE - Static variable in class org.jmol.viewer.JC
IMAGE_TYPES - Static variable in class org.jmol.viewer.JC
imageableHeight - Variable in class jspecview.common.PrintLayout
imageableWidth - Variable in class jspecview.common.PrintLayout
imageableX - Variable in class jspecview.common.PrintLayout
imageableY - Variable in class jspecview.common.PrintLayout
imageChoices - Variable in class org.jmol.dialog.Dialog
ImageDialog - Class in org.jmol.console
ImageDialog(Viewer, String, Map) - Constructor for class org.jmol.console.ImageDialog
ImageEncoder - Class in javajs.img
  Generic abstract image creator: (1) set parameters (2) encode the image bytes, if necessary (3) generate the image
ImageEncoder() - Constructor for class javajs.img.ImageEncoder
imageExtensions - Variable in class org.jmol.dialog.Dialog
imageFontScaling - Variable in class org.jmol.render.FontLineShapeRenderer
imageFontScaling - Variable in class org.jmol.render.MeshRenderer
imageFontScaling - Variable in class org.jmol.viewer.Viewer
imageScale - Variable in class org.jmol.modelset.Text
imagestate - Static variable in class org.jmol.script.T
imageType - Variable in class org.jmol.dialog.Dialog
imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
imesh - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
implicitStringCommand - Static variable in class org.jmol.script.T
in - Static variable in class org.jmol.script.T
inchi - Variable in class org.jmol.inchi.InchiJmol
inchi - Static variable in class org.jmol.script.T
inchi() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
inchiAveAtomicMass - Static variable in class org.iupac.InchiUtils
InchiFlag - Enum Class in io.github.dan2097.jnainchi
InchiJmol - Class in org.jmol.inchi
InchiJmol() - Constructor for class org.jmol.inchi.InchiJmol
InChIJNA - Class in org.jmol.inchi
  Interface with inchi.c via JNA (see JNA-InChI github project).
InChIJNA() - Constructor for class org.jmol.inchi.InChIJNA
InChIJS - Class in org.jmol.inchi
  This class implements inchi-web.wasm from InChI-SwingJS, which is adapted from https://github.com/IUPAC-InChI/InChI-Web-Demo by Bob Hanson and Josh Charlton 2025.01.23-2025.01.24.
InChIJS() - Constructor for class org.jmol.inchi.InChIJS
inchikey - Static variable in class org.jmol.script.T
InChIStructureProvider - Interface in org.iupac
InchiUtils - Class in org.iupac
  periodic table daata from inchi C util.c
InchiUtils() - Constructor for class org.iupac.InchiUtils
includeAllRelatedFrames(BS, boolean) - Method in class org.jmol.modelset.ModelSet
increasing - Variable in class jspecview.source.AnIMLReader
increasing - Variable in class jspecview.source.NMRMLReader
increment - Static variable in class org.jmol.script.T
incrementID() - Method in class org.jmol.modelsetbio.ProteinStructure
incrementModel(int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
inDefinedStateBlock - Variable in class org.jmol.modelset.StateScript
indent - Variable in class org.jmol.util.JSONWriter
INDENT - Static variable in class org.jmol.shapecgo.CGOMesh
index - Variable in class jspecview.application.AwtTreeNode
index - Variable in class jspecview.tree.SimpleTreeNode
index - Variable in class org.jmol.adapter.smarter.Atom
index - Variable in class org.jmol.minimize.MinBond
index - Variable in class org.jmol.modelset.Measurement
index - Variable in class org.jmol.quantum.SlaterData
index - Variable in class org.jmol.script.SV
index - Variable in class org.jmol.shape.Mesh
index - Variable in class org.jmol.util.BZone
index - Variable in class org.jmol.util.Edge
indexes - Variable in class org.jmol.minimize.MMConstraint
indexInFrame(Atom) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
indexInModel - Variable in class org.jmol.util.JmolMolecule
indexOf(String) - Method in class javajs.util.SB
indexOf2(String, int) - Method in class javajs.util.SB
info - Variable in class org.jmol.atomdata.RadiusData
info - Static variable in class org.jmol.script.T
info - Variable in class org.jmol.shapespecial.Ellipsoid
info - Variable in class org.openscience.jmol.app.JmolApp
info(String) - Method in class org.jmol.util.DefaultLogger
info(String) - Static method in class org.jmol.util.Logger
  og* Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at INFO level.
INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
INFO_BIO_SYMMETRY - Static variable in class org.jmol.viewer.JC
INFO_BIO_SYMMETRY_COUNT - Static variable in class org.jmol.viewer.JC
INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
INFO_DIMENSION_TYPE - Static variable in class org.jmol.util.SimpleUnitCell
INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
INFO_FILE_SPACE_GROUP_NAME - Static variable in class org.jmol.viewer.JC
INFO_FILE_SYMMETRY - Static variable in class org.jmol.viewer.JC
INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
INFO_HALL - Static variable in class org.jmol.viewer.JC
INFO_HM - Static variable in class org.jmol.viewer.JC
INFO_IS_HEXAGONAL - Static variable in class org.jmol.util.SimpleUnitCell
INFO_IS_RHOMBOHEDRAL - Static variable in class org.jmol.util.SimpleUnitCell
INFO_ITA - Static variable in class org.jmol.viewer.JC
INFO_JDX_ATOM_SELECT - Static variable in class org.jmol.viewer.JC
INFO_JDX_MODEL_SELECT - Static variable in class org.jmol.viewer.JC
INFO_JMOL_DATA - Static variable in class org.jmol.viewer.JC
INFO_JMOL_DATA_HEADER - Static variable in class org.jmol.viewer.JC
INFO_JMOL_DATA_ORIGINATING_MODEL - Static variable in class org.jmol.viewer.JC
INFO_JMOL_DATA_PROPERTIES - Static variable in class org.jmol.viewer.JC
INFO_JMOL_DATA_SCALING - Static variable in class org.jmol.viewer.JC
INFO_MODEL_NAME - Static variable in class org.jmol.viewer.JC
INFO_OPS_CTR - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_ASSIGNED - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_F2C_TITLE - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_INDEX - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_INFO - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_NAME - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_NOTE - Static variable in class org.jmol.viewer.JC
INFO_SPACE_GROUP_TITLE - Static variable in class org.jmol.viewer.JC
INFO_START_JSPECVIEW - Static variable in class org.jmol.viewer.JC
INFO_SYMMETRY_INFO - Static variable in class org.jmol.viewer.JC
INFO_SYMMETRY_OPERATIONS - Static variable in class org.jmol.viewer.JC
INFO_SYMOPS_TEMP - Static variable in class org.jmol.viewer.JC
INFO_TRAJECTORY_STEPS - Static variable in class org.jmol.viewer.JC
INFO_UNIT_CELL - Static variable in class org.jmol.viewer.JC
INFO_UNIT_CELL_CONVENTIONAL - Static variable in class org.jmol.viewer.JC
INFO_UNIT_CELL_OFFSET - Static variable in class org.jmol.viewer.JC
INFO_UNIT_CELL_PARAMS - Static variable in class org.jmol.viewer.JC
INFO_UNIT_CELL_RANGE - Static variable in class org.jmol.viewer.JC
  used to set atom symmetry 555 556 etc.
INFO_UNIT_CELLS - Static variable in class org.jmol.viewer.JC
INFO_VIBRATION_STEPS - Static variable in class org.jmol.viewer.JC
INFO_VOLUME - Static variable in class org.jmol.util.SimpleUnitCell
infofontsize - Static variable in class org.jmol.script.T
INFORMATION_MESSAGE - Static variable in class jspecview.dialog.DialogManager
infoText - Variable in class jme.JME
inFront - Variable in class org.jmol.modelset.Measurement
inGreyscaleMode - Variable in class org.jmol.util.GData
INHERIT - Static variable in class org.jmol.util.ColorEncoder
INHERIT_ALL - Static variable in class org.jmol.util.C
INHERIT_COLOR - Static variable in class org.jmol.util.C
init() - Method in class jspecview.appletjs.JSVApplet
  Initializes applet with parameters and load the `JDXSource` called by the browser
init() - Method in class jspecview.appletjs.JSVAppletPro
init() - Method in class org.jmol.symmetry.CIPData
  initializer -- called also by CIPDataSmiles
init(float[]) - Method in class org.jmol.util.SimpleUnitCell
init(Object) - Method in class org.jmol.scriptext.MathExt
init(Object) - Method in class org.jmol.scriptext.ScriptExt
init(Object) - Method in class org.jmol.scriptext.SmilesExt
init(Object) - Method in class org.jmol.util.GenericApplet
init(String, Object, String, SC) - Method in interface org.jmol.api.SC
init(String, Object, String, SC) - Method in class org.jmol.awt.AwtSwingComponent
init(String, Object, String, SC) - Method in class org.jmol.awtjs.swing.AbstractButton
init(String, Viewer, Lst) - Method in class org.jmol.modelset.MeasurementData
init(URL, String) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
INIT - Static variable in class org.jmol.thread.JmolThread
initArrays(int) - Method in class org.jmol.quantum.NMRNoeMatrix
  create an empty atom list for subsequent population with atoms
initBS() - Method in class org.jmol.renderbio.BioMeshRenderer
initForm(JSViewer, OC) - Method in class jspecview.export.AMLExporter
initForm(JSViewer, OC) - Method in class jspecview.export.CMLExporter
initForm(JSViewer, OC) - Method in class jspecview.export.SVGExporter
initialEndIndex - Variable in class jspecview.common.JSViewer
initialize - Static variable in class org.jmol.script.T
initialize() - Method in class jme.JME
initialize(boolean, boolean) - Method in class org.jmol.viewer.Viewer
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.MOCalculation
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
initialize(int, P3[], BS) - Method in class org.jmol.bspt.Bspf
initialize(int, T3[], P4) - Method in class org.jmol.shape.Mesh
initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
initialize(T3, float, boolean) - Method in class org.jmol.bspt.CubeIterator
  initialize to return all points within the sphere defined by center and radius
initialize(JSViewer, PopupResource, String) - Method in class jspecview.popup.JSVGenericPopup
initialize(AtomSetCollectionReader, int) - Method in class org.jmol.adapter.readers.cif.MSRdr
initialize(AtomSetCollectionReader, int) - Method in interface org.jmol.adapter.smarter.MSInterface
initialize(ShapeRenderer, BioShape, int) - Method in class org.jmol.renderbio.BioMeshRenderer
initialize(Viewer, GenericPlatform) - Method in class org.jmol.g3d.Graphics3D
initialize(Viewer, GenericPlatform) - Method in class org.jmol.util.GData
initialize(Viewer, PopupResource, String) - Method in class org.jmol.popup.JmolGenericPopup
initialize0(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
initializeAnnotation(SV, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
initializeAnnotation(SV, int, int) - Method in class org.jmol.dssx.AnnotationParser
  We create a main list of mappings, where each mapping has _atoms and _path
initializeBspf() - Method in class org.jmol.modelset.ModelSet
  ///////// iterators //////////
initializeBspt(int) - Method in class org.jmol.modelset.ModelSet
initializeExporter(Map) - Method in class org.jmol.viewer.Viewer
initializeExporter(Viewer, double, GData, Map) - Method in interface org.jmol.api.JmolRendererInterface
initializeExporter(Viewer, double, GData, Map) - Method in class org.jmol.export.Export3D
initializeExporter(Viewer, double, GData, Map) - Method in class org.jmol.g3d.Graphics3D
initializeHydrogenAddition() - Method in class org.jmol.modelsetbio.BioResolver
initializeModelForSmiles() - Method in interface org.iupac.InChIStructureProvider
initializeModelForSmiles() - Method in class org.jmol.inchi.InChIJNA
initializeModelForSmiles() - Method in class org.jmol.inchi.InChIJS
initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
initializeOnePointQC() - Method in class org.jmol.quantum.QuantumCalculation
initializeOrientation(M3) - Method in interface org.jmol.api.SymmetryInterface
initializeOrientation(M3) - Method in class org.jmol.symmetry.Symmetry
initializeOutput(Viewer, double, Map) - Method in interface org.jmol.api.JmolRendererInterface
initializeOutput(Viewer, double, Map) - Method in class org.jmol.export.Export3D
initializeOutput(Viewer, double, Map) - Method in class org.jmol.g3d.Graphics3D
initializeReader() - Method in class org.jmol.adapter.readers.cif.CifReader
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
initializeReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
initializeReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
initializeReader() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
initializeReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
initializeReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.AdfReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.AmsReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.JSONReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.OrcaReader
initializeReader() - Method in class org.jmol.adapter.readers.spartan.OdysseyReader
initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
  //////////// file reader option //////////////
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CmdfReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.FSGOutputReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  not sure how to work with symmetry here...
initializeReader() - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeShape(Viewer, ModelSet, int) - Method in class org.jmol.shape.Shape
initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeSymmetryOptions() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeTrajectoryFile() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initialStartIndex - Variable in class jspecview.common.JSViewer
initMany(Lst, int, int) - Method in class jspecview.common.PanelData
initModelSet() - Method in class org.jmol.shape.AtomShape
initModelSet() - Method in class org.jmol.shape.Measures
initModelSet() - Method in class org.jmol.shape.Shape
initModelSet() - Method in class org.jmol.shape.TextShape
initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
initModelSet() - Method in class org.jmol.shapespecial.Vectors
initOne(Spectrum) - Method in class jspecview.common.PanelData
initOptions() - Method in class org.jmol.util.GenericApplet
initOutput(Viewer, double, GData, Map) - Method in class org.jmol.export.___Exporter
initOutput(Viewer, double, GData, Map) - Method in class org.jmol.export._PovrayExporter
initOutput(Viewer, double, GData, Map) - Method in class org.jmol.export._TachyonExporter
initParams(String) - Method in class jspecview.app.JSVApp
  starts or restarts applet display from scratch or from a JSVApplet.script() JavaScript command Involves a two-pass sequence through parsing the parameters, because order is not important in this sort of call.
initRenderer() - Method in class org.jmol.render.AxesRenderer
initRenderer() - Method in class org.jmol.render.BbcageRenderer
initRenderer() - Method in class org.jmol.render.MeasuresRenderer
initRenderer() - Method in class org.jmol.render.ShapeRenderer
initRenderer() - Method in class org.jmol.render.UccageRenderer
initRenderer() - Method in class org.jmol.renderspecial.DotsRenderer
initShape() - Method in class org.jmol.shape.AtomShape
initShape() - Method in class org.jmol.shape.Axes
initShape() - Method in class org.jmol.shape.Bbcage
initShape() - Method in class org.jmol.shape.Echo
initShape() - Method in class org.jmol.shape.FontLineShape
initShape() - Method in class org.jmol.shape.Frank
initShape() - Method in class org.jmol.shape.Hover
initShape() - Method in class org.jmol.shape.Labels
initShape() - Method in class org.jmol.shape.Measures
initShape() - Method in class org.jmol.shape.MeshCollection
initShape() - Method in class org.jmol.shape.Shape
initShape() - Method in class org.jmol.shape.Sticks
initShape() - Method in class org.jmol.shape.Uccage
initShape() - Method in class org.jmol.shapebio.Backbone
initShape() - Method in class org.jmol.shapebio.BioShapeCollection
initShape() - Method in class org.jmol.shapebio.Cartoon
initShape() - Method in class org.jmol.shapebio.MeshRibbon
initShape() - Method in class org.jmol.shapebio.Rockets
initShape() - Method in class org.jmol.shapebio.Trace
initShape() - Method in class org.jmol.shapespecial.Dipoles
initShape() - Method in class org.jmol.shapespecial.Dots
initShape() - Method in class org.jmol.shapespecial.Draw
initShape() - Method in class org.jmol.shapespecial.Ellipsoids
initShape() - Method in class org.jmol.shapespecial.GeoSurface
initShape() - Method in class org.jmol.shapesurface.Contact
initShape() - Method in class org.jmol.shapesurface.Isosurface
initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
initShape() - Method in class org.jmol.shapesurface.NBO
initShape() - Method in class org.jmol.shapesurface.Plot3D
initShape() - Method in class org.jmol.shapesurface.Pmesh
initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
initSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
initSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
initSwing(String, PopupResource, Object, boolean, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
initVars() - Method in class org.jmol.export._PovrayExporter
initVars() - Method in class org.jmol.export._TachyonExporter
initViewer() - Method in class jspecview.appletjs.JSVApplet
inline - Static variable in class org.jmol.script.T
inp - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
input - Variable in class org.jmol.console.GenericConsole
INPUT_DEVICE - Static variable in class com.sparshui.common.ConnectionType
InputDeviceConnection - Class in com.sparshui.server
  Represents a connection to the input device.
InputDeviceConnection(GestureServer, Socket) - Constructor for class com.sparshui.server.InputDeviceConnection
  Create a new input device connection with the given gesture server and socket.
inputFileName - Variable in class org.jmol.dialog.Dialog
inputInChI - Variable in class org.jmol.inchi.InchiJmol
InputReader - Class in org.jmol.adapter.readers.simple
InputReader() - Constructor for class org.jmol.adapter.readers.simple.InputReader
InputScannerThread - Class in org.openscience.jmol.app
inRange(int, int, int) - Method in class org.jmol.viewer.MouseState
inscode - Static variable in class org.jmol.script.T
insert(int, String) - Method in class javajs.util.SB
insert(SC, int) - Method in interface org.jmol.api.SC
insert(SC, int) - Method in class org.jmol.awt.AwtSwingComponent
insert(SC, int) - Method in class org.jmol.awtjs.swing.AbstractButton
insertComponent(Component, int) - Method in class org.jmol.awtjs.swing.Container
insertion - Static variable in class org.jmol.script.T
INSERTION - Enum constant in enum class org.jmol.c.PAL
insertionCode - Variable in class org.jmol.adapter.smarter.Atom
insertNodeInto(JSVTreeNode, JSVTreeNode, int) - Method in class jspecview.tree.SimpleTreeModel
insertString(int, String, Object) - Method in interface org.jmol.awtjs.swing.Document
insertString(int, String, Object) - Method in class org.jmol.awtjs.swing.JTextPane
Insets - Class in org.jmol.awtjs.swing
Insets(int, int, int, int) - Constructor for class org.jmol.awtjs.swing.Insets
insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
insideout - Static variable in class org.jmol.script.T
insideOut - Variable in class org.jmol.jvxl.data.JvxlData
insideOut - Variable in class org.jmol.shape.Mesh
INSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
Int2IntHash - Class in org.jmol.util
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
integer - Static variable in class org.jmol.script.T
integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptError
Integral - Class in jspecview.common
Integral() - Constructor for class jspecview.common.Integral
IntegralData - Class in jspecview.common
  from IntegralGraph a data structure for integration settings
IntegralData(double, double, double, Spectrum) - Constructor for class jspecview.common.IntegralData
IntegralData(Spectrum, Parameters) - Constructor for class jspecview.common.IntegralData
IntegralData.IntMode - Enum Class in jspecview.common
integralDrawAll - Variable in class jspecview.common.Parameters
integralMinY - Variable in class jspecview.common.Parameters
integralOffset - Variable in class jspecview.common.Parameters
INTEGRALOFFSET - Enum constant in enum class jspecview.common.ScriptToken
integralPlotColor - Variable in class jspecview.common.PanelData
INTEGRALPLOTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
integralRange - Variable in class jspecview.common.Parameters
INTEGRALRANGE - Enum constant in enum class jspecview.common.ScriptToken
integralShiftMode - Variable in class jspecview.common.PanelData
INTEGRATE - Enum constant in enum class jspecview.common.ScriptToken
integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
integration - Variable in class org.jmol.jvxl.data.JvxlData
integration - Variable in class org.jmol.quantum.QuantumCalculation
Integration - Enum constant in enum class jspecview.common.Annotation.AType
INTEGRATION - Enum constant in enum class jspecview.common.ScriptToken
IntegrationDialog - Class in jspecview.dialog
  Dialog for managing the integral listing for a Spectrum within a GraphSet
IntegrationDialog() - Constructor for class jspecview.dialog.IntegrationDialog
INTEGRATIONRATIOS - Enum constant in enum class jspecview.common.ScriptToken
Interface - Class in javajs.api
Interface - Class in org.jmol.api
Interface() - Constructor for class javajs.api.Interface
Interface() - Constructor for class org.jmol.api.Interface
INTERFACE - Enum constant in enum class jspecview.common.ScriptToken
interfaceOverlaid - Variable in class jspecview.common.JSViewer
interior - Static variable in class org.jmol.script.T
intermolecular - Static variable in class org.jmol.script.T
internal - Static variable in class org.jmol.script.T
INTERNAL - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
internal_feedback - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
internal_gui - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
internal_gui_control_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
internal_gui_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
internal_gui_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
internal_prompt - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
internalSlab - Variable in class org.jmol.viewer.TransformManager
internalTranslation - Variable in class org.jmol.viewer.TransformManager
interrupt() - Method in interface org.jmol.api.JmolNavigatorInterface
interrupt() - Method in class org.jmol.thread.AnimationThread
interrupt() - Method in class org.jmol.thread.JmolThread
interrupt() - Method in class org.jmol.thread.MoveToThread
intersection - Variable in class org.jmol.jvxl.readers.Parameters
intersection - Static variable in class org.jmol.script.T
intersection(int[], int[]) - Static method in class jme.JMEUtil
intersectLine(P3[], int, P3, V3) - Method in class org.jmol.util.Triangulator
intersectPlane(P4, T3[], int) - Method in class org.jmol.util.Triangulator
  a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.
intersects(BS) - Method in class javajs.util.BS
  Returns true if the specified `BitSet` has any bits set to `true` that are also set to `true` in this `BitSet`.
intparam - Static variable in class org.jmol.script.T
intParameter(int) - Method in class org.jmol.script.ScriptParam
intParameter(int) - Method in class org.jmol.scriptext.ScriptExt
intParameterRange(int, int, int) - Method in class org.jmol.script.ScriptParam
intproperty - Static variable in class org.jmol.script.T
intramolecular - Variable in class org.jmol.modelset.MeasurementData
intramolecular - Static variable in class org.jmol.script.T
intToByteArray(byte[], int, int) - Static method in class com.sparshui.common.utils.Converter
intToByteArray(int) - Static method in class com.sparshui.common.utils.Converter
  Converts an integer intBits into a byte array.
intToFloat(int) - Static method in class javajs.util.BC
intToSignedInt(int) - Static method in class javajs.util.BC
intValue - Variable in class org.jmol.script.T
inv() - Method in class javajs.util.Quat
INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
invalidatePolygons() - Method in class org.jmol.util.MeshSurface
invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
  //////////// meshDataServer interface /////////////////
invalidateVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
InvalidSmilesException - Exception Class in org.jmol.smiles
  Exception thrown for invalid SMILES String
InvalidSmilesException(String) - Constructor for exception class org.jmol.smiles.InvalidSmilesException
  Constructs a `InvalidSmilesException` with a detail message.
invArg() - Method in class org.jmol.script.ScriptError
invArg() - Method in class org.jmol.scriptext.ScriptExt
invArgStr(String) - Method in class org.jmol.script.ScriptError
inverse() - Method in class javajs.util.Matrix
  Matrix inverse or pseudoinverse
invert() - Method in class javajs.util.M3
  Sets the value of this matrix to its inverse.
invert() - Method in class javajs.util.M4
  Sets the value of this matrix to its inverse.
invertAtomCoord(P3, P4, BS, int, boolean) - Method in class org.jmol.viewer.Viewer
invertInPlace(BS, int) - Static method in class org.jmol.util.BSUtil
  inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertM(M3) - Method in class javajs.util.M3
  Sets the value of this matrix to the matrix inverse of the passed matrix m1.
invertSelected - Static variable in class org.jmol.script.T
invertSelected(P3, P4, int, BS) - Method in class org.jmol.modelset.ModelSet
  Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.
invertSelected(P3, P4, int, BS) - Method in class org.jmol.viewer.Viewer
INVERTY - Enum constant in enum class jspecview.common.ScriptToken
invertYAxis() - Method in class jspecview.source.JDXDataObject
invPO() - Method in class org.jmol.scriptext.ScriptExt
io.github.dan2097.jnainchi - package io.github.dan2097.jnainchi
ipadx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
ipady - Variable in class org.jmol.awtjs.swing.GridBagConstraints
IRMODE - Enum constant in enum class jspecview.common.ScriptToken
iRowColSelected - Variable in class jspecview.dialog.JSVDialog
  /////////// protected methods
is(int) - Method in class org.jmol.modelset.Bond
is(MouseState) - Method in class org.jmol.viewer.MouseState
IS - Static variable in class org.jmol.quantum.QS
IS_APPEND - Static variable in class org.jmol.viewer.FileManager
IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
is1D() - Method in class jspecview.source.JDXDataObject
is2D - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
is2D() - Method in class org.jmol.viewer.Viewer
is2DPoint(T3) - Static method in class org.jmol.shapespecial.Draw
isAB(Object) - Static method in class javajs.util.AU
isAB(Object) - Static method in class jspecview.common.JSVFileManager
isAbsorbance() - Method in class jspecview.source.JDXDataObject
isActive - Variable in class org.jmol.shape.AtomShape
isActive() - Method in class org.jmol.shapespecial.Ellipsoids
isActiveLevel(int) - Static method in class org.jmol.util.Logger
  Tells if a logging level is active.
isAD(Object) - Static method in class javajs.util.AU
isADD(Object) - Static method in class javajs.util.AU
isADDD(Object) - Static method in class javajs.util.AU
isAdded(int) - Method in class org.jmol.modelset.Group
isADF - Variable in class org.jmol.adapter.readers.quantum.AdfReader
isAF(Object) - Static method in class javajs.util.AU
isAFF(Object) - Static method in class javajs.util.AU
isAFFF(Object) - Static method in class javajs.util.AU
isAFloat(Object) - Static method in class javajs.util.AU
isAI(Object) - Static method in class javajs.util.AU
isAII(Object) - Static method in class javajs.util.AU
isAll - Variable in class org.jmol.modelset.MeasurementData
isAmide - Variable in class org.jmol.minimize.MinBond
isAngstroms - Variable in class org.jmol.jvxl.readers.JvxlReader
isAngstroms - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
isAngstroms - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
isAntialiased() - Method in interface org.jmol.api.JmolGraphicsInterface
isAntialiased() - Method in class org.jmol.export.Export3D
  is full scene / oversampling antialiasing in effect
isAntialiased() - Method in class org.jmol.util.GData
  is full scene / oversampling antialiasing in effect
isAP(Object) - Static method in class javajs.util.AU
isAppendSelected() - Method in class org.jmol.dialog.FilePreview
isApplet - Variable in class jspecview.common.JSViewer
isApplet - Variable in class org.jmol.popup.GenericPopup
isApplet - Variable in class org.jmol.viewer.Viewer
isApplet() - Method in class jspecview.common.JSVFileManager
isApprox(V3d, V3d, double) - Static method in class org.jmol.minimize.Util
isaromatic - Static variable in class org.jmol.script.T
isAromatic - Variable in class org.jmol.minimize.MinBond
isAromatic() - Method in class org.jmol.modelset.Bond
isArrayParameter(int) - Method in class org.jmol.script.ScriptParam
isAS(Object) - Static method in class javajs.util.AU
isASS(Object) - Static method in class javajs.util.AU
isAtomExpression(int) - Method in class org.jmol.script.ScriptEval
isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
isAtomPDB(int) - Method in class org.jmol.modelset.ModelSet
isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
isAtropism(int) - Static method in class org.jmol.util.Edge
isAutoOverlayFromJmolClick() - Method in class jspecview.source.JDXDataObject
isAV(Object) - Static method in class org.jmol.util.Escape
isBarb - Variable in class org.jmol.shapespecial.DrawMesh
isBase64() - Method in class javajs.util.OC
isBase64(SB) - Static method in class javajs.util.Rdr
isBiColor() - Method in enum class org.jmol.c.STER
isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
isBicolorMap - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
isBigEndian - Variable in class javajs.util.BinaryDocument
isBigEndian() - Method in interface javajs.api.GenericOutputChannel
isBigEndian() - Method in class javajs.util.OC
isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isBinary(BufferedInputStream, int) - Static method in class javajs.util.Rdr
  Just looking for non-printable characters.
isBinaryUrl(String) - Method in interface javajs.api.js.J2SObjectInterface
isBio - Variable in class org.jmol.symmetry.Symmetry
isBio() - Method in interface org.jmol.api.SymmetryInterface
isBio() - Method in class org.jmol.symmetry.Symmetry
isBioModel - Variable in class org.jmol.modelset.Model
isBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
isBioShape - Variable in class org.jmol.shape.Shape
isBondable(float, float, float, float, float) - Method in class org.jmol.modelset.ModelSet
isBonded(Atom) - Method in class org.jmol.modelset.Atom
isBondSet - Variable in class org.jmol.script.ScriptParam
isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
isBound(int, int) - Method in class org.jmol.viewer.Viewer
isBZip2B(byte[]) - Static method in class javajs.util.Rdr
isBZip2S(InputStream) - Static method in class javajs.util.Rdr
isCA2(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isCapturing() - Method in class org.jmol.viewer.Viewer
isCarbohydrate - Variable in class org.jmol.renderbio.BackboneRenderer
isCarbohydrate - Variable in class org.jmol.renderbio.CartoonRenderer
isCarbohydrate - Variable in class org.jmol.renderbio.MeshRibbonRenderer
isCarbohydrate - Variable in class org.jmol.renderbio.RibbonsRenderer
isCarbohydrate - Variable in class org.jmol.renderbio.RocketsRenderer
isCarbohydrate - Variable in class org.jmol.renderbio.StrandsRenderer
isCarbohydrate - Variable in class org.jmol.renderbio.TraceRenderer
isCarbohydrate() - Method in class org.jmol.modelset.Group
isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
  /////////////////////////////////////////////////////////////
isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
isCartoonsSelected() - Method in class org.jmol.dialog.FilePreview
isCDX - Variable in class org.jmol.adapter.readers.xml.XmlCdxReader
isCellEditable(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
isCenterParameter(int) - Method in class org.jmol.script.ScriptParam
isCentrosymmetric() - Method in class org.jmol.symmetry.HallInfo
isChain - Variable in class org.jmol.smiles.SmilesBond
isChanged() - Method in class com.sparshui.server.TouchPoint
  Get the value of the changed flag.
isCIF2 - Variable in class org.jmol.adapter.writers.CIFWriter
isClaimed() - Method in class com.sparshui.server.TouchPoint
  The GestureServer needs to know whether an incoming touchPoint is bound to a client or not so that it can tell the input device whether or not to consume the event.
isClearAll() - Method in class jspecview.common.PeakInfo
isClickable() - Method in class org.jmol.modelset.Atom
isClipped(int, int) - Method in class org.jmol.export.Export3D
isClipped(int, int) - Method in class org.jmol.util.GData
isClipped(int, int, int) - Method in class org.jmol.export.Export3D
isClipped3(int, int, int) - Method in class org.jmol.util.GData
isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
isClippedXY(int, int, int) - Method in class org.jmol.util.GData
isClippedZ(int) - Method in class org.jmol.util.GData
isColixColorInherited(short) - Static method in class org.jmol.util.C
isColixLastAvailable(short) - Static method in class org.jmol.util.C
isColixTranslucent(short) - Static method in class org.jmol.util.C
isColorParam(int) - Method in class org.jmol.script.ScriptParam
isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
isColorSolid - Variable in class org.jmol.util.MeshSurface
isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptCompiler
isCommensurate - Variable in class org.jmol.adapter.readers.cif.MSRdr
isComplete - Variable in class org.jmol.script.ScriptContext
isCompoundDocumentB(byte[]) - Static method in class javajs.util.Rdr
isCompoundDocumentS(InputStream) - Static method in class javajs.util.Rdr
isCompoundSource - Variable in class jspecview.source.JDXSource
isConcatenated - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isConnect() - Method in class org.jmol.modelset.StateScript
isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
isContainedIn(BS) - Method in class org.jmol.modelset.Model
isContinuous() - Method in class jspecview.source.JDXDataObject
  Returns true if spectrum is continuous
isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
isContoured - Variable in class org.jmol.jvxl.data.JvxlData
isContoured - Variable in class org.jmol.jvxl.readers.Parameters
isCore - Variable in class org.jmol.quantum.SlaterData
isCourseGrained - Variable in class org.jmol.adapter.readers.cif.CifReader
isCovalent() - Method in class org.jmol.modelset.Bond
isCovalent() - Method in class org.jmol.smiles.SmilesBond
isCovalent() - Method in class org.jmol.util.Edge
isCovalent() - Method in interface org.jmol.util.SimpleEdge
isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
isCovalentNotPartial0() - Method in class org.jmol.modelset.Bond
iscroll - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
isCrossLinked(Group) - Method in class org.jmol.modelset.Group
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
isCrossLinked(Node) - Method in class org.jmol.modelset.Atom
isCrossLinked(Node) - Method in class org.jmol.smiles.SmilesAtom
isCrossLinked(Node) - Method in interface org.jmol.util.Node
isCurrentGraphSet(GraphSet) - Method in class jspecview.common.PanelData
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
isCyclic() - Method in class org.jmol.modelsetbio.BioPolymer
isDatabaseCode(char) - Static method in class org.jmol.viewer.Viewer
isDataFlavorSupported(DataFlavor) - Method in class jspecview.java.AwtClipboard
isDataFlavorSupported(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
isDefault - Variable in class jspecview.common.ColorParameters
isDefaultSetting() - Method in class org.jmol.symmetry.CLEG.ClegNode
isDefined() - Method in class org.jmol.smiles.SmilesAtom
isDeleted() - Method in class org.jmol.modelset.Atom
isDeleted() - Method in class org.jmol.smiles.SmilesAtom
isDeleted() - Method in interface org.jmol.util.Node
isDeleted(Atom) - Static method in class org.jmol.modelset.AtomCollection
isDialog() - Method in interface jspecview.api.AnnotationData
isDialog() - Method in class jspecview.common.MeasurementData
isDialog() - Method in class jspecview.dialog.JSVDialog
isDigit(char) - Static method in class javajs.util.PT
isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
isDirectory() - Method in interface org.jmol.api.GenericFileInterface
isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
isDna() - Method in class org.jmol.modelset.Group
  group ID-based definition
isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
  /////////////////////////////////////////////////////////////
isDnaByID() - Method in class org.jmol.modelset.Group
  group ID-based definition
isDrawPolygon - Variable in class org.jmol.util.MeshSurface
isDSSP1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isDssrSet - Variable in class org.jmol.modelsetbio.NucleicPolymer
isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
isEcho - Variable in class org.jmol.modelset.Text
isEditor - Variable in class org.jmol.script.ScriptContext
isEditorScript - Variable in class org.jmol.script.ScriptContext
iSelected - Variable in class jspecview.dialog.JSVDialog
isElement(int, int) - Static method in class org.jmol.util.Elements
isEmbeddable(String) - Static method in class org.jmol.viewer.FileManager
  Check to see if it is possible that this file has been embedded by Jmol using JC.EMBEDDED_SCRIPT_TAG.
isEmbedded - Variable in class jspecview.common.JSViewer
isEmbeddedExpression - Variable in class org.jmol.script.ScriptCompiler
isEmpty() - Method in class javajs.util.BS
  Returns true if this `BitSet` contains no bits that are set to `true`.
isEmpty() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
isEnabled() - Method in interface jspecview.api.JSVViewPanel
isEnabled() - Method in class jspecview.js2d.JsMainPanel
isEnabled() - Method in class jspecview.js2d.JsPanel
isEnabled() - Method in interface org.jmol.api.JmolModulationSet
isEnabled() - Method in interface org.jmol.api.SC
isEnabled() - Method in class org.jmol.awt.AwtSwingComponent
isEnabled() - Method in class org.jmol.awtjs.swing.Component
isEnabled() - Method in class org.jmol.util.ModulationSet
isEquiv(Tensor) - Method in class org.jmol.util.Tensor
iSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
isExecuting() - Method in interface org.jmol.api.JmolScriptEvaluator
isExecuting() - Method in class org.jmol.script.ScriptEval
isExport - Variable in class org.jmol.render.ShapeRenderer
isExportMode(String) - Static method in enum class jspecview.common.ExportType
isExportXAxisLeftToRight() - Method in class jspecview.common.Spectrum
isFieldValid() - Method in class org.jmol.adapter.readers.cif.BCIFReader
isFieldValid() - Method in class org.jmol.adapter.readers.cif.CifReader
isFinalized - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isFinite(double) - Static method in class org.jmol.minimize.Util
isFixed - Variable in class org.jmol.shape.MeshCollection
isFloatInfo(String) - Static method in class org.jmol.util.Tensor
isFloatParameter(int) - Method in class org.jmol.script.ScriptParam
isFloatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
isFocusable() - Method in interface jspecview.api.JSVViewPanel
isFocusable() - Method in class jspecview.js2d.JsMainPanel
isFocusable() - Method in class jspecview.js2d.JsPanel
isForcedSubset() - Method in class jspecview.common.Spectrum
isFractional - Variable in class org.jmol.util.Vibration
isFrom000 - Variable in class org.jmol.util.Vibration
isFullyLit() - Method in class org.jmol.jvxl.readers.Parameters
isFuncReturn - Variable in class org.jmol.script.ScriptEval
isFunction(String) - Method in class org.jmol.script.ScriptEval
isFunction(String) - Method in class org.jmol.viewer.Viewer
isGC() - Method in class jspecview.source.JDXDataObject
isGenerated() - Method in class org.jmol.symmetry.HallInfo
isGhostPass - Variable in class org.jmol.render.MeshRenderer
isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
isGzipB(byte[]) - Static method in class javajs.util.Rdr
isGzipS(InputStream) - Static method in class javajs.util.Rdr
isHeadless() - Method in class jspecview.application.JSpecView
isHeadless() - Method in class jspecview.java.AwtPlatform
isHeadless() - Method in class jspecview.js2d.JsPlatform
isHeadless() - Method in interface org.jmol.api.GenericPlatform
  //// Display
isHeadless() - Method in class org.jmol.awt.Platform
isHeadless() - Method in class org.jmol.awtjs2d.Platform
isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
isHelix() - Method in class org.jmol.modelsetbio.Monomer
isHetero - Variable in class org.jmol.adapter.smarter.Atom
isHetero() - Method in class org.jmol.modelset.Atom
isHetero(String) - Method in class org.jmol.modelsetbio.BioResolver
  MMCif, Gromacs, MdTop, Mol2 readers only
isHexagonal(float[]) - Static method in class org.jmol.util.SimpleUnitCell
isHexagonalSG(int, float[]) - Method in class org.jmol.symmetry.SpaceGroup
isHidden - Variable in class org.jmol.modelset.Measurement
isHidden() - Method in class org.jmol.modelkit.ModelKit
isHighDPI() - Static method in class jme.JMEUtil
  Check if the applet is showing in highDPI or not.
isHighPrecision - Variable in class org.jmol.adapter.writers.XtlWriter
  in SwingJS this is always true
isHighPrecision - Static variable in class org.jmol.viewer.Viewer
  adjustable
isHNMR() - Method in class jspecview.source.JDXDataObject
  Determines if a spectrum is an HNMR spectrum
isHoverable() - Method in class org.jmol.viewer.ActionManager
iShowSolid - Variable in class org.jmol.renderspecial.DotsRenderer
isHydrogen() - Method in class org.jmol.modelset.Bond
isHydrogen() - Method in class org.jmol.smiles.SmilesBond
isHydrogen() - Method in class org.jmol.util.Edge
isHZtoPPM() - Method in class jspecview.source.JDXDataObject
  Determines if the spectrum should be displayed with abscissa unit of Part Per Million (PPM) instead of Hertz (HZ)
isIDcmd(int) - Static method in class org.jmol.script.T
  commands that allow implicit ID as first parameter
isImaginary() - Method in class jspecview.source.JDXDataObject
isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
isInDisplayRange(int, int) - Method in class org.jmol.util.GData
isInitializedIndex(int) - Method in class org.jmol.bspt.Bspf
isInPosition(V3, float) - Method in class org.jmol.viewer.TransformManager
isInRange(float, int, boolean, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
isInRange(Atom, Atom, float, float, boolean, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
  Consider the min/max option for CONNECT
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
isInsideOut() - Method in class org.jmol.jvxl.readers.Parameters
isIntegralDrag - Variable in class jspecview.common.PanelData
isInTetrahedron(P3, P3, P3, P3, P3, P4, V3, V3, boolean) - Static method in class javajs.util.Measure
isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
isInTriangle(P3, P3, P3, P3, V3, V3, V3) - Static method in class javajs.util.Measure
isInverted() - Method in class jspecview.source.JDXDataObject
isIsotropic - Variable in class org.jmol.util.Tensor
isJmolD - Static variable in class org.jmol.viewer.Viewer
  legacy Jmol
isJmolDataFrame - Variable in class org.jmol.modelset.Model
isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
isJmolDataFrame(int) - Method in class org.jmol.modelset.ModelSet
isJmolType(String) - Static method in class org.jmol.viewer.FileManager
  Check to see if this is a Jmol WRITE file type that might be or have attached a ZIP collection .
isJNLP - Variable in class org.jmol.viewer.Viewer
isJS - Static variable in class jspecview.common.JSViewer
isJS - Variable in class org.jmol.popup.GenericPopup
isJS - Variable in class org.jmol.script.ScriptEval
isJS - Variable in class org.jmol.thread.JmolThread
isJS - Static variable in class org.jmol.util.GenericApplet
isJS - Static variable in class org.jmol.viewer.Viewer
isJSNoAWT - Variable in class org.jmol.viewer.Viewer
isJSThread - Variable in class org.jmol.script.ScriptContext
isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
iskiosk - Static variable in class org.jmol.script.T
isKiosk - Variable in class org.openscience.jmol.app.JmolApp
isKnownPDBGroup(String, int) - Method in class org.jmol.modelsetbio.BioResolver
isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  after reading a model, Q: Is this the last model?
isLeadAtom() - Method in class org.jmol.modelset.Atom
isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
isLeadAtom() - Method in interface org.jmol.util.Node
isLeadAtom(int) - Method in class org.jmol.modelset.Group
isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
isLeaf() - Method in interface jspecview.api.JSVTreeNode
isLeaf() - Method in class jspecview.tree.SimpleTreeNode
isLetter(char) - Static method in class javajs.util.PT
isLetterOrDigit(char) - Static method in class javajs.util.PT
isLigand - Variable in class org.jmol.adapter.readers.cif.CifReader
isLike(String, String) - Static method in class javajs.util.PT
  a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
isLike(SV, SV) - Static method in class org.jmol.script.SV
  a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
isLikelyPDB(String) - Static method in class org.jmol.viewer.JC
isLocal(String) - Static method in class javajs.util.OC
isLocal(String) - Static method in class jspecview.common.JSVFileManager
isLoggable(int[], int) - Method in class org.jmol.minimize.Minimizer
isLoop - Variable in class org.jmol.adapter.readers.cif.CifReader
isLoopKey() - Method in class org.jmol.adapter.readers.cif.CifReader
isLowerCase(char) - Static method in class javajs.util.PT
isM3D - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
isMagCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
isMapped - Variable in class org.jmol.jvxl.readers.Parameters
isMatch(String, String) - Static method in class jspecview.common.Parameters
isMatch(String, String, boolean, boolean) - Static method in class javajs.util.PT
  A general non-regex (for performance) text matcher that utilizes ? and *.
isMathExpressionCommand - Variable in class org.jmol.script.ScriptCompiler
isMeasure - Variable in class org.jmol.modelset.Text
isMenuItem(Object) - Method in class org.jmol.console.GenericConsole
isMenuItem(Object) - Method in class org.jmol.console.JmolConsole
isMenuItem(Object) - Method in class org.jmol.consolejs.AppletConsole
isMerged - Variable in class org.jmol.util.MeshSurface
isMessagePackB(byte[]) - Static method in class javajs.util.Rdr
isMessagePackS(InputStream) - Static method in class javajs.util.Rdr
isMin(Map) - Method in class org.jmol.modelset.Measurement
isMMCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
isModelConnected - Variable in class org.jmol.jvxl.data.JvxlData
isModelConnected - Variable in class org.jmol.jvxl.readers.Parameters
isModelConnected - Variable in class org.jmol.shape.Mesh
isModelKit - Variable in class org.jmol.modelset.Model
isModelKitOption(char, String) - Method in class org.jmol.viewer.Viewer
  Check for an option type 'M' 'S' 'U' 'B'.
isModelkitPickingRotateBond() - Method in class org.jmol.viewer.Viewer
isModelPDB(int) - Method in class org.jmol.viewer.Viewer
isModulated - Variable in class org.jmol.util.Tensor
isModulated(int) - Method in class org.jmol.modelset.AtomCollection
isMolecular - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isMouseDown - Variable in class jspecview.app.GenericMouse
isMouseUp() - Method in class jspecview.common.PanelData
isMovie - Variable in class org.jmol.viewer.AnimationManager
isMS() - Method in class jspecview.source.JDXDataObject
isMTClient() - Method in class org.jmol.viewer.ActionManager
isMTServer() - Method in class org.jmol.viewer.ActionManager
isMultiTouch - Variable in class org.jmol.viewer.ActionManager
isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
isNaN() - Method in class org.jmol.script.SV
isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
isNavigating() - Method in class org.jmol.viewer.TransformManager
isNear(double, double) - Static method in class org.jmol.minimize.Util
isNear(TouchPoint) - Method in class com.sparshui.server.TouchPoint
isNear3(double, double, double) - Static method in class org.jmol.minimize.Util
isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
isNearZero(double) - Static method in class org.jmol.minimize.Util
isNearZero2(double, double) - Static method in class org.jmol.minimize.Util
isNegligible(double, double) - Static method in class org.jmol.minimize.Util
isNegligible3(double, double, double) - Static method in class org.jmol.minimize.Util
isNewSet - Variable in class org.jmol.script.ScriptCompiler
isNext(String) - Method in class org.jmol.jvxl.readers.XmlReader
isNMR() - Method in class jspecview.source.JDXDataObject
isNonStringPrimitive(Object) - Static method in class javajs.util.PT
isNonzero() - Method in class org.jmol.util.ModulationSet
isNonzero() - Method in class org.jmol.util.Vibration
isNucleic - Variable in class org.jmol.renderbio.BackboneRenderer
isNucleic - Variable in class org.jmol.renderbio.CartoonRenderer
isNucleic - Variable in class org.jmol.renderbio.MeshRibbonRenderer
isNucleic - Variable in class org.jmol.renderbio.RibbonsRenderer
isNucleic - Variable in class org.jmol.renderbio.RocketsRenderer
isNucleic - Variable in class org.jmol.renderbio.StrandsRenderer
isNucleic - Variable in class org.jmol.renderbio.TraceRenderer
isNucleic() - Method in class org.jmol.modelset.Group
  group ID-based definition
isNucleic() - Method in class org.jmol.modelsetbio.BioPolymer
isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isNucleic() - Method in class org.jmol.smiles.SmilesAtom
isNucleicMonomer() - Method in class org.jmol.modelset.Group
isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
isNull(String) - Method in class org.jmol.adapter.readers.cif.CifReader
isNumericAndNonZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
isOccupied() - Method in class org.jmol.modelset.Atom
IsoExt - Class in org.jmol.scriptext
IsoExt() - Constructor for class org.jmol.scriptext.IsoExt
isOffsetAbsolute(int) - Static method in class org.jmol.viewer.JC
isomesh_auto_state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
isomeshes - Variable in class org.jmol.shapesurface.Isosurface
isOneOf(String, String) - Static method in class javajs.util.PT
isOpen(Lst, String) - Static method in class jspecview.common.PanelNode
isOpenShell() - Method in class org.jmol.adapter.readers.quantum.NBOParser
isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
isOrderH(int) - Static method in class org.jmol.util.Edge
isOrderly - Variable in class org.jmol.modelset.Model
  a flag that, when false, indicates that the model has atoms in different regions of the Atom[] array
isosurface - Static variable in class org.jmol.script.T
Isosurface - Class in org.jmol.shapesurface
Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
isosurfacekey - Static variable in class org.jmol.script.T
IsosurfaceMesh - Class in org.jmol.shapesurface
isosurfacepropertysmoothing - Static variable in class org.jmol.script.T
isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.T
IsosurfaceRenderer - Class in org.jmol.rendersurface
IsosurfaceRenderer() - Constructor for class org.jmol.rendersurface.IsosurfaceRenderer
ISOTOPE_MASS_OFFSET - Static variable in class org.jmol.util.Elements
ISOTOPE_NUMBER_MASK - Static variable in class org.jmol.util.Elements
isotopeMass - Static variable in class org.jmol.util.Elements
isotropy() - Method in class org.jmol.util.Tensor
  isotropy = average of eigenvalues
isP1 - Variable in class org.jmol.adapter.writers.CIFWriter
isPaletteVariable(byte) - Static method in enum class org.jmol.c.PAL
isParallel() - Method in class org.jmol.viewer.Viewer
isPartial() - Method in class org.jmol.smiles.SmilesBond
isPartial() - Method in class org.jmol.util.Edge
isPass2 - Variable in class org.jmol.util.GData
isPaused - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
isPaused() - Method in interface org.jmol.api.JmolScriptEvaluator
isPaused() - Method in class org.jmol.script.ScriptEval
isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
isPeriodic - Variable in class org.jmol.jvxl.readers.SurfaceReader
isPhosphorusOnly - Variable in class org.jmol.renderbio.BackboneRenderer
isPhosphorusOnly - Variable in class org.jmol.renderbio.CartoonRenderer
isPhosphorusOnly - Variable in class org.jmol.renderbio.MeshRibbonRenderer
isPhosphorusOnly - Variable in class org.jmol.renderbio.RibbonsRenderer
isPhosphorusOnly - Variable in class org.jmol.renderbio.RocketsRenderer
isPhosphorusOnly - Variable in class org.jmol.renderbio.StrandsRenderer
isPhosphorusOnly - Variable in class org.jmol.renderbio.TraceRenderer
isPickAtomAssignCharge() - Method in class org.jmol.modelkit.ModelKit
isPickleB(byte[]) - Static method in class javajs.util.Rdr
isPickleS(InputStream) - Static method in class javajs.util.Rdr
isPixels - Variable in class jspecview.common.Annotation
isPlugin - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
isPlugin() - Method in class org.openscience.jmol.app.janocchio.Nmr
isPngZipB(byte[]) - Static method in class javajs.util.Rdr
isPngZipStream(InputStream) - Static method in class javajs.util.Rdr
isPoint3f(int) - Method in class org.jmol.script.ScriptParam
isPolygonDisplayable(int) - Method in class org.jmol.render.MeshRenderer
isPolygonDisplayable(int) - Method in class org.jmol.renderspecial.DrawRenderer
isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
isPolymer - Variable in class org.jmol.render.AxesRenderer
isPolymer - Variable in class org.jmol.render.BbcageRenderer
isPolymer - Variable in class org.jmol.render.UccageRenderer
isPolymer() - Method in interface org.jmol.api.SymmetryInterface
isPolymer() - Method in class org.jmol.symmetry.Symmetry
isPolymer() - Method in class org.jmol.util.SimpleUnitCell
isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
isPossibleHBond(HB, HB) - Static method in enum class org.jmol.c.HB
isPreviewOnly - Variable in class org.jmol.viewer.Viewer
isPrimitive - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isPrinting - Variable in class jspecview.common.PanelData
isPrintOnly - Variable in class org.jmol.viewer.Viewer
isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
isPro() - Method in interface jspecview.api.JSVAppletInterface
isPro() - Method in class jspecview.app.JSVApp
isPro() - Method in class jspecview.app.JSVAppPro
isPro() - Method in class jspecview.appletjs.JSVApplet
isPro() - Method in class jspecview.appletjs.JSVAppletPro
isProbableClegSetting(String) - Static method in class org.jmol.symmetry.CLEG
  Determine if the string is of the general form [<type>/]<n>:...,....
isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
isProtein() - Method in class org.jmol.modelset.Group
  group ID-based definition
isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
isPurine() - Method in class org.jmol.modelset.Atom
isPurine() - Method in class org.jmol.modelset.Group
  group ID-based definition
isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isPurine() - Method in class org.jmol.smiles.SmilesAtom
isPurine() - Method in interface org.jmol.util.Node
isPurineByID() - Method in class org.jmol.modelset.Group
  group ID-based definition
isPyrimidine() - Method in class org.jmol.modelset.Atom
isPyrimidine() - Method in class org.jmol.modelset.Group
  group ID-based definition
isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
isPyrimidine() - Method in interface org.jmol.util.Node
isPyrimidineByID() - Method in class org.jmol.modelset.Group
isQuantumBasisSupported(char) - Static method in class org.jmol.quantum.QS
isQueueProcessing() - Method in interface org.jmol.api.JmolScriptManager
isQueueProcessing() - Method in class org.jmol.script.ScriptManager
isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
isQuote(char) - Method in class javajs.util.CifDataParser
  CIF 1.0 only; we handle various quote types here
isQuote(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Includes all possible operator tokens
isRadio - Variable in class org.jmol.awtjs.swing.JRadioButtonMenuItem
isRandom - Variable in class javajs.util.BinaryDocument
isRemote(String) - Static method in class javajs.util.OC
isRenderScalable() - Method in class org.jmol.shapespecial.DrawMesh
isRepaintPending() - Method in interface org.jmol.api.JmolRepaintManager
isRepaintPending() - Method in class org.jmol.render.RepaintManager
isRepaintPending() - Method in class org.jmol.viewer.Viewer
isReset - Variable in class org.jmol.thread.JmolThread
isReversed - Variable in class org.jmol.util.ColorEncoder
isRhombohedral(float[]) - Static method in class org.jmol.util.SimpleUnitCell
isRna() - Method in class org.jmol.modelset.Group
  group ID-based definition
isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isRnaByID() - Method in class org.jmol.modelset.Group
  group ID-based definition
isRotation() - Method in class javajs.util.M3
isScalable() - Method in class jspecview.source.JDXDataObject
isScalar(SV) - Static method in class org.jmol.script.SV
isScaleSet - Variable in class org.jmol.shapespecial.DrawMesh
isScript() - Static method in class jme.JMEUtil.GWT
isScriptExecuting() - Method in class org.jmol.api.JmolViewer
isScriptExecuting() - Method in class org.jmol.viewer.Viewer
isScriptQueued() - Method in interface org.jmol.api.JmolScriptManager
isScriptQueued() - Method in class org.jmol.script.ScriptManager
isScriptType(String) - Static method in class org.jmol.viewer.FileManager
isSelected - Variable in class jspecview.common.PanelNode
isSelected() - Method in interface org.jmol.api.JmolAbstractButton
isSelected() - Method in interface org.jmol.api.SC
isSelected() - Method in class org.jmol.awt.AwtSwingComponent
isSelected() - Method in class org.jmol.awtjs.swing.AbstractButton
isSelected() - Method in class org.jmol.console.JmolLabel
isSelected(int) - Method in class org.jmol.viewer.SelectionManager
isSelected(Object) - Method in interface jspecview.api.PlatformDialog
isSelected(Object) - Method in class jspecview.java.AwtDialog
isSelected(Object) - Method in class jspecview.js2d.JsDialog
isSelected(BS) - Method in class org.jmol.modelset.Group
isSelected(BS, int) - Method in class org.jmol.util.Tensor
isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
isServer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
isSet - Variable in class org.jmol.shape.AtomShape
isSetBrace - Variable in class org.jmol.script.ScriptCompiler
isSetOrDefine - Variable in class org.jmol.script.ScriptCompiler
isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
isSheet() - Method in class org.jmol.modelsetbio.Monomer
isShell - Variable in class org.jmol.render.MeshRenderer
isShell - Variable in class org.jmol.shape.Mesh
isShowAllStacked() - Method in class jspecview.common.PanelData
isSigned - Variable in class jspecview.common.JSViewer
isSigned - Variable in class org.jmol.popup.GenericPopup
isSigned - Variable in class org.jmol.util.GenericApplet
isSigned() - Method in interface jspecview.api.JSVAppletInterface
isSigned() - Method in interface jspecview.api.ScriptInterface
isSigned() - Method in class jspecview.app.JSVApp
isSigned() - Method in class jspecview.app.JSVAppPro
isSigned() - Method in class jspecview.appletjs.JSVApplet
isSigned() - Method in class jspecview.application.JSpecView
isSignedApplet - Variable in class org.jmol.viewer.Viewer
isSilent - Variable in class org.jmol.jvxl.readers.Parameters
isSilent - Variable in class org.openscience.jmol.app.JmolApp
isSimple() - Method in interface org.jmol.api.SymmetryInterface
isSimple() - Method in class org.jmol.symmetry.Symmetry
isSimulation - Variable in class jspecview.common.PanelNode
isSimulation - Variable in class jspecview.source.JDXDataObject
isSingleThreaded - Variable in class jspecview.common.JSViewer
isSingleThreaded - Variable in class org.jmol.viewer.Viewer
isSingleThreaded() - Method in class jspecview.java.AwtPlatform
isSingleThreaded() - Method in class jspecview.js2d.JsPlatform
isSingleThreaded() - Method in interface org.jmol.api.GenericPlatform
isSingleThreaded() - Method in class org.jmol.awt.Platform
isSingleThreaded() - Method in class org.jmol.awtjs2d.Platform
isSlab - Variable in class org.jmol.render.AxesRenderer
isSlab - Variable in class org.jmol.render.BbcageRenderer
isSlab - Variable in class org.jmol.render.UccageRenderer
isSlab() - Method in interface org.jmol.api.SymmetryInterface
isSlab() - Method in class org.jmol.symmetry.Symmetry
isSlab() - Method in class org.jmol.util.SimpleUnitCell
isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
isSlabEnabled - Variable in class org.jmol.export._PovrayExporter
isSlabEnabled - Variable in class org.jmol.export._TachyonExporter
isSmilesCanonical(String) - Static method in class org.jmol.viewer.JC
isSorting() - Method in class org.openscience.jmol.app.janocchio.TableSorter
isSpaceGroupInfoKey(String) - Static method in class org.jmol.viewer.JC
  When UNITCELL NONE is given, clear out all space group and unit cell keys from model info.
isSpinCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
isSpinFixed - Variable in class org.jmol.viewer.TransformManager
isSpinInternal - Variable in class org.jmol.viewer.TransformManager
isSplitFrameSelectable(int) - Method in class org.jmol.viewer.AnimationManager
isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
isSquared - Variable in class org.jmol.jvxl.readers.Parameters
isSquaredLinear - Variable in class org.jmol.jvxl.readers.Parameters
isSSG - Variable in class org.jmol.symmetry.SpaceGroup
isStackable() - Method in class jspecview.source.JDXDataObject
isStarted() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
isStarted() - Method in interface org.openscience.jmol.app.JmolPlugin
isStateScript - Variable in class org.jmol.script.ScriptEval
isStateScript - Variable in class org.jmol.script.ScriptCompiler
isStateScript() - Method in interface org.jmol.api.JmolScriptEvaluator
isStateScript() - Method in class org.jmol.script.ScriptEval
isStepping() - Method in interface org.jmol.api.JmolScriptEvaluator
isStepping() - Method in class org.jmol.script.ScriptEval
isStereo() - Method in class org.jmol.util.Edge
isStereoOpposite(int, int, int) - Method in class org.jmol.smiles.SmilesAtom
isStereoSlave - Variable in class org.jmol.util.GenericApplet
isStopped() - Method in interface org.jmol.api.JmolScriptEvaluator
isStopped() - Method in class org.jmol.script.ScriptEval
isStringArray(String) - Static method in class org.jmol.util.Escape
isSubstructure(String, String) - Method in class org.jmol.viewer.Viewer
isSupercell() - Method in interface org.jmol.api.SymmetryInterface
isSupercell() - Method in class org.jmol.symmetry.Symmetry
isSupercell() - Method in class org.jmol.util.SimpleUnitCell
isSUPERCELL - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
  actual SUPERCELL keyword, not just "cell="
isSurface - Variable in class org.jmol.shapespecial.Dots
isSwingJS - Static variable in class jspecview.common.JSViewer
isSwingJS - Static variable in class org.jmol.viewer.Viewer
isSymmetryCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
isSymmetryCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
isSyntaxAndFileCheck - Variable in class org.jmol.viewer.Viewer
isSyntaxCheck - Variable in class org.jmol.viewer.Viewer
isTainted - Variable in class org.jmol.popup.GenericPopup
isTainted() - Method in class org.jmol.modelset.Measurement
isTar(BufferedInputStream) - Static method in class javajs.util.Rdr
isTerminator(char) - Method in class javajs.util.CifDataParser
  The token terminator is space or tab in CIF 1.0, but it can be quoted strings in CIF 2.0.
isTracker() - Method in class org.jmol.symmetry.CIPData
  Subclass identifier
isTracker() - Method in class org.jmol.symmetry.CIPDataTracker
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isTrajectory - Variable in class org.jmol.modelset.Measurement
isTrajectory - Variable in class org.jmol.modelset.ModelLoader
isTrajectory(int) - Method in class org.jmol.modelset.ModelSet
  could be the base model or one of the subframes
isTrajectoryMeasurement(int[]) - Method in class org.jmol.modelset.ModelSet
isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelSet
isTransform(String, boolean) - Static method in class org.jmol.symmetry.CLEG
isTransformOnly(String) - Static method in class org.jmol.symmetry.CLEG
isTranslation(M4) - Static method in class org.jmol.symmetry.SymmetryOperation
isTranslucent - Variable in class org.jmol.render.MeshRenderer
isTranslucent - Variable in class org.jmol.util.ColorEncoder
isTranslucentInherit - Variable in class org.jmol.render.MeshRenderer
isTransmittance() - Method in class jspecview.source.JDXDataObject
  ///////////// derived info /////////////
isTransparent(short) - Static method in class org.jmol.util.C
isTrue(String) - Static method in class jspecview.common.Parameters
isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
isTwoSided - Variable in class org.jmol.shape.Mesh
isUnits(String) - Static method in class org.jmol.modelset.Measurement
isUnmodulated - Variable in class org.jmol.util.Tensor
isUpperCase(char) - Static method in class javajs.util.PT
isURL(String) - Static method in class jspecview.common.JSVFileManager
isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
isUserFunction(String) - Method in class org.jmol.script.ScriptCompiler
isValid - Variable in class org.jmol.bspt.Bspf
isValid - Variable in class org.jmol.jvxl.data.JvxlData
isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
isValid - Variable in class org.jmol.modelset.Measurement
isValid - Variable in class org.jmol.shape.Mesh
isValid - Variable in class org.jmol.shapespecial.Ellipsoid
isValid - Variable in class org.jmol.shapespecial.Polyhedron
isValid() - Method in class jspecview.common.SubSpecChangeEvent
isValid() - Method in class org.jmol.modelset.Measurement
isValid() - Method in class org.jmol.modelset.StateScript
isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.readers.xtal.ShelxReader
isValidFontName(String) - Method in class jspecview.common.ColorParameters
isValidFontName(String) - Method in class jspecview.java.AwtParameters
isValidFontName(String) - Method in class jspecview.js2d.JsParameters
isValidSym1(char) - Static method in class org.jmol.adapter.smarter.Atom
isValidSym2(char, char) - Static method in class org.jmol.adapter.smarter.Atom
isValidSymNoCase(char, char) - Static method in class org.jmol.adapter.smarter.Atom
isVariableType(Object) - Static method in class org.jmol.script.SV
  Must be updated if getVariable is updated!
isVector - Variable in class org.jmol.shapespecial.DrawMesh
isView - Variable in class jspecview.common.PanelNode
isView - Variable in class jspecview.source.JDXSource
isVisible - Variable in class org.jmol.modelset.Measurement
isVisible - Variable in class org.jmol.shape.Bbcage
isVisible() - Method in interface jspecview.api.AnnotationData
isVisible() - Method in interface jspecview.api.JSVViewPanel
isVisible() - Method in interface jspecview.api.PlatformDialog
isVisible() - Method in class jspecview.common.MeasurementData
isVisible() - Method in class jspecview.dialog.JSVDialog
isVisible() - Method in class jspecview.js2d.JsMainPanel
isVisible() - Method in class jspecview.js2d.JsPanel
isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
isVisible() - Method in class org.jmol.awtjs.swing.Component
isVisible(int) - Method in class org.jmol.modelset.Atom
isVisibleForMe(Atom) - Method in class org.jmol.render.ShapeRenderer
isVisibleNormix(short) - Method in class org.jmol.render.MeshRenderer
isWebGL - Variable in class org.jmol.popup.GenericPopup
isWebGL - Variable in class org.jmol.viewer.Viewer
isWebGL() - Method in interface org.jmol.api.JmolRendererInterface
isWebGL() - Method in class org.jmol.export.Export3D
isWebGL() - Method in class org.jmol.g3d.Graphics3D
isWhitespace(char) - Static method in class javajs.util.PT
isWhiteSpace(String, int) - Static method in class javajs.util.PT
isWild(String) - Static method in class javajs.util.PT
isWindowCentered() - Method in class org.jmol.viewer.TransformManager
isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
isWithin(P3) - Method in class org.jmol.util.BoxInfo
isWithinStructure(STR) - Method in class org.jmol.modelset.Group
isWithinStructure(STR) - Method in class org.jmol.modelsetbio.AlphaMonomer
isWithinSupercell(int, P3, float, float, float, float, float, float, float) - Static method in class org.jmol.adapter.smarter.XtalSymmetry
isWithinUnitCell(P3, float, float, float, float) - Method in interface org.jmol.api.SymmetryInterface
isWithinUnitCell(P3, float, float, float, float) - Method in class org.jmol.symmetry.Symmetry
isXIncreasing() - Method in class jspecview.source.JDXDataObject
  Returns true if the spectrum is increasing; used by SVGExporter only
isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
isXtalState() - Method in class org.jmol.modelkit.ModelKit
isXYZ - Variable in class org.jmol.modelset.ModelSet
isYInRange(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
  Determines if the y values of a spectrum are in a certain range
isZipB(byte[]) - Static method in class javajs.util.Rdr
isZipFile(InputStream) - Static method in class jspecview.common.JSVFileManager
isZipS(InputStream) - Static method in class javajs.util.Rdr
  Check for a ZIP input stream - starting with "PKinvalid input: '<'03>invalid input: '<'04>"
isZipStream(Object) - Method in interface javajs.api.GenericZipTools
isZipStream(Object) - Method in class javajs.util.ZipTools
isZipStream(Object) - Method in class org.jmol.viewer.FileManager
itaIndex - Variable in class org.jmol.symmetry.SpaceGroup
  index in cleg_settings.tab; "-" if in Jmol's list but not at ITA -- 152:_2 and 154:_2
itaNo - Variable in class org.jmol.symmetry.SpaceGroup
  X in X.n or X:a...
itaNumber - Variable in class org.jmol.symmetry.SpaceGroup
itemKeys - Variable in class org.jmol.console.KeyJMenu
itemStateChanged(ItemEvent) - Method in class org.jmol.awt.AwtPopupHelper
itemStateChanged(ItemEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
itemStateChanged(ItemEvent) - Method in class org.jmol.dialog.Dialog.ExportChoiceListener
iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelsetbio.BioResolver
  Pull in all spans of helix, etc.
iToken - Variable in class org.jmol.script.ScriptParam
itokenInfix - Variable in class org.jmol.script.ScriptCompiler
iType - Variable in class com.sparshui.GestureType
iType - Variable in class org.jmol.util.Tensor
iValue(T) - Static method in class org.jmol.script.SV
ivspoints - Variable in class jspecview.source.AnIMLReader
ivspoints - Variable in class jspecview.source.NMRMLReader

## J

j2sHeadless - Static variable in class org.jmol.smiles.SmilesMatcher
J2SIgnoreImport - Annotation Interface in javajs
J2SObjectInterface - Interface in javajs.api.js
  methods in j2s JavaScript accessed in Jmol
J2SRequireImport - Annotation Interface in javajs
JaguarReader - Class in org.jmol.adapter.readers.quantum
  Jaguar reader tested for the two samples files in CVS.
JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
JanaReader - Class in org.jmol.adapter.readers.xtal
  A reader for Jana M50+M40 file pairs.
JanaReader() - Constructor for class org.jmol.adapter.readers.xtal.JanaReader
javaConsoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
javajs - package javajs
javajs.api - package javajs.api
javajs.api.js - package javajs.api.js
javajs.export - package javajs.export
javajs.img - package javajs.img
javajs.util - package javajs.util
javascript - Static variable in class org.jmol.script.T
JButton - Class in org.jmol.awtjs.swing
JButton() - Constructor for class org.jmol.awtjs.swing.JButton
jc - Variable in class org.jmol.awt.AwtSwingComponent
JC - Class in org.jmol.viewer
JC() - Constructor for class org.jmol.viewer.JC
jcampdx - Variable in class jspecview.source.JDXHeader
JcampdxReader - Class in org.jmol.adapter.readers.more
  A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= <Models> acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...
JcampdxReader() - Constructor for class org.jmol.adapter.readers.more.JcampdxReader
jcd - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
JCH3_AYDIN_GUETHER - Static variable in class org.jmol.quantum.NMRCalculation
JCH3_NONE - Static variable in class org.jmol.quantum.NMRCalculation
JCH3_TVAROSKA_TARAVEL - Static variable in class org.jmol.quantum.NMRCalculation
JCH3_WASYLISHEN_SCHAEFER - Static variable in class org.jmol.quantum.NMRCalculation
JCheckBox - Class in org.jmol.awtjs.swing
JCheckBox() - Constructor for class org.jmol.awtjs.swing.JCheckBox
JCheckBoxMenuItem - Class in org.jmol.awtjs.swing
JCheckBoxMenuItem() - Constructor for class org.jmol.awtjs.swing.JCheckBoxMenuItem
JComboBox<T> - Class in org.jmol.awtjs.swing
JComboBox(String[]) - Constructor for class org.jmol.awtjs.swing.JComboBox
JComponent - Class in org.jmol.awtjs.swing
JComponent(String) - Constructor for class org.jmol.awtjs.swing.JComponent
JContentPane - Class in org.jmol.awtjs.swing
JContentPane() - Constructor for class org.jmol.awtjs.swing.JContentPane
JDialog - Class in org.jmol.awtjs.swing
  There is really no need here for awt.Dialog.
JDialog() - Constructor for class org.jmol.awtjs.swing.JDialog
JDXDataObject - Class in jspecview.source
  spectrum data AS READ FROM FILE
JDXDataObject() - Constructor for class jspecview.source.JDXDataObject
JDXDecompressor - Class in jspecview.source
  JDXDecompressor contains static methods to decompress the data part of JCAMP-DX spectra that have been compressed using DIF, FIX, SQZ or PAC formats.
JDXDecompressor(String, int) - Constructor for class jspecview.source.JDXDecompressor
JDXDecompressor(JDXSourceStreamTokenizer, double, double, double, double, int) - Constructor for class jspecview.source.JDXDecompressor
  Initialises the `JDXDecompressor` from the compressed data, the x factor, the y factor and the deltaX value
JDXDecompressorTest - Class in jspecview.source
JDXDecompressorTest() - Constructor for class jspecview.source.JDXDecompressorTest
JDXExporter - Class in jspecview.export
  class `JDXExporter` contains methods for exporting a JCAMP-DX Spectrum in one of the compression formats DIF, FIX, PAC, SQZ or as x, y values.
JDXExporter() - Constructor for class jspecview.export.JDXExporter
JDXHeader - Class in jspecview.source
  could be a spectrum or a source
JDXHeader() - Constructor for class jspecview.source.JDXHeader
JDXHeader.DataLDRTable - Class in jspecview.source
JDXMOLParser - Class in org.jmol.jsv
  Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
JDXMOLParser() - Constructor for class org.jmol.jsv.JDXMOLParser
JDXReader - Class in jspecview.source
  `JDXFileReader` reads JDX data, including complex BLOCK files that contain NTUPLE blocks or nested BLOCK data.
JDXSource - Class in jspecview.source
  `JDXSource` is representation of all the data in the JCAMP-DX file or source.
JDXSource(int, String) - Constructor for class jspecview.source.JDXSource
JDXSourceStreamTokenizer - Class in jspecview.source
JEditorPane - Class in org.jmol.awtjs.swing
  A simple implementation of a Swing JTextPane.
JEditorPane() - Constructor for class org.jmol.awtjs.swing.JEditorPane
JLabel - Class in org.jmol.awtjs.swing
JLabel(String) - Constructor for class org.jmol.awtjs.swing.JLabel
jme - package jme
JME - Class in jme
JME() - Constructor for class jme.JME
JME(JFrame, boolean) - Constructor for class jme.JME
jmeFile() - Method in class jme.JME
jmeh - Variable in class jme.JME
JMEmol - Class in jme
JMEmol(JME, JmolAdapterAtomIterator, JmolAdapterBondIterator) - Constructor for class jme.JMEmol
JMenu - Class in org.jmol.awtjs.swing
JMenu() - Constructor for class org.jmol.awtjs.swing.JMenu
JMenuItem - Class in org.jmol.awtjs.swing
JMenuItem(String) - Constructor for class org.jmol.awtjs.swing.JMenuItem
JMenuItem(String, int) - Constructor for class org.jmol.awtjs.swing.JMenuItem
JmeReader - Class in org.jmol.adapter.readers.simple
JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
jmeToMolecule(String) - Static method in class org.jmol.smiles.SmilesMatcher
JMEUtil - Class in jme
JMEUtil() - Constructor for class jme.JMEUtil
JMEUtil.GWT - Class in jme
  Do nothing , support for JSME code splitting.
JMEUtil.JSME_RunAsyncCallback - Class in jme
JMEUtil.RunAsyncCallback - Interface in jme
  A callback meant to be used by
JMEUtil.RunWhenDataReadyCallback - Interface in jme
jmol - Variable in class jspecview.application.JSpecView
jmol - Static variable in class org.jmol.script.T
Jmol - Class in org.jmol.appletjs
  Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
Jmol - Class in org.openscience.jmol.app
Jmol(Map) - Constructor for class org.jmol.appletjs.Jmol
Jmol(JmolApp, Splash, JFrame, Jmol, int, int, Map, Point) - Constructor for class org.openscience.jmol.app.Jmol
Jmol() - Static method in class org.jmol.awtjs2d.Platform
JMOL - Enum constant in enum class jspecview.common.ScriptToken
JMOL - Enum constant in enum class org.jmol.c.PAL
JMOL - Enum constant in enum class org.jmol.c.VDW
JMOL - Static variable in class org.jmol.util.ColorEncoder
jmol_atoms - Variable in class org.jmol.adapter.writers.CIFWriter
JMOL_DIAMETER - Static variable in class org.jmol.shapecgo.CGOMesh
JMOL_MODEL_KIT - Static variable in class org.jmol.viewer.JC
JMOL_PS - Static variable in class org.jmol.shapecgo.CGOMesh
JMOL_SCREEN - Static variable in class org.jmol.shapecgo.CGOMesh
JMOL_UVMAP - Static variable in class org.jmol.shapecgo.CGOMesh
JmolAbstractButton - Interface in org.jmol.api
JmolAdapter - Class in org.jmol.api
  The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapter() - Constructor for class org.jmol.api.JmolAdapter
JmolAdapterAtomIterator - Interface in org.jmol.api
JmolAdapterBondIterator - Class in org.jmol.api
JmolAdapterBondIterator() - Constructor for class org.jmol.api.JmolAdapterBondIterator
JmolAdapterStructureIterator - Class in org.jmol.api
JmolAdapterStructureIterator() - Constructor for class org.jmol.api.JmolAdapterStructureIterator
JmolAnnotationParser - Interface in org.jmol.api
jmolApp - Variable in class org.openscience.jmol.app.JmolData
jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
JmolApp - Class in org.openscience.jmol.app
JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
  standard Jmol application entry point
JmolAppAPI - Interface in org.jmol.api
JmolAppConsoleInterface - Interface in org.jmol.api
JmolAppletInterface - Interface in org.jmol.api
  This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAsyncException - Exception Class in org.jmol.viewer
JmolAsyncException(String) - Constructor for exception class org.jmol.viewer.JmolAsyncException
JmolAudio - Class in org.jmol.util
JmolAudio() - Constructor for class org.jmol.util.JmolAudio
JmolAudioPlayer - Interface in org.jmol.api
JmolBinding - Class in org.jmol.viewer.binding
JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
JmolButton - Class in org.jmol.console
JmolButton(String) - Constructor for class org.jmol.console.JmolButton
JmolButton(ImageIcon) - Constructor for class org.jmol.console.JmolButton
JmolCallbackListener - Interface in org.jmol.api
JmolChimeMessenger - Interface in org.jmol.viewer
JmolConsole - Class in org.jmol.console
JmolConsole() - Constructor for class org.jmol.console.JmolConsole
JmolData - Class in org.openscience.jmol.app
JmolDataManager - Interface in org.jmol.api
JmolDataReader - Class in org.jmol.adapter.readers.pdb
  JmolData file reader, for a modified PDB format This class also holds pseudo-static methods for spin
JmolDataReader() - Constructor for class org.jmol.adapter.readers.pdb.JmolDataReader
JmolDialogInterface - Interface in org.jmol.api
JmolDropEditor - Interface in org.jmol.api
JmolEnvCalc - Interface in org.jmol.api
JmolFilesReaderInterface - Interface in org.jmol.api
JmolFrame - Interface in jspecview.java
JmolFrame - Interface in org.jmol.awt
jmolFrameType - Variable in class org.jmol.modelset.Model
jmolFrameTypeInt - Variable in class org.jmol.modelset.Model
JmolGenericPopup - Class in org.jmol.popup
  An abstract popup class that is instantiated for a given platform and context as one of:
JmolGenericPopup() - Constructor for class org.jmol.popup.JmolGenericPopup
JmolGestureServerInterface - Interface in org.jmol.api
JmolGraphicsInterface - Interface in org.jmol.api
JmolInChI - Interface in org.jmol.api
jmolinjspecview - Static variable in class org.jmol.script.T
JmolJDXMOLParser - Interface in org.jmol.api
JmolJDXMOLReader - Interface in org.jmol.api
jmolJME - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
JmolJME - Class in org.openscience.jmol.app.jmolpanel
  ONLY for legacy Jmol, not for JmolD (which uses jme.jmeJmol
JmolJME() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolJME
JmolJniClientAdapter - Class in org.jmol.multitouch.jni
JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
JmolJSpecView - Interface in org.jmol.api
JmolLabel - Class in org.jmol.console
JmolLabel(String, int) - Constructor for class org.jmol.console.JmolLabel
JmolMeasurementClient - Interface in org.jmol.api
JmolModulationSet - Interface in org.jmol.api
JmolMolecule - Class in org.jmol.util
  an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
JmolMovieCreatorInterface - Interface in org.jmol.api
JmolMultiTouchAdapter - Interface in org.jmol.multitouch
JmolMultiTouchClient - Interface in org.jmol.multitouch
JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
JmolNavigatorInterface - Interface in org.jmol.api
JmolNMRInterface - Interface in org.jmol.api
jmolObject - Static variable in class org.jmol.viewer.Viewer
jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
JmolPanel - Class in org.openscience.jmol.app.jmolpanel
JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, Map, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.AnimButton - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
  To shutdown when run as an application.
JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
  An Action to copy the current image into the clipboard.
JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.CreditsAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.TwoDEditorAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
JmolParallelProcessor - Interface in org.jmol.api
JmolPdfCreatorInterface - Interface in org.jmol.api
JmolPlugin - Interface in org.openscience.jmol.app
JmolPopup - Class in org.jmol.popup
  An abstract popup class that is instantiated for a given platform and context as one of:
JmolPopup() - Constructor for class org.jmol.popup.JmolPopup
jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
JmolPropertyManager - Interface in org.jmol.api
JmolRendererInterface - Interface in org.jmol.api
JmolRepaintManager - Interface in org.jmol.api
JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
  Provides access to resources (for example, strings and images).
JmolSceneGenerator - Interface in org.jmol.api
JmolScriptEditorInterface - Interface in org.jmol.api
JmolScriptEvaluator - Interface in org.jmol.api
JmolScriptFunction - Interface in org.jmol.api
JmolScriptManager - Interface in org.jmol.api
JmolSelectionListener - Interface in org.jmol.api
  listen to atom selections in a Jmol Viewer
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS - Section in package org.jmol.smiles
Jmol SMILES and Jmol SMARTS Definition of "aromatic" - Section in package org.jmol.smiles
JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
JmolStateCreator - Class in org.jmol.viewer
JmolStateCreator() - Constructor for class org.jmol.viewer.JmolStateCreator
JmolStatusListener - Interface in org.jmol.api
JmolSyncInterface - Interface in org.jmol.api
JmolThread - Class in org.jmol.thread
JmolThread() - Constructor for class org.jmol.thread.JmolThread
JmolToggleButton - Class in org.jmol.console
JmolToggleButton(ImageIcon) - Constructor for class org.jmol.console.JmolToggleButton
JmolToJSmolInterface - Interface in org.jmol.api.js
  methods in JSmol JavaScript accessed in Jmol
JmolTouchSimulator - Class in com.sparshui.inputdevice
  allows Jmol to implement multitouch testing using the mouse press CTRL-LEFT and drag twice for a two-stroke multitouch gesture that will be sent to the server in an interlaced fashion.
JmolTouchSimulator() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator
JmolTouchSimulator.TouchData - Class in com.sparshui.inputdevice
JmolTouchSimulator.TouchDataComparator - Class in com.sparshui.inputdevice
JmolTouchSimulatorInterface - Interface in org.jmol.api
JmolUtil - Class in org.jmol.io
JmolUtil() - Constructor for class org.jmol.io.JmolUtil
JmolViewer - Class in org.jmol.api
  JmolViewer is the main API for the Viewer class.
JmolViewer() - Constructor for class org.jmol.api.JmolViewer
JmolWriter - Interface in org.jmol.api
JmolZipUtilities - Interface in org.jmol.api
join - Static variable in class org.jmol.script.T
join(String[], char, int) - Static method in class javajs.util.PT
JPanel - Class in org.jmol.awtjs.swing
JPanel(LayoutManager) - Constructor for class org.jmol.awtjs.swing.JPanel
JPEG_CONTINUE_STRING - Static variable in class org.jmol.viewer.FileManager
JPEG_EXTENSIONS - Static variable in class org.jmol.viewer.JC
JPG - Enum constant in enum class jspecview.common.ExportType
Jpg64Encoder - Class in javajs.img
Jpg64Encoder() - Constructor for class javajs.img.Jpg64Encoder
JpgEncoder - Class in javajs.img
  JpegEncoder - The JPEG main program which performs a jpeg compression of an image.
JpgEncoder() - Constructor for class javajs.img.JpgEncoder
jpiDispose() - Method in class jspecview.popup.JSVGenericPopup
jpiDispose() - Method in interface org.jmol.api.GenericMenuInterface
jpiDispose() - Method in class org.jmol.popup.GenericPopup
jpiDispose() - Method in class org.jmol.popup.JmolGenericPopup
jpiDispose() - Method in class org.jmol.popup.JmolPopup
jpiGetMenuAsObject() - Method in class jspecview.popup.JSVGenericPopup
jpiGetMenuAsObject() - Method in interface org.jmol.api.GenericMenuInterface
jpiGetMenuAsObject() - Method in class org.jmol.popup.JmolGenericPopup
jpiGetMenuAsString(String) - Method in interface org.jmol.api.GenericMenuInterface
jpiGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
jpiInitialize(PlatformViewer, String) - Method in class jspecview.java.AwtPopup
jpiInitialize(PlatformViewer, String) - Method in class jspecview.js2d.JsPopup
jpiInitialize(PlatformViewer, String) - Method in interface org.jmol.api.GenericMenuInterface
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.popup.JmolGenericPopup
jpiShow(int, int) - Method in class jspecview.popup.JSVGenericPopup
jpiShow(int, int) - Method in interface org.jmol.api.GenericMenuInterface
jpiShow(int, int) - Method in class org.jmol.modelkit.ModelKitPopup
jpiShow(int, int) - Method in class org.jmol.popup.JmolGenericPopup
jpiUpdateComputedMenus() - Method in class jspecview.popup.JSVGenericPopup
jpiUpdateComputedMenus() - Method in interface org.jmol.api.GenericMenuInterface
jpiUpdateComputedMenus() - Method in class org.jmol.modelkit.ModelKitPopup
jpiUpdateComputedMenus() - Method in class org.jmol.popup.JmolPopup
JPopupMenu - Class in org.jmol.awtjs.swing
JPopupMenu(String) - Constructor for class org.jmol.awtjs.swing.JPopupMenu
JRadioButtonMenuItem - Class in org.jmol.awtjs.swing
JRadioButtonMenuItem() - Constructor for class org.jmol.awtjs.swing.JRadioButtonMenuItem
JSAppletObject - Interface in javajs.api.js
JSConsole - Interface in org.jmol.api.js
JScrollPane - Class in org.jmol.awtjs.swing
JScrollPane(JComponent) - Constructor for class org.jmol.awtjs.swing.JScrollPane
JsDialog - Class in jspecview.js2d
  just a class I made to separate the construction of the AnnotationDialogs from their use
JsDialog(DialogManager, JSVDialog, String) - Constructor for class jspecview.js2d.JsDialog
JsDialogManager - Class in jspecview.js2d
  A DialogManager for JavaScript.
JsDialogManager() - Constructor for class jspecview.js2d.JsDialogManager
jsDocumentBase - Static variable in class jspecview.common.JSVFileManager
jsDocumentBase - Static variable in class org.jmol.viewer.Viewer
jsEval(String) - Method in class org.jmol.viewer.Viewer
jsEvalSV(String) - Method in class org.jmol.viewer.Viewer
JSExporter - Class in org.jmol.export
  A class to output WebGL graphics.
JSExporter() - Constructor for class org.jmol.export.JSExporter
JsFileHelper - Class in jspecview.js2d
JsFileHelper() - Constructor for class jspecview.js2d.JsFileHelper
JSFunction - Interface in javajs.api
  A flag that this object is really a JavaScript function that, for example, might be called from setTimeout().
JsG2D - Class in jspecview.js2d
  generic 2D drawing methods for JSpecView -- JavaScript version
JsG2D - Class in org.jmol.awtjs2d
  generic 2D drawing methods -- JavaScript version
JsG2D() - Constructor for class jspecview.js2d.JsG2D
JsG2D() - Constructor for class org.jmol.awtjs2d.JsG2D
JSInterface - Interface in javajs.api
  called by JSmol JavaScript methods using this._applet.xxxx()
JSJmolPopup - Class in org.jmol.awtjs2d
JSJmolPopup() - Constructor for class org.jmol.awtjs2d.JSJmolPopup
  The main popup window for the applet -- as JavaScript
JSJSONParser - Class in javajs.util
  a very simple JSON parser for JSON objects that are compatible with JavaScript A gross simplification of https://github.com/douglascrockford/JSON-java A SUBSET of JSON with similarly to window.JSON.parse(): In JavaScript returns "null" for a null value, not null -- requires quoted strings for keys and values -- does not allow /xxx/ objects
JSJSONParser() - Constructor for class javajs.util.JSJSONParser
JsMainPanel - Class in jspecview.js2d
JsMainPanel() - Constructor for class jspecview.js2d.JsMainPanel
JSME_RunAsyncCallback() - Constructor for class jme.JMEUtil.JSME_RunAsyncCallback
JSModelKitPopup - Class in org.jmol.awtjs2d
JSModelKitPopup() - Constructor for class org.jmol.awtjs2d.JSModelKitPopup
JSmolAppletObject - Interface in org.jmol.api.js
jsmolObject - Static variable in class jspecview.common.JSViewer
json - Static variable in class org.jmol.script.T
JSONEncodable - Interface in javajs.api
JSONException - Exception Class in javajs.util
JSONException(String) - Constructor for exception class javajs.util.JSONException
JsonNioClient - Interface in org.openscience.jmol.app.jsonkiosk
  a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
JsonNioClient.TouchHandler - Class in org.openscience.jmol.app.jsonkiosk
JsonNioClientThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
JsonNioServer - Interface in org.openscience.jmol.app.jsonkiosk
JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
JsonNioService - Class in org.openscience.jmol.app.jsonkiosk
  A class for interacting with Jmol over local sockets.
JsonNioService() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService
JsonNioService.JsonNioClientThread - Class in org.openscience.jmol.app.jsonkiosk
JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jsonkiosk
JSONReader - Class in org.jmol.adapter.readers.simple
JSONReader() - Constructor for class org.jmol.adapter.readers.simple.JSONReader
JSONWriter - Class in org.jmol.util
JSONWriter() - Constructor for class org.jmol.util.JSONWriter
JsPanel - Class in jspecview.js2d
  The JavaScript extension of a JSVPanel.
JsParameters - Class in jspecview.js2d
JsParameters() - Constructor for class jspecview.js2d.JsParameters
JSPattern(String, boolean) - Constructor for class org.jmol.util.PatternMatcher.JSPattern
JSpecView - Class in jspecview.application
  The Main Class or Entry point of the JSpecView Application.
JSpecView(boolean, JSVInterface) - Constructor for class jspecview.application.JSpecView
  The entry point constructor, from Jmol's StatusListener or from the AppletPro object (via MainFrame) or from MainFrame itself.
jspecview.api - package jspecview.api
jspecview.api.js - package jspecview.api.js
jspecview.app - package jspecview.app
jspecview.appletjs - package jspecview.appletjs
jspecview.application - package jspecview.application
jspecview.common - package jspecview.common
jspecview.dialog - package jspecview.dialog
jspecview.exception - package jspecview.exception
jspecview.export - package jspecview.export
jspecview.java - package jspecview.java
jspecview.js2d - package jspecview.js2d
jspecview.popup - package jspecview.popup
jspecview.source - package jspecview.source
jspecview.tree - package jspecview.tree
JsPlatform - Class in jspecview.js2d
  JavaScript 2D canvas version requires Ajax-based URL stream processing.
JsPlatform() - Constructor for class jspecview.js2d.JsPlatform
JSplitPane - Class in org.jmol.awtjs.swing
JSplitPane(int) - Constructor for class org.jmol.awtjs.swing.JSplitPane
JsPopup - Class in jspecview.js2d
JsPopup() - Constructor for class jspecview.js2d.JsPopup
JSPopupHelper - Class in org.jmol.awtjs2d
  For menus, popup-related awt/swing class references are in this file.
JSPopupHelper(GenericPopup) - Constructor for class org.jmol.awtjs2d.JSPopupHelper
jsSurface(Object, T3[], T3[], int[][], int, int, int, BS, int, int, int[], int[]) - Method in class org.jmol.export.JSExporter
JSV - Class in org.jmol.jsv
JSV - Enum constant in enum class jspecview.common.ScriptToken
JSV() - Constructor for class org.jmol.jsv.JSV
JSV_CLOSE - Static variable in class org.jmol.viewer.JC
JSV_NOT - Static variable in class org.jmol.viewer.JC
JSV_SELECT - Static variable in class org.jmol.viewer.JC
JSV_SEND_C13SIMULATE - Static variable in class org.jmol.viewer.JC
JSV_SEND_H1SIMULATE - Static variable in class org.jmol.viewer.JC
JSV_SEND_JDXMOL - Static variable in class org.jmol.viewer.JC
JSV_SETPEAKS - Static variable in class org.jmol.viewer.JC
JSV_STRUCTURE - Static variable in class org.jmol.viewer.JC
JSV_SYNC_KEYWORD_PREFIX - Static variable in class org.jmol.viewer.JC
JSV_SYNC_KEYWORD_PREFIX_LENGTH - Static variable in class org.jmol.viewer.JC
JSVApp - Class in jspecview.app
  JSpecView Applet class.
JSVApp(AppletFrame, boolean) - Constructor for class jspecview.app.JSVApp
JSVAppInterface - Interface in jspecview.api
JSVApplet - Class in jspecview.appletjs
  Entry point for the web.
JSVApplet(Map) - Constructor for class jspecview.appletjs.JSVApplet
JSVAppletInterface - Interface in jspecview.api
JSVAppletObject - Interface in jspecview.api.js
JSVAppletPro - Class in jspecview.appletjs
  A signed applet that has an Advanced...
JSVAppletPro(Map) - Constructor for class jspecview.appletjs.JSVAppletPro
JSVAppPro - Class in jspecview.app
JSVAppPro(AppletFrame, boolean) - Constructor for class jspecview.app.JSVAppPro
JSVDialog - Class in jspecview.dialog
JSVDialog() - Constructor for class jspecview.dialog.JSVDialog
JSVersion - Class in jspecview.common
JSVersion() - Constructor for class jspecview.common.JSVersion
JSVException - Exception Class in jspecview.exception
  JSVException is the base class from which all exceptions in JSpecView is inherited.
JSVException(String) - Constructor for exception class jspecview.exception.JSVException
  Constructor that takes a string specifying exception details
JSVExporter - Interface in jspecview.api
JSVFileDropper - Interface in jspecview.api
JSVFileHelper - Interface in jspecview.api
JSVFileManager - Class in jspecview.common
JSVFileManager() - Constructor for class jspecview.common.JSVFileManager
JSVGenericPopup - Class in jspecview.popup
JSVGenericPopup() - Constructor for class jspecview.popup.JSVGenericPopup
JSViewer - Class in jspecview.common
  This class encapsulates all general functionality of applet and app.
JSViewer(ScriptInterface, boolean, boolean, boolean) - Constructor for class jspecview.common.JSViewer
JSVInterface - Interface in org.jmol.api
  and interface for JSpecView for the Jmol application
JSVMainPanel - Interface in jspecview.api
jsvp - Variable in class jspecview.app.GenericMouse
jsvp - Variable in class jspecview.common.PanelData
jsvp - Variable in class jspecview.common.PanelNode
jsvp - Variable in class jspecview.dialog.JSVDialog
JSVPanel - Interface in jspecview.api
  JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
JSVPdfWriter - Interface in jspecview.api
JSVPopupResourceBundle - Class in jspecview.popup
JSVPopupResourceBundle() - Constructor for class jspecview.popup.JSVPopupResourceBundle
jsvpPopupMenu - Variable in class jspecview.common.JSViewer
JSVPrintDialog - Interface in jspecview.api
JSVToJSmolInterface - Interface in jspecview.api.js
JSVTree - Interface in jspecview.api
JSVTreeNode - Interface in jspecview.api
JSVTreePath - Interface in jspecview.api
jsvViewer - Variable in class jspecview.application.ApplicationMenu
JSVViewPanel - Interface in jspecview.api
JSVZipFileSequentialReader - Class in jspecview.common
  Reads the entire contents of a ZIP file as though it were one straight file Skips and entry that contains '\0' Allows for a moderate amount of buffered reading via mark()
JSVZipFileSequentialReader() - Constructor for class jspecview.common.JSVZipFileSequentialReader
JSVZipInterface - Interface in jspecview.api
JSVZipReader - Interface in jspecview.api
JSVZipUtil - Class in jspecview.common
JSVZipUtil() - Constructor for class jspecview.common.JSVZipUtil
JTable - Class in org.jmol.awtjs.swing
JTable(AbstractTableModel) - Constructor for class org.jmol.awtjs.swing.JTable
JTextField - Class in org.jmol.awtjs.swing
JTextField(String) - Constructor for class org.jmol.awtjs.swing.JTextField
JTextPane - Class in org.jmol.awtjs.swing
  A simple implementation of a Swing JTextPane.
JTextPane() - Constructor for class org.jmol.awtjs.swing.JTextPane
jumpBestFrame() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
JumpBestFrameAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
jumpToSpectrum(Spectrum) - Method in class jspecview.common.PanelData
jumpToSpectrumIndex(int, boolean) - Method in class jspecview.common.PanelData
justifymeasurements - Static variable in class org.jmol.script.T
Jvxl - Class in org.openscience.jvxl
Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
jvxlAppendEncodedNumber(SB, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
JvxlCoder - Class in org.jmol.jvxl.data
JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
  //// string data compression/decompression
jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlCreateHeader(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
  Creates a two-line header for the XJVXL file.
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlCutoffRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlData - Variable in class org.jmol.shape.MeshCollection
jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
JvxlData - Class in org.jmol.jvxl.data
JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlDecodeBitSetRange(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  decode vertex data found within <jvxlVertexData> element as created by jvxlEncodeVertexData (see above)
jvxlDecompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlEncodeBitSet(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEncodeBitSet0(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEncodeBitSetBuffer(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEncodeColorData(float[], float, float, int, int, boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFileSource - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlFractionAsCharacterRange(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], Lst, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetInfoData(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
JvxlReader - Class in org.jmol.jvxl.readers
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  "edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
JvxlWrite - Class in org.openscience.jvxl.simplewriter
JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
JvxlXmlReader - Class in org.jmol.jvxl.readers
jzt - Variable in class javajs.util.CompoundDocument

## K

ka - Variable in class org.jmol.minimize.MinAngle
keep_alive - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
keepHydrogens - Variable in class jme.JME
KET - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Account for keto-enol tautomerism (experimental)
key - Variable in class org.jmol.minimize.MinObject
KEY_MAX - Static variable in class javajs.util.CifDataParser
  The maximum number of columns (data keys) passed to the parser or found in the file for a given loop_ or category.subkey listing.
keybuf - Variable in class org.jmol.viewer.MouseState
keyDown(KeyEvent, int) - Method in class jme.JME
KeyJCheckBox - Class in org.jmol.console
KeyJCheckBox(String, String, Map, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
KeyJCheckBoxMenuItem - Class in org.jmol.console
KeyJCheckBoxMenuItem(String, String, Map, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
KeyJMenu - Class in org.jmol.console
KeyJMenu(String, String, Map) - Constructor for class org.jmol.console.KeyJMenu
KeyJMenuItem - Class in org.jmol.console
KeyJMenuItem(String, String, Map) - Constructor for class org.jmol.console.KeyJMenuItem
KeyJRadioButtonMenuItem - Class in org.jmol.console
KeyJRadioButtonMenuItem(String, String, Map) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
keyPressed(int) - Method in class jspecview.application.CommandHistory
keyPressed(int, int) - Method in class jspecview.common.PanelData
keyPressed(int, int) - Method in interface org.jmol.api.EventManager
keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
  called by MouseManager.keyPressed
keyPressed(KeyEvent) - Method in class jme.JME
keyPressed(KeyEvent) - Method in class jspecview.app.GenericMouse
keyPressed(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
keyPressedEvent(int, char) - Method in class jspecview.application.MainFrame
keyReleased(int) - Method in class jspecview.common.PanelData
keyReleased(int) - Method in interface org.jmol.api.EventManager
keyReleased(int) - Method in class org.jmol.viewer.ActionManager
keyReleased(KeyEvent) - Method in class jme.JME
keyReleased(KeyEvent) - Method in class jspecview.app.GenericMouse
keyReleased(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
keys - Static variable in class org.jmol.script.T
keyType - Variable in class org.jmol.modelkit.ModelKit
  from SET ELEMENTKEY ON/OFF or SET LABELKEY ON/OFF; TRUE to automatically set element keys for all model s; off to turn them off
keyTyped(int, int) - Method in class jspecview.common.PanelData
keyTyped(int, int) - Method in interface org.jmol.api.EventManager
keyTyped(int, int) - Method in class org.jmol.viewer.ActionManager
keyTyped(KeyEvent) - Method in class jme.JME
keyTyped(KeyEvent) - Method in class jspecview.app.GenericMouse
keyTyped(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
keyXy - Variable in class org.jmol.shapesurface.Isosurface
kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
KioskFrame - Class in org.openscience.jmol.app.jsonkiosk
  A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in https://molecularPlayground.org
KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jsonkiosk.KioskFrame
knownGroupID(String) - Static method in class org.jmol.modelsetbio.BioResolver

## L

label - Static variable in class org.jmol.script.T
label - Variable in class org.jmol.shapespecial.Ellipsoid
LABEL - Enum constant in enum class jspecview.common.ScriptToken
label_anchor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_angle_digits - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
LABEL_DEFAULT_OFFSET - Static variable in class org.jmol.viewer.JC
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JC
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JC
label_digits - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_dihedral_digits - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_distance_digits - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LABEL_EXPLICIT - Static variable in class org.jmol.viewer.JC
LABEL_FLAGS - Static variable in class org.jmol.viewer.JC
label_font_id - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
  ////////////// LABEL and ECHO ///////////////////////
LABEL_OFFSET_MAX - Static variable in class org.jmol.viewer.JC
label_outline_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_placement_offset - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LABEL_POINTER_BACKGROUND - Static variable in class org.jmol.viewer.JC
LABEL_POINTER_NONE - Static variable in class org.jmol.viewer.JC
LABEL_POINTER_ON - Static variable in class org.jmol.viewer.JC
label_position - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_shadow_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
label_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LABEL_ZPOS_FRONT - Static variable in class org.jmol.viewer.JC
LABEL_ZPOS_GROUP - Static variable in class org.jmol.viewer.JC
label1 - Variable in class org.jmol.console.GenericConsole
labelColix - Variable in class org.jmol.modelset.Measurement
labelColix - Variable in class org.jmol.render.LabelsRenderer
labelFormat - Variable in class org.jmol.shape.Hover
labelkey - Static variable in class org.jmol.script.T
LabelNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
labelpointerwidth - Static variable in class org.jmol.script.T
labelPointerWidth - Variable in class org.jmol.viewer.GlobalSettings
labels - Static variable in class org.jmol.console.GenericConsole
labels - Variable in class org.jmol.shape.Axes
labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
Labels - Class in org.jmol.shape
Labels() - Constructor for class org.jmol.shape.Labels
labelSetter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
LabelSetter - Class in org.openscience.jmol.app.janocchio
LabelSetter(NMR_Viewer, NoeTable, CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.LabelSetter
LabelsRenderer - Class in org.jmol.render
LabelsRenderer() - Constructor for class org.jmol.render.LabelsRenderer
LabelToken - Class in org.jmol.modelset
LabelToken() - Constructor for class org.jmol.modelset.LabelToken
labelX - Variable in class jme.AtomDisplayLabel
labelY - Variable in class jme.AtomDisplayLabel
labToXyz(P3, P3) - Method in class javajs.img.GifEncoder
language - Variable in class org.jmol.i18n.Language
language - Static variable in class org.jmol.script.T
language - Variable in class org.jmol.util.GenericApplet
Language - Class in org.jmol.i18n
languagetranslation - Static variable in class org.jmol.script.T
LargeMolecules - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Allows input of molecules up to 32767 atoms [Produces 'InChI=1B' indicating beta status of resulting identifiers]
last - Static variable in class org.jmol.script.T
LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.C
lastAtomIndex - Variable in class org.jmol.modelset.Group
lastDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
lastElement() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
lastFlowCommand - Variable in class org.jmol.script.ScriptCompiler
lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
lastIndexOf(String) - Method in class javajs.util.SB
lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
lastModelIndex - Variable in class org.jmol.atomdata.AtomData
lastModelSet - Variable in class org.jmol.modelkit.ModelKit
lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
lastPressTime - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
lastRepaintTime - Variable in class org.jmol.thread.JmolThread
lastToken - Variable in class org.jmol.script.ScriptCompiler
lastX - Variable in class jspecview.export.AMLExporter
lastX - Variable in class jspecview.export.CMLExporter
lastX - Variable in class jspecview.source.AnIMLReader
lastX - Variable in class jspecview.source.NMRMLReader
latestMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
lattice - Static variable in class org.jmol.script.T
lattice - Variable in class org.jmol.shape.Mesh
LATTICE_VECTOR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
latticeOffset - Variable in class org.jmol.render.MeshRenderer
latticeScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
latticeType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
launchMainFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
launchMainFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
layout - Variable in class jspecview.common.PrintLayout
  The paper orientation ("portrait" or "landscape")
layoutDialog() - Method in class jspecview.dialog.JSVDialog
LayoutManager - Class in org.jmol.awtjs.swing
LayoutManager() - Constructor for class org.jmol.awtjs.swing.LayoutManager
layoutWindow(String) - Method in class org.jmol.console.AppletConsole
layoutWindow(String) - Method in class org.jmol.console.GenericConsole
layoutWindow(String) - Method in class org.jmol.consolejs.AppletConsole
layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
lcaocartoon - Static variable in class org.jmol.script.T
LcaoCartoon - Class in org.jmol.shapesurface
LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
LcaoCartoonRenderer - Class in org.jmol.rendersurface
LcaoCartoonRenderer() - Constructor for class org.jmol.rendersurface.LcaoCartoonRenderer
leadatom - Static variable in class org.jmol.script.T
leadAtomIndex - Variable in class org.jmol.modelset.Group
leadAtomIndices - Variable in class org.jmol.modelsetbio.BioPolymer
leadAtomIndices - Variable in class org.jmol.renderbio.BackboneRenderer
leadAtomIndices - Variable in class org.jmol.renderbio.CartoonRenderer
leadAtomIndices - Variable in class org.jmol.renderbio.MeshRibbonRenderer
leadAtomIndices - Variable in class org.jmol.renderbio.RibbonsRenderer
leadAtomIndices - Variable in class org.jmol.renderbio.RocketsRenderer
leadAtomIndices - Variable in class org.jmol.renderbio.StrandsRenderer
leadAtomIndices - Variable in class org.jmol.renderbio.TraceRenderer
leadMidpoints - Variable in class org.jmol.modelsetbio.BioPolymer
leadPoints - Variable in class org.jmol.modelsetbio.BioPolymer
left - Variable in class jspecview.common.PanelData
left - Static variable in class org.jmol.script.T
LEFT - Static variable in class org.jmol.awtjs.swing.SwingConstants
LEFT - Static variable in class org.jmol.viewer.binding.Binding
leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
leftbrace - Static variable in class org.jmol.script.T
leftDifference(Quat) - Method in class javajs.util.Quat
leftdivide - Static variable in class org.jmol.script.T
leftJustify(SB, String, String) - Static method in class javajs.util.PT
leftMargin - Static variable in class jspecview.common.PanelData
leftPanel - Variable in class jspecview.java.AwtDialog
leftPanel - Variable in class jspecview.js2d.JsDialog
leftparen - Static variable in class org.jmol.script.T
leftsquare - Static variable in class org.jmol.script.T
legacy_mouse_zoom - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
legacy_vdw_radii - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
legacyautobonding - Static variable in class org.jmol.script.T
legacyhaddition - Static variable in class org.jmol.script.T
legacyjavafloat - Static variable in class org.jmol.script.T
legacyJavaFloat - Variable in class org.jmol.viewer.GlobalSettings
legend - Variable in class jspecview.common.PanelNode
length - Static variable in class org.jmol.script.T
length() - Method in class javajs.util.BS
  Returns the "logical size" of this `BitSet`: the index of the highest set bit in the `BitSet` plus one.
length() - Method in class javajs.util.SB
length() - Method in class javajs.util.T3
  Returns the length of this vector.
length() - Method in class javajs.util.V3d
  Returns the length of this vector.
length() - Method in interface org.jmol.api.GenericFileInterface
lengthSquared() - Method in class javajs.util.T3
  Returns the squared length of this vector.
lengthSquared() - Method in class javajs.util.V3d
  Returns the squared length of this vector.
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
LEVEL_INFO - Static variable in class org.jmol.util.Logger
LEVEL_MAX - Static variable in class org.jmol.util.Logger
LEVEL_WARN - Static variable in class org.jmol.util.Logger
LEXICAL_COMPARATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
light - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light_count - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LIGHT_GRAY - Static variable in class jspecview.common.ColorParameters
light2 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light3 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light4 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light5 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light6 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light7 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light8 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
light9 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
lighting - Static variable in class org.jmol.script.T
lighting - Variable in class org.jmol.shape.Mesh
lightSource - Variable in class org.jmol.export.___Exporter
LIME - Static variable in class org.jmol.util.C
LimitedLineReader - Class in javajs.util
  A simple class to read a designated number of bytes from a file and then return them line by line, skipping lines that start with #, and including the \n or \r characters at line ends.
LimitedLineReader(BufferedReader, int) - Constructor for class javajs.util.LimitedLineReader
line - Variable in class javajs.util.CifDataParser
  from buffered reader
line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
line - Variable in class org.jmol.jvxl.readers.JvxlReader
line - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
line - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
line - Static variable in class org.jmol.script.T
LINE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
line_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
line_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
line_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
LINE_SEGMENT - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
line_smooth - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
line_stick_helper - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
line_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
line_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
lineCurrent - Variable in class org.jmol.script.ScriptCompiler
linedata - Static variable in class org.jmol.script.T
lineData - Variable in class org.jmol.shape.Mesh
lineHeight - Variable in class org.jmol.modelset.Text
lineIndices - Variable in class org.jmol.script.ScriptContext
lines - Variable in class org.jmol.modelset.Text
lines - Static variable in class org.jmol.script.T
lineto(int, int) - Method in class javajs.export.PDFCreator
lineTo(Object, int, int) - Method in class jspecview.common.PDFWriter
lineTo(Object, int, int) - Method in class jspecview.java.AwtG2D
lineTo(Object, int, int) - Method in class jspecview.js2d.JsG2D
lineTo(Object, int, int) - Method in interface org.jmol.api.GenericGraphics
lineTo(Object, int, int) - Method in class org.jmol.awt.AwtG2D
lineTo(Object, int, int) - Method in class org.jmol.awtjs2d.JsG2D
LINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
lineWidthMad - Variable in class org.jmol.export.___Exporter
link - Static variable in class org.jmol.script.T
LINK - Enum constant in enum class jspecview.common.ScriptToken
LINK_TYPE_AROM - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_BITS - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_DELO - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_DOUBLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_GENERIC_LINK - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
  types set by filter TOPOSE_TYPES in the format of one or more of {v, vw, hb} separated by "+"; default is v+hb
LINK_TYPE_HBOND - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_OCTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_OTHER - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_PI - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_POLY - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_QUADRUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_QUINTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_SEPTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_SEXTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_SINGLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_TRIPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
LINK_TYPE_VDW - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
  Opens a web page in an external browser
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
  Follows the reference in an link.
linkedMesh - Variable in class org.jmol.shape.Mesh
linkedMesh - Variable in class org.jmol.shape.MeshCollection
linkSpectra(PanelData.LinkMode) - Method in class jspecview.common.PanelData
linkTypes - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
list - Variable in class org.jmol.awtjs.swing.Container
list - Static variable in class org.jmol.script.T
list(SB) - Method in class org.jmol.shapespecial.Polyhedron
LIST - Enum constant in enum class jspecview.common.IntegralData.IntMode
listBS(BS) - Method in class org.jmol.script.ScriptEval
listCommands - Variable in class org.jmol.viewer.Viewer
ListDataReader - Class in javajs.util
  VectorDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with Vector<String> arrays without any further adaptation.
ListDataReader() - Constructor for class javajs.util.ListDataReader
listf - Static variable in class org.jmol.script.T
listParameter(int, int, int) - Method in class org.jmol.script.ScriptParam
listParameter4(int, int, int, boolean) - Method in class org.jmol.script.ScriptParam
listSavedStates() - Method in class org.jmol.viewer.StateManager
ListSelectionModel - Interface in org.jmol.awtjs.swing
lo - Variable in class org.jmol.util.ColorEncoder
load - Static variable in class org.jmol.script.T
load(BufferedReader) - Method in class jspecview.application.DisplaySchemesProcessor
  Loads the display schemes into memory and stores them in a `Vector`
load(String) - Method in class jspecview.application.DisplaySchemesProcessor
  Loads the display schemes into memory and stores them in a `Vector`
LOAD - Enum constant in enum class jspecview.common.ScriptToken
LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JC
LOAD_OPTION_FILL_RANGE - Static variable in class org.jmol.viewer.JC
loadAndRun(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
loadatomdatatolerance - Static variable in class org.jmol.script.T
loadButton - Variable in class org.jmol.console.GenericConsole
loadContent(String) - Method in interface org.jmol.api.JmolDropEditor
  Deprecated.
loadContent(String) - Method in class org.jmol.console.ScriptEditor
loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
loadData() - Method in class jspecview.dialog.JSVDialog
loadDefault() - Method in class jspecview.application.DisplaySchemesProcessor
  Load a default DisplayScheme if xml file not found
loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
loadDefaultXML() - Method in class jspecview.application.DisplaySchemesProcessor
loadDOMNode(Object) - Method in interface org.jmol.api.JmolAppletInterface
loadDOMNode(Object) - Method in class org.jmol.util.GenericApplet
loadFile(String) - Method in interface org.jmol.api.JmolDropEditor
loadFile(String) - Method in class org.jmol.console.ScriptEditor
loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
  When dropped, if the data are 2D, then read directly into JME.
loadFileAsync(String, String, int, boolean) - Method in class org.jmol.script.ScriptEval
  Allows asynchronous file loading from the LOAD or SCRIPT command.
loadFileAsynchronously(Object, JSAppletObject, String, Object) - Method in interface javajs.api.js.J2SObjectInterface
LOADFILECALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
loadFileResourceAsync(String) - Method in interface org.jmol.api.JmolScriptEvaluator
loadFileResourceAsync(String) - Method in class org.jmol.script.ScriptEval
  load a static file asynchronously
loadformat - Static variable in class org.jmol.script.T
loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
loadImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
  Load an image
loadImage(GenericPlatform, String, String, byte[], Object) - Method in interface org.jmol.api.js.JmolToJSmolInterface
loadImageData(Object, String, String, Object) - Method in class org.jmol.viewer.Viewer
  NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage
loadImaginary - Variable in class jspecview.common.JSViewer
LOADIMAGINARY - Enum constant in enum class jspecview.common.ScriptToken
loadInline(String) - Method in interface jspecview.api.JSVAppletInterface
  Loads in-line JCAMP-DX data into the existing applet window
loadInline(String) - Method in class jspecview.app.JSVApp
  Loads in-line JCAMP-DX data into the existing applet window
loadInline(String) - Method in class jspecview.appletjs.JSVApplet
loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String) - Method in class org.jmol.api.JmolViewer
loadInline(String) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String) - Method in class org.jmol.viewer.Viewer
  from Applet and external applications only
loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String[]) - Method in class org.jmol.api.JmolViewer
loadInline(String[]) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String[]) - Method in class org.jmol.viewer.Viewer
  external apps only
loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
  external apps and applet only
loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String[], String) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String, char) - Method in class org.jmol.api.JmolViewer
loadInline(String, char) - Method in class org.jmol.viewer.Viewer
  external apps only
loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String, String) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(List, boolean) - Method in class org.jmol.api.JmolViewer
  NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
loadInline(List, boolean) - Method in class org.jmol.viewer.Viewer
  External applications only; does not preserve state -- intentionally!
loadInlineAppend(String, boolean) - Method in class org.jmol.api.JmolViewer
loadInlineAppend(String, boolean) - Method in class org.jmol.viewer.Viewer
  used by applet and console
loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
loadInlineArray(String[], String, boolean) - Method in class org.jmol.util.GenericApplet
loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
loadInlineString(String, String, boolean) - Method in class org.jmol.util.GenericApplet
loadligandformat - Static variable in class org.jmol.script.T
LoadMeasureThread - Class in org.openscience.jmol.app.janocchio
LoadMeasureThread() - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
LoadMeasureThread(NMR_JmolPanel, String) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
LoadMeasureThreadJSON - Class in org.openscience.jmol.app.janocchio
LoadMeasureThreadJSON(NMR_JmolPanel, Map) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
loadModelFromFile(String, String, String[], Object, boolean, Map, SB, SB, int, String) - Method in class org.jmol.viewer.Viewer
  Used by the ScriptEvaluator LOAD command to open one or more files.
loadScript - Variable in class org.jmol.modelset.Model
loadShape(int) - Method in class org.jmol.viewer.ShapeManager
loadState - Variable in class org.jmol.modelset.Model
LOADSTRUCT - Enum constant in enum class org.jmol.c.CBK
loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
lobe - Static variable in class org.jmol.script.T
Location - Class in com.sparshui.common
  Represents a 2D location with float values.
Location() - Constructor for class com.sparshui.common.Location
  Cosntruct a default location.
Location(float, float) - Constructor for class com.sparshui.common.Location
  Construct a specific location.
LocContact - Variable in class jspecview.source.AnIMLReader
LocContact - Variable in class jspecview.source.NMRMLReader
LOCCRC - Static variable in class javajs.api.GenericZipInputStream
LOCEXT - Static variable in class javajs.api.GenericZipInputStream
LOCFLG - Static variable in class javajs.api.GenericZipInputStream
LOCHDR - Static variable in class javajs.api.GenericZipInputStream
LOCHOW - Static variable in class javajs.api.GenericZipInputStream
LOCLEN - Static variable in class javajs.api.GenericZipInputStream
LOCNAM - Static variable in class javajs.api.GenericZipInputStream
LocName - Variable in class jspecview.source.AnIMLReader
LocName - Variable in class jspecview.source.NMRMLReader
LOCSIG - Static variable in class javajs.api.GenericZipInputStream
LOCSIZ - Static variable in class javajs.api.GenericZipInputStream
LOCTIM - Static variable in class javajs.api.GenericZipInputStream
LOCVER - Static variable in class javajs.api.GenericZipInputStream
log - Static variable in class org.jmol.script.T
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
  Method to output a log.
log(String) - Static method in class jme.JMEUtil.GWT
log(String) - Method in interface org.jmol.atomdata.AtomDataServer
log(String) - Method in class org.jmol.minimize.forcefield.ForceField
log(String) - Method in class org.jmol.viewer.Viewer
log_box_selections - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
log_conformations - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
logcommands - Static variable in class org.jmol.script.T
logCommands - Variable in class org.jmol.viewer.GlobalSettings
logfile - Static variable in class org.jmol.script.T
Logger - Class in org.jmol.util
  Logger mechanism.
LoggerInterface - Interface in org.jmol.util
  Interface used for the logging mechanism.
loggestures - Static variable in class org.jmol.script.T
logGestures - Variable in class org.jmol.viewer.GlobalSettings
logging - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
logging - Variable in class javajs.img.ImageEncoder
logInfo(String) - Method in class org.jmol.symmetry.CIPChirality
loglevel - Static variable in class org.jmol.script.T
logLevel() - Static method in class org.jmol.util.Logger
  Indicates if the level is logged.
logMessages - Variable in class org.jmol.script.ScriptCompiler
lonepair - Static variable in class org.jmol.script.T
longdate - Variable in class jspecview.export.AMLExporter
longdate - Variable in class jspecview.export.CMLExporter
longDate - Variable in class jspecview.source.JDXHeader
LongDate - Variable in class jspecview.source.AnIMLReader
LongDate - Variable in class jspecview.source.NMRMLReader
longToByteArray(byte[], int, long) - Static method in class com.sparshui.common.utils.Converter
lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEval
lookupInterpolatedVoxelValue(T3, boolean) - Method in class org.jmol.jvxl.data.VolumeData
lookupSpecialAtomID(String) - Method in class org.jmol.modelsetbio.BioResolver
loop - Static variable in class org.jmol.script.T
LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
LooseTSACheck - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Relax criteria of ambiguous drawing for in-ring tetrahedral stereo
LOW - Static variable in class org.jmol.util.ColorEncoder
lowPrecision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
lp - Static variable in class org.jmol.script.T
Lst<V> - Class in javajs.util
  created to remove ambiguities in add and remove
Lst() - Constructor for class javajs.util.Lst
lstDipoles - Variable in class org.jmol.shapespecial.Dipole
lstNCS - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
lumo - Static variable in class org.jmol.script.T

## M

m - Variable in class javajs.util.Matrix
m - Variable in class org.jmol.util.MeshSlicer
m00 - Variable in class javajs.util.M34
  The first element of the first row
m01 - Variable in class javajs.util.M34
  The second element of the first row.
m02 - Variable in class javajs.util.M34
  third element of the first row.
m03 - Variable in class javajs.util.M4
  The fourth element of the first row.
m10 - Variable in class javajs.util.M34
  The first element of the second row.
m11 - Variable in class javajs.util.M34
  The second element of the second row.
m12 - Variable in class javajs.util.M34
  The third element of the second row.
m13 - Variable in class javajs.util.M4
  The fourth element of the second row.
m20 - Variable in class javajs.util.M34
  The first element of the third row.
m21 - Variable in class javajs.util.M34
  The second element of the third row.
m22 - Variable in class javajs.util.M34
  The third element of the third row.
m23 - Variable in class javajs.util.M4
  The fourth element of the third row.
M3 - Class in javajs.util
  A single precision floating point 3 by 3 matrix.
M3() - Constructor for class javajs.util.M3
  Constructs and initializes a Matrix3f to all zeros.
m30 - Variable in class javajs.util.M4
  The first element of the fourth row.
m31 - Variable in class javajs.util.M4
  The second element of the fourth row.
m32 - Variable in class javajs.util.M4
  The third element of the fourth row.
m33 - Variable in class javajs.util.M4
  The fourth element of the fourth row.
M34 - Class in javajs.util
  A base class for both M3 and M4 to conserve code size.
M34() - Constructor for class javajs.util.M34
M4 - Class in javajs.util
  A single precision floating point 4 by 4 matrix.
M4() - Constructor for class javajs.util.M4
  all zeros
MAC_COMMAND - Static variable in class org.jmol.awtjs.Event
MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
macro - Static variable in class org.jmol.script.T
macrodirectory - Static variable in class org.jmol.script.T
mad - Variable in class org.jmol.modelset.Bond
mad - Variable in class org.jmol.modelset.Measurement
mad - Variable in class org.jmol.modelset.MeasurementData
mad - Variable in class org.jmol.render.ShapeRenderer
mad - Variable in class org.jmol.shape.AtomShape
mad - Variable in class org.jmol.shapespecial.Dipole
MAD_GLOBAL - Static variable in class org.jmol.modelset.Atom
madAtom - Variable in class org.jmol.modelset.Atom
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JC
mads - Variable in class org.jmol.renderbio.BackboneRenderer
mads - Variable in class org.jmol.renderbio.CartoonRenderer
mads - Variable in class org.jmol.renderbio.MeshRibbonRenderer
mads - Variable in class org.jmol.renderbio.RibbonsRenderer
mads - Variable in class org.jmol.renderbio.RocketsRenderer
mads - Variable in class org.jmol.renderbio.StrandsRenderer
mads - Variable in class org.jmol.renderbio.TraceRenderer
mads - Variable in class org.jmol.shape.AtomShape
MAGENTA - Static variable in class org.jmol.util.C
magMoment - Variable in class org.jmol.util.Vibration
magneticshielding - Static variable in class org.jmol.script.T
MagresReader - Class in org.jmol.adapter.readers.xtal
MagresReader() - Constructor for class org.jmol.adapter.readers.xtal.MagresReader
main(String[]) - Static method in class jme.JME
main(String[]) - Static method in class jspecview.application.JSpecView
main(String[]) - Static method in class jspecview.application.MainFrame
main(String[]) - Static method in class jspecview.source.JDXDecompressorTest
main(String[]) - Static method in class jspecview.source.JDXReader
main(String[]) - Static method in class org.jmol.adapter.writers.CDXMLWriter
main(String[]) - Static method in class org.jmol.quantum.NMRNoeMatrix
main(String[]) - Static method in class org.jmol.symmetry.SpaceGroupFinder
main(String[]) - Static method in class org.molecularplayground.MPJmolApp
main(String[]) - Static method in class org.openscience.jmol.app.janocchio.Nmr
main(String[]) - Static method in class org.openscience.jmol.app.Jmol
main(String[]) - Static method in class org.openscience.jmol.app.JmolData
main(String[]) - Static method in class org.openscience.jmol.app.jmolpanel.JmolJME
main(String[]) - Static method in class org.openscience.jvxl.Jvxl
main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
MAIN - Static variable in class org.jmol.thread.JmolThread
mainFrame - Variable in class jspecview.application.ApplicationMenu
mainFrame - Variable in class jspecview.application.AppToolBar
MainFrame - Class in jspecview.application
  The Main Class or Entry point of the JSpecView Application.
MainFrame(JSpecView, Component, JSVInterface) - Constructor for class jspecview.application.MainFrame
  Constructor
mainPanel - Variable in class jspecview.common.JSViewer
MainPopupResourceBundle - Class in org.jmol.popup
MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
mainSplitPane - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
majorVersion - Static variable in class jspecview.common.JSVersion
majorVersion - Static variable in class org.jmol.viewer.JC
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
  // super-overloaded methods ///////
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
makeConnections2(float, float, int, int, BS, BS, BS, boolean, boolean, float, SB) - Method in class org.jmol.modelset.ModelSet
manager - Variable in class jspecview.dialog.JSVDialog
manager - Variable in class jspecview.java.AwtDialog
manager - Variable in class jspecview.js2d.JsDialog
manifest - Static variable in class org.jmol.script.T
map(Object, String, String, Map) - Static method in class org.jmol.console.GenericConsole
map_auto_expand_sym - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mapAddKey(String) - Method in class org.jmol.util.JSONWriter
mapAddKeyValue(String, Object, String) - Method in class org.jmol.util.JSONWriter
mapAddKeyValueRaw(String, Object, String) - Method in class org.jmol.util.JSONWriter
  Add a key:value pair where value is already quoted
mapAddMapAllExcept(String, Map, String) - Method in class org.jmol.util.JSONWriter
mapCloned - Variable in class org.jmol.adapter.readers.xml.CDXMLParser
mapClose() - Method in class org.jmol.util.JSONWriter
mapGet(String) - Method in class org.jmol.script.SV
mapLattice - Variable in class org.jmol.jvxl.data.JvxlData
mapLattice - Variable in class org.jmol.jvxl.readers.Parameters
mapOpen() - Method in class org.jmol.util.JSONWriter
mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
mapPolyhedra(int, int, boolean, M4) - Method in class org.jmol.scriptext.SmilesExt
mapproperty - Static variable in class org.jmol.script.T
mapPut(String, SV) - Method in class org.jmol.script.SV
mapSpins(Map) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
mapSpins(Map) - Method in class org.jmol.symmetry.SpaceGroup
mapString - Variable in class jme.AtomDisplayLabel
mapUnique - Variable in class org.jmol.smiles.SmilesSearch
marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
MarchingCubes - Class in org.jmol.jvxl.calc
MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
MarchingCubes(VertexDataServer, VolumeData, Parameters, BS) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
  /////////////////////////////////////////////////////////////
MarchingSquares - Class in org.jmol.jvxl.calc
MarchingSquares(VertexDataServer, VolumeData, P4, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
mark() - Method in class jme.JMEmol
mark(int) - Method in class jspecview.common.JSVZipFileSequentialReader
mark(long) - Method in class javajs.util.ArrayDataReader
mark(long) - Method in class javajs.util.ListDataReader
MARK - Enum constant in enum class jspecview.common.IntegralData.IntMode
markLines(String, char) - Static method in class org.jmol.util.Parser
markUsed - Variable in class jme.JME
MAROON - Static variable in class org.jmol.util.C
mass - Static variable in class org.jmol.script.T
mat4 - Variable in class org.jmol.modelset.Model
  mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
mat4 - Variable in class org.jmol.util.MeshSurface
match(String) - Method in class org.jmol.symmetry.CIPData
  Return a bit set corresponding to a SMARTS
match(String) - Method in class org.jmol.symmetry.CIPDataSmiles
matcher(String) - Method in class org.jmol.util.PatternMatcher.JSPattern
matchesFilePath(String) - Method in class jspecview.source.JDXSource
matchesPeakTypeModel(String, String) - Method in class jspecview.common.Spectrum
  Find a matching spectrum by type (IR, 1HNMR,...) and model name
matFor(String) - Method in class org.jmol.symmetry.CLEG.ClegData
mathExpressionCommand - Static variable in class org.jmol.script.T
MathExt - Class in org.jmol.scriptext
MathExt() - Constructor for class org.jmol.scriptext.MathExt
mathfunc - Static variable in class org.jmol.script.T
mathop - Static variable in class org.jmol.script.T
mathproperty - Static variable in class org.jmol.script.T
matrix - Static variable in class org.jmol.script.T
Matrix - Class in javajs.util
  streamlined and refined for Jmol by Bob Hanson from http://math.nist.gov/javanumerics/jama/ Jama = Java Matrix class.
Matrix(double[][], int, int) - Constructor for class javajs.util.Matrix
  Construct a matrix quickly without checking arguments.
matrix_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
matrix3f - Static variable in class org.jmol.script.T
matrix4f - Static variable in class org.jmol.script.T
matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
matrixCtoFNoOffset - Variable in class org.jmol.util.SimpleUnitCell
matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
matrixFtoCNoOffset - Variable in class org.jmol.util.SimpleUnitCell
matrixRotate - Variable in class org.jmol.viewer.TransformManager
matrixStereo - Variable in class org.jmol.viewer.TransformManager
matrixTemp - Variable in class org.jmol.viewer.TransformManager
matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
matrixTest - Variable in class org.jmol.viewer.TransformManager
matrixToRationalString(M34) - Static method in class org.jmol.symmetry.SymmetryOperation
  rxyz option creates tab-separated string representation of a 3x4 (r,t) or 3x3 matrix with rational fractions adds "|" prior to translation; does NOT add last row of 0 0 0 1 `( 1 -1 0 | 1/2 0 0 1 | -1/2 0 1 0 | 0 )`
matrixToScript(Object) - Static method in class org.jmol.util.Escape
matrixTransform - Variable in class org.jmol.viewer.TransformManager
matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
max - Static variable in class org.jmol.script.T
MAX_ALPHA_SIZE - Static variable in interface org.apache.tools.bzip2.BZip2Constants
MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
MAX_CODE_LEN - Static variable in interface org.apache.tools.bzip2.BZip2Constants
MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
MAX_SELECTORS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
max_threads - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
max_triangles - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MAX_TYPE_SUPPORTED - Static variable in class org.jmol.quantum.QS
max_ups - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MAXABS - Static variable in class jspecview.common.Spectrum
maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JC
MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
maxSerial - Variable in class org.jmol.adapter.readers.cif.CifReader
maxset - Static variable in class org.jmol.script.T
maxSphereCache - Static variable in class org.jmol.util.Shader
maxXOnScale - Variable in class jspecview.common.ScaleData
  the maximim X value on the scale, usually maxX
maxYOnScale - Variable in class jspecview.common.ScaleData
maybeGetBaseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
mayScript - Variable in class org.jmol.util.GenericApplet
mc - Variable in class org.jmol.modelset.ModelSet
  model count
MdCrdReader - Class in org.jmol.adapter.readers.more
  Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
MdTopReader - Class in org.jmol.adapter.readers.more
  A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
measure - Static variable in class org.jmol.script.T
Measure - Class in javajs.util
Measure - Class in org.openscience.jmol.app.janocchio
Measure() - Constructor for class javajs.util.Measure
MEASURE - Enum constant in enum class org.jmol.c.CBK
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
measureallmodels - Static variable in class org.jmol.script.T
MeasureCouple - Class in org.openscience.jmol.app.janocchio
MeasureCouple(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureCouple
MeasureDist - Class in org.openscience.jmol.app.janocchio
  Calculates the difference between calculated and experimental values for coloring table
MeasureDist(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureDist
measureDistanceUnits - Variable in class org.jmol.viewer.GlobalSettings
Measurement - Class in jspecview.common
  The `Measurement` class stores an annotation that is a measurement
Measurement - Class in org.jmol.modelset
Measurement() - Constructor for class jspecview.common.Measurement
Measurement() - Constructor for class org.jmol.modelset.Measurement
measurementCount - Variable in class org.jmol.shape.Measures
MeasurementData - Class in jspecview.common
MeasurementData - Class in org.jmol.modelset
MeasurementData() - Constructor for class org.jmol.modelset.MeasurementData
measurementlabels - Static variable in class org.jmol.script.T
measurementnumbers - Static variable in class org.jmol.script.T
MeasurementPending - Class in org.jmol.modelset
MeasurementPending() - Constructor for class org.jmol.modelset.MeasurementPending
measurements - Static variable in class org.jmol.script.T
measurements - Variable in class org.jmol.shape.Measures
Measurements - Enum constant in enum class jspecview.common.Annotation.AType
measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
MeasurementsDialog - Class in jspecview.dialog
  Dialog for managing the measurement list for a Spectrum within a GraphSet
MeasurementsDialog() - Constructor for class jspecview.dialog.MeasurementsDialog
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
MeasurementTable(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
  Constructor
measurementunits - Static variable in class org.jmol.script.T
MeasureNoe - Class in org.openscience.jmol.app.janocchio
MeasureNoe(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureNoe
Measures - Class in org.jmol.shape
Measures() - Constructor for class org.jmol.shape.Measures
MeasuresRenderer - Class in org.jmol.render
MeasuresRenderer() - Constructor for class org.jmol.render.MeasuresRenderer
menu - Static variable in class org.jmol.script.T
menuAddButtonGroup(SC) - Method in class org.jmol.awt.AwtPopupHelper
menuAddButtonGroup(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuAddButtonGroup(SC) - Method in interface org.jmol.popup.PopupHelper
menuAddSeparator(SC) - Method in class org.jmol.popup.GenericPopup
menuAddSubMenu(SC, SC) - Method in class org.jmol.popup.GenericPopup
menuCheckBoxCallback(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
menuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
menuClearListeners(SC) - Method in class org.jmol.awt.AwtPopupHelper
  Listener methods
menuClearListeners(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuClearListeners(SC) - Method in interface org.jmol.popup.PopupHelper
menuClickCallback(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
menuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
menuCreateCheckboxItem(SC, String, String, String, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
menuCreateItem(SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
menuCreatePopup(String, Object) - Method in class org.jmol.awt.AwtPopupHelper
menuCreatePopup(String, Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuCreatePopup(String, Object) - Method in interface org.jmol.popup.PopupHelper
menuEnable(SC, boolean) - Method in class org.jmol.popup.GenericPopup
menuEnabled() - Method in class org.jmol.viewer.Viewer
menuFocusCallback(String, String, boolean) - Method in class jspecview.java.AwtPopup
menuFocusCallback(String, String, boolean) - Method in class jspecview.js2d.JsPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.popup.GenericPopup
  //// run time event-driven methods
menuGetId(SC) - Method in class org.jmol.popup.GenericPopup
menuGetListPosition(SC) - Method in class org.jmol.popup.GenericPopup
menuHidePopup(SC) - Method in class org.jmol.awt.AwtModelKitPopup
menuHidePopup(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
menuHidePopup(SC) - Method in class org.jmol.modelkit.ModelKitPopup
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awt.AwtPopupHelper
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuInsertSubMenu(SC, SC, int) - Method in interface org.jmol.popup.PopupHelper
menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
menuMap - Variable in class org.jmol.console.GenericConsole
menuName - Variable in class org.jmol.popup.GenericPopup
menuNewSubMenu(String, String) - Method in class org.jmol.popup.GenericPopup
MENUON - Enum constant in enum class jspecview.common.ScriptToken
menuRemoveAll(SC, int) - Method in class org.jmol.popup.GenericPopup
menuSetAutoscrolls(SC) - Method in class org.jmol.popup.GenericPopup
menuSetLabel(SC, String) - Method in class org.jmol.popup.GenericPopup
menuShowPopup(SC, int, int) - Method in class jspecview.java.AwtPopup
menuShowPopup(SC, int, int) - Method in class jspecview.js2d.JsPopup
  could be frank menu or regular context menu
menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtJmolPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtModelKitPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSJmolPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSModelKitPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.popup.GenericPopup
menuStructure - Variable in class org.jmol.api.JmolViewer
menuText - Variable in class org.jmol.popup.JmolGenericPopup
mep - Static variable in class org.jmol.script.T
mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
MepCalculation - Class in org.jmol.quantum
MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
merge(MeshCollection) - Method in class org.jmol.shape.MeshCollection
  called by ParallelProcessor at completion
merge(MeshCollection) - Method in class org.jmol.shapesurface.LcaoCartoon
merge(MeshCollection) - Method in class org.jmol.shapesurface.MolecularOrbital
mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
mergeBufferPixel(int, int, int) - Static method in class org.jmol.g3d.Graphics3D
mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelSet
  initial transfer of model data from old to new model set.
mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
mesh - Variable in class org.jmol.render.MeshRenderer
mesh - Static variable in class org.jmol.script.T
Mesh - Class in org.jmol.shape
Mesh() - Constructor for class org.jmol.shape.Mesh
  always use Mesh().mesh1(thisID, colix, index)
mesh_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_carve_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_carve_selection - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_carve_state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_clear_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_clear_selection - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_clear_state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_grid_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_lighting - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_negative_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_negative_visible - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_normals - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_skip - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_solvent - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_type - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mesh1(Viewer, String, short, int) - Method in class org.jmol.shape.Mesh
MeshCapper - Class in org.jmol.util
  A class to properly cap a convoluted, closed slice of an isosurface inspired by: Computational Geometry: Algorithms and Applications Mark de Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
MeshCapper() - Constructor for class org.jmol.util.MeshCapper
MeshCapper.MeshCapperSorter - Class in org.jmol.util
MeshCapperSorter() - Constructor for class org.jmol.util.MeshCapper.MeshCapperSorter
meshColix - Variable in class org.jmol.shape.Mesh
MeshCollection - Class in org.jmol.shape
MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
meshColor - Variable in class org.jmol.jvxl.data.JvxlData
meshCount - Variable in class org.jmol.shape.MeshCollection
meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
MeshData - Class in org.jmol.jvxl.data
MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
MeshData.SortSet - Class in org.jmol.jvxl.data
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
MeshDataServer - Interface in org.jmol.jvxl.api
meshes - Variable in class org.jmol.shape.MeshCollection
meshes - Variable in class org.jmol.shapebio.BioShape
meshReady - Variable in class org.jmol.shapebio.BioShape
MeshRenderer - Class in org.jmol.render
  an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
MeshRenderer() - Constructor for class org.jmol.render.MeshRenderer
meshRibbon - Static variable in class org.jmol.script.T
MeshRibbon - Class in org.jmol.shapebio
MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
MeshRibbonRenderer - Class in org.jmol.renderbio
MeshRibbonRenderer() - Constructor for class org.jmol.renderbio.MeshRibbonRenderer
meshscale - Static variable in class org.jmol.script.T
meshSlabValue - Variable in class org.jmol.render.MeshRenderer
MeshSlicer - Class in org.jmol.util
MeshSlicer() - Constructor for class org.jmol.util.MeshSlicer
MeshSurface - Class in org.jmol.util
MeshSurface() - Constructor for class org.jmol.util.MeshSurface
meshType - Variable in class org.jmol.util.MeshSurface
meshWidth - Variable in class org.jmol.shapecgo.CGOMesh
message - Static variable in class org.jmol.script.T
MESSAGE - Enum constant in enum class org.jmol.c.CBK
MessagePackReader - Class in javajs.util
  A simple MessagePack reader.
MessagePackReader() - Constructor for class javajs.util.MessagePackReader
MessagePackReader(GenericBinaryDocumentReader, boolean) - Constructor for class javajs.util.MessagePackReader
messageQueue - Variable in class org.jmol.viewer.StatusManager
messagestylechime - Static variable in class org.jmol.script.T
MessageType() - Constructor for class com.sparshui.common.ClientProtocol.MessageType
META_MASK - Static variable in class org.jmol.awtjs.Event
mf - Variable in class org.jmol.util.JmolMolecule
mi - Variable in class org.jmol.util.Point3fi
  model index -- may be to a trajectory
middle - Static variable in class org.jmol.script.T
MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
min - Static variable in class org.jmol.script.T
MIN - Enum constant in enum class jspecview.common.IntegralData.IntMode
MIN_ADDH - Static variable in class org.jmol.viewer.Viewer
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
MIN_GROUP_SELECT - Static variable in class org.jmol.viewer.Viewer
MIN_HAVE_FIXED - Static variable in class org.jmol.viewer.Viewer
min_mesh_spacing - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MIN_MODELKIT - Static variable in class org.jmol.viewer.Viewer
MIN_QUICK - Static variable in class org.jmol.viewer.Viewer
MIN_SELECT_ONLY - Static variable in class org.jmol.viewer.Viewer
MIN_SELECTED - Static variable in class org.jmol.viewer.Viewer
MIN_SILENT - Static variable in class org.jmol.viewer.Viewer
MIN_XX - Static variable in class org.jmol.viewer.Viewer
MinAngle - Class in org.jmol.minimize
minAngles - Variable in class org.jmol.minimize.Minimizer
MinAtom - Class in org.jmol.minimize
minAtoms - Variable in class org.jmol.minimize.Minimizer
MinBond - Class in org.jmol.minimize
minbonddistance - Static variable in class org.jmol.script.T
minBonds - Variable in class org.jmol.minimize.Minimizer
minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
minGrid - Variable in class org.jmol.jvxl.data.VolumeData
minHeight - Variable in class org.jmol.awtjs.swing.Component
MINIMIZATION - Enum constant in enum class org.jmol.c.CBK
minimizationcriterion - Static variable in class org.jmol.script.T
minimizationmaxatoms - Static variable in class org.jmol.script.T
minimizationOn() - Method in class org.jmol.minimize.Minimizer
minimizationrefresh - Static variable in class org.jmol.script.T
minimizationreportsteps - Static variable in class org.jmol.script.T
minimizationsilent - Static variable in class org.jmol.script.T
minimizationsteps - Static variable in class org.jmol.script.T
MinimizationThread - Class in org.jmol.minimize
MinimizationThread() - Constructor for class org.jmol.minimize.MinimizationThread
minimize - Static variable in class org.jmol.script.T
minimize(int, double, BS, BS, BS, int, String) - Method in class org.jmol.minimize.Minimizer
minimize(JmolScriptEvaluator, int, float, BS, BS, BS, float, int) - Method in class org.jmol.viewer.Viewer
  From the MINIMIZE command and other sources.
MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JC
minimizeEnd(BS, boolean) - Method in class org.jmol.modelkit.ModelKit
Minimizer - Class in org.jmol.minimize
Minimizer() - Constructor for class org.jmol.minimize.Minimizer
MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
minList - Variable in class org.jmol.minimize.MMConstraint
minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
minmaxmask - Static variable in class org.jmol.script.T
MinObject - Class in org.jmol.minimize
MinObject() - Constructor for class org.jmol.minimize.MinObject
minpixelselradius - Static variable in class org.jmol.script.T
MinPosition - Class in org.jmol.minimize
  not implemented -- would be a force toward a given position in space
minScreenDimension - Variable in class org.jmol.export._PovrayExporter
minScreenDimension - Variable in class org.jmol.export._TachyonExporter
minset - Static variable in class org.jmol.script.T
MinTorsion - Class in org.jmol.minimize
minTorsions - Variable in class org.jmol.minimize.Minimizer
minus - Static variable in class org.jmol.script.T
minusMinus - Static variable in class org.jmol.script.T
minWidth - Variable in class org.jmol.awtjs.swing.Component
minXOnScale - Variable in class jspecview.common.ScaleData
  the minimum X value on the scale, usually minX
minYOnScale - Variable in class jspecview.common.ScaleData
misc - Static variable in class org.jmol.script.T
mlp - Static variable in class org.jmol.script.T
MlpCalculation - Class in org.jmol.quantum
MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
mm - Variable in class org.jmol.viewer.Viewer
MMCifReader - Class in org.jmol.adapter.readers.cif
  mmCIF files are recognized prior to class creation.
MMCifReader() - Constructor for class org.jmol.adapter.readers.cif.MMCifReader
MMCifValidationParser - Class in org.jmol.adapter.readers.cif
MMCifValidationParser() - Constructor for class org.jmol.adapter.readers.cif.MMCifValidationParser
MMConstraint - Class in org.jmol.minimize
MMConstraint(int[], double) - Constructor for class org.jmol.minimize.MMConstraint
MMTFReader - Class in org.jmol.adapter.readers.cif
  JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md Note added 2024.01.19 Jose Duarte 2:03 PM (email) to MMTF-Users From July 2024 the PDB file archive will not be offered in the compressed MMTF format anymore.
MMTFReader() - Constructor for class org.jmol.adapter.readers.cif.MMTFReader
mo - Static variable in class org.jmol.script.T
MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
MOCalculation - Class in org.jmol.quantum
MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
moData - Variable in class org.jmol.jvxl.readers.Parameters
modAverage - Variable in class org.jmol.adapter.readers.cif.MSRdr
modAxes - Variable in class org.jmol.adapter.readers.cif.MSRdr
modDim - Variable in class org.jmol.adapter.readers.cif.MSRdr
modDim - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
modDim - Variable in class org.jmol.util.Vibration
  modDim will be > 0 for modulation
mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
mode - Variable in class org.jmol.render.LabelsRenderer
mode - Static variable in class org.jmol.script.T
mode - Variable in class org.jmol.viewer.TransformManager
MODE_ABC - Static variable in class org.jmol.symmetry.SymmetryOperation
MODE_CALC_2JHH - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_3JCH - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_3JHH - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_ALL - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_INVALID - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_J - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_JHH - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CALC_NOE - Static variable in class org.jmol.quantum.NMRCalculation
MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_MODEL - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
MODE_MASK - Static variable in class org.jmol.viewer.binding.Binding
MODE_MXYZ - Static variable in class org.jmol.symmetry.SymmetryOperation
MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
MODE_P_ALLOW_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
MODE_P_CONVERT_TO_CARTESIAN - Static variable in class org.jmol.script.ScriptParam
MODE_P_IMPLICIT_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
MODE_P_INT_ONLY - Static variable in class org.jmol.script.ScriptParam
MODE_P_NULL_ON_ERROR - Static variable in class org.jmol.script.ScriptParam
MODE_P3 - Static variable in class org.jmol.script.ScriptParam
MODE_P34 - Static variable in class org.jmol.script.ScriptParam
MODE_P4 - Static variable in class org.jmol.script.ScriptParam
MODE_PERSPECTIVE_PYMOL - Static variable in class org.jmol.viewer.TransformManager
MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
MODE_UVW - Static variable in class org.jmol.symmetry.SymmetryOperation
MODE_XYZ - Static variable in class org.jmol.symmetry.SymmetryOperation
mode2d - Static variable in class org.jmol.script.T
model - Variable in class jspecview.export.AMLExporter
model - Variable in class jspecview.export.CMLExporter
model - Variable in class org.jmol.modelset.Chain
model - Variable in class org.jmol.modelsetbio.BioPolymer
model - Static variable in class org.jmol.script.T
model(int, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
Model - Class in org.jmol.modelset
Model() - Constructor for class org.jmol.modelset.Model
modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
modelbased - Static variable in class org.jmol.script.T
modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelSet
modelFileNumbers - Variable in class org.jmol.modelset.ModelSet
modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
modelindex - Static variable in class org.jmol.script.T
modelIndex - Variable in class org.jmol.adapter.writers.CIFWriter
modelIndex - Variable in class org.jmol.atomdata.AtomData
modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
modelIndex - Variable in class org.jmol.modelset.Measurement
modelIndex - Variable in class org.jmol.modelset.MeasurementData
modelIndex - Variable in class org.jmol.modelset.Model
modelIndex - Variable in class org.jmol.modelset.Text
modelIndex - Variable in class org.jmol.popup.JmolPopup
modelIndex - Variable in class org.jmol.shape.Mesh
modelIndex - Variable in class org.jmol.shape.MeshCollection
modelIndex - Variable in class org.jmol.shapebio.BioShape
modelIndex - Variable in class org.jmol.shapespecial.Polyhedron
modelIndex - Variable in class org.jmol.util.JmolMolecule
modelIndex - Variable in class org.jmol.util.Tensor
modelIndex(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
modelInfo - Variable in class org.jmol.adapter.writers.CIFWriter
modelInfo - Variable in class org.jmol.popup.JmolPopup
modelInvRotation - Variable in class org.jmol.jvxl.readers.Parameters
modelIsRawPDB() - Method in class org.jmol.modelset.Atom
modelIsRawPDB() - Method in class org.jmol.smiles.SmilesAtom
modelIsRawPDB() - Method in interface org.jmol.util.Node
ModelKit - Class in org.jmol.modelkit
  An abstract popup class that is instantiated for a given platform and context as one of:
ModelKit() - Constructor for class org.jmol.modelkit.ModelKit
MODELKIT - Enum constant in enum class org.jmol.c.CBK
MODELKIT_ADDCONSTRAINT - Static variable in class org.jmol.viewer.JC
MODELKIT_ADDHYDROGEN - Static variable in class org.jmol.viewer.JC
MODELKIT_ADDHYDROGENS - Static variable in class org.jmol.viewer.JC
MODELKIT_ALLOPERATORS - Static variable in class org.jmol.viewer.JC
MODELKIT_APPLYFULL - Static variable in class org.jmol.viewer.JC
MODELKIT_APPLYLOCAL - Static variable in class org.jmol.viewer.JC
MODELKIT_ASSIGN_BOND - Static variable in class org.jmol.viewer.JC
MODELKIT_ATOMPICKINGMODE - Static variable in class org.jmol.viewer.JC
MODELKIT_ATOMTYPE - Static variable in class org.jmol.viewer.JC
MODELKIT_AUTOBOND - Static variable in class org.jmol.viewer.JC
MODELKIT_BONDINDEX - Static variable in class org.jmol.viewer.JC
MODELKIT_BONDPICKINGMODE - Static variable in class org.jmol.viewer.JC
MODELKIT_BONDTYPE - Static variable in class org.jmol.viewer.JC
MODELKIT_BRANCH_ATOM_DRAGGED - Static variable in class org.jmol.viewer.JC
MODELKIT_BRANCH_ATOM_PICKED - Static variable in class org.jmol.viewer.JC
MODELKIT_CENTER - Static variable in class org.jmol.viewer.JC
MODELKIT_CLICKTOSETELEMENT - Static variable in class org.jmol.viewer.JC
MODELKIT_CONSTRAINT - Static variable in class org.jmol.viewer.JC
MODELKIT_DATA - Static variable in class org.jmol.viewer.JC
MODELKIT_DELETE_BOND - Static variable in class org.jmol.viewer.JC
MODELKIT_DISTANCE - Static variable in class org.jmol.viewer.JC
MODELKIT_DRAGATOM - Static variable in class org.jmol.viewer.JC
MODELKIT_ELEMENT_KEY - Static variable in class org.jmol.viewer.JC
MODELKIT_ELEMENT_KEY_ID - Static variable in class org.jmol.viewer.JC
MODELKIT_EXISTS - Static variable in class org.jmol.viewer.JC
MODELKIT_FRAME_RESIZED - Static variable in class org.jmol.viewer.JC
MODELKIT_HIDDEN - Static variable in class org.jmol.viewer.JC
MODELKIT_HIDEMENU - Static variable in class org.jmol.viewer.JC
MODELKIT_HIGHLIGHT - Static variable in class org.jmol.viewer.JC
MODELKIT_HOVERLABEL - Static variable in class org.jmol.viewer.JC
MODELKIT_INITIALIZE_MODEL - Static variable in class org.jmol.viewer.JC
MODELKIT_INVARIANT - Static variable in class org.jmol.viewer.JC
MODELKIT_ISMOLECULAR - Static variable in class org.jmol.viewer.JC
MODELKIT_KEY - Static variable in class org.jmol.viewer.JC
MODELKIT_LABEL_KEY - Static variable in class org.jmol.viewer.JC
MODELKIT_MINIMIZING - Static variable in class org.jmol.viewer.JC
MODELKIT_MODE - Static variable in class org.jmol.viewer.JC
MODELKIT_MODEL_KEY - Static variable in class org.jmol.viewer.JC
MODELKIT_NEW_MODEL_ATOM_KEYS - Static variable in class org.jmol.viewer.JC
MODELKIT_OFFSET - Static variable in class org.jmol.viewer.JC
MODELKIT_REMOVEALLCONSTRAINTS - Static variable in class org.jmol.viewer.JC
MODELKIT_REMOVECONSTRAINT - Static variable in class org.jmol.viewer.JC
MODELKIT_RESET - Static variable in class org.jmol.viewer.JC
MODELKIT_RETAINLOCAL - Static variable in class org.jmol.viewer.JC
MODELKIT_ROTATE_BOND_ATOM_INDEX - Static variable in class org.jmol.viewer.JC
MODELKIT_ROTATEBONDINDEX - Static variable in class org.jmol.viewer.JC
MODELKIT_SCREENXY - Static variable in class org.jmol.viewer.JC
MODELKIT_SET_ELEMENT_KEY - Static variable in class org.jmol.viewer.JC
MODELKIT_SET_LABEL_KEY - Static variable in class org.jmol.viewer.JC
MODELKIT_SHOWSYMOPINFO - Static variable in class org.jmol.viewer.JC
MODELKIT_SYMMETRY - Static variable in class org.jmol.viewer.JC
MODELKIT_SYMOP - Static variable in class org.jmol.viewer.JC
MODELKIT_UDPATE_KEY_STATE - Static variable in class org.jmol.viewer.JC
MODELKIT_UNITCELL - Static variable in class org.jmol.viewer.JC
MODELKIT_UPDATE_ATOM_KEYS - Static variable in class org.jmol.viewer.JC
MODELKIT_UPDATE_MODEL_KEYS - Static variable in class org.jmol.viewer.JC
MODELKIT_VIBRATION - Static variable in class org.jmol.viewer.JC
MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JC
MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JC
modelkitmode - Static variable in class org.jmol.script.T
ModelKitPopup - Class in org.jmol.modelkit
  An abstract popup class that is instantiated for a given platform and context as one of:
ModelKitPopup() - Constructor for class org.jmol.modelkit.ModelKitPopup
ModelKitPopupResourceBundle - Class in org.jmol.modelkit
ModelKitPopupResourceBundle(String, Properties) - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
ModelLoader - Class in org.jmol.modelset
ModelLoader(Viewer, String, SB, Object, ModelSet, BS) - Constructor for class org.jmol.modelset.ModelLoader
modelMap - Variable in class org.jmol.adapter.readers.cif.CifReader
modelName - Variable in class org.jmol.atomdata.AtomData
modelNames - Variable in class org.jmol.modelset.ModelSet
modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
modelNumberParameter(int) - Method in class org.jmol.script.ScriptParam
modelNumbers - Variable in class org.jmol.modelset.ModelSet
modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelSet
modelRadius - Variable in class org.jmol.viewer.TransformManager
modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
ModelSet - Class in org.jmol.modelset
ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
modelSetName - Variable in class org.jmol.modelset.ModelSet
modelSetProperties - Variable in class org.jmol.modelset.ModelSet
modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
modelStartEnd - Variable in class org.jmol.adapter.smarter.Structure
modelType - Variable in class jspecview.source.AnIMLReader
modelType - Variable in class jspecview.source.NMRMLReader
modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
modeMultipleBond - Variable in class org.jmol.viewer.GlobalSettings
modifiersWhenPressed10 - Variable in class jspecview.app.GenericMouse
modify - Static variable in class org.jmol.script.T
MODIFY_ASSIGN_ATOM - Static variable in class org.jmol.viewer.Viewer
MODIFY_ASSIGN_BOND - Static variable in class org.jmol.viewer.Viewer
MODIFY_DELETE_ATOM - Static variable in class org.jmol.viewer.Viewer
MODIFY_DELETE_ATOMS - Static variable in class org.jmol.viewer.Viewer
MODIFY_DELETE_BONDS - Static variable in class org.jmol.viewer.Viewer
MODIFY_DELETE_MODEL - Static variable in class org.jmol.viewer.Viewer
MODIFY_SET_COORD - Static variable in class org.jmol.viewer.Viewer
modifyorcreate - Static variable in class org.jmol.script.T
modo - Static variable in class org.jmol.script.T
modScale - Variable in class org.jmol.util.Vibration
modt1 - Static variable in class org.jmol.script.T
modt2 - Static variable in class org.jmol.script.T
modt3 - Static variable in class org.jmol.script.T
modulateoccupancy - Static variable in class org.jmol.script.T
modulation - Static variable in class org.jmol.script.T
Modulation - Class in org.jmol.util
  A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
Modulation(char, char, double[], String, double[]) - Constructor for class org.jmol.util.Modulation
  Each atomic modulation involves a fractional coordinate wave vector q, a Fourier power n, a modulation axis (x, y, or, z), and specified parameters that depend upon the type of function.
modulationscale - Static variable in class org.jmol.script.T
modulationScale - Variable in class org.jmol.viewer.GlobalSettings
ModulationSet - Class in org.jmol.util
  A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
ModulationSet() - Constructor for class org.jmol.util.ModulationSet
MODULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
modx - Static variable in class org.jmol.script.T
modxyz - Static variable in class org.jmol.script.T
mody - Static variable in class org.jmol.script.T
modz - Static variable in class org.jmol.script.T
moe_separate_chains - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MOEnergySorter() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
mol - Variable in class jme.JME
Mol2Reader - Class in org.jmol.adapter.readers.more
  A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
Mol3DReader - Class in org.jmol.adapter.readers.molxyz
  3D only
Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
MoldenReader - Class in org.jmol.adapter.readers.quantum
  A molecular structure and orbital reader for MolDen files.
MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
molecular - Static variable in class org.jmol.script.T
MolecularOrbital - Class in org.jmol.shapesurface
MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
MolecularOrbitalRenderer - Class in org.jmol.rendersurface
MolecularOrbitalRenderer() - Constructor for class org.jmol.rendersurface.MolecularOrbitalRenderer
molecule - Static variable in class org.jmol.script.T
MOLECULE - Enum constant in enum class org.jmol.c.PAL
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND_STEREO - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_FORMULA - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
moleculeCount - Variable in class org.jmol.modelset.BondCollection
moleculeCount - Variable in class org.jmol.modelset.Model
moleculeID - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
moleculeIndex - Variable in class org.jmol.util.JmolMolecule
molecules - Variable in class org.jmol.modelset.BondCollection
moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
molFile() - Method in class jme.JME
molform - Variable in class jspecview.export.AMLExporter
molform - Variable in class jspecview.export.CMLExporter
molForm - Variable in class jspecview.source.AnIMLReader
molForm - Variable in class jspecview.source.NMRMLReader
MolReader - Class in org.jmol.adapter.readers.molxyz
  A reader for MDLI mol and sdf files.
MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
mols - Variable in class jme.JME
MOLWriter - Class in org.jmol.adapter.writers
MOLWriter() - Constructor for class org.jmol.adapter.writers.MOLWriter
monitorenergy - Static variable in class org.jmol.script.T
monomer - Static variable in class org.jmol.script.T
Monomer - Class in org.jmol.modelsetbio
  A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
Monomer() - Constructor for class org.jmol.modelsetbio.Monomer
MONOMER - Enum constant in enum class org.jmol.c.PAL
monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
monomerCount - Variable in class org.jmol.renderbio.BackboneRenderer
monomerCount - Variable in class org.jmol.renderbio.CartoonRenderer
monomerCount - Variable in class org.jmol.renderbio.MeshRibbonRenderer
monomerCount - Variable in class org.jmol.renderbio.RibbonsRenderer
monomerCount - Variable in class org.jmol.renderbio.RocketsRenderer
monomerCount - Variable in class org.jmol.renderbio.StrandsRenderer
monomerCount - Variable in class org.jmol.renderbio.TraceRenderer
monomerCount - Variable in class org.jmol.shape.AtomShape
monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
monomers - Variable in class org.jmol.modelsetbio.BioPolymer
monomers - Variable in class org.jmol.renderbio.BackboneRenderer
monomers - Variable in class org.jmol.renderbio.CartoonRenderer
monomers - Variable in class org.jmol.renderbio.MeshRibbonRenderer
monomers - Variable in class org.jmol.renderbio.RibbonsRenderer
monomers - Variable in class org.jmol.renderbio.RocketsRenderer
monomers - Variable in class org.jmol.renderbio.StrandsRenderer
monomers - Variable in class org.jmol.renderbio.TraceRenderer
monomers - Variable in class org.jmol.shapebio.BioShape
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
MopacArchiveReader - Class in org.jmol.adapter.readers.simple
  Mopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cell
MopacArchiveReader() - Constructor for class org.jmol.adapter.readers.simple.MopacArchiveReader
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.CsfReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
  Reads Mopac 2007 GRAPHF output files
MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
MopacReader - Class in org.jmol.adapter.readers.simple
  Reads Mopac 93, 6, 7, 2002, or 2009 output files
MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
MOReader - Class in org.jmol.adapter.readers.quantum
  General methods for reading molecular orbital data, including embedded output from the NBO program.
MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
moreLabels(Map) - Method in class org.openscience.jmol.app.janocchio.NmrGuiMap
  See NMR_JmolPanel where "NMR." is processed, and ./Properties/Nmr.properties where they are defined
moreLabels(Map) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
  Add more labels if desired
morph - Static variable in class org.jmol.script.T
morph(float) - Method in class org.jmol.viewer.AnimationManager
morphAtoms(BS, P3[][], int, float, P3) - Method in class org.jmol.modelset.ModelSet
morphTrajectories(int, int, float) - Method in class org.jmol.modelset.ModelSet
moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
motion_bias - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
motion_hand - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
motion_linear - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
motion_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
motion_simple - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
motionDisabled - Variable in class org.molecularplayground.MPJmolApp
moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
mouse - Static variable in class org.jmol.script.T
Mouse - Class in org.jmol.awtjs2d
  JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
Mouse(double, Viewer, Object) - Constructor for class org.jmol.awtjs2d.Mouse
MOUSE_DOWN - Static variable in class org.jmol.awtjs.Event
MOUSE_DRAG - Static variable in class org.jmol.awtjs.Event
MOUSE_ENTER - Static variable in class org.jmol.awtjs.Event
MOUSE_EXIT - Static variable in class org.jmol.awtjs.Event
mouse_grid - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MOUSE_LEFT - Static variable in class org.jmol.awtjs.Event
mouse_limit - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MOUSE_MIDDLE - Static variable in class org.jmol.awtjs.Event
MOUSE_MOVE - Static variable in class org.jmol.awtjs.Event
MOUSE_NONE - Static variable in class org.jmol.viewer.JC
mouse_restart_movie_delay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MOUSE_RIGHT - Static variable in class org.jmol.awtjs.Event
mouse_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mouse_selection_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
MOUSE_UP - Static variable in class org.jmol.awtjs.Event
MOUSE_WHEEL - Static variable in class org.jmol.awtjs.Event
mouse_wheel_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mouse_z_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mouseAction(int, long, int, int, int, int) - Method in class jspecview.common.PanelData
mouseAction(int, long, int, int, int, int) - Method in interface org.jmol.api.EventManager
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
mouseClicked(MouseEvent) - Method in class jme.JME
mouseClicked(MouseEvent) - Method in class jspecview.app.GenericMouse
mouseClicked(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseClicked(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseDown(MouseEvent, int, int) - Method in class jme.JME
mouseDrag(MouseEvent, int, int) - Method in class jme.JME
mousedragfactor - Static variable in class org.jmol.script.T
mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
mouseDragged(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
mouseDragged(MouseEvent) - Method in class jme.JME
mouseDragged(MouseEvent) - Method in class jspecview.app.GenericMouse
mouseDragged(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseEntered(MouseEvent) - Method in class jme.JME
mouseEntered(MouseEvent) - Method in class jspecview.app.GenericMouse
mouseEntered(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseEnterExit(long, int, int, boolean) - Method in class jspecview.common.PanelData
mouseEnterExit(long, int, int, boolean) - Method in interface org.jmol.api.EventManager
mouseEnterExit(long, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
mouseExited(MouseEvent) - Method in class jme.JME
mouseExited(MouseEvent) - Method in class jspecview.app.GenericMouse
mouseExited(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseListener - Variable in class org.jmol.awtjs.swing.Component
mouseMove(MouseEvent, int, int) - Method in class jme.JME
mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
mouseMoved(MouseEvent) - Method in class jme.JME
mouseMoved(MouseEvent) - Method in class jspecview.app.GenericMouse
mouseMoved(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mousePressed(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
mousePressed(MouseEvent) - Method in class jme.JME
mousePressed(MouseEvent) - Method in class jspecview.app.GenericMouse
mousePressed(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mousePressed(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseReleased(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
mouseReleased(MouseEvent) - Method in class jme.JME
mouseReleased(MouseEvent) - Method in class jspecview.app.GenericMouse
mouseReleased(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseReleased(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseShift - Variable in class jme.JME
MouseState - Class in org.jmol.viewer
mouseUp(MouseEvent, int, int) - Method in class jme.JME
mousewheelfactor - Static variable in class org.jmol.script.T
mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
mouseWheelMoved(MouseWheelEvent) - Method in class jspecview.app.GenericMouse
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseX - Variable in class jspecview.common.PanelData
mouseY - Variable in class jspecview.common.PanelData
movableBitSet - Variable in class org.jmol.viewer.Viewer
movableX - Variable in class org.jmol.modelset.Text
movableXPercent - Variable in class org.jmol.modelset.Text
movableY - Variable in class org.jmol.modelset.Text
movableYPercent - Variable in class org.jmol.modelset.Text
movableZ - Variable in class org.jmol.modelset.Text
movableZPercent - Variable in class org.jmol.modelset.Text
move - Static variable in class org.jmol.script.T
move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.Viewer
MOVE - Static variable in class com.sparshui.common.TouchState
MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
moveAtoms(M4, M3, M3, V3, BS, P3, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
moveAtoms(M4, M3, M3, V3, P3, boolean, BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
moveAtomWithHydrogens(int, int, int, int, P3, BS) - Method in class org.jmol.viewer.Viewer
moved - Variable in class org.jmol.viewer.ActionManager
moved(long, int, int, int) - Method in class jspecview.app.GenericMouse
MOVED - Static variable in class org.jmol.awtjs.Event
moveMinConstrained(int, P3, BS) - Method in class org.jmol.modelkit.ModelKit
movePossible - Variable in class jme.JME
moveRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
moveto - Static variable in class org.jmol.script.T
moveto(int, int) - Method in class javajs.export.PDFCreator
moveTo(JmolScriptEvaluator, float, P3, V3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.Viewer
MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
moveToPyMOL(JmolScriptEvaluator, float, float[]) - Method in class org.jmol.viewer.TransformManager
movetoThread - Variable in class org.jmol.viewer.TransformManager
MoveToThread - Class in org.jmol.thread
MoveToThread() - Constructor for class org.jmol.thread.MoveToThread
moveUpdate(float) - Method in class org.jmol.viewer.Viewer
movie - Static variable in class org.jmol.script.T
movie_animate_by_frame - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_auto_interpolate - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_auto_store - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_delay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_fps - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_loop - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_panel - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_panel_row_height - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
movie_rock - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
mp - Variable in class jspecview.export.AMLExporter
mp - Variable in class jspecview.export.CMLExporter
mPending - Variable in class org.jmol.shape.Measures
MPJmolApp - Class in org.molecularplayground
MPJmolApp() - Constructor for class org.molecularplayground.MPJmolApp
MPJmolApp(int) - Constructor for class org.molecularplayground.MPJmolApp
mrc - Static variable in class org.jmol.script.T
ms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ms - Variable in class org.jmol.modelset.Measurement
ms - Variable in class org.jmol.modelset.Model
  BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
ms - Variable in class org.jmol.modelset.ModelLoader
ms - Variable in class org.jmol.render.ShapeRenderer
ms - Variable in class org.jmol.shape.Shape
ms - Variable in class org.jmol.viewer.Viewer
MSCifParser - Class in org.jmol.adapter.readers.cif
MSCifParser() - Constructor for class org.jmol.adapter.readers.cif.MSCifParser
msg - Variable in class org.jmol.jvxl.data.JvxlData
msInfo - Variable in class org.jmol.modelset.ModelSet
MSInterface - Interface in org.jmol.adapter.smarter
  Modulated Structure Reader Interface
msms - Static variable in class org.jmol.script.T
MSRdr - Class in org.jmol.adapter.readers.cif
  generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth, Legendre; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
MSRdr() - Constructor for class org.jmol.adapter.readers.cif.MSRdr
mul - Static variable in class org.jmol.script.T
mul(float) - Method in class javajs.util.Quat
mul(M3) - Method in class javajs.util.M3
  Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(M4) - Method in class javajs.util.M4
  Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(Matrix) - Method in class javajs.util.Matrix
  Linear algebraic matrix multiplication, A * B
mul2(M3, M3) - Method in class javajs.util.M3
  Sets the value of this matrix to the result of multiplying the two argument matrices together.
mul2(M4, M4) - Method in class javajs.util.M4
  Sets the value of this matrix to the result of multiplying the two argument matrices together.
mul3 - Static variable in class org.jmol.script.T
mul33(float) - Method in class javajs.util.M34
mulQ(Quat) - Method in class javajs.util.Quat
MULTI_POINT_DRAG_GESTURE - Static variable in class com.sparshui.GestureType
MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JC
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JC
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JC
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JC
multipart - Variable in class jme.JME
MULTIPLE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
multiplebondbananas - Static variable in class org.jmol.script.T
multiplebondradiusfactor - Static variable in class org.jmol.script.T
multiplebondspacing - Static variable in class org.jmol.script.T
multiplex - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
multiprocessor - Static variable in class org.jmol.script.T
mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
mustFinalizeModelSet - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
mustResumeEval - Variable in class org.jmol.script.ScriptContext
mutate - Static variable in class org.jmol.script.T
mutate(BS, String, String[], String, float[]) - Method in class org.jmol.modelsetbio.BioModelSet
mxyz - Variable in class org.jmol.util.ModulationSet
  the modulated magnetic spin
myAtoms - Variable in class org.jmol.util.ContactPair
MyFileFilter - Class in org.openscience.jmol.app.janocchio
MyFileFilter(String[], String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
MyFileFilter(String, String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
myFrame - Variable in class jme.JME
myName - Variable in class org.jmol.script.SV
myName - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
myParams - Variable in class jspecview.common.MeasurementData
myParams - Variable in class jspecview.dialog.JSVDialog
myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
myType - Variable in class org.jmol.shape.Shape
myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
myVisibilityFlag - Variable in class org.jmol.render.ShapeRenderer

## N

n - Variable in class javajs.util.Matrix
n(int, int) - Static method in class org.jmol.script.T
N_GROUPS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
N_ITERS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
NA - Enum constant in enum class jspecview.common.IntegralData.IntMode
nada - Static variable in class org.jmol.script.T
NADA - Enum constant in enum class org.jmol.c.VDW
name - Variable in class jspecview.common.Parameters
name - Variable in class org.jmol.awtjs.swing.Component
name - Variable in class org.jmol.minimize.forcefield.ForceField
name - Static variable in class org.jmol.script.T
name - Variable in class org.jmol.symmetry.UnitCell
name - Variable in class org.jmol.thread.JmolThread
name - Variable in class org.jmol.viewer.binding.Binding
name - Variable in class org.jmol.viewer.MouseState
namedSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
nameOf(int) - Static method in class org.jmol.script.T
  note: nameOf is a very inefficient mechanism for getting the name of a token.
NamfisReader - Class in org.openscience.jmol.app.janocchio
NamfisReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisReader
NamfisSaver - Class in org.openscience.jmol.app.janocchio
NamfisSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisSaver
nativeLanguage - Variable in class org.jmol.i18n.Language
natoms - Variable in class jme.JMEmol
nAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
nAtoms - Variable in class org.jmol.minimize.MMConstraint
nAtoms0 - Variable in class org.jmol.adapter.readers.cif.CifReader
NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager
  //////////////////////// old TransfomManager11 ////////////////////
NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager
navfps - Static variable in class org.jmol.script.T
navFps - Variable in class org.jmol.viewer.TransformManager
navigate - Static variable in class org.jmol.script.T
navigateAxis(V3, float) - Method in interface org.jmol.api.JmolNavigatorInterface
navigateAxis(V3, float) - Method in class org.jmol.navigate.Navigator
navigateAxis(V3, float) - Method in class org.jmol.viewer.TransformManager
  scripted entry point for navigation
navigateAxis(V3, float) - Method in class org.jmol.viewer.Viewer
navigateKey(int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
navigateKey(int, int) - Method in class org.jmol.navigate.Navigator
navigateList(JmolScriptEvaluator, Lst) - Method in interface org.jmol.api.JmolNavigatorInterface
navigateList(JmolScriptEvaluator, Lst) - Method in class org.jmol.navigate.Navigator
navigateList(JmolScriptEvaluator, Lst) - Method in class org.jmol.viewer.TransformManager
navigatePt(P3) - Method in class org.jmol.viewer.Viewer
navigating - Variable in class org.jmol.viewer.TransformManager
navigationCenter - Variable in class org.jmol.viewer.TransformManager
navigationdepth - Static variable in class org.jmol.script.T
navigationDepthPercent - Variable in class org.jmol.viewer.TransformManager
navigationmode - Static variable in class org.jmol.script.T
navigationOffset - Variable in class org.jmol.viewer.TransformManager
navigationperiodic - Static variable in class org.jmol.script.T
navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
navigationslab - Static variable in class org.jmol.script.T
navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager
navigationspeed - Static variable in class org.jmol.script.T
Navigator - Class in org.jmol.navigate
  Navigator is a user input mechanism that utilizes the keypad to drive through the model.
Navigator() - Constructor for class org.jmol.navigate.Navigator
navMode - Variable in class org.jmol.viewer.TransformManager
navOn - Variable in class org.jmol.viewer.TransformManager
navTranslatePercent(float, float) - Method in class org.jmol.viewer.Viewer
navTranslatePercentOrTo(float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.navigate.Navigator
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.viewer.TransformManager
  seconds invalid input: '<' 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"
navx - Static variable in class org.jmol.script.T
navX - Variable in class org.jmol.viewer.TransformManager
navy - Static variable in class org.jmol.script.T
navY - Variable in class org.jmol.viewer.TransformManager
NAVY - Static variable in class org.jmol.util.C
navz - Static variable in class org.jmol.script.T
navZ - Variable in class org.jmol.viewer.TransformManager
nb_spheres_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nb_spheres_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nb_spheres_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
nbo - Static variable in class org.jmol.script.T
NBO - Class in org.jmol.shapesurface
NBO() - Constructor for class org.jmol.shapesurface.NBO
NBO_CONFIG - Static variable in class org.jmol.viewer.JC
NBO_MODEL - Static variable in class org.jmol.viewer.JC
NBO_RUN - Static variable in class org.jmol.viewer.JC
NBO_SEARCH - Static variable in class org.jmol.viewer.JC
NBO_TYPES - Static variable in class org.jmol.viewer.JC
NBO_VIEW - Static variable in class org.jmol.viewer.JC
nbocharges - Static variable in class org.jmol.script.T
nbonds - Variable in class jme.JMEmol
nBonds - Variable in class org.jmol.minimize.MinAtom
NBOParser - Class in org.jmol.adapter.readers.quantum
NBOParser() - Constructor for class org.jmol.adapter.readers.quantum.NBOParser
NBORenderer - Class in org.jmol.rendersurface
NBORenderer() - Constructor for class org.jmol.rendersurface.NBORenderer
nBytes - Variable in class javajs.util.BinaryDocument
nBytes - Variable in class org.jmol.jvxl.data.JvxlData
nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
  /////////////////////////////////////////////////////////////
nci - Static variable in class org.jmol.script.T
NciCalculation - Class in org.jmol.quantum
NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
nCoef - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
nContours - Variable in class org.jmol.jvxl.data.JvxlData
nData - Variable in class org.jmol.jvxl.readers.JvxlReader
nData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
nData - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
nDim - Variable in class org.jmol.symmetry.SpaceGroup
  number of dimesions -- 2 (plane, frieze) or 3 (layer, rod, space)
nDims - Variable in class org.jmol.render.AxesRenderer
nDims - Variable in class org.jmol.render.BbcageRenderer
nDims - Variable in class org.jmol.render.UccageRenderer
ndots - Static variable in class org.jmol.render.FontLineShapeRenderer
ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
nEdges - Variable in class org.jmol.jvxl.data.JvxlData
needRecentering - Variable in class jme.JMEmol
needTranslucent - Variable in class org.jmol.render.MeshRenderer
negate() - Method in class javajs.util.Quat
negativeAtomCount - Variable in class org.jmol.jvxl.readers.JvxlReader
negativeAtomCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
negativeAtomCount - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
neighbor_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nElements - Variable in class org.jmol.util.JmolMolecule
nError - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
NetworkConfiguration - Class in com.sparshui.common
  Defines the port the server will be listening for connections on.
NetworkConfiguration() - Constructor for class com.sparshui.common.NetworkConfiguration
NEW_NO_HALL_GROUP - Static variable in class org.jmol.symmetry.SpaceGroup
new3(float, float, float) - Static method in class javajs.util.P3
new3(float, float, float) - Static method in class javajs.util.V3
new3(int, int, int) - Static method in class javajs.util.P3i
new4(float, float, float, float) - Static method in class javajs.util.A4
  Constructs and initializes an AxisAngle4f from the specified x, y, z, and angle.
new4(float, float, float, float) - Static method in class javajs.util.P4
new4(float, float, float, float) - Static method in class javajs.util.Quat
  Note that q0 is the last parameter here
new4(float, float, float, int) - Static method in class org.jmol.util.Point3fi
newA(float[]) - Static method in class javajs.util.P3
newA(float[]) - Static method in class org.jmol.util.SimpleUnitCell
newA16(float[]) - Static method in class javajs.util.M4
  Constructs and initializes a Matrix4f from the specified 16 element array.
newA9(float[]) - Static method in class javajs.util.M3
  Constructs and initializes a Matrix3f from the specified 9 element array.
newAA(A4) - Static method in class javajs.util.A4
  Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
newAA(A4) - Static method in class javajs.util.Quat
newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
newAndSetBit(int) - Static method in class org.jmol.util.BSUtil
newAntialiasing - Variable in class org.jmol.util.GData
newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Create a new atoms set, clearing the atom map
newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
newAtomSetClear(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Create a new atom set, optionally clearing the atom map.
newBinding(Viewer, String) - Static method in class org.jmol.viewer.binding.Binding
newBitSet2(int, int) - Static method in class org.jmol.util.BSUtil
newBS(BS) - Static method in class org.jmol.modelset.BondSet
newBufferedImage(Object, int, int) - Method in class jspecview.java.AwtPlatform
newBufferedImage(Object, int, int) - Method in class jspecview.js2d.JsPlatform
newBufferedImage(Object, int, int) - Method in interface org.jmol.api.GenericPlatform
newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs.Platform
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs2d.Platform
newByte2(int) - Static method in class javajs.util.AU
newBZip2InputStream(InputStream) - Method in interface javajs.api.GenericZipTools
newBZip2InputStream(InputStream) - Method in class javajs.util.ZipTools
newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
newDocument(int, int, boolean) - Method in class javajs.export.PDFCreator
newDouble2(int) - Static method in class javajs.util.AU
newDouble3n(int) - Static method in class javajs.util.AU
newEcho(Viewer, Font, String, short, int, int, float) - Static method in class org.jmol.modelset.Text
newF(float) - Static method in class org.jmol.script.SV
newFile(String) - Method in class jspecview.java.AwtPlatform
newFile(String) - Method in class jspecview.js2d.JsPlatform
newFile(String) - Method in interface org.jmol.api.GenericPlatform
newFile(String) - Method in class org.jmol.awt.Platform
newFile(String) - Method in class org.jmol.awtjs2d.Platform
newFileSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
newFileSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
newFloat2(int) - Static method in class javajs.util.AU
newFloat3(int, int) - Static method in class javajs.util.AU
newFont(String, boolean, boolean, float) - Method in class jspecview.java.AwtPlatform
newFont(String, boolean, boolean, float) - Method in class jspecview.js2d.JsPlatform
newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.FontManager
newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs2d.Platform
newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface javajs.api.js.J2SObjectInterface
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.common.PDFWriter
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.java.AwtG2D
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.js2d.JsG2D
newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface org.jmol.api.GenericGraphics
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awt.AwtG2D
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awtjs2d.JsG2D
newGZIPInputStream(InputStream) - Method in interface javajs.api.GenericZipTools
newGZIPInputStream(InputStream) - Method in class javajs.util.ZipTools
newGZIPInputStream(InputStream) - Method in interface jspecview.api.JSVZipInterface
newGZIPInputStream(InputStream) - Method in class jspecview.common.JSVZipUtil
newI(int) - Static method in class org.jmol.script.SV
newI(int) - Static method in class org.jmol.util.Rgb16
newID(String) - Static method in class org.jmol.awtjs.swing.Component
newInt2(int) - Static method in class javajs.util.AU
newInt3(int, int) - Static method in class javajs.util.AU
newInt4(int) - Static method in class javajs.util.AU
newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJMenu(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
newJMenu(String) - Method in class org.jmol.console.JmolConsole
newJMenu(String) - Method in class org.jmol.consolejs.AppletConsole
newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJMenuItem(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
newJMenuItem(String) - Method in class org.jmol.console.JmolConsole
newJMenuItem(String) - Method in class org.jmol.consolejs.AppletConsole
newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJSVZipFileSequentialReader(InputStream, String[], String) - Method in interface jspecview.api.JSVZipInterface
newJSVZipFileSequentialReader(InputStream, String[], String) - Method in class jspecview.common.JSVZipUtil
newLabel(Viewer, Font, String, short, short, int, float) - Static method in class org.jmol.modelset.Text
newLatticePts - Variable in class org.jmol.util.BZone
newLine - Static variable in class jspecview.export.JDXExporter
newList() - Static method in class org.qcschema.QCSchemaUnits
newM(M3) - Static method in class javajs.util.Quat
newM3(M3) - Static method in class javajs.util.M3
  Constructs a new matrix with the same values as the Matrix3f parameter.
newM4(M4) - Static method in class javajs.util.M4
  Constructs a new matrix with the same values as the Matrix4f parameter.
newMeasure(Viewer, Font, short) - Static method in class org.jmol.modelset.Text
newMeasurementData(String, Lst) - Method in class org.jmol.viewer.Viewer
newMesh(boolean, T3[], int, int[][], T3[], int) - Static method in class org.jmol.util.MeshSurface
newModel(int) - Method in class org.jmol.adapter.readers.cif.CifReader
newMolecule - Variable in class jme.JME
newMV(M3, T3) - Static method in class javajs.util.M4
  Constructs and initializes a Matrix4f from the rotation matrix and translation.
newN(int) - Static method in class javajs.util.BS
  Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range `0` through `nbits-1`.
newN(int) - Static method in class javajs.util.SB
newOffScreenImage(int, int) - Method in class jspecview.java.AwtPlatform
newOffScreenImage(int, int) - Method in class jspecview.js2d.JsPlatform
newOffScreenImage(int, int) - Method in interface org.jmol.api.GenericPlatform
newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
newOffScreenImage(int, int) - Method in class org.jmol.awtjs.Platform
newOffScreenImage(int, int) - Method in class org.jmol.awtjs2d.Platform
newP(T3) - Static method in class javajs.util.P3
newP4(P4) - Static method in class javajs.util.Quat
newParams(float[], float) - Static method in class org.jmol.util.SimpleUnitCell
newPF(T3, int) - Static method in class org.jmol.util.Point3fi
newPlanes - Variable in class org.jmol.util.BZone
NEWPSOFF - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Both ends of wedge point to stereocenters [compatible with standard InChI]
newPt(P4) - Static method in class javajs.util.P4
newQ(Quat) - Static method in class javajs.util.Quat
newS(String) - Static method in class javajs.util.SB
newS(String) - Static method in class org.jmol.script.SV
newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
newSg() - Method in class org.jmol.shapesurface.Isosurface
newShort2(int) - Static method in class javajs.util.AU
newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
newSpectrum(Lst) - Method in class jspecview.common.ViewData
newSpectrum(Spectrum, Coordinate[], String) - Static method in class jspecview.common.Spectrum
  copy spectrum with new coordinates
newStereo(SmilesSearch) - Static method in class org.jmol.smiles.SmilesStereo
newT(T3, boolean) - Static method in class javajs.util.Matrix
newT(T) - Static method in class org.jmol.script.SV
newToolbar(String[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
newTreePath(Object[]) - Method in interface jspecview.api.JSVTree
newTreePath(Object[]) - Method in class jspecview.application.AwtTree
newTreePath(Object[]) - Method in class jspecview.tree.SimpleTree
newV(int, Object) - Static method in class org.jmol.script.SV
newV(T3) - Static method in class javajs.util.V3
newVA(T3, float) - Static method in class javajs.util.Quat
newVA(V3, float) - Static method in class javajs.util.A4
  Constructs and initializes an AxisAngle4f from the specified axis and angle.
newVertex(P3, V3, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
newVertexBitSet() - Static method in class org.jmol.util.Normix
newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
newVsub(T3, T3) - Static method in class javajs.util.V3
newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
newWindow(boolean) - Method in interface jspecview.api.AppletFrame
newWindow(boolean) - Method in class jspecview.appletjs.JSVApplet
newWindowHeight - Variable in class org.jmol.util.GData
newWindowWidth - Variable in class org.jmol.util.GData
newXYCoords - Variable in class jspecview.export.AMLExporter
newXYCoords - Variable in class jspecview.export.CMLExporter
newZipInputStream(InputStream) - Method in interface javajs.api.GenericZipTools
newZipInputStream(InputStream) - Method in class javajs.util.ZipTools
next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
next - Variable in class org.jmol.jvxl.readers.JvxlReader
next - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
next - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
next - Static variable in class org.jmol.script.T
next() - Method in class jspecview.source.JDXDecompressor
next() - Method in interface org.jmol.api.AtomIndexIterator
next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
next() - Method in interface org.jmol.modelset.BondIterator
next() - Method in class org.jmol.symmetry.UnitCellIterator
nextAtomSet() - Method in class org.jmol.adapter.readers.cif.CifReader
nextClearBit(int) - Method in class javajs.util.BS
  Returns the index of the first bit that is set to `false` that occurs on or after the specified starting index.
nextData(StringTokenizer, String) - Static method in class jme.JMEmol
nextData(StringTokenizer, String) - Static method in class jme.JMEUtil
nextElement() - Method in class jspecview.tree.SimpleTreeEnumeration
nextElement() - Method in class org.jmol.bspt.CubeIterator
  normal iterator method
nextEvent() - Method in class jspecview.source.XMLParser
nextFileName(String, int) - Method in class org.jmol.console.GenericConsole
nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
nextFileName(String, int) - Method in class org.jmol.consolejs.AppletConsole
nextID() - Method in class org.jmol.adapter.readers.xml.CDXMLParser
nextIndex() - Method in interface org.jmol.modelset.BondIterator
nextRandom8Bit() - Method in class org.jmol.util.Shader
  Implements RANDU algorithm for random noise in lighting/shading.
nextSetBit(int) - Method in class javajs.util.BS
  Returns the index of the first bit that is set to `true` that occurs on or after the specified starting index.
nextStartTag() - Method in class jspecview.source.XMLParser
nextTag() - Method in class jspecview.source.XMLParser
nextToken() - Method in class jspecview.common.ScriptTokenizer
nextValue() - Method in class jspecview.source.XMLParser
nextView() - Method in class jspecview.common.PanelData
  Displays the next view zoomed
nextVoxel() - Method in class org.jmol.jvxl.readers.JvxlReader
nextVoxel() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
nextVoxel() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
nFast - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
nFrankList - Variable in class org.jmol.popup.JmolGenericPopup
nGaussians - Variable in class org.jmol.quantum.MOCalculation
nihresolverformat - Static variable in class org.jmol.script.T
nIn - Variable in class org.jmol.util.Shader
nioClosed(JsonNioServer) - Method in class org.molecularplayground.MPJmolApp
nioClosed(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  /////// JSON/NIO SERVICE //////////
nioClosed(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
nioSync(Viewer, Map) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
  process touch or gesture commands driven by hardware.
nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
nList - Variable in class org.jmol.shapecgo.CGOMesh
nmols - Variable in class jme.JME
nmr - Static variable in class org.jmol.script.T
Nmr - Class in org.openscience.jmol.app.janocchio
Nmr(String[]) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
Nmr(String[], NmrPlugin) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
NMR_DC - Static variable in class org.jmol.modelset.Measurement
NMR_DisplayPanel - Class in org.openscience.jmol.app.janocchio
NMR_JC - Static variable in class org.jmol.modelset.Measurement
NMR_JmolPanel - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel(JmolApp, Splash, JFrame, Jmol, int, int, Map, Point) - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel
NMR_JmolPanel.DetachAppletAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.JumpBestFrameAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.LabelNmrAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.ReadNamfisAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.ReadNmrAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.ReattachAppletAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.ViewCoupleTableAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.ViewNoeTableAction - Class in org.openscience.jmol.app.janocchio
NMR_JmolPanel.WriteNamfisAction - Class in org.openscience.jmol.app.janocchio
NMR_NOE_OR_J - Static variable in class org.jmol.modelset.Measurement
NMR_NOT - Static variable in class org.jmol.modelset.Measurement
NMR_Viewer - Class in org.openscience.jmol.app.janocchio
  Implements some lost interfaces.
NMR_Viewer(Map) - Constructor for class org.openscience.jmol.app.janocchio.NMR_Viewer
NmrApplet - Class in org.openscience.jmol.app.janocchio
NmrApplet() - Constructor for class org.openscience.jmol.app.janocchio.NmrApplet
NMRCalculation - Class in org.jmol.quantum
NMRCalculation() - Constructor for class org.jmol.quantum.NMRCalculation
NmrGuiMap - Class in org.openscience.jmol.app.janocchio
NmrGuiMap() - Constructor for class org.openscience.jmol.app.janocchio.NmrGuiMap
nmrMaxY - Variable in class jspecview.common.JSViewer
NMRMLReader - Class in jspecview.source
  Representation of an nmrML Source.
NMRMLReader() - Constructor for class jspecview.source.NMRMLReader
NmrMolecule - Class in org.openscience.jmol.app.janocchio
NmrMolecule(NMR_JmolPanel, BS, String[], boolean) - Constructor for class org.openscience.jmol.app.janocchio.NmrMolecule
NMRNoeMatrix - Class in org.jmol.quantum
  Class for calculating NOE intensities by full matrix relaxation approach.
NMRNoeMatrix.NOEParams - Class in org.jmol.quantum
nmrPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
nmrPanel - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
NmrPlugin - Class in org.openscience.jmol.app.janocchio
NmrPlugin() - Constructor for class org.openscience.jmol.app.janocchio.NmrPlugin
nmrpredictformat - Static variable in class org.jmol.script.T
NmrReader - Class in org.openscience.jmol.app.janocchio
NmrReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrReader
NmrResourceHandler - Class in org.openscience.jmol.app.janocchio
  Provides access to resources (for example, strings and images).
NmrSaver - Class in org.openscience.jmol.app.janocchio
NmrSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrSaver
nmrType(String) - Static method in class org.jmol.modelset.Measurement
nmrurlformat - Static variable in class org.jmol.script.T
NO_AUTOPLAY - Static variable in class org.jmol.viewer.FileManager
NO_CONVERT - Enum constant in enum class jspecview.common.Spectrum.IRMode
no_idle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
NO_SCRIPT - Static variable in class org.jmol.viewer.FileManager
noArgs - Static variable in class org.jmol.script.T
nobackshell - Static variable in class org.jmol.script.T
nocenter - Variable in class jme.JME
noColor - Variable in class org.jmol.export.__CartesianExporter
nocontourlines - Static variable in class org.jmol.script.T
noCopy(int, int) - Method in class org.jmol.script.ScriptEval
nocross - Static variable in class org.jmol.script.T
noCross - Variable in class org.jmol.shapespecial.Dipole
Node - Interface in org.jmol.util
nodebug - Static variable in class org.jmol.script.T
nodelay - Static variable in class org.jmol.script.T
noDelay - Variable in class org.jmol.viewer.GlobalSettings
  ensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1
nodes - Variable in class org.jmol.util.JmolMolecule
nodots - Static variable in class org.jmol.script.T
noeColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
NoeColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
NoeColourSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
noedges - Static variable in class org.jmol.script.T
NoEdits - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Disable polymer CRU frame shift and folding
noeMatrix - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
noeParameterSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
NoeParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
NoeParameterSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
NOEParams() - Constructor for class org.jmol.quantum.NMRNoeMatrix.NOEParams
noeTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
NoeTable - Class in org.openscience.jmol.app.janocchio
NoeTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.NoeTable
  Constructor
nofill - Static variable in class org.jmol.script.T
NoFrameShift - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Disable polymer CRU frame shift
noFrankEcho - Variable in class org.jmol.viewer.Viewer
noGraphicsAllowed - Variable in class org.jmol.viewer.Viewer
nohead - Static variable in class org.jmol.script.T
noHead - Variable in class org.jmol.shapespecial.DrawMesh
NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
noHydrogens - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
NOJMOL - Enum constant in enum class org.jmol.c.VDW
noLabelAtom - Variable in class jme.AtomDisplayLabel
noload - Static variable in class org.jmol.script.T
nomesh - Static variable in class org.jmol.script.T
noMinimize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
nonArrayString(Object) - Static method in class javajs.util.PT
  Checks to see if an object is an array (including typed arrays), and if it is, returns null; otherwise it returns the string equivalent of that object.
nonbonded_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nonbonded_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nonbonded_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
nonbonded_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
none - Static variable in class org.jmol.script.T
NONE - Enum constant in enum class javajs.util.Encoding
NONE - Enum constant in enum class jspecview.common.Annotation.AType
NONE - Enum constant in enum class jspecview.common.PanelData.LinkMode
NONE - Enum constant in enum class org.jmol.c.PAL
NONE - Enum constant in enum class org.jmol.c.STER
NONE - Enum constant in enum class org.jmol.c.STR
NONE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
NONE - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
NONE - Static variable in interface javajs.api.GenericCifDataParser
NONE - Static variable in class org.jmol.adapter.readers.cif.CifReader
NONE - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
noneSelected - Variable in class org.jmol.viewer.SelectionManager
  a flag to indicate that labels and fonts should be set to default values; set only by SELECT NONE;
nonisomericSmiles() - Method in class jme.JME
noPack - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
noplane - Static variable in class org.jmol.script.T
nops - Variable in class org.jmol.adapter.writers.CIFWriter
nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
NORM_NBO - Static variable in class org.jmol.quantum.MOCalculation
NORM_NONE - Static variable in class org.jmol.quantum.MOCalculation
NORM_NWCHEM - Static variable in class org.jmol.quantum.MOCalculation
NORM_STANDARD - Static variable in class org.jmol.quantum.MOCalculation
normal - Static variable in class org.jmol.script.T
NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
normal_workaround - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
normalCount - Variable in class org.jmol.util.MeshSurface
normalise(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
  Normalises the y values of a spectrum to a certain range
normalize() - Method in class javajs.util.T3
  Normalizes this vector in place.
normalize() - Method in class javajs.util.V3d
  Normalizes this vector in place.
normalize_ccp4_maps - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
normalize_grd_maps - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
normalize_o_maps - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
normalize12ths(V3) - Static method in class org.jmol.symmetry.SymmetryOperation
normalizeIntegral() - Method in class jspecview.common.PanelData
normalizeOperationToCentroid(int, M4, P3[], int, int) - Static method in class org.jmol.symmetry.SymmetryOperation
  Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.
normalizeSimulation(double) - Method in class jspecview.source.JDXDataObject
normals - Variable in class org.jmol.util.MeshSurface
normalsTemp - Variable in class org.jmol.util.MeshSurface
Normix - Class in org.jmol.util
  Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix() - Constructor for class org.jmol.util.Normix
NORMIX_NULL - Static variable in class org.jmol.util.Normix
normixCount - Static variable in class org.jmol.util.GData
normixCount - Variable in class org.jmol.util.MeshSurface
normixes - Variable in class org.jmol.render.MeshRenderer
normixes - Variable in class org.jmol.shape.Mesh
normType - Variable in class org.jmol.quantum.MOCalculation
NORTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
NOT - Enum constant in enum class org.jmol.c.HB
NOT - Enum constant in enum class org.jmol.c.STR
NOT_LOADED - Enum constant in enum class org.jmol.c.FIL
NOT_SORTED - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
note - Variable in class org.jmol.modelset.MeasurementData
NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JC
notfrontonly - Static variable in class org.jmol.script.T
notify(int, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
notify(int, Object[]) - Method in class org.jmol.console.ScriptEditor
notifyAtomPositionsChanged(int, BS, M4) - Method in class org.jmol.viewer.ShapeManager
notifyAtoms(String, BS[]) - Method in class org.jmol.viewer.ShapeManager
notifyAudioEnded(Object) - Method in interface org.jmol.api.JmolAppletInterface
notifyAudioEnded(Object) - Method in class org.jmol.util.GenericApplet
notifyAudioStatus(Map) - Method in class org.jmol.viewer.StatusManager
  called from JmolAudio
notifyCallback(CBK, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
notifyCallback(CBK, Object[]) - Method in class org.jmol.console.GenericConsole
notifyCallback(CBK, Object[]) - Method in class org.jmol.util.GenericApplet
notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
notifyCallback(CBK, Object[]) - Method in interface org.openscience.jmol.app.JmolPlugin
notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.status.StatusListener
notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
notifyEnabled(CBK) - Method in interface org.jmol.api.JmolCallbackListener
notifyEnabled(CBK) - Method in class org.jmol.console.GenericConsole
  ////////// JmolCallbackListener interface
notifyEnabled(CBK) - Method in class org.jmol.util.GenericApplet
  ////////// JmolStatusListener ///////////
notifyEnabled(CBK) - Method in class org.openscience.jmol.app.status.StatusListener
notifyEndOfRendering() - Method in class jspecview.java.AwtPlatform
notifyEndOfRendering() - Method in class jspecview.js2d.JsPlatform
notifyEndOfRendering() - Method in interface org.jmol.api.GenericPlatform
notifyEndOfRendering() - Method in class org.jmol.awt.Platform
notifyEndOfRendering() - Method in class org.jmol.awtjs2d.Platform
notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
notifyExitingJspecView(boolean, boolean) - Method in class jspecview.application.JSpecView
  From MainFrame only
notifyFileOpen(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyGaussian(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyGeneralCallback(CBK, Object[], String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyLanguage() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyListeners(Object) - Method in class jspecview.common.PanelData
notifyMeasure(Object[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
notifyNBO(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyNBO(Map) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyPeakPickedListeners(PeakPickEvent) - Method in class jspecview.common.PanelData
  Notifies CoordinatePickedListeners
notifyPreferences(Object[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyResumeStatus() - Method in interface org.jmol.api.JmolScriptEvaluator
notifyResumeStatus() - Method in class org.jmol.script.ScriptEval
notifyScriptEditor(int, Object[]) - Method in class org.jmol.viewer.Viewer
notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
notifyScriptTermination(String) - Method in class org.jmol.console.ScriptEditor
notifyServer(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyStatusReady(boolean) - Method in class org.jmol.api.JmolViewer
notifyStatusReady(boolean) - Method in class org.jmol.viewer.Viewer
notifySubSpectrumChange(int, Spectrum) - Method in class jspecview.common.PanelData
notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
notInCentroid(ModelSet, BS, int[]) - Method in interface org.jmol.api.SymmetryInterface
notInCentroid(ModelSet, BS, int[]) - Method in class org.jmol.symmetry.Symmetry
notriangles - Static variable in class org.jmol.script.T
nOut - Variable in class org.jmol.util.Shader
now - Static variable in class org.jmol.script.T
NoWarnings - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Suppress all warning messages
npoints - Variable in class jspecview.export.AMLExporter
npoints - Variable in class jspecview.export.CMLExporter
npoints - Variable in class jspecview.source.AnIMLReader
npoints - Variable in class jspecview.source.NMRMLReader
nPoints - Variable in class org.jmol.jvxl.data.VolumeData
nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
nProcessors - Static variable in class org.jmol.viewer.Viewer
NPZz - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Allow non-polymer-related Zz atoms (pseudo element placeholders)
nRes - Variable in class org.jmol.modelsetbio.ProteinStructure
nRotations - Variable in class org.jmol.symmetry.HallInfo
nSets - Variable in class org.jmol.util.MeshSurface
nSkipX - Variable in class org.jmol.jvxl.readers.JvxlReader
nSkipX - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
nSkipX - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
nSkipY - Variable in class org.jmol.jvxl.readers.JvxlReader
nSkipY - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
nSkipY - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
nSkipZ - Variable in class org.jmol.jvxl.readers.JvxlReader
nSkipZ - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
nSkipZ - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
nSpins - Variable in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
nSurfaces - Variable in class org.jmol.jvxl.readers.JvxlReader
nSurfaces - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
nSurfaces - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
nTab - Variable in class org.jmol.console.GenericConsole
nTokens - Variable in class org.jmol.script.ScriptCompiler
nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
nucleic - Static variable in class org.jmol.script.T
NUCLEIC - Enum constant in enum class org.jmol.c.PAL
NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
NucleicMonomer - Class in org.jmol.modelsetbio
NucleicPolymer - Class in org.jmol.modelsetbio
NucleicRenderer - Class in org.jmol.renderbio
  extends CartoonRenderer for nucleics
NucleicRenderer() - Constructor for class org.jmol.renderbio.NucleicRenderer
nucleusX - Variable in class jspecview.source.JDXDataObject
nucleusY - Variable in class jspecview.source.JDXDataObject
nullDeletedAtoms - Static variable in class org.jmol.viewer.Viewer
nullString - Static variable in class javajs.util.CifDataParser
  string to return for CIF data value .
NUM_OVERSHOOT_BYTES - Static variable in interface org.apache.tools.bzip2.BZip2Constants
number - Variable in class jme.JME
numberAtoms() - Method in class jme.JMEmol
numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptError
numCached - Variable in class org.jmol.modelset.BondCollection
numSet - Variable in class org.jmol.modelset.MeasurementPending
numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
nUnnamed - Variable in class org.jmol.shape.MeshCollection
nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
nvidia_bugs - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
NWChemReader - Class in org.jmol.adapter.readers.quantum
  A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
nX - Variable in class org.jmol.quantum.QuantumCalculation
nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
nY - Variable in class org.jmol.quantum.QuantumCalculation
nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
nZ - Variable in class org.jmol.quantum.QuantumCalculation

## O

o(int, Object) - Static method in class org.jmol.script.T
o(String, Object) - Static method in class org.jmol.i18n.GT
oabc - Variable in class org.jmol.jvxl.data.VolumeData
oabc - Variable in class org.jmol.util.MeshSurface
obFreq - Variable in class jspecview.export.AMLExporter
obFreq - Variable in class jspecview.export.CMLExporter
obFreq - Variable in class jspecview.source.AnIMLReader
obFreq - Variable in class jspecview.source.NMRMLReader
obj - Static variable in class org.jmol.script.T
OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
object - Static variable in class org.jmol.script.T
objectNameParameter(int) - Method in class org.jmol.script.ScriptParam
objects - Variable in class org.jmol.shape.TextShape
obNucleus - Variable in class jspecview.export.AMLExporter
obNucleus - Variable in class jspecview.export.CMLExporter
obNucleus - Variable in class jspecview.source.AnIMLReader
obNucleus - Variable in class jspecview.source.NMRMLReader
OBSCURE - Enum constant in enum class jspecview.common.ScriptToken
obscureTitleFromUser - Variable in class jspecview.common.JSViewer
oc - Variable in class org.jmol.adapter.writers.CIFWriter
oc - Variable in class org.jmol.adapter.writers.CMLWriter
oc - Variable in class org.jmol.util.JSONWriter
OC - Class in javajs.util
  A generic output method.
OC() - Constructor for class javajs.util.OC
OC(String) - Constructor for class javajs.util.OC
occupancies - Variable in class org.jmol.modelset.AtomCollection
occupancy - Static variable in class org.jmol.script.T
occupancythreshold - Static variable in class org.jmol.script.T
OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
OdysseyReader - Class in org.jmol.adapter.readers.spartan
OdysseyReader() - Constructor for class org.jmol.adapter.readers.spartan.OdysseyReader
off - Static variable in class org.jmol.script.T
OFF - Enum constant in enum class jspecview.common.IntegralData.IntMode
officialRelease - Static variable in class org.jmol.viewer.JC
offscreen_rendering_for_antialiasing - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
offscreen_rendering_multiplier - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
offset - Static variable in class org.jmol.script.T
offset - Variable in class org.jmol.util.MeshSurface
offset(BS, int, int) - Static method in class org.jmol.util.BSUtil
  offset the bitset in place by the specified number of bits starting at a given position
OFFSET - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
offsetPt - Variable in class org.jmol.shapespecial.Dipole
offsets - Variable in class org.jmol.modelsetbio.Monomer
offsets - Variable in class org.jmol.shape.Labels
offsetside - Static variable in class org.jmol.script.T
offsetSide - Variable in class org.jmol.shapespecial.Dipole
offsetX - Variable in class org.jmol.modelset.Text
offsetY - Variable in class org.jmol.modelset.Text
ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
OLIVE - Static variable in class org.jmol.util.C
omega - Static variable in class org.jmol.script.T
on - Static variable in class org.jmol.script.T
ON - Enum constant in enum class jspecview.common.IntegralData.IntMode
once - Static variable in class org.jmol.script.T
ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
OneFiveT - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Account for 1,5-tautomerism (experimental)
onFailure(Throwable) - Method in class jme.JMEUtil.JSME_RunAsyncCallback
onFailure(Throwable) - Method in interface jme.JMEUtil.RunAsyncCallback
  Called when, for some reason, the necessary code cannot be loaded.
onFailure(Throwable) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
  Called when, for some reason, the necessary code cannot be loaded.
onFocus() - Method in class jspecview.js2d.JsDialog
only - Static variable in class org.jmol.script.T
onSuccess() - Method in interface jme.JMEUtil.RunAsyncCallback
  Called once the necessary code for it has been loaded.
onSuccess(String) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
  Called once the necessary code for it has been loaded.
onWarning(String) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
oops(Exception) - Method in class org.jmol.minimize.MinimizationThread
oops(Exception) - Method in class org.jmol.navigate.Navigator
oops(Exception) - Method in class org.jmol.thread.JmolThread
opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
opAnd - Static variable in class org.jmol.script.T
opAND - Static variable in class org.jmol.script.T
opaque - Static variable in class org.jmol.script.T
opaque_background - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
OPAQUE_MASK - Static variable in class org.jmol.util.C
open() - Method in class org.jmol.console.ScriptEditor
openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
openBufferedReader(String, BufferedReader, Map) - Method in class org.jmol.api.JmolAdapter
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
openConnection(URL) - Method in class javajs.util.AjaxURLStreamHandler
openDataOrFile(Object, String, Lst, String, int, int, boolean, String) - Method in class jspecview.common.JSViewer
openDocument(SB) - Static method in class javajs.util.XmlUtil
openDocument(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
openDOM(Object) - Method in class org.jmol.api.JmolViewer
openDOM(Object) - Method in class org.jmol.viewer.Viewer
  applet DOM method -- does not preserve state
openExportChannel(double, String, boolean) - Method in class org.jmol.viewer.Viewer
openFile(String) - Method in class jspecview.appletjs.JSVApplet
  possibly called from JSmolJSV.js upon start up
openFile(String) - Method in class org.jmol.api.JmolViewer
openFile(String) - Method in class org.jmol.util.GenericApplet
  possibly called from JSmolApplet.js upon start up
openFile(String) - Method in class org.jmol.viewer.Viewer
  for JmolSimpleViewer -- external applications only (and no-script JavaScript)
openFile(String, boolean) - Method in class jspecview.common.JSViewer
  Opens and displays a file
openFileAsync(String) - Method in class org.jmol.api.JmolViewer
openFileAsync(String, int, String) - Method in class org.jmol.viewer.FileManager
  From file dropping.
openFileAsyncSpecial(String, int) - Method in interface javajs.api.JSInterface
openFileAsyncSpecial(String, int) - Method in class jspecview.appletjs.JSVApplet
openFileAsyncSpecial(String, int) - Method in class jspecview.common.JSViewer
openFileAsyncSpecial(String, int) - Method in class org.jmol.api.JmolViewer
openFileAsyncSpecial(String, int) - Method in class org.jmol.util.GenericApplet
openFileAsyncSpecial(String, int) - Method in class org.jmol.viewer.Viewer
  opens a file as a model, a script, or a surface via the creation of a script that is queued.
openFileAsyncSpecialType(String, int, String) - Method in interface javajs.api.JSInterface
openFileAsyncSpecialType(String, int, String) - Method in class jspecview.appletjs.JSVApplet
openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.api.JmolViewer
openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.util.GenericApplet
openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.viewer.Viewer
openFileFromDialog(boolean, boolean, String, String) - Method in class jspecview.common.JSViewer
openFiles(String[]) - Method in class org.jmol.api.JmolViewer
openFiles(String[]) - Method in class org.jmol.viewer.Viewer
  for JmolSimpleViewer -- external applications only
openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
openReader(String, Object) - Method in class org.jmol.api.JmolViewer
  Opens the file and creates the model set, given the reader.
openReader(String, String, Object) - Method in class org.jmol.api.JmolViewer
  Opens the file and creates the model set, given the reader.
openReader(String, String, Object) - Method in class org.jmol.viewer.Viewer
  Opens the file, given an already-created reader.
openSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
openStringInline(String) - Method in class org.jmol.api.JmolViewer
openStringInline(String) - Method in class org.jmol.viewer.Viewer
  only used by file dropper.
openStringInlineParamsAppend(String, Map, boolean) - Method in class org.jmol.viewer.Viewer
  Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
openTag(SB, String) - Static method in class javajs.util.XmlUtil
openTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
openTagAttr(SB, String, Object[]) - Static method in class javajs.util.XmlUtil
openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
opEQ - Static variable in class org.jmol.script.T
opGE - Static variable in class org.jmol.script.T
opGT - Static variable in class org.jmol.script.T
opIf - Static variable in class org.jmol.script.T
opIsLong - Variable in class org.jmol.symmetry.SymmetryOperation
opLE - Static variable in class org.jmol.script.T
opLIKE - Static variable in class org.jmol.script.T
opLT - Static variable in class org.jmol.script.T
opNE - Static variable in class org.jmol.script.T
opNot - Static variable in class org.jmol.script.T
opOr - Static variable in class org.jmol.script.T
oPt - Variable in class org.jmol.script.ScriptMathProcessor
OptimadeReader - Class in org.jmol.adapter.readers.xtal
  A (preliminary) reader for OPTIMADE resources.
OptimadeReader() - Constructor for class org.jmol.adapter.readers.xtal.OptimadeReader
optimize2D - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
optionalFixedH - Variable in class org.jmol.inchi.InchiJmol
optionKey - Variable in class jspecview.dialog.JSVDialog
optionKey - Variable in class jspecview.java.AwtDialog
optionKey - Variable in class jspecview.js2d.JsDialog
options - Variable in class jspecview.common.PanelData
options - Variable in class jspecview.dialog.JSVDialog
options - Variable in class jspecview.java.AwtDialog
options - Variable in class jspecview.js2d.JsDialog
options - Static variable in class org.jmol.script.T
options - Variable in class org.jmol.shapespecial.Ellipsoid
options(String) - Method in class jme.JME
optionsSaved - Variable in class jspecview.common.PanelData
opToggle - Static variable in class org.jmol.script.T
optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
optParameterAsString(int) - Method in class org.jmol.script.ScriptParam
opXor - Static variable in class org.jmol.script.T
or(BS) - Method in class javajs.util.BS
  Performs a logical OR of this bit set with the bit set argument.
ORANGE - Static variable in class org.jmol.util.C
orbital - Static variable in class org.jmol.script.T
orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
Orbitals - Class in org.openscience.jmol.app.webexport
Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
OrcaReader - Class in org.jmol.adapter.readers.quantum
  Reads ORCA input and output files
OrcaReader - Class in org.jmol.adapter.readers.simple
  Reads ORCA input and output files
OrcaReader() - Constructor for class org.jmol.adapter.readers.quantum.OrcaReader
OrcaReader() - Constructor for class org.jmol.adapter.readers.simple.OrcaReader
order - Variable in class org.jmol.adapter.smarter.Bond
order - Variable in class org.jmol.minimize.MinBond
order - Variable in class org.jmol.util.Edge
ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_HEX - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_QUAD - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_QUINT - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PYMOL_MULT - Static variable in class org.jmol.api.JmolAdapter
ORDER_PYMOL_SINGLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_STEREO_EITHER - Static variable in class org.jmol.api.JmolAdapter
ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
org.apache.tools.bzip2 - package org.apache.tools.bzip2
org.iupac - package org.iupac
org.jmol.adapter.readers.cif - package org.jmol.adapter.readers.cif
org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
org.jmol.adapter.readers.pdb - package org.jmol.adapter.readers.pdb
org.jmol.adapter.readers.pymol - package org.jmol.adapter.readers.pymol
org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
org.jmol.adapter.readers.spartan - package org.jmol.adapter.readers.spartan
org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
org.jmol.adapter.smarter - package org.jmol.adapter.smarter
org.jmol.adapter.writers - package org.jmol.adapter.writers
org.jmol.api - package org.jmol.api
org.jmol.api.js - package org.jmol.api.js
org.jmol.appletjs - package org.jmol.appletjs
org.jmol.atomdata - package org.jmol.atomdata
org.jmol.awt - package org.jmol.awt
org.jmol.awtjs - package org.jmol.awtjs
org.jmol.awtjs.swing - package org.jmol.awtjs.swing
org.jmol.awtjs2d - package org.jmol.awtjs2d
org.jmol.bspt - package org.jmol.bspt
  Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
org.jmol.c - package org.jmol.c
org.jmol.console - package org.jmol.console
org.jmol.consolejs - package org.jmol.consolejs
org.jmol.dialog - package org.jmol.dialog
org.jmol.dssx - package org.jmol.dssx
org.jmol.export - package org.jmol.export
org.jmol.g3d - package org.jmol.g3d
  Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
org.jmol.geodesic - package org.jmol.geodesic
org.jmol.i18n - package org.jmol.i18n
org.jmol.image - package org.jmol.image
org.jmol.inchi - package org.jmol.inchi
org.jmol.io - package org.jmol.io
org.jmol.jsv - package org.jmol.jsv
org.jmol.jvxl.api - package org.jmol.jvxl.api
org.jmol.jvxl.calc - package org.jmol.jvxl.calc
org.jmol.jvxl.data - package org.jmol.jvxl.data
org.jmol.jvxl.readers - package org.jmol.jvxl.readers
org.jmol.minimize - package org.jmol.minimize
org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
org.jmol.modelkit - package org.jmol.modelkit
org.jmol.modelset - package org.jmol.modelset
org.jmol.modelsetbio - package org.jmol.modelsetbio
org.jmol.multitouch - package org.jmol.multitouch
org.jmol.multitouch.jni - package org.jmol.multitouch.jni
org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
org.jmol.navigate - package org.jmol.navigate
org.jmol.popup - package org.jmol.popup
org.jmol.quantum - package org.jmol.quantum
org.jmol.quantum.mo - package org.jmol.quantum.mo
org.jmol.render - package org.jmol.render
org.jmol.renderbio - package org.jmol.renderbio
org.jmol.rendercgo - package org.jmol.rendercgo
org.jmol.renderspecial - package org.jmol.renderspecial
org.jmol.rendersurface - package org.jmol.rendersurface
org.jmol.script - package org.jmol.script
org.jmol.scriptext - package org.jmol.scriptext
org.jmol.shape - package org.jmol.shape
org.jmol.shapebio - package org.jmol.shapebio
org.jmol.shapecgo - package org.jmol.shapecgo
org.jmol.shapespecial - package org.jmol.shapespecial
org.jmol.shapesurface - package org.jmol.shapesurface
org.jmol.smiles - package org.jmol.smiles
  Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
org.jmol.symmetry - package org.jmol.symmetry
org.jmol.thread - package org.jmol.thread
org.jmol.translation - package org.jmol.translation
org.jmol.util - package org.jmol.util
org.jmol.viewer - package org.jmol.viewer
org.jmol.viewer.binding - package org.jmol.viewer.binding
org.molecularplayground - package org.molecularplayground
org.openscience.jmol.app - package org.openscience.jmol.app
org.openscience.jmol.app.janocchio - package org.openscience.jmol.app.janocchio
org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
org.openscience.jmol.app.jmolpanel.console - package org.openscience.jmol.app.jmolpanel.console
org.openscience.jmol.app.jsonkiosk - package org.openscience.jmol.app.jsonkiosk
org.openscience.jmol.app.status - package org.openscience.jmol.app.status
org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
org.openscience.jvxl - package org.openscience.jvxl
org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
org.qcschema - package org.qcschema
orientation - Variable in class org.jmol.modelset.Model
orientation - Static variable in class org.jmol.script.T
Orientation - Class in org.jmol.modelset
Orientation(Viewer, boolean, float[]) - Constructor for class org.jmol.modelset.Orientation
origin - Variable in class jspecview.export.AMLExporter
origin - Variable in class jspecview.export.CMLExporter
origin - Variable in class jspecview.source.JDXHeader
origin - Variable in class jspecview.source.AnIMLReader
origin - Variable in class jspecview.source.NMRMLReader
origin - Variable in class org.jmol.jvxl.data.VolumeData
origin - Variable in class org.jmol.jvxl.readers.Parameters
origin - Static variable in class org.jmol.script.T
origin - Variable in class org.jmol.shapespecial.Dipole
originBohr - Variable in class org.jmol.quantum.QuantumCalculation
originPoint - Variable in class org.jmol.shape.Axes
orthoscopic - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
out - Variable in class javajs.img.ImageEncoder
out - Variable in class javajs.util.BinaryDocument
out - Variable in class jspecview.export.AMLExporter
out - Variable in class jspecview.export.CMLExporter
out - Variable in class jspecview.export.SVGExporter
out - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
out - Variable in class org.jmol.export.___Exporter
out - Variable in class org.jmol.jvxl.readers.JvxlReader
out - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
out - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
out - Static variable in class org.jmol.script.T
OutErrInChI - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Output an empty InChI ("InChI=1//" or "InChI=1S//") on error
output - Variable in class org.jmol.console.GenericConsole
output(String) - Method in class org.jmol.console.ScriptEditor
output(String) - Method in class org.jmol.export.___Exporter
output(String) - Method in class org.jmol.export._StlExporter
output(String) - Method in class org.jmol.util.GenericApplet
  called by mystatuslisteners
output(T3) - Method in class org.jmol.export.___Exporter
output(T3) - Method in class org.jmol.export._IdtfExporter
output(T3) - Method in class org.jmol.export._MayaExporter
output(T3) - Method in class org.jmol.export._ObjExporter
output(T3) - Method in class org.jmol.export._PovrayExporter
output(T3) - Method in class org.jmol.export._TachyonExporter
output(T3) - Method in class org.jmol.export._VrmlExporter
output(T3) - Method in class org.jmol.export.JSExporter
outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
outputAttr(String, float, float, float) - Method in class org.jmol.export._StlExporter
outputAttr(String, float, float, float) - Method in class org.jmol.export._VrmlExporter
outputAttr(String, float, float, float) - Method in class org.jmol.export._X3dExporter
outputAttrPt(String, T3) - Method in class org.jmol.export._StlExporter
outputAttrPt(String, T3) - Method in class org.jmol.export._VrmlExporter
outputAttrPt(String, T3) - Method in class org.jmol.export._X3dExporter
outputBuffer - Variable in class org.jmol.script.ScriptContext
outputBuffer - Variable in class org.jmol.script.ScriptEval
outputBytes(byte[]) - Method in class javajs.util.AjaxURLConnection
outputChildClose() - Method in class org.jmol.export._StlExporter
outputChildClose() - Method in class org.jmol.export._VrmlExporter
outputChildClose() - Method in class org.jmol.export._X3dExporter
outputChildShapeClose() - Method in class org.jmol.export._VrmlExporter
outputChildShapeClose() - Method in class org.jmol.export._X3dExporter
outputChildShapeStart() - Method in class org.jmol.export._VrmlExporter
outputChildShapeStart() - Method in class org.jmol.export._X3dExporter
outputChildStart() - Method in class org.jmol.export._StlExporter
outputChildStart() - Method in class org.jmol.export._VrmlExporter
outputChildStart() - Method in class org.jmol.export._X3dExporter
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._StlExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._X3dExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
outputCloseTag() - Method in class org.jmol.export._VrmlExporter
outputCloseTag() - Method in class org.jmol.export._X3dExporter
outputColorIndices(int[][], int, BS, int, Map, short[], short[]) - Method in class org.jmol.export._VrmlExporter
outputColors(Lst) - Method in class org.jmol.export._VrmlExporter
outputComment(String) - Method in class org.jmol.export.___Exporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export.__CartesianExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._IdtfExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._MayaExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._VrmlExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export.JSExporter
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._IdtfExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._MayaExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._ObjExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._VrmlExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.JSExporter
outputCylinderChildScaled(short, byte) - Method in class org.jmol.export._VrmlExporter
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._PovrayExporter
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._TachyonExporter
outputDefChildFaceSet(String) - Method in class org.jmol.export._VrmlExporter
outputDefChildFaceSet(String) - Method in class org.jmol.export._X3dExporter
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._PovrayExporter
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._TachyonExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.__CartesianExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._IdtfExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._MayaExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._ObjExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._VrmlExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.JSExporter
outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
outputFace(int[], int[], int) - Method in class org.jmol.export.JSExporter
outputFaceSetClose() - Method in class org.jmol.export._VrmlExporter
outputFaceSetClose() - Method in class org.jmol.export._X3dExporter
outputFaceSetStart() - Method in class org.jmol.export._VrmlExporter
outputFaceSetStart() - Method in class org.jmol.export._X3dExporter
outputFileName - Variable in class org.jmol.dialog.Dialog
outputFooter() - Method in class org.jmol.export.___Exporter
outputFooter() - Method in class org.jmol.export._IdtfExporter
outputFooter() - Method in class org.jmol.export._TachyonExporter
outputFooter() - Method in class org.jmol.export._VrmlExporter
outputFooter() - Method in class org.jmol.export._X3dExporter
outputFooter() - Method in class org.jmol.export.JSExporter
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst, Map, P3) - Method in class org.jmol.export._StlExporter
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst, Map, P3) - Method in class org.jmol.export._VrmlExporter
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst, Map, P3) - Method in class org.jmol.export._X3dExporter
outputHeader() - Method in class org.jmol.export.___Exporter
outputHeader() - Method in class org.jmol.export._IdtfExporter
outputHeader() - Method in class org.jmol.export._MayaExporter
outputHeader() - Method in class org.jmol.export._ObjExporter
outputHeader() - Method in class org.jmol.export._PovrayExporter
outputHeader() - Method in class org.jmol.export._StlExporter
outputHeader() - Method in class org.jmol.export._TachyonExporter
outputHeader() - Method in class org.jmol.export._VrmlExporter
outputHeader() - Method in class org.jmol.export._X3dExporter
outputHeader() - Method in class org.jmol.export.JSExporter
  ///////////////// standard exporter methods //////////////////
outputIndices(int[][], int[], int, BS, int) - Method in class org.jmol.export.__CartesianExporter
outputInitialTransform() - Method in class org.jmol.export._VrmlExporter
outputJmolPerspective() - Method in class org.jmol.export.___Exporter
OutputManagerAwt - Class in org.jmol.viewer
OutputManagerAwt() - Constructor for class org.jmol.viewer.OutputManagerAwt
OutputManagerJS - Class in org.jmol.viewer
OutputManagerJS() - Constructor for class org.jmol.viewer.OutputManagerJS
outputNormals(Lst) - Method in class org.jmol.export._VrmlExporter
outputQuaternionFrame(P3, P3, P3, P3, float, float, float) - Method in class org.jmol.export._VrmlExporter
outputRotation(A4) - Method in class org.jmol.export._StlExporter
outputRotation(A4) - Method in class org.jmol.export._VrmlExporter
outputRotation(A4) - Method in class org.jmol.export._X3dExporter
outputShapeClose() - Method in class org.jmol.export._VrmlExporter
outputShapeClose() - Method in class org.jmol.export._X3dExporter
outputShapeStart() - Method in class org.jmol.export._VrmlExporter
outputShapeStart() - Method in class org.jmol.export._X3dExporter
outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export.__CartesianExporter
outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export._VrmlExporter
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
outputString(String) - Method in class javajs.util.AjaxURLConnection
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export.___Exporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export._IdtfExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export._MayaExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export._PovrayExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export._TachyonExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export._VrmlExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst, Map, P3) - Method in class org.jmol.export.JSExporter
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
outputTextPixel(P3, int) - Method in class org.jmol.export.__CartesianExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._IdtfExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._MayaExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._ObjExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._VrmlExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._X3dExporter
outputTextPixel(P3, int) - Method in class org.jmol.export.JSExporter
outputToFile(Map) - Method in class org.jmol.api.JmolViewer
outputToFile(Map) - Method in class org.jmol.viewer.Viewer
outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._VrmlExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__CartesianExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._IdtfExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._MayaExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._PovrayExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._TachyonExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._X3dExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.JSExporter
outputUseChildClose(String) - Method in class org.jmol.export._VrmlExporter
outputUseChildClose(String) - Method in class org.jmol.export._X3dExporter
outputVertex(T3, T3) - Method in class org.jmol.export.___Exporter
outputVertex(T3, T3) - Method in class org.jmol.export._PovrayExporter
outputVertex(T3, T3) - Method in class org.jmol.export._TachyonExporter
outputVertices(T3[], int, T3) - Method in class org.jmol.export.___Exporter
outSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
OUTSOCKET - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OUTSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
oValue(Object) - Static method in class org.jmol.script.SV
overlaps(double, double) - Method in class jspecview.common.Measurement
overlay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
OVERLAY - Enum constant in enum class jspecview.common.ScriptToken
OVERLAY_DIALOG - Static variable in class jspecview.common.JSViewer
overlay_lines - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
OVERLAY_OFFSET - Static variable in class jspecview.common.JSViewer
OverlayLegend - Enum constant in enum class jspecview.common.Annotation.AType
OverlayLegendDialog - Class in jspecview.dialog
  Dialog for showing the legend or key for overlaid plots in a `JSVPanel`.
OverlayLegendDialog() - Constructor for class jspecview.dialog.OverlayLegendDialog
OVERLAYSTACKED - Enum constant in enum class jspecview.common.ScriptToken
owner - Variable in class jspecview.export.AMLExporter
owner - Variable in class jspecview.export.CMLExporter
owner - Variable in class jspecview.source.JDXHeader
owner - Variable in class jspecview.source.AnIMLReader
owner - Variable in class jspecview.source.NMRMLReader

## P

P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
P - Static variable in class org.jmol.quantum.QS
P_CHECK - Static variable in class org.jmol.util.MeshSurface
P_CONTOUR - Static variable in class org.jmol.util.MeshSurface
P_EXPLICIT_COLOR - Static variable in class org.jmol.util.MeshSurface
P2nReader - Class in org.jmol.adapter.readers.pdb
  P2N file reader.
P2nReader() - Constructor for class org.jmol.adapter.readers.pdb.P2nReader
P3 - Class in javajs.util
  A 3 element point that is represented by single precision floating point x,y,z coordinates.
P3() - Constructor for class javajs.util.P3
P3i - Class in javajs.util
  A 3 element point that is represented by signed integer x,y,z coordinates.
P3i() - Constructor for class javajs.util.P3i
p3Screens - Variable in class org.jmol.render.AxesRenderer
p3Screens - Variable in class org.jmol.render.BbcageRenderer
p3Screens - Variable in class org.jmol.render.UccageRenderer
p3Screens - Variable in class org.jmol.render.MeshRenderer
P4 - Class in javajs.util
  A 4 element point that is represented by single precision floating point x,y,z,w coordinates.
P4() - Constructor for class javajs.util.P4
PAC - Enum constant in enum class jspecview.common.ExportType
pack() - Method in interface jspecview.api.PlatformDialog
pack() - Method in class org.jmol.awtjs.swing.JDialog
packageJSON(String, String) - Static method in class javajs.util.PT
packed - Static variable in class org.jmol.script.T
pageUpBuffer - Variable in class org.jmol.console.GenericConsole
paint(Graphics) - Method in class jme.JME
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
paintComponent(Graphics) - Method in class jspecview.java.AwtPanel
  Overrides paintComponent in class JPanel in order to draw the spectrum
paintComponent(Object) - Method in interface jspecview.api.JSVPanel
paintComponent(Object) - Method in class jspecview.java.AwtPanel
paintComponent(Object) - Method in class jspecview.js2d.JsPanel
  Overrides paintComponent in class JPanel in order to draw the spectrum
paintMolecularArea(BufferedImage) - Method in class jme.JME
PAL - Enum Class in org.jmol.c
  Enum for animation mode.
PALETTE_ALTLOC - Static variable in enum class org.jmol.c.PAL
PALETTE_AMINO - Static variable in enum class org.jmol.c.PAL
PALETTE_CHAIN - Static variable in enum class org.jmol.c.PAL
PALETTE_CPK - Static variable in enum class org.jmol.c.PAL
PALETTE_ENERGY - Static variable in enum class org.jmol.c.PAL
PALETTE_FIXEDTEMP - Static variable in enum class org.jmol.c.PAL
PALETTE_FORMAL_CHARGE - Static variable in enum class org.jmol.c.PAL
PALETTE_GROUP - Static variable in enum class org.jmol.c.PAL
PALETTE_INSERTION - Static variable in enum class org.jmol.c.PAL
PALETTE_JMOL - Static variable in enum class org.jmol.c.PAL
PALETTE_MOLECULE - Static variable in enum class org.jmol.c.PAL
PALETTE_MONOMER - Static variable in enum class org.jmol.c.PAL
PALETTE_NONE - Static variable in enum class org.jmol.c.PAL
PALETTE_NUCLEIC - Static variable in enum class org.jmol.c.PAL
PALETTE_PARTIAL_CHARGE - Static variable in enum class org.jmol.c.PAL
PALETTE_POLYMER - Static variable in enum class org.jmol.c.PAL
PALETTE_PROPERTY - Static variable in enum class org.jmol.c.PAL
PALETTE_RASMOL - Static variable in enum class org.jmol.c.PAL
PALETTE_SHAPELY - Static variable in enum class org.jmol.c.PAL
PALETTE_STRAIGHTNESS - Static variable in enum class org.jmol.c.PAL
PALETTE_STRUCTURE - Static variable in enum class org.jmol.c.PAL
PALETTE_SURFACE - Static variable in enum class org.jmol.c.PAL
PALETTE_TEMP - Static variable in enum class org.jmol.c.PAL
PALETTE_TYPE - Static variable in enum class org.jmol.c.PAL
PALETTE_VARIABLE - Static variable in enum class org.jmol.c.PAL
PALETTE_VOLATILE - Static variable in enum class org.jmol.c.PAL
paletteID - Variable in class org.jmol.modelset.Atom
paletteIDs - Variable in class org.jmol.shape.AtomShape
palindrome - Static variable in class org.jmol.script.T
panel() - Method in class org.openscience.jmol.app.webexport.Test
PanelData - Class in jspecview.common
  JSVPanel class draws a plot from the data contained a instance of one or more `GraphSet` objects.
PanelData(JSVPanel, JSViewer) - Constructor for class jspecview.common.PanelData
PanelData.LinkMode - Enum Class in jspecview.common
panelEvent(Object) - Method in interface jspecview.api.PanelListener
panelEvent(Object) - Method in class jspecview.app.JSVApp
  called by notifyPeakPickedListeners in JSVPanel
panelEvent(Object) - Method in class jspecview.application.MainFrame
PanelListener - Interface in jspecview.api
panelNode - Variable in class jspecview.application.AwtTreeNode
panelNode - Variable in class jspecview.tree.SimpleTreeNode
PanelNode - Class in jspecview.common
PanelNode(String, String, JDXSource, JSVPanel) - Constructor for class jspecview.common.PanelNode
panelNodes - Variable in class jspecview.common.JSViewer
paper - Variable in class jspecview.common.PrintLayout
  The size of the paper to be printed on
paperHeight - Variable in class jspecview.common.PrintLayout
paperWidth - Variable in class jspecview.common.PrintLayout
parabolicInterpolation(Coordinate[], int) - Static method in class jspecview.common.Coordinate
  see https://ccrma.stanford.edu/~jos/sasp/Quadratic_Interpolation_Spectral_Peaks.html
parallel - Static variable in class org.jmol.script.T
PARAM_COUNT - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_M33 - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_M4 - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_OXYZ - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_SCALE - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_SLOP - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_STD - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_SUPERCELL - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_VAX - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_VBX - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_VCX - Static variable in class org.jmol.util.SimpleUnitCell
PARAM_VCZ - Static variable in class org.jmol.util.SimpleUnitCell
paramAsStr(int) - Method in class org.jmol.script.ScriptParam
paramAsStr(int) - Method in class org.jmol.scriptext.ScriptExt
ParamCheck(float[], boolean, boolean) - Constructor for class org.jmol.symmetry.SpaceGroup.ParamCheck
parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptEval
parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptEval
parameterExpressionSelect(Map, T[]) - Method in class org.jmol.script.ScriptEval
parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptEval
parameterExpressionToken(int) - Method in class org.jmol.script.ScriptEval
parameters - Variable in class jspecview.common.JSViewer
parameters - Static variable in class org.jmol.script.T
Parameters - Class in jspecview.common
Parameters - Class in org.jmol.jvxl.readers
Parameters() - Constructor for class jspecview.common.Parameters
Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
params - Variable in class org.jmol.jvxl.readers.SurfaceReader
paramsCentroid - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
paramsLattice - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
paramTypes - Static variable in class org.jmol.script.T
parBorU - Variable in class org.jmol.util.Tensor
parent - Variable in class jspecview.source.JDXDataObject
parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
parent - Variable in class org.jmol.awtjs.swing.Component
parentContext - Variable in class org.jmol.script.ScriptContext
parse(String, boolean) - Method in class javajs.util.JSJSONParser
  Could return Integer, Float, Boolean, String, Mapinvalid input: '<'String, Object>, Lst
parseCalc(Viewer, String) - Static method in class org.jmol.util.SimpleUnitCell
parseCalcFunctions(Viewer, String[], String) - Static method in class org.jmol.util.SimpleUnitCell
parseCartesianField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
parseCartesianField() - Method in class org.jmol.adapter.readers.cif.CifReader
parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
parseDataBlockParameters(String[], String, String, int[], int[]) - Method in interface javajs.api.GenericCifDataParser
parseDataBlockParameters(String[], String, String, int[], int[]) - Method in class javajs.util.CifDataParser
  Process a data block, with or without a loop_.
parsedContext - Variable in class org.jmol.console.ScriptEditor
parsedData - Variable in class org.jmol.console.ScriptEditor
parseDSV(String, double, double) - Static method in class jspecview.common.Coordinate
  Parses data stored in x, y format
parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseFloat() - Method in class org.jmol.jvxl.readers.JvxlReader
parseFloat() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseFloat() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseFloat(String) - Static method in class javajs.util.PT
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.JvxlReader
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseFloatArray(String) - Static method in class javajs.util.PT
parseFloatArrayBsData(String[], BS, float[]) - Static method in class org.jmol.util.Parser
parseFloatArrayData(String[], float[]) - Static method in class javajs.util.PT
  parses a string array for floats.
parseFloatArrayDataN(String[], float[], int) - Static method in class javajs.util.PT
  parses a string array for floats.
parseFloatArrayFromMatchAndField(String, BS, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
  the major lifter here.
parseFloatArrayInfested(String[], float[]) - Static method in class javajs.util.PT
parseFloatArrayNext(String, int[], float[], String, String) - Static method in class javajs.util.PT
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseFloatChecked(String, int, int[], boolean) - Static method in class javajs.util.PT
  A float parser that is 30% faster than Float.parseFloat(x) and also accepts x.yD+-n
parseFloatField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
parseFloatField() - Method in class org.jmol.adapter.readers.cif.CifReader
parseFloatFraction(String) - Static method in class javajs.util.PT
  parse a float or "float/float"
parseFloatNext(String, int[]) - Static method in class javajs.util.PT
parseFloatRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseFloatRange(String, int, int[]) - Static method in class javajs.util.PT
parseFloatStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseFloatStrict(String) - Static method in class javajs.util.PT
parseInitScript(String) - Method in class jspecview.common.JSViewer
  Parses the JavaScript call parameters and executes them accordingly
parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseInt() - Method in class org.jmol.jvxl.readers.JvxlReader
parseInt() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseInt() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseInt(String) - Static method in class javajs.util.PT
parseIntAt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseIntChecked(String, int, int[]) - Static method in class javajs.util.PT
parseIntField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
parseIntField() - Method in class org.jmol.adapter.readers.cif.CifReader
parseIntFieldTok(byte) - Method in class org.jmol.adapter.readers.cif.BCIFReader
  Get a specific column's item for this category on this row.
parseIntFieldTok(byte) - Method in class org.jmol.adapter.readers.cif.MMCifReader
parseIntNext(String) - Method in class org.jmol.jvxl.readers.JvxlReader
parseIntNext(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseIntNext(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseIntNext(String, int[]) - Static method in class javajs.util.PT
parseIntRadix(String, int) - Static method in class javajs.util.PT
parseIntRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseIntRange(String, int, int[]) - Static method in class javajs.util.PT
parseIntStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseIntStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
parseIntStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
parseIntStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
parseJSON(String) - Method in class org.jmol.viewer.Viewer
parseJSONArray(String) - Method in class org.jmol.viewer.Viewer
parseJSONMap(String) - Method in class org.jmol.viewer.Viewer
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.BCIFReader
  This is the callback the that the MMCifReader and CifReader process.....() methods call initially.
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
  sets up arrays and variables for tokenizer.getData() after the first tag of the loop has been checked.
parseMap(String, boolean) - Method in class javajs.util.JSJSONParser
  requires { "key":"value", "key":"value",....}
parsePrecision(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  Track the precision (count of y digits in "xx.yyyy") for setting cellSlop.
parser - Variable in class jspecview.source.AnIMLReader
parser - Variable in class jspecview.source.NMRMLReader
Parser - Class in org.jmol.util
Parser() - Constructor for class org.jmol.util.Parser
parseScript(String, int) - Method in class org.jmol.console.ScriptEditor
parseSimpleMath(Viewer, String) - Static method in class org.jmol.util.SimpleUnitCell
  parse math such as "1/sqrt(3)" or "2sqrt(3) or "2cos(3pi/2)"
parseStringInfestedFloatArray(String, BS, float[]) - Static method in class org.jmol.util.Parser
  parses a "dirty" string for floats.
parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseToken(String) - Static method in class javajs.util.PT
parseTokenChecked(String, int, int[]) - Static method in class javajs.util.PT
parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseTokenNext(String, int[]) - Static method in class javajs.util.PT
parseTokenRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseTokenRange(String, int, int[]) - Static method in class javajs.util.PT
parseTokenStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseTrimmed(String) - Static method in class javajs.util.PT
parseTrimmedAt(String, int) - Static method in class javajs.util.PT
parseTrimmedChecked(String, int, int) - Static method in class javajs.util.PT
parseTrimmedRange(String, int, int) - Static method in class javajs.util.PT
part - Variable in class org.jmol.adapter.smarter.Atom
PARTIAL_CHARGE - Enum constant in enum class org.jmol.c.PAL
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JC
partialcharge - Static variable in class org.jmol.script.T
partialCharge - Variable in class org.jmol.adapter.smarter.Atom
partialCharge - Variable in class org.jmol.minimize.MinAtom
partialdots - Static variable in class org.jmol.script.T
particleradius - Static variable in class org.jmol.script.T
pass2Flag01 - Variable in class org.jmol.g3d.Graphics3D
pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
path - Static variable in class org.jmol.script.T
path - Static variable in class org.openscience.jmol.app.janocchio.Nmr
PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
  AtomSetCollectionReader.readData() will close any BufferedReader
PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
pathforallfiles - Static variable in class org.jmol.script.T
pathlength - Variable in class jspecview.export.AMLExporter
pathlength - Variable in class jspecview.export.CMLExporter
pathlength - Variable in class jspecview.source.AnIMLReader
pathlength - Variable in class jspecview.source.NMRMLReader
pattern - Static variable in class org.jmol.script.T
PatternMatcher - Class in org.jmol.util
PatternMatcher() - Constructor for class org.jmol.util.PatternMatcher
PatternMatcher.JSPattern - Class in org.jmol.util
  Super-simplified for JavaScript
pause - Static variable in class org.jmol.script.T
pauseExecution(boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
pauseExecution(boolean) - Method in class org.jmol.script.ScriptEval
pauseScript(Viewer, boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
pbuf - Variable in class org.jmol.g3d.Graphics3D
pbufT - Variable in class org.jmol.g3d.Graphics3D
pc - Variable in class org.jmol.script.ScriptContext
pc - Variable in class org.jmol.script.ScriptEval
pc - Variable in class org.jmol.util.MeshSurface
  polygon count
pc0 - Variable in class org.jmol.script.ScriptContext
pcEnd - Variable in class org.jmol.script.ScriptContext
pcResume - Variable in class org.jmol.script.ScriptEval
pcs - Variable in class org.jmol.util.MeshSurface
  polygon color index "colix" array
pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
pd - Variable in class jspecview.app.GenericMouse
pd() - Method in class jspecview.common.JSViewer
pd() - Method in class jspecview.common.PanelNode
pdb - Static variable in class org.jmol.script.T
PDB_ANNOTATIONS - Static variable in class org.jmol.viewer.JC
PDB_CARTOONS - Static variable in class org.jmol.viewer.FileManager
pdb_conect_all - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_discrete_chains - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_echo_tags - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_formal_charges - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_hetatm_guess_valences - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_hetatm_sort - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_honor_model_number - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_ignore_conect - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_insertions_go_first - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_insure_orthogonal - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_literal_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_no_end_record - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_reformat_names_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_retain_ids - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_standard_order - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_truncate_residue_name - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_unbond_cations - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdb_use_ter_records - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pdbaddhydrogens - Static variable in class org.jmol.script.T
pdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
  pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid.
pdbgetheader - Static variable in class org.jmol.script.T
pdbheader - Static variable in class org.jmol.script.T
pdbID - Variable in class org.jmol.adapter.readers.cif.CifReader
pdbID - Variable in class org.jmol.adapter.readers.pdb.PdbReader
pdbID - Variable in class org.jmol.modelset.Model
PdbReader - Class in org.jmol.adapter.readers.pdb
  PDB file reader.
PdbReader() - Constructor for class org.jmol.adapter.readers.pdb.PdbReader
pdbsequential - Static variable in class org.jmol.script.T
PDBWriter - Class in org.jmol.adapter.writers
  An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
PDBWriter() - Constructor for class org.jmol.adapter.writers.PDBWriter
PDF - Enum constant in enum class jspecview.common.ExportType
PDF_NO_SUCH_PAGE - Static variable in class jspecview.common.JSViewer
PDF_PAGE_EXISTS - Static variable in class jspecview.common.JSViewer
PDFCreator - Class in javajs.export
PDFCreator() - Constructor for class javajs.export.PDFCreator
PdfEncoder - Class in javajs.img
  A relatively primitive PDF generator that just makes a document with an image in it.
PdfEncoder() - Constructor for class javajs.img.PdfEncoder
PDFWriter - Class in jspecview.common
  A class that creates the PDF document specific to JSpecView using javajs.export.PDFCreator.
PDFWriter() - Constructor for class jspecview.common.PDFWriter
PEAK - Enum constant in enum class jspecview.common.ScriptToken
PEAKCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
peakCount - Variable in class jspecview.source.JDXSource
PeakData - Class in jspecview.common
  a data structure for peak lists
PeakData(Annotation.AType, Spectrum) - Constructor for class jspecview.common.PeakData
PeakInfo - Class in jspecview.common
PeakInfo() - Constructor for class jspecview.common.PeakInfo
PeakInfo(String) - Constructor for class jspecview.common.PeakInfo
peakInfoModelSentToJmol - Variable in class jspecview.common.JSViewer
PeakList - Enum constant in enum class jspecview.common.Annotation.AType
PEAKLIST - Enum constant in enum class jspecview.common.ScriptToken
PeakListDialog - Class in jspecview.dialog
  Dialog for managing the peak listing for a Spectrum within a GraphSet
PeakListDialog() - Constructor for class jspecview.dialog.PeakListDialog
peakListInterpolation - Variable in class jspecview.common.Parameters
peakListThreshold - Variable in class jspecview.common.Parameters
peakOverColor - Variable in class jspecview.common.PanelData
PEAKOVERCOLOR - Enum constant in enum class jspecview.common.ScriptToken
PeakPickEvent - Class in jspecview.common
PeakPickEvent(Object, Coordinate, PeakInfo) - Constructor for class jspecview.common.PeakPickEvent
peakTabColor - Variable in class jspecview.common.PanelData
PEAKTABCOLOR - Enum constant in enum class jspecview.common.ScriptToken
peakTabsOn - Variable in class jspecview.common.PanelData
PEAKTABSON - Enum constant in enum class jspecview.common.ScriptToken
peek() - Method in class jspecview.source.XMLParser
peekToken() - Method in interface javajs.api.GenericCifDataParser
peekToken() - Method in class javajs.util.CifDataParser
  Just look at the next token.
per - Static variable in class org.jmol.script.T
percent - Static variable in class org.jmol.script.T
percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
percentvdwatom - Static variable in class org.jmol.script.T
period - Static variable in class org.jmol.script.T
periodicity - Variable in class org.jmol.render.AxesRenderer
periodicity - Variable in class org.jmol.render.BbcageRenderer
periodicity - Variable in class org.jmol.render.UccageRenderer
periodicity - Variable in class org.jmol.symmetry.SpaceGroup
PeriodicVolumeFileReader - Class in org.jmol.jvxl.readers
PeriodicVolumeFileReader() - Constructor for class org.jmol.jvxl.readers.PeriodicVolumeFileReader
perpendicular - Static variable in class org.jmol.script.T
perper - Static variable in class org.jmol.script.T
perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
perspectivedepth - Static variable in class org.jmol.script.T
perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
perspectivemodel - Static variable in class org.jmol.script.T
perspectiveModel - Variable in class org.jmol.viewer.TransformManager
perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
PfaatBinding - Class in org.jmol.viewer.binding
PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
phase - Static variable in class org.jmol.script.T
phi - Static variable in class org.jmol.script.T
phongexponent - Static variable in class org.jmol.script.T
PhosphorusMonomer - Class in org.jmol.modelsetbio
PhosphorusMonomer() - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
PhosphorusPolymer - Class in org.jmol.modelsetbio
PICK - Enum constant in enum class org.jmol.c.CBK
PICK_COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
pickable - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pickedMesh - Variable in class org.jmol.shape.MeshCollection
pickedModel - Variable in class org.jmol.shape.MeshCollection
pickedPt - Variable in class org.jmol.shape.MeshCollection
pickedVertex - Variable in class org.jmol.shape.MeshCollection
picking - Static variable in class org.jmol.script.T
PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_LIGAND - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MODEL - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_SPIN - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
PICKING_MK_RESET - Static variable in class org.jmol.viewer.ActionManager
PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_SPIN - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
PICKING_SYMOP - Static variable in class org.jmol.viewer.ActionManager
pickingspinrate - Static variable in class org.jmol.script.T
pickingstyle - Static variable in class org.jmol.script.T
PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
  picking styles
PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
picklabel - Static variable in class org.jmol.script.T
pidOf(Object) - Static method in enum class org.jmol.c.PAL
ping() - Method in class jme.JME
PINK - Static variable in class org.jmol.util.C
pis - Variable in class org.jmol.util.MeshSurface
  polygon indexes
pivot - Static variable in class org.jmol.script.T
pivot2 - Static variable in class org.jmol.script.T
pixelLocation(Location) - Static method in class com.sparshui.common.Location
pixels - Variable in class javajs.img.ImageEncoder
PLAIN_MESSAGE - Static variable in class jspecview.dialog.DialogManager
planarparam - Static variable in class org.jmol.script.T
plane - Static variable in class org.jmol.script.T
PLANE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
planeParameter(int, boolean) - Method in class org.jmol.script.ScriptParam
planeValue(T) - Method in class org.jmol.script.ScriptParam
Platform - Class in org.jmol.awt
Platform - Class in org.jmol.awtjs
  WebGL interface
Platform - Class in org.jmol.awtjs2d
  JavaScript 2D canvas version requires Ajax-based URL stream processing.
Platform() - Constructor for class org.jmol.awt.Platform
Platform() - Constructor for class org.jmol.awtjs.Platform
Platform() - Constructor for class org.jmol.awtjs2d.Platform
PlatformDialog - Interface in jspecview.api
platformspeed - Static variable in class org.jmol.script.T
PlatformViewer - Interface in org.jmol.api
play - Static variable in class org.jmol.script.T
playAudio(Map) - Method in class org.jmol.viewer.StatusManager
playAudio(JSmolAppletObject, Map) - Method in interface org.jmol.api.js.JmolToJSmolInterface
playAudio(Viewer, Map) - Method in class org.jmol.util.JmolAudio
  WAV only for application
playrev - Static variable in class org.jmol.script.T
plLabel - Variable in class jspecview.source.AnIMLReader
plLabel - Variable in class jspecview.source.NMRMLReader
plot - Static variable in class org.jmol.script.T
plot3d - Static variable in class org.jmol.script.T
Plot3D - Class in org.jmol.shapesurface
Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
Plot3DRenderer - Class in org.jmol.rendersurface
Plot3DRenderer() - Constructor for class org.jmol.rendersurface.Plot3DRenderer
plotAreaColor - Variable in class jspecview.common.PanelData
PLOTAREACOLOR - Enum constant in enum class jspecview.common.ScriptToken
PLOTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
plotColors - Variable in class jspecview.common.ColorParameters
PLOTCOLORS - Enum constant in enum class jspecview.common.ScriptToken
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.util.GData
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in interface org.jmol.api.JmolRendererInterface
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.export.Export3D
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.g3d.Graphics3D
plotPixelClippedP3i(P3i) - Method in interface org.jmol.api.JmolRendererInterface
plotPixelClippedP3i(P3i) - Method in class org.jmol.export.Export3D
plotPixelClippedP3i(P3i) - Method in class org.jmol.g3d.Graphics3D
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.util.GData
pluginFile - Variable in class org.openscience.jmol.app.JmolApp
pluginFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
plus - Static variable in class org.jmol.script.T
plusPlus - Static variable in class org.jmol.script.T
PLYWriter - Class in org.jmol.shapesurface
  A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
PLYWriter() - Constructor for class org.jmol.shapesurface.PLYWriter
pmesh - Static variable in class org.jmol.script.T
Pmesh - Class in org.jmol.shapesurface
Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
PmeshRenderer - Class in org.jmol.rendersurface
PmeshRenderer() - Constructor for class org.jmol.rendersurface.PmeshRenderer
PMeshWriter - Class in org.jmol.shapesurface
  A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
PMeshWriter() - Constructor for class org.jmol.shapesurface.PMeshWriter
PNG - Enum constant in enum class jspecview.common.ExportType
png_file_gamma - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
png_screen_gamma - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pngBytes - Variable in class javajs.img.PngEncoder
PngEncoder - Class in javajs.img
  Modified by Bob Hanson hansonr@stolaf.edu to be a subclass of ImageEncoder and to use javajs.util.OutputChannel instead of just returning bytes.
PngEncoder() - Constructor for class javajs.img.PngEncoder
pngjCache - Variable in class org.jmol.viewer.FileManager
PO - Class in org.jmol.translation
  Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.
PO() - Constructor for class org.jmol.translation.PO
pocket - Static variable in class org.jmol.script.T
point - Static variable in class org.jmol.script.T
POINT - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
point3f - Static variable in class org.jmol.script.T
Point3fi - Class in org.jmol.util
  The Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points) associated symmetry operation (generating equivalent atoms in UnitCell.java)
Point3fi() - Constructor for class org.jmol.util.Point3fi
point4f - Static variable in class org.jmol.script.T
pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
pointer - Variable in class org.jmol.modelset.Text
pointerPt - Variable in class org.jmol.modelset.Text
pointgroup - Static variable in class org.jmol.script.T
pointGroup - Variable in class org.jmol.modelset.AtomCollection
pointgroupdistancetolerance - Static variable in class org.jmol.script.T
pointgrouplineartolerance - Static variable in class org.jmol.script.T
PointIterator - Class in org.jmol.bspt
PointIterator() - Constructor for class org.jmol.bspt.PointIterator
pointPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d, boolean) - Static method in class org.jmol.minimize.Util
  calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
points - Variable in class org.jmol.jvxl.readers.Parameters
points - Variable in class org.jmol.modelset.MeasurementData
points - Variable in class org.jmol.quantum.QuantumCalculation
pointScale - Variable in class org.jmol.shapespecial.Polyhedron
pointSize - Variable in class org.jmol.jvxl.data.JvxlData
pointSize - Variable in class org.jmol.jvxl.readers.Parameters
POINTSONLY - Enum constant in enum class jspecview.common.ScriptToken
pointsperangstrom - Static variable in class org.jmol.script.T
pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
pointT - Variable in class org.jmol.render.FontLineShapeRenderer
pointT2 - Variable in class org.jmol.render.FontLineShapeRenderer
pointT3 - Variable in class org.jmol.render.FontLineShapeRenderer
polar_neighbor_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
polarnitro - Variable in class jme.JME
polygon - Static variable in class org.jmol.script.T
POLYGON - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
polygonCount0 - Variable in class org.jmol.util.MeshSurface
polyhedra - Static variable in class org.jmol.script.T
Polyhedra - Class in org.jmol.shapespecial
Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
POLYHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
PolyhedraRenderer - Class in org.jmol.renderspecial
PolyhedraRenderer() - Constructor for class org.jmol.renderspecial.PolyhedraRenderer
Polyhedron - Class in org.jmol.shapespecial
polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
polyhedronStereo - Variable in class org.jmol.smiles.SmilesSearch
  indicates that we have [XxPHn] with no connected atoms
polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in interface org.jmol.api.SmilesMatcherInterface
polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in class org.jmol.smiles.SmilesMatcher
  Generate a topological SMILES string from a set of faces
polymer - Static variable in class org.jmol.script.T
POLYMER - Enum constant in enum class org.jmol.c.PAL
polymerlength - Static variable in class org.jmol.script.T
Polymers - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Allow processing of polymers (experimental)
Polymers105 - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Allow processing of polymers (experimental, legacy mode of v.
polySmiles - Variable in class org.jmol.shapespecial.Polyhedron
polySmilesCenter - Variable in class org.jmol.smiles.SmilesGenerator
pop - Static variable in class org.jmol.script.T
popHoldRepaint(boolean, String) - Method in interface org.jmol.api.JmolRepaintManager
popHoldRepaint(boolean, String) - Method in class org.jmol.render.RepaintManager
popHoldRepaint(String) - Method in class org.jmol.api.JmolViewer
popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
popMatrix() - Method in class org.jmol.export._StlExporter
popMatrix() - Method in class org.jmol.export._VrmlExporter
popMatrix() - Method in class org.jmol.export._X3dExporter
popStack(int) - Method in class org.jmol.viewer.StateManager
  Remove the last item on the specified stack, and save the current state to the other stack provided that state is not null.
popState() - Method in class org.jmol.util.CommandHistory
popState() - Method in class org.jmol.viewer.Viewer
populateVariables() - Method in class jspecview.source.AnIMLReader
populateVariables() - Method in class jspecview.source.NMRMLReader
populationDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
PopulationDisplay - Class in org.openscience.jmol.app.janocchio
PopulationDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.PopulationDisplay
  Constructor
PopupHelper - Interface in org.jmol.popup
popupMenu - Variable in class org.jmol.popup.GenericPopup
PopupResource - Class in org.jmol.popup
PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
port - Variable in class org.openscience.jmol.app.JmolApp
  The data model.
port - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
PORTRAIT - Static variable in class jspecview.common.JSViewer
position - Variable in class jspecview.common.PrintLayout
  The position of the graph on the paper ("center", "default", "fit to page")
postByteArray(String, byte[]) - Method in interface javajs.api.BytePoster
postByteArray(String, byte[]) - Static method in class jspecview.common.JSVFileManager
postByteArray(String, byte[]) - Method in class jspecview.common.JSViewer
postByteArray(String, byte[]) - Method in class org.jmol.viewer.FileManager
  / BytePoster interface
postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
postSymmetrySetMagneticMoments(AtomSetCollection, boolean) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
  At the end, we need to rescale the vectors using SpinFramePp.
povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
  A dialog for controling the creation of a povray input file from a Chemframe and a display.
PovrayDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Creates a dialog for getting info related to output frames in povray format.
povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
PpmEncoder - Class in javajs.img
  see http://netpbm.sourceforge.net/doc/ppm.html
PpmEncoder() - Constructor for class javajs.img.PpmEncoder
pqr_workarounds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
PqrReader - Class in org.jmol.adapter.readers.pdb
  PQR file reader.
PqrReader() - Constructor for class org.jmol.adapter.readers.pdb.PqrReader
precision - Variable in class jspecview.common.MeasurementData
precision - Variable in class jspecview.common.Parameters
precision - Variable in class jspecview.common.ScaleData
  The precision (number of decimal places) of the X and Y values
precision - Variable in class jspecview.dialog.JSVDialog
precision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
  maximum of the decimal length of unit cell lengths and fractional coordinates
precision - Variable in class org.jmol.adapter.writers.XtlWriter
PrecisionRenderer - Class in org.jmol.g3d
  Note added 4/2015 BH: Well, it turns out that the calculation of the intermediate pixel z value in all methods involving rasterization of lines is incorrect and has been incorrect since Jmol's inception.
PrecisionRenderer() - Constructor for class org.jmol.g3d.PrecisionRenderer
predefinedset - Static variable in class org.jmol.script.T
predefinedStatic - Static variable in class org.jmol.viewer.JC
predefinedVariable - Static variable in class org.jmol.viewer.JC
  /////////////////////////////////////////////////////////////
preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PreferencesDialog - Class in jspecview.application
  Dialog to change the preferences for the application.
PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
PreferencesDialog(Frame, JSViewer, String, boolean, DisplaySchemesProcessor) - Constructor for class jspecview.application.PreferencesDialog
  Initialises the `PreferencesDialog`
PreferencesDialog(JmolPanel, JFrame, GuiMap, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
PREFIX_FRIEZE - Static variable in class org.jmol.symmetry.SpaceGroup
PREFIX_LAYER - Static variable in class org.jmol.symmetry.SpaceGroup
PREFIX_PLANE - Static variable in class org.jmol.symmetry.SpaceGroup
PREFIX_ROD - Static variable in class org.jmol.symmetry.SpaceGroup
PREFIX_SPACE - Static variable in class org.jmol.symmetry.SpaceGroup
prepareAtomSet(BS) - Method in class org.jmol.adapter.writers.CIFWriter
prepareAtomSet(BS) - Method in class org.jmol.adapter.writers.FSG2SCIFConverter
prepareBinaryOutput(SV) - Method in class org.jmol.scriptext.CmdExt
prepareNextLine() - Method in class javajs.util.CifDataParser
  sets the string for parsing to be from the next line when the token buffer is empty, and if ';' is at the beginning of that line, extends the string to include that full multiline string.
preprocessSemiString() - Method in class javajs.util.CifDataParser
  Encapsulate a multi-line ; ....
preprocessString() - Method in class javajs.util.CifDataParser
  Preprocess the string on a line starting with a semicolon to produce a string with a \1 ...
preprocessString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  initial processing; returns a string bounded by \1
presentation - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
presentation_auto_quit - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
presentation_auto_start - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
presentation_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
preserve_chempy_ids - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
preservestate - Static variable in class org.jmol.script.T
preserveState - Variable in class org.jmol.modelset.AtomCollection
preserveState - Variable in class org.jmol.viewer.GlobalSettings
pressed - Variable in class org.jmol.viewer.ActionManager
pressed(long, int, int, int, boolean) - Method in class jspecview.app.GenericMouse
PRESSED - Static variable in class org.jmol.awtjs.Event
pressedCount - Variable in class org.jmol.viewer.ActionManager
preSymmetryFinalizeMoments(AtomSetCollectionReader, AtomSetCollection, String, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
  Scale the magnetic moments of magCIF and spinCIF files.
prev - Static variable in class org.jmol.script.T
prevBondCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
previewXML(BufferedReader) - Method in class org.jmol.adapter.readers.xml.XmlNmrmlReader
  fixing unterminated cv element and unclosed chemicalShiftStandard start element not fixing trailing '"' after bond elements Just two times through this before we are done.
previewXML(BufferedReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
  An opportunity to fix XML (nmrML issues)
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
previousMeshID - Variable in class org.jmol.shape.MeshCollection
previousMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
previousView() - Method in class jspecview.common.PanelData
  Displays the previous view zoomed
previousX - Variable in class org.jmol.viewer.TransformManager
previousY - Variable in class org.jmol.viewer.TransformManager
prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
primitiveToCrystal - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
print - Static variable in class org.jmol.script.T
print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  added print command, so that it can be used by RasmolScriptHandler
print(Graphics, PageFormat, int) - Method in class jspecview.java.AwtPanel
  Implements method print in interface printable
print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
print(Object, double, double, double, double, double, double, boolean, int) - Method in class jspecview.common.PanelData
print(String) - Method in interface jspecview.api.JSVAppletInterface
print(String) - Method in class jspecview.app.JSVApp
print(String) - Method in class jspecview.appletjs.JSVApplet
print(String) - Method in class jspecview.common.JSViewer
PRINT - Enum constant in enum class jspecview.common.ScriptToken
printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
printFilePath(Object, int, int, String) - Method in class jspecview.common.PanelData
PrintLayout - Class in jspecview.common
  `PrintLayout` class stores all the information needed from the `PrintLayoutDialog`
PrintLayout(PanelData) - Constructor for class jspecview.common.PrintLayout
printPanel(PrintLayout, OutputStream, String) - Method in interface jspecview.api.JSVPanel
printPanel(PrintLayout, OutputStream, String) - Method in class jspecview.java.AwtPanel
  Send a print job of the spectrum to the default printer on the system
printPanel(PrintLayout, OutputStream, String) - Method in class jspecview.js2d.JsPanel
  Send a print job of the spectrum to the default printer on the system
printPdf(GenericGraphics, PrintLayout) - Method in class jspecview.common.PanelData
  from jspecview.export.PDFCreator -- does not use iText --
printPDF(JSViewer, String) - Method in interface jspecview.export.ExportInterface
printVersion(Object, int) - Method in class jspecview.common.PanelData
privat - Static variable in class org.jmol.script.T
privateFuncs - Variable in class org.jmol.script.ScriptContext
privateFuncs - Variable in class org.jmol.script.ScriptEval
privateKey - Variable in class org.jmol.export.___Exporter
privateKey - Variable in class org.jmol.viewer.OutputManagerAwt
privateKey - Variable in class org.jmol.viewer.OutputManagerJS
probe - Static variable in class org.jmol.script.T
probes - Variable in class org.jmol.jvxl.readers.Parameters
probeValues - Variable in class org.jmol.jvxl.readers.Parameters
process - Static variable in class org.jmol.script.T
process() - Method in class org.jmol.quantum.MepCalculation
process() - Method in class org.jmol.quantum.MOCalculation
process() - Method in class org.jmol.quantum.NciCalculation
process() - Method in class org.jmol.quantum.QuantumCalculation
process(int, boolean) - Method in class jspecview.source.AnIMLReader
  Process the audit XML events
process(int, boolean) - Method in class jspecview.source.NMRMLReader
  Process the audit XML events
process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
  Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
process(int, int, float) - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
process(Lst, Spectrum.IRMode) - Static method in class jspecview.common.Spectrum
processAssemblyGenBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processAtom(Atom, String, char, String, int, int, char, boolean, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
  reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.BCIFReader
  The primare method initiating this reader
processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.MMTFReader
processBinaryDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
processBinaryDocument() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
processBinaryDocument() - Method in class org.jmol.adapter.readers.xtal.CmdfReader
processBinaryDocument() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processBlock(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
processCellParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
  unit cell parameters -- two options, so we use MOD 6
processChange(List, TouchPoint) - Method in interface com.sparshui.gestures.Gesture
  Process a touch point change in the gesture.
processChange(List, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
  incorporates double-click gesture
processChange(List, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  a general name definition field.
processCitationListBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
processClick(String) - Method in class jspecview.dialog.DialogManager
  processing click event from platform DialogManager
processCompBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
  //////////// DOM option //////////////
processDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlNmrmlReader
processEndMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
processEndTag(int) - Method in class jspecview.source.AnIMLReader
processEndTag(int) - Method in class jspecview.source.NMRMLReader
processEntry() - Method in class org.jmol.adapter.readers.cif.MSCifParser
processError(int) - Method in class com.sparshui.server.ServerToClientProtocol
  Send an error message to the client.
processErrors(String) - Method in class jspecview.source.AnIMLReader
processErrors(String) - Method in class jspecview.source.NMRMLReader
processEvent(int, int, int, int, long) - Method in class jspecview.app.GenericMouse
processEvent(int, int, int, int, long) - Method in interface org.jmol.api.GenericMouseInterface
processEvent(int, int, int, int, long) - Method in class org.jmol.awtjs2d.Mouse
processEvent(int, Event) - Method in interface com.sparshui.client.SparshClient
  This method processes events from the Gesture Server.
processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
  Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
processEvents(int, Lst) - Method in class com.sparshui.server.ServerToClientProtocol
  Instruct the client to process the events that have been generated by a group.
processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
processKey(int, int, boolean) - Method in class org.jmol.console.GenericConsole
processKeyEvent(Object) - Method in interface javajs.api.JSInterface
processKeyEvent(Object) - Method in interface jspecview.api.JSVPanel
processKeyEvent(Object) - Method in class jspecview.app.GenericMouse
processKeyEvent(Object) - Method in class jspecview.appletjs.JSVApplet
processKeyEvent(Object) - Method in class jspecview.common.JSViewer
processKeyEvent(Object) - Method in class jspecview.java.AwtPanel
processKeyEvent(Object) - Method in class jspecview.js2d.JsPanel
processKeyEvent(Object) - Method in interface org.jmol.api.GenericMouseInterface
processKeyEvent(Object) - Method in class org.jmol.awtjs2d.Mouse
processKeyEvent(Object) - Method in class org.jmol.util.GenericApplet
processKeyEvent(Object) - Method in class org.jmol.viewer.Viewer
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
  processes loop_ blocks of interest or skips the data
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
  creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.
processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
processMKPropertyItem(String, boolean) - Method in class org.jmol.modelkit.ModelKit
processModelData(String, String, String, String, String, float, float, boolean) - Method in class jspecview.source.JDXReader
processModelData(String, String, String, String, String, float, float, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
processModelData(String, String, String, String, String, float, float, boolean) - Method in interface org.jmol.api.JmolJDXMOLReader
processMouseEvent(int, int, int, int, long) - Method in interface javajs.api.JSInterface
processMouseEvent(int, int, int, int, long) - Method in interface jspecview.api.JSVPanel
processMouseEvent(int, int, int, int, long) - Method in class jspecview.appletjs.JSVApplet
processMouseEvent(int, int, int, int, long) - Method in class jspecview.common.JSViewer
  called by JSmol.js mouse event
processMouseEvent(int, int, int, int, long) - Method in class jspecview.java.AwtPanel
processMouseEvent(int, int, int, int, long) - Method in class jspecview.js2d.JsPanel
  called only by JavaScript
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.util.GenericApplet
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.multitouch.ActionManagerMT
processMultitouchEvent(int, int, int, int, P3, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.viewer.ActionManager
  Specific to ActionManagerMT -- for processing SparshUI gestures
processNextMeasure(MeasurementData, Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
processNextMeasure(MeasurementData, Measurement) - Method in class org.jmol.modelset.MeasurementData
  if this is the client, then this method is called by MeasurementData when a measurement is ready
processNextMeasure(MeasurementData, Measurement) - Method in class org.jmol.shape.Measures
processNioMessage(byte[]) - Method in class org.molecularplayground.MPJmolApp
processNioMessage(byte[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
processNioMessage(byte[]) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
processPeakPickEvent(Object, boolean) - Method in class jspecview.common.JSViewer
  this method is called as a result of the user clicking on a peak (eventObject instanceof PeakPickEvent) or from PEAK command execution
processPoints() - Method in class org.jmol.quantum.MOCalculation
processPoints() - Method in class org.jmol.quantum.QuantumCalculation
processPt(T3) - Method in class org.jmol.quantum.QuantumCalculation
ProcessRecord(String, String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  process _topol_node.id 1
processRequest(SparshClient) - Method in class com.sparshui.client.ClientToServerProtocol
  Processes a request from the Gesture Server
processSemiString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Sets a multiline semicolon-eclipsed string to be parsed from the beginning, allowing for CIF 2.0-type prefixed text lines and removing line folding.
processSequence() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  get canonical 1-letter DNA/RNA sequence code from 3-letter code.
processService(Map) - Method in class org.jmol.viewer.StatusManager
  service is expected to return a value in the "ret" key
processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlNmrmlReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
processStartElement(String, Map) - Method in class org.jmol.adapter.readers.xml.CDXMLParser
processStartMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  identifies ranges for HELIX and TURN
processStructConnLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processStructOperListBlock(boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  identifies sheet ranges
processStructSiteBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  identifies structure sites
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.CifReader
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processSymop(String, boolean) - Method in class org.jmol.modelkit.ModelKit
processSync(String, int) - Method in interface org.jmol.api.JmolJSpecView
processSync(String, int) - Method in class org.jmol.jsv.JSV
processTableEvent(String, int, int, boolean) - Method in class jspecview.dialog.DialogManager
  processing table cell click event from platform DialogManager; takes two hits in AWT -- one a row, the other a column
processTag(int) - Method in class jspecview.source.AnIMLReader
  Process the XML events.
processTag(int) - Method in class jspecview.source.NMRMLReader
  Process the XML events.
processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
processTwoPointGesture(float[][][]) - Method in interface javajs.api.JSInterface
processTwoPointGesture(float[][][]) - Method in interface jspecview.api.JSVPanel
processTwoPointGesture(float[][][]) - Method in class jspecview.app.GenericMouse
processTwoPointGesture(float[][][]) - Method in class jspecview.appletjs.JSVApplet
processTwoPointGesture(float[][][]) - Method in class jspecview.common.JSViewer
processTwoPointGesture(float[][][]) - Method in class jspecview.java.AwtPanel
processTwoPointGesture(float[][][]) - Method in class jspecview.js2d.JsPanel
processTwoPointGesture(float[][][]) - Method in interface org.jmol.api.GenericMouseInterface
processTwoPointGesture(float[][][]) - Method in class org.jmol.awtjs2d.Mouse
  called by JSmol as processTwoPointGesture(canvas.touches);
processTwoPointGesture(float[][][]) - Method in class org.jmol.util.GenericApplet
processTwoPointGesture(float[][][]) - Method in class org.jmol.viewer.Viewer
processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cif.CifReader
  the PDB transformation matrix cartesian --> fractional key and field have been set already
processUpdate(String) - Method in interface org.jmol.api.JmolAudioPlayer
processUpdate(String) - Method in class org.jmol.util.JmolAudio
  In JavaScript, this is called directly from the page in response to events; in Java it is called from the audio player via update(LineEvent).
processWindowClosing(String) - Method in class jspecview.dialog.DialogManager
  processing window closing event from platform DialogManager
processWriteOrCapture(Map) - Method in class org.jmol.viewer.Viewer
  from eval write command only includes option to write set of files
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
  the current state
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
processXML(int, int) - Method in class jspecview.source.AnIMLReader
processXML(int, int) - Method in class jspecview.source.NMRMLReader
processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.more.CDXReader
processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
programInfo - Variable in class org.jmol.atomdata.AtomData
projectOntoAxis(P3, P3, V3, V3) - Static method in class javajs.util.Measure
  project point onto a line containing ptA and having axis unitVector axisUnitVector, returning the result in point and a vector from ptA to pt in vectorProjection
prompt - Static variable in class org.jmol.script.T
prompt(String, String, String[], boolean) - Method in class jspecview.java.AwtPlatform
prompt(String, String, String[], boolean) - Method in class jspecview.js2d.JsPlatform
prompt(String, String, String[], boolean) - Method in interface org.jmol.api.GenericPlatform
prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
prompt(String, String, String[], boolean) - Method in class org.jmol.awtjs2d.Platform
prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
PROP_ATOMS_DELETED - Static variable in class org.jmol.viewer.JC
PROP_ATOMS_LABELED - Static variable in class org.jmol.viewer.JC
PROP_ATOMS_MOVED - Static variable in class org.jmol.viewer.JC
PROP_DELETE_MODEL_ATOMS - Static variable in class org.jmol.viewer.JC
PROP_JSPECVIEW - Static variable in class org.jmol.viewer.JC
PROP_MODEL_TYPE - Static variable in class org.jmol.viewer.JC
properties - Variable in class jspecview.common.JSViewer
properties - Variable in class org.jmol.modelset.Model
property - Variable in class org.jmol.modelset.Measurement
property - Variable in class org.jmol.modelset.MeasurementData
property - Static variable in class org.jmol.script.T
PROPERTY - Enum constant in enum class org.jmol.c.PAL
propertyatomnumbercolumncount - Static variable in class org.jmol.script.T
propertyatomnumberfield - Static variable in class org.jmol.script.T
propertyChange(PropertyChangeEvent) - Method in class org.jmol.dialog.FilePreview
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  /////////////////////////////////////////////////////////////
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
propertycolorscheme - Static variable in class org.jmol.script.T
propertydatacolumncount - Static variable in class org.jmol.script.T
propertydatafield - Static variable in class org.jmol.script.T
propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
PROPERTYFLAGS - Static variable in class org.jmol.script.T
PropertyManager - Class in org.jmol.viewer
  The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
propOp(T, SV) - Method in class org.jmol.script.ScriptMathProcessor
propselector - Static variable in class org.jmol.script.T
protein - Static variable in class org.jmol.script.T
proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
ProteinStructure - Class in org.jmol.modelsetbio
ProteinStructure() - Constructor for class org.jmol.modelsetbio.ProteinStructure
proteinStructureTainted - Variable in class org.jmol.modelset.ModelSet
PS_CLOSEPATH - Static variable in class org.jmol.shapecgo.CGOMesh
PS_LINETO - Static variable in class org.jmol.shapecgo.CGOMesh
PS_MOVETO - Static variable in class org.jmol.shapecgo.CGOMesh
PS_NEWPATH - Static variable in class org.jmol.shapecgo.CGOMesh
PS_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
PS_SETLINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
PS_SHOWPAGE - Static variable in class org.jmol.shapecgo.CGOMesh
PS_STROKE - Static variable in class org.jmol.shapecgo.CGOMesh
psi - Static variable in class org.jmol.script.T
psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
PsiReader - Class in org.jmol.adapter.readers.quantum
  Reader for Psi3 output files.
PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
pt - Variable in enum class org.jmol.c.VDW
pt - Variable in class org.jmol.render.AxesRenderer
pt - Variable in class org.jmol.render.BbcageRenderer
pt - Variable in class org.jmol.render.UccageRenderer
pt - Variable in class org.jmol.util.ContactPair
PT - Class in javajs.util
  a combination of Parsing and Text-related utility classes
PT() - Constructor for class javajs.util.PT
PT_INT_LABEL - Static variable in class jspecview.common.Measurement
PT_ON_LINE - Static variable in class jspecview.common.Measurement
PT_ON_LINE1 - Static variable in class jspecview.common.Measurement
PT_ON_LINE2 - Static variable in class jspecview.common.Measurement
PT_XY1 - Static variable in class jspecview.common.Measurement
PT_XY2 - Static variable in class jspecview.common.Measurement
pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
pt0 - Variable in class org.jmol.modelsetbio.AlphaPolymer
  Specifically for mmTF bitset setting of structures
pt0 - Variable in class org.jmol.render.FontLineShapeRenderer
pt0 - Variable in class org.jmol.renderspecial.DrawRenderer
pt0i - Variable in class org.jmol.render.FontLineShapeRenderer
pt0i - Variable in class org.jmol.renderspecial.DrawRenderer
pt1 - Variable in class org.jmol.render.FontLineShapeRenderer
pt1 - Variable in class org.jmol.renderspecial.DrawRenderer
pt1f - Variable in class org.jmol.render.MeshRenderer
pt1i - Variable in class org.jmol.render.MeshRenderer
pt2 - Variable in class org.jmol.renderspecial.DrawRenderer
pt2f - Variable in class org.jmol.render.MeshRenderer
pt2i - Variable in class org.jmol.render.FontLineShapeRenderer
pt2i - Variable in class org.jmol.render.MeshRenderer
pt3i - Variable in class org.jmol.render.MeshRenderer
pt4Value(SV) - Static method in class org.jmol.script.SV
ptCenter - Variable in class org.jmol.shape.Mesh
pTemp - Variable in class org.jmol.render.LabelsRenderer
ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ptMark - Variable in class javajs.util.DataReader
ptNewSetModifier - Variable in class org.jmol.script.ScriptCompiler
pts - Variable in class org.jmol.modelset.Measurement
ptSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
  ////////////// MarchingReader Interface Methods ///////////////////
ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
ptTest1 - Variable in class org.jmol.viewer.TransformManager
ptTest2 - Variable in class org.jmol.viewer.TransformManager
ptTest3 - Variable in class org.jmol.viewer.TransformManager
ptToIJK(T3, int) - Static method in class org.jmol.util.SimpleUnitCell
  Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}
ptValue(SV) - Static method in class org.jmol.script.SV
ptValue(SV, BS) - Method in class org.jmol.script.ScriptMathProcessor
purine - Static variable in class org.jmol.script.T
PURINE_MASK - Static variable in class org.jmol.viewer.JC
PURPLE - Static variable in class org.jmol.util.C
push - Static variable in class org.jmol.script.T
pushContextDown(String) - Method in interface org.jmol.api.JmolScriptEvaluator
pushContextDown(String) - Method in class org.jmol.script.ScriptEval
pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
pushHoldRepaint(String) - Method in interface org.jmol.api.JmolRepaintManager
pushHoldRepaint(String) - Method in class org.jmol.render.RepaintManager
pushHoldRepaintWhy(String) - Method in class org.jmol.viewer.Viewer
pushMatrix() - Method in class org.jmol.export._StlExporter
pushMatrix() - Method in class org.jmol.export._VrmlExporter
pushMatrix() - Method in class org.jmol.export._X3dExporter
pushPop(SV, SV) - Method in class org.jmol.script.SV
  Script variables are pushed after cloning, because the name comes with them when we do otherwise they are not mutable anyway.
pushState() - Method in class org.jmol.viewer.Viewer
pushState(String) - Method in class org.jmol.util.CommandHistory
put(int, int) - Method in class org.jmol.util.Int2IntHash
putBox(int, float[]) - Method in class org.jmol.shape.Labels
putByte(int) - Method in class javajs.img.ImageEncoder
putCoord(V3d, double[]) - Static method in class org.jmol.minimize.Util
putInfo(String, Map, String, Object) - Static method in class jspecview.common.Parameters
putLabel(int, Text) - Method in class org.jmol.shape.Labels
putP(T3) - Method in class javajs.util.T3
putString(String) - Method in class javajs.img.ImageEncoder
PWmatReader - Class in org.jmol.adapter.readers.xtal
  crude PWmat atom.config reader http://pwmatus.com/manual
PWmatReader() - Constructor for class org.jmol.adapter.readers.xtal.PWmatReader
PWMATWriter - Class in org.jmol.adapter.writers
  A writer for PWMAT atom.config files.
PWMATWriter() - Constructor for class org.jmol.adapter.writers.PWMATWriter
Pwr2 - Static variable in class org.jmol.util.TriangleData
pymol - Static variable in class org.jmol.script.T
PYMOL_LABEL_OFFSET_ABS - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_ABS_ANG - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_ABS_PIX - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_ANG - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_JMOL - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_PIX - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_REL - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_REL_ANG - Static variable in class org.jmol.modelset.Text
PYMOL_LABEL_OFFSET_REL_PIX - Static variable in class org.jmol.modelset.Text
pymol_space_max_blue - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pymol_space_max_green - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pymol_space_max_red - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
pymol_space_min_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
PymolAtomReader - Interface in org.jmol.api
pymoldashes - Static variable in class org.jmol.render.FontLineShapeRenderer
pymolOffset - Variable in class org.jmol.modelset.Text
pymolRadius - Variable in class org.jmol.adapter.smarter.Bond
PyMOLReader - Class in org.jmol.adapter.readers.pymol
  PyMOL PSE (binary Python session) file reader.
PyMOLReader() - Constructor for class org.jmol.adapter.readers.pymol.PyMOLReader
PyMOLSettings - Enum Class in org.jmol.adapter.readers.pymol
pyrimidine - Static variable in class org.jmol.script.T
PYRIMIDINE_MASK - Static variable in class org.jmol.viewer.JC

## Q

q0 - Variable in class javajs.util.Quat
q1 - Variable in class javajs.util.Quat
q2 - Variable in class javajs.util.Quat
q3 - Variable in class javajs.util.Quat
QchemReader - Class in org.jmol.adapter.readers.quantum
  A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
QCJSONReader - Class in org.jmol.adapter.readers.quantum
  A molecular structure and orbital reader for MolDen files.
QCJSONReader() - Constructor for class org.jmol.adapter.readers.quantum.QCJSONReader
QCJSONWriter - Class in org.jmol.adapter.writers
  A very experimental class for writing QCJSON files.
QCJSONWriter() - Constructor for class org.jmol.adapter.writers.QCJSONWriter
QCJSONWriter.SparseArray - Class in org.jmol.adapter.writers
  / sparse array handling ////
QCSchemaUnits - Class in org.qcschema
  A general Java class for working with QCShema units and array types.
QCSchemaUnits() - Constructor for class org.qcschema.QCSchemaUnits
qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
QS - Class in org.jmol.quantum
  Constants and static methods for quantum shells.
QS() - Constructor for class org.jmol.quantum.QS
QUADRIC - Static variable in class org.jmol.shapecgo.CGOMesh
qualifiedValue() - Method in class jspecview.source.XMLParser
  for <xxxx> value </xxxx>
quality - Variable in class javajs.img.ImageEncoder
qualityJ - Variable in class org.jmol.dialog.Dialog
qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
QualityListener(boolean, JSlider) - Constructor for class org.jmol.dialog.Dialog.QualityListener
qualityP - Variable in class org.jmol.dialog.Dialog
qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
  gets the value at the color boundary for this color range fraction
quantize4(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
QuantumCalculation - Class in org.jmol.quantum
QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
QuantumPlaneCalculation - Class in org.jmol.quantum
  Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
QuantumPlaneCalculation() - Constructor for class org.jmol.quantum.QuantumPlaneCalculation
Quat - Class in javajs.util
Quat() - Constructor for class javajs.util.Quat
quaternion - Static variable in class org.jmol.script.T
quaternionframe - Static variable in class org.jmol.script.T
query - Variable in class jme.JME
QUESTION_MESSAGE - Static variable in class jspecview.dialog.DialogManager
queueOnHold - Variable in class org.jmol.viewer.Viewer
queueThreadFinished(int) - Method in interface org.jmol.api.JmolScriptManager
queueThreadFinished(int) - Method in class org.jmol.script.ScriptManager
quiet - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
quit - Static variable in class org.jmol.script.T

## R

r - Variable in class org.jmol.quantum.SlaterData
r - Variable in class org.jmol.util.Rgb16
R3 - Static variable in class org.jmol.minimize.forcefield.ForceField
R4 - Static variable in class org.jmol.minimize.forcefield.ForceField
R5 - Static variable in class org.jmol.minimize.forcefield.ForceField
rad - Static variable in class org.jmol.script.T
RAD_COV_BODR_2014_02_22 - Static variable in class org.jmol.util.Elements
RAD_COV_IONIC_OB1_100_1 - Static variable in class org.jmol.util.Elements
RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
radiansPerDegree - Static variable in class javajs.util.Measure
radiansPerDegree - Static variable in class org.jmol.viewer.JC
radical - Static variable in class org.jmol.script.T
radii - Variable in class org.jmol.util.ContactPair
radius - Variable in class org.jmol.adapter.smarter.Atom
radius - Static variable in class org.jmol.script.T
RADIUS_GLOBAL - Static variable in class org.jmol.modelset.Atom
RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
RADIUS_MAX - Static variable in class org.jmol.shape.Shape
radiusData - Variable in class org.jmol.atomdata.AtomData
radiusData - Variable in class org.jmol.modelset.MeasurementData
RadiusData - Class in org.jmol.atomdata
RadiusData(float[], float, RadiusData.EnumType, VDW) - Constructor for class org.jmol.atomdata.RadiusData
RadiusData.EnumType - Enum Class in org.jmol.atomdata
raise_exceptions - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ramachandran - Static variable in class org.jmol.script.T
ramp_blend_nearby_colors - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
random - Static variable in class org.jmol.script.T
randomPoint() - Static method in class org.jmol.shapespecial.Draw
randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
range - Static variable in class org.jmol.script.T
rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
rangeselected - Static variable in class org.jmol.script.T
rangeSelected - Variable in class org.jmol.viewer.GlobalSettings
rank_assisted_sorts - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
Raromatic - Static variable in class org.jmol.minimize.forcefield.ForceField
rasmol - Static variable in class org.jmol.script.T
RASMOL - Enum constant in enum class org.jmol.c.PAL
RASMOL - Enum constant in enum class org.jmol.c.VDW
RASMOL - Static variable in class org.jmol.util.ColorEncoder
RasmolBinding - Class in org.jmol.viewer.binding
RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
rawBondCount - Variable in class org.jmol.minimize.Minimizer
rawIndex - Variable in class org.jmol.minimize.MinBond
rawLine - Variable in class jspecview.source.JDXSourceStreamTokenizer
ray_blend_blue - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_blend_colors - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_blend_green - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_blend_red - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_clip_shadows - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_color_ramps - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_default_renderer - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_direct_shade - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_hint_camera - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_hint_shadow - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_improve_shadows - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_interior_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_interior_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_interior_reflect - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_interior_shadows - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_interior_texture - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_label_specular - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_legacy_lighting - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_max_passes - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_opaque_background - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_orthoscopic - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_oversample_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_pixel_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_scatter - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_shadow_decay_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_shadow_decay_range - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_shadow_fudge - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_shadows - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_spec_local - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_texture - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_texture_settings - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_depth_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_disco_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_fog - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_fog_start - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_frames - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_gain - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_persist_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_slope_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_trace_trans_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_transparency_contrast - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_transparency_oblique - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_transparency_oblique_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_transparency_shadows - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_transparency_spec_cut - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_transparency_specular - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_triangle_fudge - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ray_volume - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
RBOND - Static variable in class jme.JMEmol
rButton - Variable in class jme.JME
rd - Variable in class org.jmol.viewer.Viewer
rd() - Method in class jspecview.source.JDXReader
rd() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
rd() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
rd() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
rd() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  filter out unnecessary lines
rd() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
rd() - Method in interface org.jmol.api.JmolJDXMOLReader
rd() - Method in class org.jmol.jvxl.readers.JvxlReader
rd() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
rd() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
rdline() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
rdr - Variable in class org.jmol.adapter.readers.xml.CDXMLParser
Rdr - Class in javajs.util
  A general helper class for a variety of stream and reader functionality including: stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams various stream/reader methods, including UTF-encoded stream reading reflection-protected access to a CIF parser and ZIP tools
Rdr(BufferedReader) - Constructor for class javajs.util.Rdr
Rdr.StreamReader - Class in javajs.util
rdSiesta() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
reaction - Variable in class jme.JME
reactionPart() - Method in class jme.JMEmol
read() - Method in class org.apache.tools.bzip2.CBZip2InputStream
read(byte[], int, int) - Method in class org.apache.tools.bzip2.CBZip2InputStream
read(char[], int, int) - Method in class javajs.util.ArrayDataReader
read(char[], int, int) - Method in class javajs.util.ListDataReader
read(char[], int, int) - Method in class jspecview.common.JSVZipFileSequentialReader
read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
readACDAssignments(int, boolean, Lst) - Method in interface org.jmol.api.JmolJDXMOLParser
readACDAssignments(int, boolean, Lst) - Method in class org.jmol.jsv.JDXMOLParser
readACDMolFile() - Method in interface org.jmol.api.JmolJDXMOLParser
readACDMolFile() - Method in class org.jmol.jsv.JDXMOLParser
  MOL file embedded in JDX file
readAllAsString(BufferedReader, int, boolean, String[], int) - Static method in class javajs.util.Rdr
  This method fills data[i] with string data from a file that may or may not be binary even though it is being read by a reader.
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readBonds() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readBrukerDir(String) - Method in class jspecview.source.BrukerReader
  Read through a Bruker directory (Java only) looking for title, acqus, procs, 1r, 1i, 2rr.
readBrukerZip(byte[], String) - Method in class jspecview.source.BrukerReader
  Read through a ZIP file (Java or JavaScript) looking for title, acqus, procs, 1r, 1i, 2rr.
readBuf(char[], int, int) - Method in class javajs.util.DataReader
readByte() - Method in interface javajs.api.GenericBinaryDocumentReader
readByte() - Method in class javajs.util.BinaryDocument
readByteArray(byte[], int, int) - Method in interface javajs.api.GenericBinaryDocument
readByteArray(byte[], int, int) - Method in class javajs.util.BinaryDocument
readByteAsInt() - Method in class org.apache.tools.bzip2.CBZip2InputStream
readBytes(int) - Method in interface javajs.api.GenericBinaryDocumentReader
readBytes(int) - Method in class javajs.util.BinaryDocument
readCifData(String, Object, String) - Method in interface org.jmol.atomdata.AtomDataServer
readCifData(String, Object, String) - Method in class org.jmol.viewer.Viewer
readCifData(String, String) - Method in class org.jmol.viewer.Viewer
readCifData(GenericCifDataParser, BufferedReader, String[]) - Static method in class javajs.util.Rdr
readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
  Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
readDataObject(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readDouble() - Method in interface javajs.api.GenericBinaryDocumentReader
readDouble() - Method in class javajs.util.BinaryDocument
readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readEnergy() - Method in class org.jmol.adapter.readers.quantum.GamessReader
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
READER_NOT_FOUND - Static variable in class org.jmol.viewer.JC
readerClosed - Variable in class org.jmol.jvxl.readers.JvxlReader
readerClosed - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
readerClosed - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
readFileAsMap(BufferedInputStream, Map, String) - Method in interface javajs.api.GenericZipTools
readFileAsMap(BufferedInputStream, Map, String) - Method in class javajs.util.ZipTools
readFileAsMap(BufferedInputStream, Map, String) - Method in class org.jmol.viewer.Viewer
readFloat() - Method in interface javajs.api.GenericBinaryDocumentReader
readFloat() - Method in class javajs.util.BinaryDocument
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
  Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readFrequencies(String, boolean) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Interprets the Harmonic frequencies section.
readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
readInputRecords() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readInt() - Method in interface javajs.api.GenericBinaryDocumentReader
readInt() - Method in class javajs.util.BinaryDocument
readIntLE() - Method in interface javajs.api.GenericBinaryDocument
readIntLE() - Method in class javajs.util.BinaryDocument
readLine() - Method in interface javajs.api.GenericCifDataParser
readLine() - Method in class javajs.util.ArrayDataReader
readLine() - Method in class javajs.util.CifDataParser
readLine() - Method in class javajs.util.ListDataReader
readLine() - Method in class jspecview.common.JSVZipFileSequentialReader
readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
readLineTrimmed() - Method in class jspecview.source.JDXSourceStreamTokenizer
readLineWithNewline() - Method in class javajs.util.LimitedLineReader
readList() - Method in class javajs.util.CifDataParser
  Read a CIF 2.0 list structure, converting it to either a JSON string or to a Java data structure
readLong() - Method in interface javajs.api.GenericBinaryDocumentReader
readLong() - Method in class javajs.util.BinaryDocument
readMap() - Method in class javajs.util.MessagePackReader
readModels() - Method in interface org.jmol.api.JmolJDXMOLParser
readModels() - Method in class org.jmol.jsv.JDXMOLParser
readMolecularFormula() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
  try various ways to read the optional atom labels.
readMolecularObitals() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
readMolecule(String) - Method in class jme.JME
readMolFile(String) - Method in class jme.JME
ReadNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
readNBOCoefficients(Map, String, Viewer) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
  Called by setNBOType in IsoExt when use issues NBO TYPE xxx
readNextLine() - Method in interface javajs.api.GenericLineReader
readNextLine() - Method in class javajs.util.Rdr
readNextLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
ReadNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
readNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
readNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
readOldFrequency() - Method in class org.jmol.adapter.readers.quantum.AdfReader
readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readParameters() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readPeaks(boolean, int) - Method in interface org.jmol.api.JmolJDXMOLParser
readPeaks(boolean, int) - Method in class org.jmol.jsv.JDXMOLParser
readShort() - Method in interface javajs.api.GenericBinaryDocumentReader
readShort() - Method in class javajs.util.BinaryDocument
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
READSPT - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
readString(int) - Method in interface javajs.api.GenericBinaryDocumentReader
readString(int) - Method in class javajs.util.BinaryDocument
readStructure(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readSurfaceDataJXR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readSurfaceDataXML() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
readTable() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Read a CIF 2.0 table into either a JSON string or a java data structure
readUInt8() - Method in interface javajs.api.GenericBinaryDocumentReader
readUInt8() - Method in class javajs.util.BinaryDocument
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
readUnsignedShort() - Method in interface javajs.api.GenericBinaryDocumentReader
readUnsignedShort() - Method in class javajs.util.BinaryDocument
readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  //////////reading the format///////////
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JvxlReader
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
ReattachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
rebond() - Method in class org.jmol.api.JmolViewer
rebond() - Method in class org.jmol.viewer.Viewer
rebondState(boolean) - Method in class org.jmol.viewer.Viewer
recachePngjBytes(String, byte[]) - Method in class org.jmol.viewer.FileManager
recalcAltVertices - Variable in class org.jmol.shape.Mesh
reCalculate(BS, M3) - Method in class org.jmol.geodesic.EnvelopeCalculation
  problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
recalculateAllPolymers(BS, Group[]) - Method in class org.jmol.modelsetbio.BioModelSet
recalculateEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelSet
recalculatePoints(int) - Method in class org.jmol.modelsetbio.BioModelSet
recalculatePolymers(BS) - Method in class org.jmol.modelset.ModelSet
recalculatePositionDependentQuantities(BS, M4) - Method in class org.jmol.modelset.ModelSet
recallCommand(boolean, boolean) - Method in class org.jmol.console.GenericConsole
recallCommand(boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
  Recall command history.
recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
recentSimulation - Variable in class jspecview.common.JSViewer
RecMet - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Include reconnected metals results
recordData(float) - Method in class org.jmol.jvxl.readers.JvxlReader
recordData(float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
recordData(float) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
Rectangle - Class in org.jmol.util
Rectangle() - Constructor for class org.jmol.util.Rectangle
rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
RED - Static variable in class jspecview.common.ColorParameters
RED - Static variable in class org.jmol.util.C
REDBLUE - Enum constant in enum class org.jmol.c.STER
REDCYAN - Enum constant in enum class org.jmol.c.STER
REDGREEN - Enum constant in enum class org.jmol.c.STER
redo - Static variable in class org.jmol.script.T
redomove - Static variable in class org.jmol.script.T
reducedAnisotropy() - Method in class org.jmol.util.Tensor
  reduced anisotropy = largest difference from isotropy (may be negative)
reEnable() - Method in class jspecview.dialog.JSVDialog
REF_TYPE_BRUKER - Static variable in class jspecview.source.JDXDataObject
REF_TYPE_STANDARD - Static variable in class jspecview.source.JDXDataObject
REF_TYPE_UNSPECIFIED - Static variable in class jspecview.source.JDXDataObject
REF_TYPE_VARIAN - Static variable in class jspecview.source.JDXDataObject
reference - Variable in class org.jmol.modelset.TickInfo
reference - Static variable in class org.jmol.script.T
referenceCenter - Variable in class org.jmol.export.___Exporter
referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
reflect - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
reflect_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
reformatDistanceIfSelected(boolean) - Method in class org.jmol.modelset.Measurement
refPoint - Variable in class jspecview.source.AnIMLReader
refPoint - Variable in class jspecview.source.NMRMLReader
refresh - Static variable in class org.jmol.script.T
refresh() - Method in class jspecview.common.PanelData
refresh() - Method in class jspecview.common.RepaintManager
refresh(boolean) - Method in class org.jmol.script.ScriptEval
  Refresh the display NOW
refresh(int, String) - Method in class org.jmol.api.JmolViewer
refresh(int, String) - Method in class org.jmol.viewer.Viewer
  initiate a repaint/update sequence if it has not already been requested.
refresh(Point3fi[]) - Method in class org.jmol.modelset.Measurement
REFRESH_REPAINT - Static variable in class org.jmol.viewer.Viewer
REFRESH_REPAINT_NO_MOTION_ONLY - Static variable in class org.jmol.viewer.Viewer
REFRESH_SEND_WEBGL_NEW_ORIENTATION - Static variable in class org.jmol.viewer.Viewer
REFRESH_SYNC - Static variable in class org.jmol.viewer.Viewer
REFRESH_SYNC_MASK - Static variable in class org.jmol.viewer.Viewer
refreshDataFramePointGroup(int) - Method in class org.jmol.modelset.ModelSet
refreshing - Static variable in class org.jmol.script.T
refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
regainFocus() - Method in interface org.jmol.api.JmolAppConsoleInterface
regainFocus() - Method in class org.jmol.console.AppletConsole
regainFocus() - Method in class org.jmol.consolejs.AppletConsole
regainFocus() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
register(String, JmolSyncInterface) - Method in class jspecview.application.JSpecView
  called by Jmol's StatusListener to register itself, indicating to JSpecView that it needs to synchronize with it
register(String, JmolSyncInterface) - Method in interface org.jmol.api.JmolSyncInterface
register(String, JmolSyncInterface) - Method in class org.jmol.util.GenericApplet
  ////// JmolSyncInterface //////////
register(String, JmolSyncInterface) - Method in class org.openscience.jmol.app.status.StatusListener
register(Component, String) - Method in interface org.jmol.awtjs.swing.SwingController
  Set c's id to a unique identifier and add it to an associative array that will associate that id with c.
registerAudio(String, Map) - Method in class org.jmol.viewer.StatusManager
registerDialog(JSVDialog) - Method in class jspecview.dialog.DialogManager
  register the JSV dialog with a unique key to be used as an ID in callbacks optionKeys ending with "!" are one-of-a-kind, such as "views"
registerSelector(String, Object) - Method in class jspecview.dialog.DialogManager
registryKey - Variable in class jspecview.java.AwtDialog
registryKey - Variable in class jspecview.js2d.JsDialog
reinitializeLightingAndColor(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
reinitShape() - Method in class org.jmol.shape.Axes
reinstateMenu(JMenuItem, MenuElement[]) - Method in class org.jmol.awt.AwtPopupHelper
  Cause the menu to persist in its open state.
rejectAtomName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Related Documentation - Section in package org.jmol.g3d
RELATIVE_DRAG_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
RELATIVE_DRAG_EVENT - Static variable in class com.sparshui.GestureType
RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
RELATIVE_DRAG_GESTURE - Static variable in class com.sparshui.GestureType
RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
RelativeDragEvent - Class in com.sparshui.common.messages.events
RelativeDragEvent() - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
RelativeDragEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
  Constructs a dragEvent from a complete serialized version of the drag event.
RelativeDragEvent(float, float) - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
relativeStereo - Variable in class jme.JME
release() - Method in interface org.jmol.api.AtomIndexIterator
release() - Method in class org.jmol.bspt.CubeIterator
  nulls internal references
release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
release() - Method in class org.jmol.symmetry.UnitCellIterator
released(long, int, int, int) - Method in class jspecview.app.GenericMouse
RELEASED - Static variable in class org.jmol.awtjs.Event
releaseModelSet() - Method in class org.jmol.modelset.ModelSet
releaseModelSetAC() - Method in class org.jmol.modelset.AtomCollection
releaseModelSetBC() - Method in class org.jmol.modelset.BondCollection
releaseScreenImage() - Method in class org.jmol.api.JmolViewer
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
releaseScreenImage() - Method in class org.jmol.util.GData
releaseScreenImage() - Method in class org.jmol.viewer.Viewer
releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
remove - Static variable in class org.jmol.script.T
remove() - Method in class jspecview.source.JDXDecompressor
remove(int) - Method in class javajs.util.Lst
remove(int) - Method in class jspecview.common.IntegralData
remove(int) - Method in interface org.jmol.api.SC
remove(int) - Method in class org.jmol.awt.AwtSwingComponent
remove(int) - Method in class org.jmol.awtjs.swing.Container
remove(Object) - Method in class javajs.util.Lst
  Deprecated.
removeAll() - Method in interface org.jmol.api.SC
removeAll() - Method in class org.jmol.awt.AwtSwingComponent
removeAll() - Method in class org.jmol.awtjs.swing.Container
removeAllHighlights() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that removes all highlights from the plot area of a `JSVPanel`
removeAllHighlights() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that removes all highlights from the plot area of a `JSVPanel`
removeAllHighlights() - Method in class jspecview.appletjs.JSVApplet
removeAllHighlights() - Method in class jspecview.common.PanelData
  Removes all highlights from the display
removeAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells
removeCommand() - Method in class org.jmol.util.CommandHistory
removeCommand() - Method in class org.jmol.viewer.Viewer
  Removes one command from the command history
removeCommand(int) - Method in class org.jmol.util.CommandHistory
removeCurrentAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
removeDialog(JSVDialog) - Method in class jspecview.common.PanelData
removeDuplicates(ModelSet, BS, boolean) - Method in interface org.jmol.api.SymmetryInterface
removeDuplicates(ModelSet, BS, boolean) - Method in class org.jmol.symmetry.Symmetry
removeFunction(String) - Method in class org.jmol.viewer.Viewer
removeHighlight(double, double) - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that removes a highlight from the plot area of a `JSVPanel`
removeHighlight(double, double) - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that removes a highlight from the plot area of a `JSVPanel`
removeHighlight(double, double) - Method in class jspecview.appletjs.JSVApplet
removeHighlight(double, double) - Method in class jspecview.common.PanelData
  Remove the highlight specified by the starting and ending x value
removeItemAt(int) - Method in class javajs.util.Lst
removeLastUnselectedAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
removeMapKeys(Map, String) - Static method in class javajs.util.AU
  remove all keys from a map that start with given root
removeNodeFromParent(JSVTreeNode) - Method in class jspecview.tree.SimpleTreeModel
removeObj(Object) - Method in class javajs.util.Lst
removeParam(String) - Method in class org.jmol.viewer.GlobalSettings
removePrevNodeTrm() - Method in class org.jmol.symmetry.CLEG.ClegData
removePropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
removeScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
  Removes the scale factor from the coordinates
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
render() - Method in class org.jmol.render.AxesRenderer
render() - Method in class org.jmol.render.BallsRenderer
render() - Method in class org.jmol.render.BbcageRenderer
render() - Method in class org.jmol.render.EchoRenderer
render() - Method in class org.jmol.render.FrankRenderer
render() - Method in class org.jmol.render.HalosRenderer
render() - Method in class org.jmol.render.HoverRenderer
render() - Method in class org.jmol.render.LabelsRenderer
render() - Method in class org.jmol.render.MeasuresRenderer
render() - Method in class org.jmol.render.ShapeRenderer
render() - Method in class org.jmol.render.StarsRenderer
render() - Method in class org.jmol.render.SticksRenderer
render() - Method in class org.jmol.render.UccageRenderer
render() - Method in class org.jmol.renderbio.BioMeshRenderer
render() - Method in class org.jmol.renderbio.BackboneRenderer
render() - Method in class org.jmol.renderbio.CartoonRenderer
render() - Method in class org.jmol.renderbio.MeshRibbonRenderer
render() - Method in class org.jmol.renderbio.RibbonsRenderer
render() - Method in class org.jmol.renderbio.RocketsRenderer
render() - Method in class org.jmol.renderbio.StrandsRenderer
render() - Method in class org.jmol.renderbio.TraceRenderer
render() - Method in class org.jmol.rendercgo.CGORenderer
render() - Method in class org.jmol.renderspecial.DipolesRenderer
render() - Method in class org.jmol.renderspecial.DotsRenderer
render() - Method in class org.jmol.renderspecial.DrawRenderer
render() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
render() - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
render() - Method in class org.jmol.renderspecial.PolyhedraRenderer
render() - Method in class org.jmol.renderspecial.VectorsRenderer
render() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
render() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
render() - Method in class org.jmol.rendersurface.PmeshRenderer
render(GData, ModelSet, boolean, int[]) - Method in interface org.jmol.api.JmolRepaintManager
render(GData, ModelSet, boolean, int[]) - Method in class org.jmol.render.RepaintManager
  //////// actual rendering ///////////
render_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
render1(Dots) - Method in class org.jmol.renderspecial.DotsRenderer
render2(boolean) - Method in class org.jmol.render.MeshRenderer
  Overridden in DrawRenderer and IsosurfaceRenderer
render2(boolean) - Method in class org.jmol.renderspecial.DrawRenderer
render2(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
render2b(boolean) - Method in class org.jmol.render.MeshRenderer
render2Strand(boolean, float, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderAllStrings(Object) - Method in interface org.jmol.api.JmolGraphicsInterface
renderAllStrings(Object) - Method in class org.jmol.export.Export3D
renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
renderAllStrings(Object) - Method in class org.jmol.util.GData
renderArc - Variable in class org.jmol.modelset.Measurement
renderArrowHeads - Variable in class org.jmol.renderbio.RocketsRenderer
renderAxis - Variable in class org.jmol.modelset.Measurement
renderBackground(JmolRendererInterface) - Method in interface org.jmol.api.JmolRendererInterface
renderBackground(JmolRendererInterface) - Method in class org.jmol.export.Export3D
renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
  ///////////////////////////////////////////////////////
renderBackground(JmolRendererInterface) - Method in class org.jmol.util.GData
renderBioShape(BioShape) - Method in class org.jmol.renderbio.BackboneRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.CartoonRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RibbonsRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RocketsRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.StrandsRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.TraceRenderer
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.AxesRenderer
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.BbcageRenderer
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.UccageRenderer
renderCageLine(int, int, int, int, boolean) - Method in class org.jmol.render.AxesRenderer
renderCageLine(int, int, int, int, boolean) - Method in class org.jmol.render.BbcageRenderer
renderCageLine(int, int, int, int, boolean) - Method in class org.jmol.render.UccageRenderer
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.DotsRenderer
  generic renderer -- dots and geosurface
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
renderCrossHairs(int[], int, int, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.export.Export3D
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.g3d.Graphics3D
renderDots(int) - Method in class org.jmol.renderspecial.DotsRenderer
  also called by GeoSurface when in motion
renderExport(GData, ModelSet, Map) - Method in interface org.jmol.api.JmolRepaintManager
renderExport(GData, ModelSet, Map) - Method in class org.jmol.render.RepaintManager
renderHeight - Variable in class org.jmol.awtjs.swing.Component
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.BackboneRenderer
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.CartoonRenderer
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.RibbonsRenderer
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.RocketsRenderer
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.StrandsRenderer
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.TraceRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.BackboneRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.CartoonRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.RibbonsRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.RocketsRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.StrandsRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.TraceRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.BackboneRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.CartoonRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.RibbonsRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.RocketsRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.StrandsRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.TraceRenderer
renderHermiteRibbon(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, int) - Method in class org.jmol.g3d.HermiteRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.BackboneRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.CartoonRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.RibbonsRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.StrandsRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.TraceRenderer
renderHermiteRope(boolean, int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
renderInfo() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderInfo() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
rendering - Variable in class org.jmol.jvxl.data.JvxlData
renderIso() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderLabelOrMeasure(Text, String) - Method in class org.jmol.render.LabelsRenderer
renderLine(P3, P3, int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
renderLow - Variable in class org.jmol.render.MeshRenderer
renderMesh2(Mesh) - Method in class org.jmol.render.MeshRenderer
  overridden in BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
renderMeshes() - Method in class org.jmol.renderbio.BioMeshRenderer
renderMeshRibbon() - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderPass2(short) - Static method in class org.jmol.util.C
renderPoints() - Method in class org.jmol.render.MeshRenderer
renderPoints() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderRockets() - Method in class org.jmol.renderbio.RocketsRenderer
renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolViewer
renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
  JmolViewer interface uses this, but that is all
renderScreenImage(Object, Object) - Method in class jspecview.java.AwtPlatform
  legacy apps will use this
renderScreenImage(Object, Object) - Method in class jspecview.js2d.JsPlatform
  legacy apps will use this
renderScreenImage(Object, Object) - Method in interface org.jmol.api.GenericPlatform
  Deprecated.
renderScreenImage(Object, Object) - Method in class org.jmol.awt.Platform
  legacy apps will use this
renderScreenImage(Object, Object) - Method in class org.jmol.awtjs2d.Platform
  legacy apps will use this
renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
  Deprecated.
renderScreenImageStereo(Object, boolean, int, int) - Method in class org.jmol.viewer.Viewer
renderShape(JmolRendererInterface, ModelSet, Shape, int) - Method in class org.jmol.render.ShapeRenderer
renderStrands() - Method in class org.jmol.renderbio.StrandsRenderer
renderStrandShape() - Method in class org.jmol.renderbio.StrandsRenderer
renderStruts - Variable in class org.jmol.renderbio.BackboneRenderer
renderStruts - Variable in class org.jmol.renderbio.CartoonRenderer
renderStruts - Variable in class org.jmol.renderbio.MeshRibbonRenderer
renderStruts - Variable in class org.jmol.renderbio.RibbonsRenderer
renderStruts - Variable in class org.jmol.renderbio.RocketsRenderer
renderStruts - Variable in class org.jmol.renderbio.StrandsRenderer
renderStruts - Variable in class org.jmol.renderbio.TraceRenderer
renderText(Text, P3i, short, int) - Method in class org.jmol.render.LabelsRenderer
renderTrace() - Method in class org.jmol.renderbio.TraceRenderer
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.render.MeshRenderer
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderWidth - Variable in class org.jmol.awtjs.swing.Component
rep(String, String, String) - Static method in class javajs.util.PT
  Does a clean ITERATIVE replace of strFrom in str with strTo.
repaint() - Method in interface jspecview.api.AppletFrame
repaint() - Method in interface jspecview.api.JSVPanel
repaint() - Method in interface jspecview.api.PlatformDialog
repaint() - Method in interface jspecview.api.ScriptInterface
repaint() - Method in class jspecview.app.JSVApp
repaint() - Method in class jspecview.appletjs.JSVApplet
repaint() - Method in class jspecview.application.JSpecView
repaint() - Method in class jspecview.common.PanelData
repaint() - Method in class jspecview.dialog.JSVDialog
repaint() - Method in class jspecview.js2d.JsPanel
repaint() - Method in class org.jmol.awtjs.swing.Component
repaint() - Method in class org.jmol.awtjs.swing.JDialog
repaint(Object) - Method in class jspecview.java.AwtPlatform
repaint(Object) - Method in class jspecview.js2d.JsPlatform
repaint(Object) - Method in interface org.jmol.api.GenericPlatform
repaint(Object) - Method in class org.jmol.awt.Platform
repaint(Object) - Method in class org.jmol.awtjs2d.Platform
repaint(JSAppletObject, boolean) - Method in interface javajs.api.js.J2SObjectInterface
REPAINT_IGNORE - Static variable in class org.jmol.viewer.JC
repaintDone() - Method in class jspecview.common.JSViewer
repaintDone() - Method in class jspecview.common.RepaintManager
repaintDone() - Method in interface org.jmol.api.JmolRepaintManager
repaintDone() - Method in class org.jmol.render.RepaintManager
repaintIfReady(String) - Method in interface org.jmol.api.JmolRepaintManager
repaintIfReady(String) - Method in class org.jmol.render.RepaintManager
repaintManager - Variable in class jspecview.common.JSViewer
RepaintManager - Class in jspecview.common
RepaintManager - Class in org.jmol.render
RepaintManager() - Constructor for class org.jmol.render.RepaintManager
RepaintManager(JSViewer) - Constructor for class jspecview.common.RepaintManager
repaintwaitms - Static variable in class org.jmol.script.T
repaintWaitMs - Variable in class org.jmol.viewer.GlobalSettings
replace - Static variable in class org.jmol.script.T
replace(int, int, String) - Method in class javajs.util.SB
replaceAllCharacters(String, String, String) - Static method in class javajs.util.PT
  Does a clean replace of any of the characters in str with strTo If strTo contains strFrom, then only a single pass is done.
replaceGroup(Group, Group) - Method in class org.jmol.shape.Shape
replaceGroup(Group, Group) - Method in class org.jmol.shapebio.BioShapeCollection
replaceGroup(Group, Group) - Method in class org.jmol.viewer.ShapeManager
replaceQuotedStrings(String, Lst, Lst) - Static method in class javajs.util.PT
replaceStrings(String, Lst, Lst) - Static method in class javajs.util.PT
replaceWithCharacter(String, String, char) - Static method in class javajs.util.PT
  Does a clean replace of any of the characters in str with chrTo If strTo contains strFrom, then only a single pass is done.
reply(int, Object) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
reply(int, Object) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
report(String, boolean) - Method in class org.jmol.minimize.Minimizer
report(String, boolean) - Method in class org.jmol.script.ScriptEval
reportAll - Variable in class org.jmol.shape.Sticks
reportSelection(int) - Method in class org.jmol.viewer.ChimeMessenger
  report atom selection in Chime format
reportSelection(int) - Method in interface org.jmol.viewer.JmolChimeMessenger
repositionWindow(String, Component) - Method in class org.openscience.jmol.app.HistoryFile
  Uses the informations in the history to reposition the window.
repositionWindow(String, Component, int, int, boolean) - Method in class org.openscience.jmol.app.HistoryFile
  Uses the informations in the history to reposition the window.
requestFocusInWindow(Object) - Method in class jspecview.java.AwtPlatform
requestFocusInWindow(Object) - Method in class jspecview.js2d.JsPlatform
requestFocusInWindow(Object) - Method in interface org.jmol.api.GenericPlatform
requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
requestFocusInWindow(Object) - Method in class org.jmol.awtjs2d.Platform
requestRepaint() - Method in class jspecview.common.JSViewer
requestRepaintAndWait(String) - Method in interface org.jmol.api.JmolRepaintManager
requestRepaintAndWait(String) - Method in class org.jmol.render.RepaintManager
requestRepaintAndWait(String) - Method in class org.jmol.viewer.Viewer
RequestThread() - Constructor for class jspecview.java.AwtPanel.RequestThread
requiresBSFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
requiresEndTag() - Method in class jspecview.source.XMLParser
reset - Static variable in class org.jmol.script.T
reset() - Method in interface javajs.api.GenericOutputChannel
reset() - Method in class javajs.util.ArrayDataReader
reset() - Method in class javajs.util.ListDataReader
reset() - Method in class javajs.util.OC
reset() - Method in class jme.JME
reset() - Method in class jspecview.common.JSVZipFileSequentialReader
reset() - Method in class org.jmol.smiles.SmilesSearch
reset() - Method in class org.jmol.thread.JmolThread
reset() - Method in class org.jmol.util.BoxInfo
reset(boolean) - Method in class org.jmol.viewer.Viewer
reset(int) - Method in class org.jmol.util.CommandHistory
  Resets instance.
RESET_NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
resetAromatic() - Method in class org.jmol.modelset.BondCollection
resetAtomPickType() - Method in class org.jmol.modelkit.ModelKit
resetBioshapes(BS) - Method in class org.jmol.viewer.ShapeManager
resetBoundCount() - Method in class org.jmol.modelset.Model
resetChanged() - Method in class com.sparshui.server.TouchPoint
  Reset the changed flag.
resetDSSR(boolean) - Method in class org.jmol.modelset.Model
  Something has changed; clear the DSSR cache and possibly remove DSSR entirely.
resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
  reset some parameters at the "MAP" keyword or initially
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
resetLighting() - Method in class org.jmol.viewer.StateManager
  Reset lighting to Jmol defaults
resetMolecules() - Method in class org.jmol.modelset.ModelSet
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
  something has arisen that requires resetting of the navigation point.
resetObjects() - Method in class org.jmol.shape.MeshCollection
resetRasmolBonds(BS, int) - Method in class org.jmol.modelsetbio.BioModel
  from Trajectory.setAtomPositions base models only; not trajectories
resetRotation() - Method in class org.jmol.viewer.TransformManager
resetRotation() - Method in class org.jmol.viewer.TransformManager4D
resetScaleFactors() - Method in class jspecview.common.ViewData
resetShapes(boolean) - Method in class org.jmol.viewer.ShapeManager
resetShapes(boolean) - Method in class org.jmol.viewer.Viewer
resetSlab() - Method in class org.jmol.util.MeshSurface
resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
resetView() - Method in class jspecview.common.PanelData
  Resets the spectrum to it's original view
residue - Static variable in class org.jmol.script.T
RESIZE - Enum constant in enum class org.jmol.c.CBK
resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
resizeApplet(Object, int[]) - Method in interface javajs.api.js.J2SObjectInterface
resizeInnerPanel(int, int) - Method in class org.jmol.api.JmolViewer
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.StatusManager
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.Viewer
resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
resizeInnerPanel(String) - Method in class org.jmol.util.GenericApplet
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.status.StatusListener
resizeInnerPanelString(String) - Method in class org.jmol.viewer.StatusManager
  called by file droppers
resLabel - Variable in class jspecview.source.AnIMLReader
resLabel - Variable in class jspecview.source.NMRMLReader
resno - Static variable in class org.jmol.script.T
resolution - Variable in class jspecview.export.AMLExporter
resolution - Variable in class jspecview.export.CMLExporter
resolution - Variable in class jspecview.source.AnIMLReader
resolution - Variable in class jspecview.source.NMRMLReader
resolution - Variable in class org.jmol.jvxl.readers.Parameters
resolution - Static variable in class org.jmol.script.T
resolveDataBase(String, String, String) - Static method in class org.jmol.viewer.JC
resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
Resolver - Class in org.jmol.adapter.smarter
Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
resourceName - Variable in class org.jmol.quantum.MepCalculation
restorativeForceAndAngleRadians(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restorativeForceAndDistance(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restorativeForceAndOutOfPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restorativeForceAndTorsionAngleRadians(V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restore - Static variable in class org.jmol.script.T
restore(float, boolean) - Method in class org.jmol.modelset.Orientation
restoreAtomPositions(P3[]) - Method in class org.jmol.modelset.ModelSet
restoreBonds(String) - Method in class org.jmol.viewer.StateManager
restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
restoreScene(String, float) - Method in class org.jmol.viewer.StateManager
restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
restoreSelection(String) - Method in class org.jmol.viewer.StateManager
restoreUnitCell(String) - Method in class org.jmol.viewer.StateManager
restoreXY(double[][]) - Method in class jme.JMEmol
restrict - Static variable in class org.jmol.script.T
restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEval
restrictSelected(boolean, boolean) - Method in class org.jmol.viewer.ShapeManager
restrictToModel(BS, int) - Method in class org.jmol.viewer.Viewer
  Restrict this bitset to the current model or its initial atom's model.
RESU - Static variable in class org.jmol.util.ColorEncoder
resume - Static variable in class org.jmol.script.T
resumeEval() - Method in class org.jmol.thread.JmolThread
resumeEval(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
resumeEval(Object) - Method in class org.jmol.script.ScriptEval
  From dispatchCommands and JmolThread resumeEval.
resumePausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
resumePausedExecution() - Method in class org.jmol.script.ScriptEval
retain_order - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
returncmd - Static variable in class org.jmol.script.T
reverse - Static variable in class org.jmol.script.T
reverse(Coordinate[]) - Static method in class jspecview.common.Coordinate
reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
  Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE.
reversecolor - Static variable in class org.jmol.script.T
reverseColor - Variable in class org.jmol.shape.Mesh
reversed - Variable in class org.jmol.modelsetbio.BioPolymer
reverseModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
reversePlot() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that toggles reversing the plot on a `JSVPanel`
reversePlot() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that toggles reversing the plot on a `JSVPanel`
reversePlot() - Method in class jspecview.appletjs.JSVApplet
REVERSEPLOT - Enum constant in enum class jspecview.common.ScriptToken
revertStereo - Variable in class jme.JME
rewind - Static variable in class org.jmol.script.T
rgb(int, int, int) - Static method in class javajs.util.CU
Rgb16 - Class in org.jmol.util
Rgb16() - Constructor for class org.jmol.util.Rgb16
rgbFractionalFromArgb(int) - Method in class org.jmol.export.___Exporter
rgbFractionalFromColix(short) - Method in class org.jmol.export.___Exporter
rgbToHSL(P3, boolean) - Static method in class javajs.util.CU
  Convert RGB values to HSL (hue/saturation/lightness)
rgbToXyz(P3, P3) - Method in class javajs.img.GifEncoder
RHOMB_TO_HEX - Static variable in class org.jmol.symmetry.CLEG
RHOMB_TO_HEX - Static variable in class org.jmol.util.SimpleUnitCell
ribbon - Static variable in class org.jmol.script.T
ribbon_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_nucleic_acid_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_power_b - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_sampling - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_side_chain_helper - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_smooth - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_throw - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_trace_atoms - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbon_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ribbonaspectratio - Static variable in class org.jmol.script.T
ribbonborder - Static variable in class org.jmol.script.T
ribbonBottomScreens - Variable in class org.jmol.renderbio.BackboneRenderer
ribbonBottomScreens - Variable in class org.jmol.renderbio.CartoonRenderer
ribbonBottomScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
ribbonBottomScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
ribbonBottomScreens - Variable in class org.jmol.renderbio.RocketsRenderer
ribbonBottomScreens - Variable in class org.jmol.renderbio.StrandsRenderer
ribbonBottomScreens - Variable in class org.jmol.renderbio.TraceRenderer
Ribbons - Class in org.jmol.shapebio
Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
RibbonsRenderer - Class in org.jmol.renderbio
RibbonsRenderer() - Constructor for class org.jmol.renderbio.RibbonsRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.BackboneRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.CartoonRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.RocketsRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.StrandsRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.TraceRenderer
right - Variable in class jspecview.common.PanelData
right - Static variable in class org.jmol.script.T
RIGHT - Static variable in class org.jmol.awtjs.swing.SwingConstants
RIGHT - Static variable in class org.jmol.viewer.binding.Binding
rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
rightbrace - Static variable in class org.jmol.script.T
rightDifference(Quat) - Method in class javajs.util.Quat
rightJustify(String, String) - Static method in class jme.JMEUtil
rightJustify(SB, String, String) - Static method in class javajs.util.PT
rightMargin - Static variable in class jspecview.common.PanelData
rightparen - Static variable in class org.jmol.script.T
rightsquare - Static variable in class org.jmol.script.T
RL() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
rldecode32(byte[], int) - Static method in class javajs.util.MessagePackReader
  mmtf type 7 Decode an array of int32 using run-length decoding.
rldecode32Delta(byte[], int) - Static method in class javajs.util.MessagePackReader
  mmtf type 8 Decode an array of int32 using run-length decoding of a difference array.
rldecode32ToChar(byte[], int) - Static method in class javajs.util.MessagePackReader
  mmtf type 6 Decode an array of int32 using run-length decoding to one char per int.
rldecode32ToStr(byte[]) - Static method in class javajs.util.MessagePackReader
  mmtf type 5 Decode each four bytes as a 1- to 4-character string label where a 0 byte indicates end-of-string.
rldecodef(byte[], int, float) - Static method in class javajs.util.MessagePackReader
  mmtf type 9 Decode an array of int32 using run-length decoding and divide by a divisor to give a float32.
rmsd - Static variable in class org.jmol.script.T
rna - Static variable in class org.jmol.script.T
RNA - Enum constant in enum class org.jmol.c.STR
RNA_MASK - Static variable in class org.jmol.viewer.JC
rna3d - Static variable in class org.jmol.script.T
rNums - Static variable in interface org.apache.tools.bzip2.BZip2Constants
  This array really shouldn't be here.
robust_logs - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
rock - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
rock - Static variable in class org.jmol.script.T
rock_delay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
rocket - Static variable in class org.jmol.script.T
rocketbarrels - Static variable in class org.jmol.script.T
RocketRenderer - Class in org.jmol.renderbio
RocketRenderer() - Constructor for class org.jmol.renderbio.RocketRenderer
Rockets - Class in org.jmol.shapebio
Rockets() - Constructor for class org.jmol.shapebio.Rockets
RocketsRenderer - Class in org.jmol.renderbio
RocketsRenderer() - Constructor for class org.jmol.renderbio.RocketsRenderer
ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
rotate - Static variable in class org.jmol.script.T
rotate(T3) - Method in class javajs.util.M34
ROTATE_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
ROTATE_EVENT - Static variable in class com.sparshui.GestureType
ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
ROTATE_GESTURE - Static variable in class com.sparshui.GestureType
ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
rotate2(T3, T3) - Method in class javajs.util.M34
  Transform the vector vec using this Matrix3f and place the result into vecOut.
rotate3DBall(float, float, BS) - Method in class org.jmol.viewer.TransformManager
rotate45 - Static variable in class org.jmol.script.T
rotate4DBall(float, float, float) - Method in class org.jmol.viewer.TransformManager4D
rotateAboutPointsInternal(JmolScriptEvaluator, P3, P3, float, float, boolean, BS, V3, Lst, float[], M3, M4, boolean, P3[][]) - Method in class org.jmol.viewer.Viewer
rotateAxes(int, V3[], P3, M3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
rotateAxes(V3[], UnitCell, P3, M3) - Method in class org.jmol.symmetry.SymmetryOperation
rotateAxisAngle(V3, float) - Method in class org.jmol.viewer.TransformManager
rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.Viewer
rotateAxisAngleRadiansFixed(float, BS) - Method in class org.jmol.viewer.TransformManager
rotateAxisAngleRadiansInternal(float, BS, M4, boolean) - Method in class org.jmol.viewer.TransformManager
RotateEvent - Class in com.sparshui.common.messages.events
RotateEvent() - Constructor for class com.sparshui.common.messages.events.RotateEvent
RotateEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.RotateEvent
  Constructs a new Rotate Event based on a serial representation of a rotate event.
RotateEvent(float, Location, long) - Constructor for class com.sparshui.common.messages.events.RotateEvent
rotateFront() - Method in class org.jmol.api.JmolViewer
rotateFront() - Method in class org.jmol.viewer.Viewer
rotateHexCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
rotateModelSpinVectors(int, M3) - Method in class org.jmol.viewer.Viewer
rotateModelSpinVectors(ModelSet, int, M3, boolean) - Method in class org.jmol.util.Vibration
rotatePoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
rotateSelected - Static variable in class org.jmol.script.T
rotateSpin(M3, M3, M3, Atom) - Method in class org.jmol.util.Vibration
rotateSpin(T3) - Method in class org.jmol.symmetry.SymmetryOperation
rotateSpins(int, int) - Method in class org.jmol.viewer.Viewer
rotateTranslate(Quat, T3, boolean) - Method in class org.jmol.shape.Mesh
rotateXRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager4D
rotateYRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
rotation - Static variable in class org.jmol.script.T
rotationradius - Static variable in class org.jmol.script.T
rotTrans(T3) - Method in class javajs.util.M4
  Transforms the point parameter with this Matrix4f and places the result back into point.
rotTrans2(T3, T3) - Method in class javajs.util.M4
  Transforms the point parameter with this Matrix4f and places the result into pointOut.
round() - Method in class org.openscience.jmol.app.janocchio.Measure
round(double) - Static method in class org.jmol.export.___Exporter
round(float) - Method in class javajs.util.M4
round(T3) - Static method in class org.jmol.export.___Exporter
roundInt(int) - Static method in class org.jmol.util.GData
  JavaScript won't really have an integer here after integer division.
roving_byres - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_cartoon - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_delay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_detail - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_isomesh - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_isosurface - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_labels - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_lines - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_map1_level - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_map1_name - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_map2_level - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_map2_name - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_map3_level - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_map3_name - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_nb_spheres - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_nonbonded - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_origin - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_origin_z - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_origin_z_cushion - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_polar_contacts - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_polar_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_ribbon - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_selection - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_spheres - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
roving_sticks - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
row - Static variable in class org.jmol.script.T
ROYGB - Static variable in class org.jmol.util.ColorEncoder
rubberband - Static variable in class org.jmol.script.T
run() - Method in class com.sparshui.client.ClientServerConnection
  Begin processing requests.
run() - Method in class com.sparshui.server.GestureServer
  Start accepting connections.
run() - Method in class com.sparshui.server.InputDeviceConnection
  Begin receiving data from the input device.
run() - Method in class jspecview.java.AwtPanel.RequestThread
run() - Method in class org.jmol.io.FileReader
run() - Method in class org.jmol.io.FilesReader
run() - Method in class org.jmol.script.CommandWatcherThread
run() - Method in class org.jmol.script.ScriptProcessRunnable
run() - Method in class org.jmol.thread.JmolThread
run() - Method in class org.openscience.jmol.app.InputScannerThread
run() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
run1(int) - Method in class org.jmol.minimize.MinimizationThread
run1(int) - Method in class org.jmol.navigate.Navigator
run1(int) - Method in class org.jmol.script.CommandWatcherThread
run1(int) - Method in class org.jmol.script.ScriptQueueThread
run1(int) - Method in class org.jmol.thread.AnimationThread
run1(int) - Method in class org.jmol.thread.HoverWatcherThread
run1(int) - Method in class org.jmol.thread.JmolThread
run1(int) - Method in class org.jmol.thread.MoveToThread
run1(int) - Method in class org.jmol.thread.SpinThread
  Java: run1(INIT) while(!interrupted()) { run1(MAIN) } run1(FINISH) JavaScript: run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or run1(FINISH) and return
run1(int) - Method in class org.jmol.thread.TimeoutThread
run1(int) - Method in class org.jmol.thread.VibrationThread
RUNA - Static variable in interface org.apache.tools.bzip2.BZip2Constants
runAllProcesses(Viewer) - Method in interface org.jmol.api.JmolParallelProcessor
runAllProcesses(Viewer) - Method in class org.jmol.script.ScriptParallelProcessor
runAsync(JMEUtil.RunAsyncCallback) - Static method in class jme.JMEUtil
RUNB - Static variable in interface org.apache.tools.bzip2.BZip2Constants
runBufferedSafely(String, SB) - Method in class org.jmol.script.ScriptEval
runButton - Variable in class org.jmol.console.GenericConsole
runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
runScript(String) - Method in interface jspecview.api.JSVAppletInterface
  runs a script in proper order as listed
runScript(String) - Method in interface jspecview.api.ScriptInterface
runScript(String) - Method in class jspecview.app.JSVApp
runScript(String) - Method in class jspecview.appletjs.JSVApplet
runScript(String) - Method in class jspecview.application.JSpecView
  ScriptInterface requires this.
runScript(String) - Method in class jspecview.common.JSViewer
runScript(String) - Method in interface org.jmol.api.JmolScriptEvaluator
runScript(String) - Method in class org.jmol.api.JmolViewer
  starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older version
runScript(String) - Method in interface org.jmol.api.JSVInterface
runScript(String) - Method in class org.jmol.script.ScriptEval
runScript(String) - Method in class org.jmol.viewer.Viewer
  Run a script immediately using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )
runScript(String) - Method in class org.openscience.jmol.app.status.StatusListener
  no queuing here -- called by MainFrame
runScriptBuffer(String, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
runScriptBuffer(String, SB, boolean) - Method in class org.jmol.script.ScriptEval
  runs a script immediately and sends selected output to a provided SB
runScriptCautiously(String) - Method in class org.jmol.api.JmolViewer
  Formerly runScript(script).
runScriptCautiously(String) - Method in class org.jmol.viewer.Viewer
  formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script.
runScriptFromThread(Lst) - Method in class org.jmol.script.ScriptManager
runScriptNow() - Method in class org.jmol.script.ScriptManager
runScriptNow(String) - Method in interface jspecview.api.JSVAppletInterface
runScriptNow(String) - Method in interface jspecview.api.ScriptInterface
runScriptNow(String) - Method in class jspecview.app.JSVApp
runScriptNow(String) - Method in class jspecview.appletjs.JSVApplet
runScriptNow(String) - Method in class jspecview.application.JSpecView
runScriptNow(String) - Method in class jspecview.common.JSViewer
runSleep(int, int) - Method in class org.jmol.thread.JmolThread
runsmi - Variable in class jme.JME
runUserAction(String, Object[], Viewer) - Static method in class org.jmol.script.ScriptEval
RWB - Static variable in class org.jmol.util.ColorEncoder
rxyz - Static variable in class org.jmol.script.T

## S

S - Static variable in class org.jmol.quantum.QS
s1 - Variable in class org.jmol.render.FontLineShapeRenderer
s2 - Variable in class org.jmol.render.FontLineShapeRenderer
SAbs - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Use absolute stereo (this is the default, so this flag is typically redundant)
safeJSON(String, Object) - Static method in class org.jmol.script.SV
  Safely create a JSON key - object pair, allowing for already-named arrays
safeTruncate(float, int) - Static method in class javajs.util.PT
sameAs(int, int) - Method in class org.jmol.modelset.Measurement
sameAsPoints(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
sampleID - Variable in class jspecview.source.AnIMLReader
sampleID - Variable in class jspecview.source.NMRMLReader
samplenum - Variable in class jspecview.source.AnIMLReader
samplenum - Variable in class jspecview.source.NMRMLReader
sampleowner - Variable in class jspecview.source.AnIMLReader
sampleowner - Variable in class jspecview.source.NMRMLReader
sampleRefNum - Variable in class jspecview.source.AnIMLReader
sampleRefNum - Variable in class jspecview.source.NMRMLReader
sasurface - Static variable in class org.jmol.script.T
SAtZz - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Allow stereo at atoms connected to Zz
SAUSAGE - Static variable in class org.jmol.shapecgo.CGOMesh
save - Static variable in class org.jmol.script.T
save() - Method in class org.openscience.jmol.app.HistoryFile
  Saves properties to the history file.
save_pdb_ss - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
saveAtomPositions() - Method in class org.jmol.modelset.ModelSet
saveBonds(String) - Method in class org.jmol.viewer.StateManager
saveContext(String, Object) - Method in class org.jmol.viewer.StateManager
saveCoordinates(String, BS) - Method in class org.jmol.viewer.StateManager
saved - Static variable in class org.jmol.script.T
saved - Variable in class org.jmol.viewer.StateManager
saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
saveImage(String, GenericFileInterface, OC, int, int) - Method in interface jspecview.api.JSVPanel
saveImage(String, GenericFileInterface, OC, int, int) - Method in class jspecview.java.AwtPanel
saveImage(String, GenericFileInterface, OC, int, int) - Method in class jspecview.js2d.JsPanel
saveImage(JSAppletObject, String, String) - Method in interface javajs.api.js.J2SObjectInterface
saveModelOrientation(int, Orientation) - Method in class org.jmol.modelset.ModelSet
saveName - Variable in class org.jmol.modelset.Orientation
SaveOpt - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Save custom InChI creation options (non-standard InChI)
saveOrientation(String, float[]) - Method in class org.jmol.viewer.StateManager
saveOrRetrieveTransformMatrix(M4) - Method in interface org.jmol.api.SymmetryInterface
saveOrRetrieveTransformMatrix(M4) - Method in class org.jmol.symmetry.Symmetry
  Saved by CLEG.assignSpaceGroup; retrieved by SpaceGroupFinder.
savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
saveProperties(Properties) - Method in class jspecview.app.JSVAppPro
saveProperties(Properties) - Method in class jspecview.application.JSpecView
saveProperties(Properties) - Method in interface org.jmol.api.JSVInterface
saveProperties(Properties) - Method in class org.openscience.jmol.app.status.StatusListener
saveproteinstructurestate - Static variable in class org.jmol.script.T
saveScene(String, Map) - Method in class org.jmol.viewer.StateManager
saveSelection(String, BS) - Method in class org.jmol.viewer.StateManager
saveState(String) - Method in class org.jmol.viewer.StateManager
saveStructure(String) - Method in class org.jmol.viewer.StateManager
saveUnitCell(String) - Method in class org.jmol.viewer.StateManager
saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
saveWindowSizes() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
saveWindowSizes() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
saveXY() - Method in class jme.JMEmol
saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Saves the currently active collection as a multistep XYZ file.
say(String) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
SB - Class in javajs.util
  Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
SB() - Constructor for class javajs.util.SB
sbKey - Variable in class org.jmol.minimize.MinAngle
sbOut - Variable in class org.jmol.jvxl.data.JvxlData
sbOut - Variable in class org.jmol.jvxl.readers.Parameters
sbType - Variable in class org.jmol.minimize.MinAngle
sc - Variable in class org.jmol.thread.JmolThread
SC - Interface in org.jmol.api
  SwingComponent interface common to javax.swing and org.jmol.awtjs.swing Can be augmented as needed, provided classes of org.jmol.awtjs.swing are also updated.
scale - Variable in class org.jmol.modelset.TickInfo
scale - Static variable in class org.jmol.script.T
scale - Variable in class org.jmol.shape.Axes
scale - Variable in class org.jmol.shapespecial.DrawMesh
scale - Variable in class org.jmol.shapespecial.Polyhedron
scale(double) - Method in class javajs.util.T3d
  Sets the value of this tuple to the scalar multiplication of itself.
scale(float) - Method in class javajs.util.M3
  Multiplies each element of this matrix by a scalar.
scale(float) - Method in class javajs.util.M4
  Multiplies each element of this matrix by a scalar.
scale(float) - Method in class javajs.util.T3
  Sets the value of this tuple to the scalar multiplication of itself.
scale3d - Variable in class org.jmol.jvxl.data.JvxlData
scale3d - Variable in class org.jmol.jvxl.readers.Parameters
scale3d - Static variable in class org.jmol.script.T
scale3d - Variable in class org.jmol.shape.Mesh
scale3D - Variable in class org.jmol.viewer.TransformManager
scale4(float) - Method in class javajs.util.T4
  Sets the value of this tuple to the scalar multiplication of itself.
scaleAdd(double, T3d, T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleAdd(int, T3i, T3i) - Method in class javajs.util.T3i
  Sets the value of this tuple to the scalar multiplication of tuple t1 plus tuple t2 (this = s*t1 + t2).
scaleAdd(Matrix, double) - Method in class javajs.util.Matrix
  X = A + B*scale
scaleAdd2(double, T3d, T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleAdd2(float, T3, T3) - Method in class javajs.util.T3
  Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleangstromsperinch - Static variable in class org.jmol.script.T
scaleAxes(float[]) - Method in class org.jmol.shapespecial.Ellipsoid
scaleBox(P3[], float) - Static method in class org.jmol.util.BoxInfo
SCALEBY - Enum constant in enum class jspecview.common.ScriptToken
scaleColor - Variable in class jspecview.common.PanelData
SCALECOLOR - Enum constant in enum class jspecview.common.ScriptToken
ScaleData - Class in jspecview.common
  Stores information about scale and range that `JSVPanel` needs to to display a graph with a single plot.
ScaleData(Coordinate[], int, int, boolean, boolean) - Constructor for class jspecview.common.ScaleData
  Calculates values that `JSVPanel` needs in order to render a graph, (eg.
scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
scaleName - Static variable in class org.jmol.viewer.JC
scaleObject - Variable in class org.jmol.shape.Echo
scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
scalePixelsPerMicron - Variable in class org.jmol.modelset.Text
scalePixelsPerMicron - Variable in class org.jmol.render.MeshRenderer
scaleSelectedBy(double) - Method in class jspecview.common.PanelData
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
  Perform implementation-specific scaling.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
  Perform implementation-specific scaling.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
  Perform implementation-specific scaling.
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.AdfReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.AmsReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.DgridReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
scaleSpectrum(int, double) - Method in class jspecview.common.ViewData
scaleT(T3) - Method in class javajs.util.T3
  {x*p.x, y*p.y, z*p.z) used for three-way scaling
scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
scaleVectorsToMax(float) - Method in class org.jmol.modelset.AtomCollection
  Scales vibrations and associated vectors such that the maximum length is the given value
scaleVibration(float) - Method in interface org.jmol.api.JmolModulationSet
scaleVibration(float) - Method in class org.jmol.util.ModulationSet
scaleYBy(double) - Method in class jspecview.common.PanelData
scalingFactor - Variable in class jspecview.common.PanelData
scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
  /////////////////////////////////////////////////////////////
scene - Static variable in class org.jmol.script.T
scene_animation - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_animation_duration - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_buttons - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_buttons_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_current_name - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_frame_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_loop - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
scene_restart_movie_delay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SCENE_TAG - Static variable in class org.jmol.viewer.OutputManagerAwt
SCENE_TAG - Static variable in class org.jmol.viewer.OutputManagerJS
scenes_changed - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
schemes - Variable in class org.jmol.util.ColorEncoder
scm - Variable in class org.jmol.viewer.Viewer
score - Variable in class org.jmol.util.ContactPair
scrCoords - Variable in class org.jmol.renderspecial.DotsRenderer
SCREEN - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
screenDotCount - Variable in class org.jmol.renderspecial.DotsRenderer
screenHeight - Variable in class org.jmol.export.___Exporter
screenLevel - Variable in class org.jmol.renderspecial.DotsRenderer
screenLocation(Location) - Static method in class com.sparshui.common.Location
screenPixelCount - Variable in class org.jmol.viewer.TransformManager
screens - Variable in class org.jmol.render.MeshRenderer
screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
screenWidth - Variable in class org.jmol.export.___Exporter
screenx - Static variable in class org.jmol.script.T
screenxyz - Static variable in class org.jmol.script.T
screeny - Static variable in class org.jmol.script.T
screenz - Static variable in class org.jmol.script.T
script - Variable in class org.jmol.jvxl.readers.Parameters
script - Variable in class org.jmol.modelset.Text
script - Variable in class org.jmol.script.ScriptContext
script - Variable in class org.jmol.script.ScriptCompiler
script - Static variable in class org.jmol.script.T
script - Variable in class org.jmol.thread.TimeoutThread
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
script(String) - Method in class jspecview.appletjs.JSVApplet
  Deprecated.
script(String) - Method in class jspecview.appletjs.JSVAppletPro
  JSVAppletPro uses "script()" for executing a real script, not a parameter initialization.
script(String) - Method in interface org.jmol.api.JmolAppletInterface
script(String) - Method in class org.jmol.api.JmolViewer
script(String) - Method in class org.jmol.util.GenericApplet
script(String) - Method in class org.jmol.viewer.Viewer
SCRIPT - Enum constant in enum class jspecview.common.ScriptToken
SCRIPT - Enum constant in enum class org.jmol.c.CBK
SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.JC
SCRIPT_CONSOLE - Static variable in class org.jmol.viewer.JC
SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JC
SCRIPT_EXT - Static variable in class org.jmol.viewer.JC
SCRIPT_GUI - Static variable in class org.jmol.viewer.JC
SCRIPT_ISEDITOR - Static variable in class org.jmol.viewer.JC
SCRIPT_NOENDCHECK - Static variable in class org.jmol.viewer.JC
SCRIPT_ONLY - Static variable in class org.jmol.viewer.FileManager
SCRIPT_QUIET - Static variable in class org.jmol.viewer.JC
SCRIPT_START - Static variable in class org.jmol.viewer.JC
SCRIPT_STEP - Static variable in class org.jmol.viewer.JC
SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
scriptCallback(String) - Method in class org.molecularplayground.MPJmolApp
scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptCheck(String) - Method in class org.jmol.api.JmolViewer
scriptCheck(String) - Method in class org.jmol.util.GenericApplet
scriptCheck(String) - Method in class org.jmol.viewer.Viewer
scriptCheckRet(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
scriptCheckRet(String, boolean) - Method in class org.jmol.script.ScriptManager
scriptCommand - Static variable in class org.jmol.script.T
scriptCommand - Variable in class org.jmol.shape.Mesh
ScriptCompiler - Class in org.jmol.script
ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
scriptCompleted(StatusManager, String, String) - Method in class org.jmol.viewer.ChimeMessenger
  called when a script exits.
scriptCompleted(StatusManager, String, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
ScriptContext - Class in org.jmol.script
scriptEcho(String) - Method in class org.jmol.viewer.Viewer
scriptEditor - Variable in class org.jmol.console.JmolConsole
ScriptEditor - Class in org.jmol.console
ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
ScriptError - Class in org.jmol.script
  Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
ScriptError() - Constructor for class org.jmol.script.ScriptError
ScriptEval - Class in org.jmol.script
ScriptEval() - Constructor for class org.jmol.script.ScriptEval
ScriptException - Exception Class in org.jmol.script
ScriptExt - Class in org.jmol.scriptext
ScriptExt() - Constructor for class org.jmol.scriptext.ScriptExt
scriptFileName - Variable in class org.jmol.script.ScriptContext
scriptFileName - Variable in class org.jmol.script.ScriptEval
ScriptFunction - Class in org.jmol.script
ScriptFunction() - Constructor for class org.jmol.script.ScriptFunction
ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
ScriptInterface - Interface in jspecview.api
ScriptInterruption - Exception Class in org.jmol.script
ScriptInterruption(ScriptEval, String, int) - Constructor for exception class org.jmol.script.ScriptInterruption
scriptLevel - Variable in class org.jmol.script.ScriptEval
ScriptManager - Class in org.jmol.script
ScriptManager() - Constructor for class org.jmol.script.ScriptManager
ScriptMathProcessor - Class in org.jmol.script
  Reverse Polish Notation Engine for IF, SET, and @{...} Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f -- Bob Hanson 2/16/2007
scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptNoWait(String) - Method in class org.jmol.util.GenericApplet
ScriptParallelProcessor - Class in org.jmol.script
ScriptParallelProcessor() - Constructor for class org.jmol.script.ScriptParallelProcessor
  parallel operations
ScriptParam - Class in org.jmol.script
  The ScriptParam class holds methods used to parse parameters in Jmol scripts.
ScriptParam() - Constructor for class org.jmol.script.ScriptParam
ScriptProcessRunnable - Class in org.jmol.script
ScriptProcessRunnable(ScriptParallelProcessor, ScriptProcess, Object, ShapeManager) - Constructor for class org.jmol.script.ScriptProcessRunnable
scriptqueue - Static variable in class org.jmol.script.T
scriptQueue - Variable in class jspecview.common.JSViewer
scriptQueue - Variable in class org.jmol.script.ScriptManager
ScriptQueueThread - Class in org.jmol.script
ScriptQueueThread(ScriptManager, Viewer, boolean, int) - Constructor for class org.jmol.script.ScriptQueueThread
scriptreportinglevel - Static variable in class org.jmol.script.T
scriptStatus(String) - Method in class org.jmol.viewer.Viewer
  scriptCallback is the primary way to monitor script status.
scriptStatusMsg(String, String) - Method in class org.jmol.viewer.Viewer
ScriptToken - Enum Class in jspecview.common
  ScriptToken takes care of script command processing
ScriptTokenizer - Class in jspecview.common
ScriptTokenizer(String, boolean) - Constructor for class jspecview.common.ScriptTokenizer
scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptWait(String) - Method in class org.jmol.api.JmolViewer
scriptWait(String) - Method in class org.jmol.util.GenericApplet
scriptWait(String) - Method in class org.jmol.viewer.Viewer
scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
scriptWait(String, String) - Method in class org.jmol.util.GenericApplet
scriptWaitOutput(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptWaitOutput(String) - Method in class org.jmol.util.GenericApplet
scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
sculpt_angl_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_auto_center - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_avd_excl - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_avd_gap - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_avd_range - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_avd_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_bond_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_field_mask - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_hb_overlap - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_hb_overlap_base - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_line_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_max_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_max_min - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_max_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_max_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_memory - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_min_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_min_min - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_min_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_min_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_nb_interval - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_plan_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_pyra_inv_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_pyra_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tors_tolerance - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tors_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tri_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tri_min - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tri_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tri_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_tri_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_scale14 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_vis_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_vis_mid - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_vis_min - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_vis_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_weight - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpt_vdw_weight14 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpting - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sculpting_cycles - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sD - Variable in class org.jmol.util.Point3fi
  screen diameter
sdof_drag_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
search - Static variable in class org.jmol.script.T
secondary_structure - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
security - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
seek(long) - Method in interface javajs.api.GenericBinaryDocumentReader
seek(long) - Method in class javajs.util.BinaryDocument
SEESAW - Static variable in class org.jmol.smiles.SmilesStereo
sel_counter - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
select - Static variable in class org.jmol.script.T
select(BS, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
SELECT - Enum constant in enum class jspecview.common.ScriptToken
SELECT - Enum constant in enum class org.jmol.c.CBK
selectAll() - Method in class org.jmol.api.JmolViewer
selectAll() - Method in class org.jmol.viewer.Viewer
selectAll(boolean) - Method in class jspecview.dialog.ViewsDialog
selectallmodels - Static variable in class org.jmol.script.T
selectBonds(BS) - Method in class org.jmol.viewer.Viewer
selectDisplayed(BS) - Method in class org.jmol.modelset.Trajectory
  Remove trajectories that are not currently displayed from the visible frames bitset.
selected - Static variable in class org.jmol.script.T
selectedfloat - Static variable in class org.jmol.script.T
selectedGroupCount - Variable in class org.jmol.modelset.Chain
  Calculated just prior to coloring by group so that the range is appropriate for each chain.
selectedIndex - Variable in class org.jmol.modelset.Group
  for coloring by group
selectedPanel - Variable in class jspecview.common.JSViewer
selectedPolyOnly - Variable in class org.jmol.render.MeshRenderer
selectedRow - Variable in class jspecview.java.AwtDialog
selectedRow - Variable in class jspecview.js2d.JsDialog
selectedTrajectory - Variable in class org.jmol.modelset.Model
selectedTreeNode(JSVTreeNode) - Method in class jspecview.common.JSViewer
selectFrameNode(JSVPanel) - Method in class jspecview.common.JSViewer
selectFromEntireSet(int) - Method in class jspecview.common.PanelData
  sets bsSelected to the specified pointer from "select 3.1*1"
selecthetero - Static variable in class org.jmol.script.T
selecthydrogen - Static variable in class org.jmol.script.T
selection - Static variable in class org.jmol.script.T
selection_overlay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
selection_round_points - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
selection_visible_only - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
selection_width - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
selection_width_max - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
selection_width_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
selectionChanged(BS) - Method in interface org.jmol.api.JmolSelectionListener
  Called when the selected atoms change
selectionhalos - Static variable in class org.jmol.script.T
SelectionManager - Class in org.jmol.viewer
selectPanel(JSVPanel, Lst) - Method in class jspecview.common.JSViewer
  From (AwtMainPanel or JsMainPanel).setSelectedPanel
selectPeakByFileIndex(String, String, String) - Method in class jspecview.common.PanelData
selectPeakByFileIndex(String, String, String) - Method in class jspecview.common.Spectrum
selectPeakByFilePathTypeModel(String, String, String) - Method in class jspecview.common.Spectrum
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
selectSpectrum(String, String, String, boolean) - Method in class jspecview.common.PanelData
selectStatus(BS, boolean, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
  "SELECT" starting with comma triggers the SELECT callback from a SELECT command.
selectTableRow(int) - Method in interface jspecview.api.PlatformDialog
selectTableRow(int) - Method in class jspecview.dialog.JSVDialog
selectTableRow(int) - Method in class jspecview.java.AwtDialog
selectTableRow(int) - Method in class jspecview.js2d.JsDialog
semicolon - Static variable in class org.jmol.script.T
sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
sendConsoleEcho(String) - Method in class org.jmol.console.GenericConsole
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
sendConsoleMessage(String) - Method in class org.jmol.console.GenericConsole
sendConsoleMessage(String) - Method in class org.jmol.viewer.Viewer
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
sendMessage(Map, String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
sendNioSyncRequest(Object, int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
sendPanelChange() - Method in class jspecview.common.JSViewer
sendToJmol(int, String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
  from JmolPanel and SYNC command
sendToJmol(int, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
  send the message - not for replies.
seq_view - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_alignment - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_discrete_by_state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_fill_char - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_fill_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_format - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_label_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_label_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_label_spacing - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_label_start - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_location - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_overlay - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_unaligned_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seq_view_unaligned_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
seqcode - Variable in class org.jmol.modelset.Group
seqcode - Static variable in class org.jmol.script.T
seqid - Static variable in class org.jmol.script.T
seqIdOrWyckoffCode - Variable in class org.jmol.adapter.smarter.Atom
sequence - Static variable in class org.jmol.script.T
sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
serialize() - Method in interface com.sparshui.common.Event
  Serializes this event for transmission over the network.
serialize() - Method in class com.sparshui.common.messages.events.DragEvent
  Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.FlickEvent
  Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
  Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.RotateEvent
  Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.SpinEvent
  Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.TouchEvent
  Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.ZoomEvent
  Constructs the data packet with this event data.
serializeDisplaySchemes(Writer) - Method in class jspecview.application.DisplaySchemesProcessor
  Serializes the display schemes to the given writer
serverCycle() - Method in class org.molecularplayground.MPJmolApp
serverCycle() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
serverCycle() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
ServerToClientProtocol - Class in com.sparshui.server
  Represents the server to client connection.
ServerToClientProtocol(Socket) - Constructor for class com.sparshui.server.ServerToClientProtocol
  Constructs a new connection to the client.
service - Variable in class org.molecularplayground.MPJmolApp
SERVICE - Enum constant in enum class org.jmol.c.CBK
SERVICE_LOST - Static variable in class com.sparshui.common.messages.events.EventType
SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
session_cache_optimize - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
session_changed - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
session_compression - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
session_file - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
session_migration - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
session_version_check - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
set - Static variable in class org.jmol.script.T
set(double, double) - Method in class jspecview.common.Coordinate
  Constructor
set(double, double, double) - Method in class javajs.util.T3d
  Sets the value of this tuple to the specified xyz coordinates.
set(float, float, float) - Method in class javajs.util.T3
  Sets the value of this tuple to the specified xyz coordinates.
set(float, float, float) - Method in interface org.jmol.util.Node
set(int) - Method in class javajs.util.BS
  Sets the bit at the specified index to `true`.
set(int) - Method in class javajs.util.Eigen
set(int, int) - Method in class org.jmol.awtjs.swing.Dimension
set(int, int, char, int, int, char, int, int) - Method in class org.jmol.adapter.smarter.Structure
set(int, int, int) - Method in class javajs.util.T3i
  Sets the value of this tuple to to the specified x, y, and z coordinates.
set(int, Map, RadiusData, String, String, String, TickInfo, boolean, boolean, Boolean, boolean, int, short, Text, float, BS) - Method in class org.jmol.modelset.MeasurementData
set(int, BS, int[]) - Method in class org.jmol.minimize.MMConstraint
set(InputStream, String[], String) - Method in interface jspecview.api.JSVZipReader
set(InputStream, String[], String) - Method in class jspecview.common.JSVZipFileSequentialReader
set(String) - Method in class org.jmol.viewer.binding.JmolBinding
set(String, int) - Method in interface org.jmol.api.JmolParallelProcessor
set(String, int) - Method in class org.jmol.script.ScriptFunction
set(GenericLineReader, BufferedReader, boolean) - Method in interface javajs.api.GenericCifDataParser
set(GenericLineReader, BufferedReader, boolean) - Method in class javajs.util.CifDataParser
  A Chemical Information File data parser.
set(Quat) - Method in class javajs.util.Quat
set(JFrame, PrintLayout, boolean) - Method in interface jspecview.api.JSVPrintDialog
set(JFrame, PrintLayout, boolean) - Method in class jspecview.java.AwtPrintDialog
  Initialises a modal `PrintLayoutDialog` with a default title of "Print Layout".
set(JSViewer) - Method in interface jspecview.api.JSVFileDropper
set(JSViewer) - Method in interface jspecview.api.JSVFileHelper
set(JSViewer) - Method in class jspecview.dialog.DialogManager
set(JSViewer) - Method in class jspecview.java.AwtFileDropper
set(JSViewer) - Method in class jspecview.java.AwtFileHelper
set(JSViewer) - Method in class jspecview.js2d.JsFileHelper
set(PanelData, ScriptToken, String) - Method in class jspecview.common.ColorParameters
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.smarter.XtalSymmetry
set(JmolJDXMOLReader, String, Map) - Method in interface org.jmol.api.JmolJDXMOLParser
set(JmolJDXMOLReader, String, Map) - Method in class org.jmol.jsv.JDXMOLParser
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.CircleRenderer
set(JmolRendererInterface, GData) - Method in interface org.jmol.g3d.G3DRenderer
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.HermiteRenderer
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.TriangleRenderer
set(SymmetryInterface, Atom, Atom[], BS, float) - Method in class org.jmol.symmetry.UnitCellIterator
set(AtomDataServer, int, short[]) - Method in interface org.jmol.api.JmolEnvCalc
set(AtomDataServer, int, short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
set(ModelSet) - Method in class org.jmol.modelset.MeasurementPending
set(ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
set(ModelSet, int, int, Map, Properties, Map) - Method in class org.jmol.modelset.Model
set(MeshSlicer) - Method in class org.jmol.util.MeshCapper
set(FileManager) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map, boolean) - Method in class org.jmol.io.FilesReader
set(TransformManager, Viewer) - Method in interface org.jmol.api.JmolNavigatorInterface
set(TransformManager, Viewer) - Method in class org.jmol.navigate.Navigator
set(Viewer) - Method in class org.jmol.adapter.readers.quantum.NBOParser
set(Viewer) - Method in interface org.jmol.api.JmolDataManager
set(Viewer) - Method in class org.jmol.quantum.MepCalculation
set(Viewer) - Method in class org.jmol.viewer.ChimeMessenger
set(Viewer) - Method in class org.jmol.viewer.DataManager
set(Viewer) - Method in interface org.jmol.viewer.JmolChimeMessenger
set(Viewer, BS) - Method in class org.jmol.symmetry.CIPData
  Actual constructor.
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CDXMLWriter
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CIFWriter
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CMLWriter
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PDBWriter
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PWMATWriter
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.QCJSONWriter
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.XSFWriter
set(Viewer, OC, Object[]) - Method in interface org.jmol.api.JmolWriter
set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioModelSet
set(Viewer, ShapeManager) - Method in interface org.jmol.api.JmolRepaintManager
set(Viewer, ShapeManager) - Method in class org.jmol.render.RepaintManager
set2(int, boolean) - Method in class org.jmol.smiles.SmilesBond
set2(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.Monomer
set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
set2DCrossHairsLinked(GraphSet, double, double, boolean) - Method in class jspecview.common.PanelData
set33(int, int, float) - Method in class javajs.util.M34
set3dContourVector(Lst, int[][], T3[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
  Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
set4(float, float, float, float) - Method in class javajs.util.A4
  Sets the value of this axis angle to the specified x,y,z,angle.
set4(float, float, float, float) - Method in class javajs.util.T4
  Sets the value of this tuple to the specified xyzw coordinates.
setA(double[]) - Method in class javajs.util.T3d
  Sets the value of this tuple from the 3 values specified in the array.
setA(double, double, Spectrum, String, boolean, boolean, int, int) - Method in class jspecview.common.Annotation
setA(float[]) - Method in class javajs.util.M3
  Sets the values in this Matrix3f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
setA(float[]) - Method in class javajs.util.M4
  Sets the values in this Matrix4f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
setA(float[]) - Method in class javajs.util.T3
  Sets the value of this tuple from the 3 values specified in the array.
setAA(A4) - Method in class javajs.util.A4
  Sets the value of this axis angle to the value of axis angle t1.
setAA(A4) - Method in class javajs.util.M3
  Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.
setAA(A4) - Method in class javajs.util.Quat
setAA33(A4) - Method in class javajs.util.M34
setAbc(String, float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
  set cell vectors by string.
setABC(int) - Method in class org.jmol.util.MeshSurface
setAbcFromParams(float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
setAbstractButtonLabels(Map, Map) - Static method in class org.jmol.console.GenericConsole
setAccessInternal(String) - Method in class org.jmol.viewer.Viewer
  Set access to the specified path only; used for restricting file read/write access to only those files within the zip block of a PNGJ file Java only.
setACDAssignments(String, String, int, Lst, String) - Method in interface org.jmol.api.JmolJDXMOLParser
setACDAssignments(String, String, int, Lst, String) - Method in class org.jmol.jsv.JDXMOLParser
setActionCommand(String) - Method in interface org.jmol.api.SC
setActionCommand(String) - Method in class org.jmol.awt.AwtSwingComponent
setActionCommand(String) - Method in class org.jmol.awtjs.swing.JComponent
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
  Changes the activation state for a logging level.
setActiveMenu(String) - Method in class org.jmol.modelkit.ModelKitPopup
  Set the active menu and request a repaint.
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.P2nReader
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PdbReader
  adaptable via subclassing
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PqrReader
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
setAlignment(int) - Method in class org.jmol.modelset.Text
setAlignmentLCR(String) - Method in class org.jmol.modelset.Text
setAll(int) - Static method in class org.jmol.util.BSUtil
setAll(P3, M3, P3, float, float, float, float, float, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
setAllConformation(BS) - Method in class org.jmol.modelsetbio.BioModelSet
setAllowJSThreads(boolean) - Method in class org.jmol.script.ScriptEval
setAllProteinType(BS, STR) - Method in class org.jmol.modelsetbio.BioModelSet
  called from state STRUCTURE command
setAllStructureList(Map) - Method in class org.jmol.modelsetbio.BioModelSet
setAmbientOcclusion(int) - Method in class org.jmol.util.GData
setAmbientPercent(int) - Method in class org.jmol.util.GData
  fractional distance from black for ambient color
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
setAnimation(int) - Method in class org.jmol.viewer.Viewer
setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.AnimationManager
setAnimDisplay(BS) - Method in class org.jmol.viewer.Viewer
setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAPa(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
setAPm(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
setApplicationProperties(boolean) - Method in class jspecview.application.JSpecView
setArrays(Atom[], BS, Bond[], int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setAsBallRotation(float, float, float) - Method in class javajs.util.M3
  3D ball rotation from dx dy in-plane mouse motion adapted from Andrew Hanson Computer Graphics beyond the Third Dimension: Geometry, Orientation Control, and Rendering for Graphics in Dimensions Greater than Three Course Notes for SIGGRAPH ’98 http://www.cse.ohio-state.edu/~hwshen/888_su02/hanson_note.pdf
setAsBallRotation(M4, float, float, float, float) - Method in class org.jmol.viewer.TransformManager4D
  4D ball rotation from nominal dx, dy, dz motion.
setAsXRotation(float) - Method in class javajs.util.M3
  Sets the value of this matrix to a rotation matrix about the x axis by the passed angle.
setAsXYRotation(float) - Method in class javajs.util.M4
  Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
setAsXZRotation(float) - Method in class javajs.util.M4
  Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
setAsYRotation(float) - Method in class javajs.util.M3
  Sets the value of this matrix to a rotation matrix about the y axis by the passed angle.
setAsYZRotation(float) - Method in class javajs.util.M4
  Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
setAsZRotation(float) - Method in class javajs.util.M3
  Sets the value of this matrix to a rotation matrix about the z axis by the passed angle.
setAtom(int) - Method in interface org.iupac.InChIStructureProvider
setAtom(int) - Method in class org.jmol.inchi.InChIJNA
setAtom(int) - Method in class org.jmol.inchi.InChIJS
setAtom(int, int, P3, float, BS, int, short, int, boolean, boolean) - Method in class org.jmol.modelset.Atom
setAtom(String, Map) - Method in class org.jmol.adapter.readers.xml.CDXMLParser
  Set the 2D or pseudo-3D coordinates of the atoms.
setAtom(Atom, int, int, int, float, float, float) - Method in class org.jmol.adapter.readers.simple.InputReader
setAtom(Atom, int, String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
setAtomBits(BS) - Method in class org.jmol.modelset.Chain
setAtomBits(BS) - Method in class org.jmol.modelset.Group
  note that we may pick up additional bits here that were added later
setAtomBits(BS) - Method in interface org.jmol.modelset.Structure
setAtomBits(BS) - Method in class org.jmol.modelsetbio.BioPolymer
setAtomBits(BS) - Method in class org.jmol.modelsetbio.ProteinStructure
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Chain
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Group
  Setting and clearing
setAtomBitsAndClear(BS, BS) - Method in interface org.jmol.modelset.Structure
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.ProteinStructure
setAtomChooser() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setAtomChooser() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setAtomClickability() - Method in class org.jmol.shape.AtomShape
setAtomClickability() - Method in class org.jmol.shape.Balls
setAtomClickability() - Method in class org.jmol.shape.Labels
setAtomClickability() - Method in class org.jmol.shape.Shape
setAtomClickability() - Method in class org.jmol.shape.Sticks
setAtomClickability() - Method in class org.jmol.shapebio.Backbone
setAtomClickability() - Method in class org.jmol.shapebio.BioShape
setAtomClickability() - Method in class org.jmol.shapebio.BioShapeCollection
setAtomClickability() - Method in class org.jmol.shapespecial.Dots
setAtomClickability() - Method in class org.jmol.shapespecial.Ellipsoids
setAtomColoring(int, int) - Method in class jme.JMEmol
setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomCoord2(BS, int, Object) - Method in class org.jmol.modelset.AtomCollection
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
setAtomCoords(BS, int, Object) - Method in class org.jmol.modelset.ModelSet
setAtomCoords(BS, int, Object) - Method in class org.jmol.viewer.Viewer
setAtomCoordScaled(Atom, String[], int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.modelset.ModelSet
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.viewer.Viewer
setAtomCoordTokens(Atom, String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  //////////////////////////
setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the atomic mass of the atom.
setAtomIndexes(int, int) - Method in class org.jmol.util.Tensor
setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
setAtomMapAnyCase() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomName(int, String, boolean) - Method in class org.jmol.modelset.AtomCollection
setAtomNamesAndNumbers(int, int, AtomCollection, boolean) - Method in class org.jmol.modelset.ModelSet
setAtomNumber(int, int, boolean) - Method in class org.jmol.modelset.AtomCollection
setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptEval
setAtomProperties(double, double, int, int) - Method in class jme.JMEmol
setAtomProperties(String, Object, int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
setAtoms(Node[], int, BS) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
setAtomsCoordRelative(BS, float, float, float) - Method in class org.jmol.modelset.AtomCollection
setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the partial atomic charges based on asc auxiliary info
setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  / for XmlChem3dReader, but could be for CUBE
setAtomSetFrequency(int, String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies
setAtomSetModelPropertyForSet(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the a property for the an AtomSet
setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the name for the current AtomSet
setAtomSetNumber(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomsForSmiles(Viewer, String) - Method in class org.jmol.symmetry.CIPDataSmiles
setAtomTensors(int, Lst) - Method in class org.jmol.modelset.AtomCollection
setAtomVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
setAtropisomerOptions() - Method in class org.jmol.modelset.Bond
setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
setAutoscrolls(boolean) - Method in interface org.jmol.api.SC
setAutoscrolls(boolean) - Method in class org.jmol.awt.AwtSwingComponent
setAutoscrolls(boolean) - Method in class org.jmol.awtjs.swing.JComponent
setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
setB(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
setBackground(GenericColor) - Method in class org.jmol.awtjs.swing.Component
setBackgroundArgb(int) - Method in class org.jmol.util.GData
  sets background color to the specified argb value
setBackgroundColor(GenericColor) - Method in interface jspecview.api.JSVPanel
setBackgroundColor(GenericColor) - Method in class jspecview.java.AwtPanel
setBackgroundColor(GenericColor) - Method in class jspecview.js2d.JsPanel
setBackgroundImage(Object) - Method in class org.jmol.util.GData
setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
setBannerLabel(String) - Method in class org.molecularplayground.MPJmolApp
setBaseModels(BS) - Method in class org.jmol.modelset.Trajectory
  set bits for all base models only
setBbcage(float) - Method in class org.jmol.util.BoxInfo
setBBox(T3, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
setBFactor(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
setBigEndian(boolean) - Method in interface javajs.api.GenericBinaryDocumentReader
setBigEndian(boolean) - Method in class javajs.util.BinaryDocument
setBigEndian(boolean) - Method in class javajs.util.OC
setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
setBioColix(short) - Method in class org.jmol.renderbio.BackboneRenderer
setBioColix(short) - Method in class org.jmol.renderbio.CartoonRenderer
setBioColix(short) - Method in class org.jmol.renderbio.MeshRibbonRenderer
setBioColix(short) - Method in class org.jmol.renderbio.RibbonsRenderer
setBioColix(short) - Method in class org.jmol.renderbio.RocketsRenderer
setBioColix(short) - Method in class org.jmol.renderbio.StrandsRenderer
setBioColix(short) - Method in class org.jmol.renderbio.TraceRenderer
setBits(int, int) - Method in class javajs.util.BS
  Sets the bits from the specified `fromIndex` (inclusive) to the specified `toIndex` (exclusive) to `true`.
setBitTo(int, boolean) - Method in class javajs.util.BS
  Sets the bit at the specified index to the specified value.
setBlockID(double) - Method in class jspecview.source.JDXDataObject
setBond(int) - Method in interface org.iupac.InChIStructureProvider
setBond(int) - Method in class org.jmol.inchi.InChIJNA
setBond(int) - Method in class org.jmol.inchi.InChIJS
setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
setBondArray() - Method in class org.jmol.smiles.SmilesAtom
setBondingRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
setBondMeasure(int, MeasurementPending) - Method in class org.jmol.modelkit.ModelKit
setBondProperties(int, int, int, int) - Method in class jme.JMEmol
setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
setBoolean(ScriptToken, boolean) - Method in class jspecview.common.PanelData
setBoolean(ScriptToken, boolean) - Method in class jspecview.common.Parameters
setBoolean(ScriptToken, ItemEvent) - Method in class jspecview.application.ApplicationMenu
setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptParam
  ///////////////// setting global parameters ////////////////////////
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
setBooleanPropertyTok(String, int, boolean) - Method in class org.jmol.viewer.Viewer
setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.modelset.ModelSet
setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.util.BoxInfo
setBoundBoxFromOABC(T3[]) - Method in class org.jmol.util.BoxInfo
setBoundingBox(P3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setBoundingBox(P3[]) - Method in class org.jmol.util.MeshSurface
setBox(float, float, P3, V3, V3, P3, float) - Method in class org.jmol.modelsetbio.Sheet
setBox(P3, P3) - Method in class org.jmol.util.MeshSurface
setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.modelset.Text
setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.modelset.Text
setBSAtomsForSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Add a full set of atoms to BSAtoms if they are not already indicated there.
setBsHidden(BS) - Method in class org.jmol.modelset.AtomCollection
setBSPeriod() - Method in class org.jmol.render.AxesRenderer
setBSPeriod() - Method in class org.jmol.render.BbcageRenderer
setBSPeriod() - Method in class org.jmol.render.UccageRenderer
setButton(String) - Method in class org.jmol.console.GenericConsole
setButton(String) - Method in class org.jmol.console.JmolConsole
setButton(String) - Method in class org.jmol.consolejs.AppletConsole
setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setBytes(byte[]) - Method in class javajs.util.OC
setC(short) - Method in interface org.jmol.api.JmolRendererInterface
  sets current color from colix color index
setC(short) - Method in class org.jmol.export.Export3D
  sets current color from colix color index
setC(short) - Method in class org.jmol.g3d.Graphics3D
  sets current color from colix color index
setC(short) - Method in class org.jmol.util.GData
setCA(double, double, Spectrum, String, GenericColor, boolean, boolean, int, int) - Method in class jspecview.common.ColoredAnnotation
setCalcNext(CLEG.ClegData, String) - Method in class org.jmol.symmetry.CLEG.ClegNode
  sup(i0, i1, indexMax, depthMax)
setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.ModulationSet
  get updated value for offset vector and for occupancy
setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.Vibration
setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
setCallback(String, Object) - Method in interface org.jmol.api.JmolAppletInterface
setCallback(String, Object) - Method in class org.jmol.util.GenericApplet
  set a callback either as a function or a function name from JavaScript
setCallbackFunction(String, Object) - Method in class org.jmol.viewer.StatusManager
  Set a JmolScript or JavaScript or Java callback.
setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
setCallbackFunction(String, String) - Method in class org.jmol.console.GenericConsole
setCallbackFunction(String, String) - Method in class org.jmol.util.GenericApplet
  From StatusManager
setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.status.StatusListener
setCamera(float, float) - Method in class org.jmol.viewer.TransformManager
setCameraDepthPercent(float, boolean) - Method in class org.jmol.viewer.TransformManager
  either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
setCanvasImage(Object, int, int) - Method in interface javajs.api.js.J2SObjectInterface
setCel(boolean) - Method in class org.jmol.util.GData
setCellSelectionEnabled(boolean) - Method in interface jspecview.api.PlatformDialog
setCellSelectionEnabled(boolean) - Method in class jspecview.java.AwtDialog
setCellSelectionEnabled(boolean) - Method in class jspecview.js2d.JsDialog
setCellSelectionEnabled(boolean) - Method in class org.jmol.awtjs.swing.JTable
setCelPower(int) - Method in class org.jmol.util.GData
setCenter(Location) - Method in class com.sparshui.common.messages.events.RotateEvent
setCenter(Location) - Method in class com.sparshui.common.messages.events.ZoomEvent
setCenter(P3) - Method in class org.jmol.shapespecial.Ellipsoid
setCenter(T3, float) - Method in interface org.jmol.api.AtomIndexIterator
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
setCenter(T3, float) - Method in class org.jmol.symmetry.UnitCellIterator
setCenter2(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
setCenterAt(int, P3) - Method in class org.jmol.viewer.TransformManager
setCenterBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
setCenterSelected() - Method in class org.jmol.api.JmolViewer
setCenterSelected() - Method in class org.jmol.viewer.Viewer
setCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
  deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell called from ScriptEval.finalizeLoad()
setCGO(Map) - Method in class org.jmol.viewer.Viewer
setChainID(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the charge of the atom.
setChemicalShiftReference(String, float) - Method in interface org.jmol.api.JmolNMRInterface
setChemicalShiftReference(String, float) - Method in class org.jmol.quantum.NMRCalculation
setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
setCIPChirality(int) - Method in class org.jmol.modelset.Atom
setCIPChirality(int) - Method in class org.jmol.modelset.Bond
  Not implemented.
setCIPChirality(int) - Method in class org.jmol.smiles.SmilesAtom
setCIPChirality(int) - Method in class org.jmol.util.Edge
setCIPChirality(int) - Method in interface org.jmol.util.Node
setCIPChirality(int) - Method in interface org.jmol.util.SimpleNode
setCIR(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
setClegId(String) - Method in class org.jmol.symmetry.SpaceGroup
setClickable(int) - Method in class org.jmol.modelset.Atom
setClipboard(Object) - Static method in class jspecview.java.AwtClipboard
  Transfers text or image into the clipboard.
setClipboard(Object) - Static method in class org.jmol.awt.AwtClipboard
  Transfers text or image into the clipboard.
setColix(short) - Method in class org.jmol.render.MeshRenderer
setColix(short) - Method in class org.jmol.renderbio.BackboneRenderer
setColix(short) - Method in class org.jmol.renderbio.CartoonRenderer
setColix(short) - Method in class org.jmol.renderbio.MeshRibbonRenderer
setColix(short) - Method in class org.jmol.renderbio.RibbonsRenderer
setColix(short) - Method in class org.jmol.renderbio.RocketsRenderer
setColix(short) - Method in class org.jmol.renderbio.StrandsRenderer
setColix(short) - Method in class org.jmol.renderbio.TraceRenderer
setColix(short) - Method in class org.jmol.util.MeshSurface
setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
setColixBack(short) - Method in class org.jmol.util.MeshSurface
setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setColor(float[], boolean) - Method in class javajs.export.PDFCreator
setColor(int) - Method in class org.jmol.util.GData
setColor(ScriptToken, GenericColor) - Method in class jspecview.common.ColorParameters
  Sets the color of an element
setColor(ScriptToken, GenericColor) - Method in class jspecview.common.PanelData
setColorBackground(String) - Method in class org.jmol.api.JmolViewer
setColorBackground(String) - Method in class org.jmol.viewer.Viewer
setColorFromString(ScriptToken, String) - Method in class jspecview.common.ColorParameters
setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.common.PanelData
setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.java.AwtPanel
setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.js2d.JsPanel
setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
setColumn3(int, float, float, float) - Method in class javajs.util.M3
  Sets the specified column of this matrix3d to the three values provided.
setColumn33(int, float[]) - Method in class javajs.util.M34
setColumn4(int, float, float, float, float) - Method in class javajs.util.M4
  Sets the specified column of this matrix4f to the four values provided.
setColumnA(int, float[]) - Method in class javajs.util.M3
  Sets the specified column of this matrix3d to the four values provided.
setColumnA(int, float[]) - Method in class javajs.util.M4
  Sets the specified column of this matrix4f to the four values provided.
setColumnComparator(Class, Comparator) - Method in class org.openscience.jmol.app.janocchio.TableSorter
setColumnV(int, T3) - Method in class javajs.util.M3
  Sets the specified column of this matrix3d to the vector provided.
setCommandHooks() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setCompiler() - Method in interface org.jmol.api.JmolScriptEvaluator
setCompiler() - Method in class org.jmol.script.ScriptEval
setConformation(BS) - Method in class org.jmol.modelset.ModelSet
setConformation(BS) - Method in class org.jmol.modelsetbio.BioPolymer
setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
  sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
setConsoleFontScale(int) - Method in class org.jmol.viewer.Viewer
setConstraint(SymmetryInterface, int, int) - Method in class org.jmol.modelkit.ModelKit
  This constraint will be set for the site only.
setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in class org.jmol.scriptext.MathExt
setContext() - Method in class jspecview.export.AMLExporter
setContext() - Method in class jspecview.export.CMLExporter
setContinuous(boolean) - Method in class jspecview.source.JDXDataObject
  Sets value to true if spectrum is continuous
setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
setContourVector(Lst, int, BS, float, short, int, SB) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
setConvertedSpectrum(Spectrum) - Method in class jspecview.common.Spectrum
setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setCorrelationTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
  set the correlation time to be used in the NOE calculation
setCorrelationTimeTauPS(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  set the correlation time to be used in the NOE calculation
setCorrelationTimeTauPS(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
setCount(int) - Method in class org.jmol.modelset.Measurement
setCount(int) - Method in class org.jmol.modelset.MeasurementPending
setCountM(int) - Method in class org.jmol.modelset.Measurement
setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
setCreatingImage(boolean) - Method in class jspecview.common.JSViewer
setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelSet
setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
setCurrentAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the number for the current AtomSet
setCurrentCage(String) - Method in class org.jmol.viewer.Viewer
setCurrentColor(String, Color) - Method in class jspecview.application.PreferencesDialog
setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
setCurrentModelID(String) - Method in class org.jmol.viewer.Viewer
setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
setCurrentModelIndexClear(int, boolean) - Method in class org.jmol.viewer.Viewer
setCurrentModelInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets auxiliary information for the AtomSet
setCurrentSubSpectrum(int) - Method in class jspecview.common.Spectrum
setCursor(int) - Method in interface jspecview.api.ScriptInterface
setCursor(int) - Method in class jspecview.app.JSVApp
setCursor(int) - Method in class jspecview.application.JSpecView
setCursor(int) - Method in class org.jmol.viewer.Viewer
setCursor(int, Object) - Method in class jspecview.java.AwtPlatform
setCursor(int, Object) - Method in class jspecview.js2d.JsPlatform
setCursor(int, Object) - Method in interface org.jmol.api.GenericPlatform
setCursor(int, Object) - Method in class org.jmol.awt.Platform
setCursor(int, Object) - Method in class org.jmol.awtjs2d.Platform
setCursor(JSmolAppletObject, int) - Method in interface org.jmol.api.js.JmolToJSmolInterface
setCursorWait(boolean) - Method in class org.jmol.script.ScriptError
setCutoff(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
  sets the cutoff distance beyond which atom interactions are not considered
setCutoffAng(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  sets the cutoff distance beyond which atom interactions are not considered
setCutoffAng(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
  sets the cutoff distance beyond which atom interactions are not considered
setData(byte[], int) - Method in class javajs.img.PngEncoder
setData(Object) - Method in class javajs.util.ArrayDataReader
setData(Object) - Method in class javajs.util.DataReader
setData(Object) - Method in class javajs.util.ListDataReader
setData(Object) - Method in class javajs.util.StringDataReader
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
  A general-purpose data storage method.
setData(String, Object[], int, int, int, int, int, int) - Method in interface org.jmol.api.JmolDataManager
setData(String, Object[], int, int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
  This method needs to be redone using a class instead of Object[]
setData(AnnotationData) - Method in class jspecview.dialog.JSVDialog
setDataClass(String) - Method in class jspecview.source.JDXHeader
  Sets the data class
setDataDistanceToPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
setDataType(String) - Method in class jspecview.source.JDXHeader
  Sets the data type
setDate(String) - Method in class jspecview.source.JDXHeader
  Sets the date the file was created
setDebugging() - Method in interface org.jmol.api.JmolScriptEvaluator
setDebugging() - Method in class org.jmol.script.ScriptEval
setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
setDefaultLattice(P3) - Method in class org.jmol.viewer.Viewer
setDefaultPrintOptions(PrintLayout) - Method in class jspecview.common.PanelData
setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
setDepth(int) - Method in class org.jmol.util.GData
  clipping from the front and the back
setDescription(String) - Method in class jspecview.java.AwtDialogFileFilter
  Sets the description for the JSpecViewFileFilter
setDialog(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  The HTML for this dialog has been generated.
setDialogLocation(Point) - Method in class org.jmol.dialog.FileChooser
setDialogSize(Dimension) - Method in class org.jmol.dialog.FileChooser
setDiffusePercent(int) - Method in class org.jmol.util.GData
  df in I = df * (N dot L) + sf * (R dot V)^p
setDihedrals(float[], BS[], float) - Method in class org.jmol.modelset.ModelSet
setDihedrals(float[], BS[], float) - Method in class org.jmol.viewer.Viewer
setDirLastExported(String) - Method in interface jspecview.api.JSVFileHelper
setDirLastExported(String) - Method in class jspecview.java.AwtFileHelper
setDirLastExported(String) - Method in class jspecview.js2d.JsFileHelper
setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setDisplay(Object) - Method in interface javajs.api.JSInterface
setDisplay(Object) - Method in class jspecview.appletjs.JSVApplet
setDisplay(Object) - Method in class jspecview.common.JSViewer
setDisplay(Object) - Method in class org.jmol.util.GenericApplet
setDisplay(Object) - Method in class org.jmol.viewer.Viewer
setDocStream(GenericZipTools, BufferedInputStream) - Method in class javajs.util.CompoundDocument
setDocumentBase(JSViewer, URL) - Static method in class jspecview.common.JSVFileManager
setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
setDragAtomIndex(int) - Method in class org.jmol.viewer.ActionManager
setDropTargetListener(boolean, JSViewer) - Method in interface jspecview.api.AppletFrame
setDropTargetListener(boolean, JSViewer) - Method in class jspecview.appletjs.JSVApplet
setDx(float) - Method in class com.sparshui.common.messages.events.DragEvent
setDy(float) - Method in class com.sparshui.common.messages.events.DragEvent
setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
setElement(int, int, float) - Method in class javajs.util.M3
  Sets the specified element of this matrix3d to the value provided.
setElement(int, int, float) - Method in class javajs.util.M4
  Sets the specified element of this matrix4f to the value provided.
setElement(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
setElementAndIsotope(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  allow 13C, 15N, 2H, etc.
setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
setElementColors(ColorParameters) - Method in class jspecview.common.ColorParameters
setEllipsoidAF(float[]) - Method in class org.jmol.jvxl.readers.Parameters
setEnabled(boolean) - Method in interface jspecview.api.JSVViewPanel
setEnabled(boolean) - Method in class jspecview.js2d.JsMainPanel
setEnabled(boolean) - Method in class jspecview.js2d.JsPanel
setEnabled(boolean) - Method in interface org.jmol.api.JmolAbstractButton
setEnabled(boolean) - Method in interface org.jmol.api.SC
setEnabled(boolean) - Method in class org.jmol.awt.AwtSwingComponent
setEnabled(boolean) - Method in class org.jmol.awtjs.swing.Component
setEnabled(boolean, boolean) - Method in class jspecview.popup.JSVGenericPopup
setEnabled(Object, boolean) - Method in interface jspecview.api.PlatformDialog
  / get/set methods ////
setEnabled(Object, boolean) - Method in class jspecview.java.AwtDialog
  / Table-related methods ////
setEnabled(Object, boolean) - Method in class jspecview.js2d.JsDialog
  / Table-related methods ////
setEnabled(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
setEnergy(float) - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
setErrorLog(String) - Method in class jspecview.source.JDXSource
  Sets the error log for this source
setErrorMessage(String) - Method in class org.jmol.script.ScriptError
setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
setEval(JmolScriptEvaluator) - Method in class org.jmol.thread.JmolThread
  JavaScript only -- -- scriptDelay, moveTo, spin -- save context for restoration later -- move program counter forward one command
setException(ScriptException, String, String) - Method in class org.jmol.script.ScriptEval
setExpCouple(String, int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setExpDist(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the number of explicit hydrogen atoms bonded with this atom.
setExpNoe(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setExportXAxisDirection(boolean) - Method in class jspecview.common.Spectrum
setF(String, float) - Method in class org.jmol.viewer.GlobalSettings
setFancyArrowHead(int) - Method in class org.jmol.renderbio.BioMeshRenderer
setFancyConic(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
setFancyRibbon(int) - Method in class org.jmol.renderbio.BioMeshRenderer
setFields() - Method in class jspecview.dialog.JSVDialog
setFileChooser(ExportType) - Method in interface jspecview.api.JSVFileHelper
setFileChooser(ExportType) - Method in class jspecview.java.AwtFileHelper
setFileChooser(ExportType) - Method in class jspecview.js2d.JsFileHelper
setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
  Set fullPathName, fileName, and nameAsGiven
setFilename(String) - Method in class org.jmol.console.ScriptEditor
setFilePath(String) - Method in interface jspecview.api.JSVAppletInterface
setFilePath(String) - Method in class jspecview.app.JSVApp
setFilePath(String) - Method in class jspecview.appletjs.JSVApplet
setFilePath(String) - Method in class jspecview.source.JDXDataObject
setFilePath(String) - Method in class jspecview.source.JDXSource
setFileType(String) - Method in class org.jmol.viewer.FileManager
setFillColor(GenericColor) - Method in class jspecview.common.Spectrum
setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setFilterAtomTypeStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setFinalOperations() - Method in class org.jmol.symmetry.SpaceGroup
setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in interface org.jmol.api.SymmetryInterface
setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in class org.jmol.symmetry.Symmetry
setFinalOperationsSafely() - Method in class org.jmol.symmetry.SpaceGroup
setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
setFloatProperty(String, float) - Method in class org.jmol.script.ScriptParam
setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
setFocus() - Method in class org.jmol.viewer.Viewer
setFocus(boolean) - Method in interface jspecview.api.PlatformDialog
setFocus(boolean) - Method in class jspecview.dialog.JSVDialog
setFocus(boolean) - Method in class jspecview.java.AwtDialog
setFocus(boolean) - Method in class jspecview.js2d.JsDialog
setFocusable(boolean) - Method in interface jspecview.api.JSVViewPanel
setFocusable(boolean) - Method in class jspecview.js2d.JsMainPanel
setFocusable(boolean) - Method in class jspecview.js2d.JsPanel
setFont(Object, int, int, float, boolean) - Method in class jspecview.common.PanelData
setFont(Object, Font) - Method in class jspecview.common.PDFWriter
setFont(Object, Font) - Method in class jspecview.java.AwtG2D
setFont(Object, Font) - Method in class jspecview.js2d.JsG2D
setFont(Object, Font) - Method in interface org.jmol.api.GenericGraphics
setFont(Object, Font) - Method in class org.jmol.awt.AwtG2D
setFont(Object, Font) - Method in class org.jmol.awtjs2d.JsG2D
setFont(String, float) - Method in class javajs.export.PDFCreator
setFont(Font) - Method in class org.jmol.g3d.Graphics3D
setFont(Font) - Method in class org.jmol.util.GData
setFont(Font, boolean) - Method in class org.jmol.modelset.Text
setFontBold(String, float) - Method in class org.jmol.util.GData
setFontFromFid(int) - Method in class org.jmol.modelset.Text
setFontScale(float) - Method in class org.jmol.modelset.Text
setFontScale(int) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
setFor(JSVPanel, ColorParameters, boolean) - Method in class jspecview.common.ColorParameters
setFormalCharge(int) - Method in class org.jmol.modelset.Atom
setFormalCharges(BS, int) - Method in class org.jmol.modelset.AtomCollection
setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setFractionalCoordPt(P3, P3, boolean) - Method in class org.jmol.modelset.Atom
setFrame(int) - Method in class org.jmol.viewer.AnimationManager
setFrame(JFrame) - Method in class jme.JME
setFrameAndTreeNode(int) - Method in class jspecview.common.JSViewer
setFrameCount(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
setFrameDelayMs(long) - Method in class org.jmol.viewer.Viewer
setFrameDelayMs(long, BS) - Method in class org.jmol.modelset.ModelSet
setFrameDeltaCouple(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setFrameDeltaNoe(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setFrameModelInfo(String, Object) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
setFrameNumberChangeViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
setFrameOffsets(BS, boolean) - Method in class org.jmol.viewer.Viewer
setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
setFrameTitle(String) - Method in class jspecview.common.PanelNode
setFrameTitle(BS, Object) - Method in class org.jmol.modelset.ModelSet
setFrameTitleObj(Object) - Method in class org.jmol.viewer.Viewer
setFrameVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
setFromAsymmetricTensor(double[][], String, String) - Method in class org.jmol.util.Tensor
  Standard constructor for QM tensors
setFromAxes(V3[]) - Method in class org.jmol.util.Tensor
  Standard constructor for ellipsoids based on axes
setFromBits(int, BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
setFromEigenVectors(T3[], float[], String, String, Tensor) - Method in class org.jmol.util.Tensor
  Standard constructor for charge and iso.
setFromMD(MeasurementData, boolean) - Method in class org.jmol.modelset.Measurement
setFromThermalEquation(double[], String) - Method in class org.jmol.util.Tensor
  standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setGraphicsColor(Object, GenericColor) - Method in class jspecview.common.PDFWriter
setGraphicsColor(Object, GenericColor) - Method in class jspecview.java.AwtG2D
setGraphicsColor(Object, GenericColor) - Method in class jspecview.js2d.JsG2D
setGraphicsColor(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
setGraphSetKey(String) - Method in interface jspecview.api.AnnotationData
setGraphSetKey(String) - Method in class jspecview.common.MeasurementData
setGraphSetKey(String) - Method in class jspecview.dialog.JSVDialog
setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
  controls greyscale rendering
setGroup(Group) - Method in class com.sparshui.server.TouchPoint
  Set the group for this touch point.
setGroup(Chain, String, int, int, int) - Method in class org.jmol.modelset.Group
setGroup1(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
setGroup1(ModelSet, int) - Method in interface org.jmol.api.JmolAnnotationParser
setGroup1(ModelSet, int) - Method in class org.jmol.dssx.AnnotationParser
setGroup1(ModelSet, int) - Method in class org.jmol.dssx.DSSR1
setGroupID(String) - Method in class org.jmol.modelset.Group
setGroupID(String) - Method in class org.jmol.modelsetbio.Monomer
setGroupLists(int) - Method in class org.jmol.modelsetbio.BioResolver
setHasUnitCell() - Method in class org.jmol.modelkit.ModelKit
setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.BioResolver
  ///////// ADDITION OF HYDROGEN ATOMS /////////////
setHeaderTable(Lst) - Method in class jspecview.source.JDXHeader
  Sets the headerTable for this Source or spectrum
setHighlightColor(GenericColor) - Method in class jspecview.common.PanelData
setHighlightedPeak(PeakInfo) - Method in class jspecview.common.Spectrum
setHistory(String) - Method in class org.jmol.viewer.Viewer
setHorizAlignment(int, int) - Static method in class org.jmol.viewer.JC
setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
setHoverLabel(String, String) - Method in class org.jmol.modelkit.ModelKit
setHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
  Finalizes the hydrogen count hydrogens in a `SmilesMolecule`.
setHydrogenCount(int) - Method in class jspecview.source.JDXDataObject
setHZtoPPM(boolean) - Method in class jspecview.source.JDXDataObject
  Sets the value to true if the spectrum should be displayed with abscissa unit of Part Per Million (PPM) instead of Hertz (HZ)
setIcon(Object) - Method in interface org.jmol.api.SC
setIcon(Object) - Method in class org.jmol.awt.AwtSwingComponent
setIcon(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
setId(String) - Method in class jspecview.common.Spectrum
setID(String) - Method in class jspecview.source.JDXSource
setIdentity() - Method in class javajs.util.M4
  Sets this Matrix4f to identity.
setImage(Object) - Method in interface org.jmol.api.GenericImageDialog
setImage(Object) - Method in class org.jmol.console.ImageDialog
setImage(Object) - Method in class org.jmol.modelset.Text
setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Sets the output image dimensions.
setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
setImageInfo(int, int, String) - Method in class org.jmol.dialog.Dialog
setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the number of implicit hydrogen atoms bonded with this atom.
setIncreasing(boolean) - Method in class jspecview.source.JDXDataObject
  Sets value to true if spectrum is increasing
setIndex(int) - Method in interface jspecview.api.JSVTreeNode
setIndex(int) - Method in class jspecview.application.AwtTreeNode
setIndex(int) - Method in class jspecview.tree.SimpleTreeNode
setIndex(int) - Method in class org.jmol.smiles.SmilesAtom
  Constructs a `SmilesAtom`.
setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Sets the indexes to the atomSetIndex values of each leaf of the node.
setInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelSet
setInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setInlineData(String) - Method in class jspecview.source.JDXDataObject
setInlineData(String) - Method in class jspecview.source.JDXSource
setInMotion(boolean) - Method in class org.jmol.api.JmolViewer
setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
setInsertedCommand(String) - Method in class org.jmol.viewer.Viewer
setInt(double, double, Spectrum, double, double, double) - Method in class jspecview.common.Integral
setInt(int) - Method in class org.jmol.util.Rgb16
setIntegrationRatios(String) - Method in class jspecview.common.PanelData
  DEPRECATED Sets the integration ratios that will be displayed
setIntLocation(int[]) - Method in interface jspecview.api.PlatformDialog
setIntLocation(int[]) - Method in class jspecview.java.AwtDialog
setIntLocation(int[]) - Method in class jspecview.js2d.JsDialog
setIntoFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setIntoFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
setIntProperty(String, int) - Method in class org.jmol.script.ScriptParam
setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
setIntPropertyTok(String, int, int) - Method in class org.jmol.viewer.Viewer
setInverseNormixes() - Static method in class org.jmol.util.Normix
setInvoker(Object) - Method in class org.jmol.awtjs.swing.JPopupMenu
setIRmode(String) - Method in class jspecview.common.JSViewer
setIRMode(Spectrum.IRMode, String) - Method in class jspecview.common.PanelData
setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setITAName(String) - Method in class org.jmol.symmetry.CLEG.ClegNode
setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelSet
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in interface org.jmol.atomdata.AtomDataServer
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.modelset.ModelSet
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.viewer.Viewer
setJcampdx(String) - Method in class jspecview.source.JDXHeader
  Sets the JCAMP-DX version number
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
setJmolDataFrame(ModelSet, String, int, int) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
  Set up the JmolDataFrame initially
setJmolDefaults() - Method in class org.jmol.api.JmolViewer
setJmolDefaults() - Method in class org.jmol.viewer.Viewer
setJmolSize(Dimension) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
setJSOptions(Map) - Method in class org.jmol.util.GenericApplet
setJSpecView(String, boolean, boolean) - Method in class org.openscience.jmol.app.status.StatusListener
setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setKeepChars(boolean) - Method in interface org.jmol.adapter.readers.xml.CDXMLParser.CDXReaderI
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
setLabel(int, String) - Method in class jme.JMEmol
setLabel(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
setLabel(Object, BS) - Method in class org.jmol.viewer.ShapeManager
setLabel(String) - Method in class org.openscience.jmol.app.jsonkiosk.BannerFrame
setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setLabels() - Method in class org.jmol.console.GenericConsole
setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
setLabelString(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
setLastColix(int, boolean) - Method in class org.jmol.util.Shader
setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
  set symmetry lattice type using Hall rotations
setLattice(int) - Method in class org.jmol.symmetry.Symmetry
setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
  Shelx and Wien2k readers
setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setLeadAtomIndex() - Method in class org.jmol.modelsetbio.Monomer
setLeftComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
setLegend(JSVDialog) - Method in class jspecview.common.PanelNode
setLength(int) - Method in class javajs.util.SB
setLengths() - Method in class org.jmol.shapespecial.Ellipsoid
setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
setLighting(int) - Method in class org.jmol.shape.Mesh
setLine(String) - Method in interface org.jmol.api.JmolJDXMOLParser
setLine(String) - Method in class org.jmol.jsv.JDXMOLParser
setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
setLineWidth(float) - Method in class javajs.export.PDFCreator
setlinkedXMove(GraphSet, double, boolean) - Method in class jspecview.common.PanelData
setLoader(ModelLoader) - Method in class org.jmol.modelsetbio.BioResolver
setLoadFormat(boolean, String, char, boolean) - Method in class org.jmol.viewer.Viewer
  Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
setLoadNote() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  //////////////////////////////////////////////////////////////////////////////////
setLoadParameters(Map, boolean) - Method in class org.jmol.viewer.Viewer
setLocalPath(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
  called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
setLocation(int[]) - Method in class org.jmol.awtjs.swing.JDialog
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
  Replaces the current logger implementation by a new one.
setLogLevel(int) - Static method in class org.jmol.util.Logger
  Activates all logging levels up through a given level.
setLongDate(String) - Method in class jspecview.source.JDXHeader
  Sets the long date of when the file was created
setlrefSingle(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setM(double[][]) - Method in interface javajs.api.EigenInterface
setM(double[][]) - Method in class javajs.util.Eigen
setM(M3) - Method in class javajs.util.A4
  Sets the value of this axis-angle to the rotational component of the passed matrix.
setM(ModelSet, Measurement, float, short, String, int) - Method in class org.jmol.modelset.Measurement
setM1(double, double, Spectrum) - Method in class jspecview.common.Measurement
setM3(M34) - Method in class javajs.util.M3
  Sets the value of this matrix to the double value of the Matrix3f argument.
setM33(M34) - Method in class javajs.util.M34
  Sets the value of this matrix to the double value of the Matrix3f argument.
setM4(M4) - Method in class javajs.util.M4
  Sets the value of this matrix to a copy of the passed matrix m1.
setMad(short) - Method in class org.jmol.modelset.Bond
setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
setMagneticMoments(boolean) - Method in class org.jmol.adapter.smarter.XtalSymmetry
  One of the last things to do for a spin space group: Set the spin vectors, possibly based on spinFrameCartXYZ.
setMainFrame(MainFrame) - Method in class jspecview.application.JSpecView
setManager(Object, Viewer, Object) - Method in class org.jmol.minimize.MinimizationThread
setManager(Object, Viewer, Object) - Method in class org.jmol.script.CommandWatcherThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.AnimationThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.JmolThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.MoveToThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.SpinThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.VibrationThread
setMapBitSet(Map, int, int, String) - Static method in class org.jmol.util.BSUtil
setMappingPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
setMarBond(short) - Method in class org.jmol.api.JmolViewer
setMarBond(short) - Method in class org.jmol.viewer.Viewer
setMargin(float) - Method in class org.jmol.util.BoxInfo
setMatchingAtom(Node, int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the number of a matching atom in a molecule.
setMatrixOperationCount(int) - Method in class org.jmol.symmetry.SpaceGroup
setMaxSize(int) - Method in class org.jmol.util.CommandHistory
  Resets maximum size of command queue.
setMeasurementText(Measurement) - Method in class jspecview.source.JDXDataObject
setMenu(String, boolean) - Method in class org.jmol.api.JmolViewer
setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
setMenu(ModelKitPopup) - Method in class org.jmol.modelkit.ModelKit
setMenuEnables(PanelNode) - Method in class jspecview.application.ApplicationMenu
setMenuItem(JMenuItem, char, String, int, int, EventListener) - Static method in class jspecview.application.ApplicationMenu
setMenuKeys(String, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setMenuKeys(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  opportunity to adjust menus for a custom application
setMenus(JMenu, JMenu, JMenu, ActionListener) - Static method in class jspecview.application.ApplicationMenu
setMenuState() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setMeshColor() - Method in class org.jmol.shape.MeshCollection
setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
  an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEval
setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
setMinimumIntegral(double) - Method in class jspecview.common.IntegralData
setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.JScrollPane
setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
setMinMax0(P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
setMinMax0(P3, P3) - Method in interface org.jmol.adapter.smarter.MSInterface
setMinMaxLatticeParameters(int, P3i, P3i, int) - Static method in class org.jmol.util.SimpleUnitCell
setMixingTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
  sets the mixing time for the NOE experiment
setMixingTimeSec(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  sets the mixing time for the NOE experiment
setMixingTimeSec(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
  sets the mixing time for the NOE experiment
setMKState(int) - Method in class org.jmol.modelkit.ModelKit
setMnemonic(char) - Method in interface org.jmol.api.JmolAbstractButton
setMnemonic(char) - Method in class org.jmol.console.JmolLabel
setMO(Map) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
setMod(String, P3, P3, int, Lst, M3, Matrix[], SymmetryInterface, int, int, Vibration, boolean) - Method in class org.jmol.util.ModulationSet
  A collection of modulations for a specific atom.
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
setModDim(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
setModel(int) - Method in interface org.jmol.api.JmolJSpecView
setModel(int) - Method in class org.jmol.jsv.JSV
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceField
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.symmetry.UnitCellIterator
setModelCage(int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
  This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command.
setModelCagePts(int, T3[], String) - Method in class org.jmol.modelset.ModelSet
setModelFields() - Method in class org.jmol.minimize.forcefield.ForceField
setModelIndex(int) - Method in class org.jmol.modelset.Measurement
setModelIndex(int) - Method in class org.jmol.modelset.StateScript
setModelInfoForSet(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets auxiliary information for an AtomSet
setModelkitPropertySafely(String, Object) - Method in class org.jmol.viewer.Viewer
  Set a ModelKit property, but only if the modelkit exists already.
setModelPDB(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setModelSet(ModelSet) - Method in class org.jmol.modelset.MeasurementData
setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
setModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
setModelSet(ModelSet) - Method in class org.jmol.viewer.Viewer
setModelVisibility() - Method in class org.jmol.viewer.Viewer
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Bbcage
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Halos
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.MeshCollection
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Shape
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.TextShape
setModelVisibilityFlags(BS) - Method in class org.jmol.shapebio.BioShapeCollection
setModelVisibilityFlags(BS) - Method in class org.jmol.shapecgo.CGO
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Dipoles
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Draw
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Ellipsoids
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Polyhedra
setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
  only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the vwr references are all removed
setModifyKeys(Map) - Method in class org.jmol.util.JSONWriter
setModTQ(T3, boolean, T3, boolean, float) - Method in interface org.jmol.api.JmolModulationSet
setModTQ(T3, boolean, T3, boolean, float) - Method in class org.jmol.util.ModulationSet
  Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
setModulation(boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Both the Jana reader and the CIF reader will call this to set the modulation for a given model.
setModulation(boolean, XtalSymmetry.FileSymmetry) - Method in interface org.jmol.adapter.smarter.MSInterface
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.modelset.ModelSet
  Sets the modulation for all atoms in bs.
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.viewer.Viewer
setMol(boolean) - Method in class jme.JME
setMol(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setMoment() - Method in interface org.jmol.api.JmolModulationSet
setMoment() - Method in class org.jmol.util.ModulationSet
setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
setMorphCount(int) - Method in class org.jmol.viewer.AnimationManager
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.AmsReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
setMotion(int, boolean) - Method in class org.jmol.viewer.ActionManager
setMotionFixed(BS) - Method in class org.jmol.viewer.Viewer
setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.Viewer
setMouseMode() - Method in class org.jmol.viewer.ActionManager
setMovableX(int) - Method in class org.jmol.modelset.Text
setMovableXPercent(int) - Method in class org.jmol.modelset.Text
setMovableY(int) - Method in class org.jmol.modelset.Text
setMovableYPercent(int) - Method in class org.jmol.modelset.Text
setMovableZPercent(int) - Method in class org.jmol.modelset.Text
setMovie(Map) - Method in class org.jmol.viewer.AnimationManager
  support for PyMOL movies and anim FRAMES [....] currently no support for scripted movies
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
setMustResume() - Method in class org.jmol.script.ScriptContext
setMV(M3, T3) - Method in class javajs.util.M4
  Initializes a Matrix4f from the rotation matrix and translation.
setName(String) - Method in class jspecview.common.Parameters
setName(String) - Method in interface org.jmol.api.SC
setName(String) - Method in class org.jmol.awt.AwtSwingComponent
setName(String) - Method in class org.jmol.awtjs.swing.Component
setName(String) - Method in class org.jmol.script.SV
setNavFps(int) - Method in class org.jmol.viewer.TransformManager
setNavigatePt(P3) - Method in class org.jmol.viewer.TransformManager
  scripted entry point for navigation
setNavigationDepthPercent(float) - Method in interface org.jmol.api.JmolNavigatorInterface
setNavigationDepthPercent(float) - Method in class org.jmol.navigate.Navigator
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
  sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be invalid input: '<'0 or >100)
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.Viewer
setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
setNavigationOffsetRelative() - Method in interface org.jmol.api.JmolNavigatorInterface
setNavigationOffsetRelative() - Method in class org.jmol.navigate.Navigator
setNavigationOffsetRelative() - Method in class org.jmol.viewer.TransformManager
setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
setNboLabels(String[], int, Lst, int, String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
setNewRotationCenter(P3) - Method in class org.jmol.viewer.Viewer
setNewWindowParametersForExport() - Method in class org.jmol.util.GData
setNextPeak(Coordinate, int) - Method in class jspecview.common.Spectrum
setNMRfreq(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
  set the NMR frequency for the NOE simulation
setNMRfreqMHz(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  set the NMR frequency for the NOE simulation
setNMRfreqMHz(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
  set the NMR frequency for the NOE simulation
setNo - Variable in class org.jmol.symmetry.SpaceGroup
  n in X.n or 9 for X:a...
setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setNode(PanelNode) - Method in class jspecview.common.JSViewer
setNodeTransform(CLEG.ClegNode) - Method in class org.jmol.symmetry.CLEG.ClegData
setNoeExprefValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setNoeNPrefIndices(int[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
setNoesy(boolean) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
  sets the experiemnt type to NOESY or ROESY
setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
setNormixes(V3[]) - Method in class org.jmol.shape.Mesh
setNth(int) - Method in class org.jmol.minimize.forcefield.ForceField
setNucleusAndFreq(String, boolean) - Method in class jspecview.source.JDXDataObject
setNullValue(String) - Method in class javajs.util.CifDataParser
  Set the string value of what is returned for "." and "?"
setNumDim(int) - Method in class jspecview.source.JDXDataObject
setO(String, Object) - Method in class org.jmol.viewer.GlobalSettings
setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
setObjectMad10(int, String, int) - Method in class org.jmol.script.ScriptEval
setObjectMad10(int, String, int) - Method in class org.jmol.viewer.Viewer
  input here is a JC.SHAPE_xxxx identifier
setObjectProp(String, int) - Method in class org.jmol.viewer.Viewer
setObjectProperty() - Method in class org.jmol.script.ScriptEval
setObjectPropSafe(String, int) - Method in interface org.jmol.api.JmolScriptEvaluator
setObjectPropSafe(String, int) - Method in class org.jmol.script.ScriptEval
  called by Viewer in setting up a PyMOL scene.
setObjectVisibility(String, boolean) - Method in class org.jmol.viewer.Viewer
setObservedFreq(double) - Method in class jspecview.source.JDXDataObject
  Sets the Observed Frequency (for NMR Spectra)
setObservedNucleus(String) - Method in class jspecview.source.JDXDataObject
setOccupancy(double[], double, double) - Method in class org.jmol.util.ModulationSet
  get the occupancy, first from the reader, then from renderer
setOccupancy(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
setOffset(int) - Method in class org.jmol.modelset.Text
setOffset(int) - Method in class org.jmol.symmetry.Symmetry
setOffsetPt(P3) - Method in class org.jmol.shapespecial.Dipole
setOffsetPt(T3) - Method in interface org.jmol.api.SymmetryInterface
setOffsetPt(T3) - Method in class org.jmol.symmetry.Symmetry
setOptions(Map) - Method in class org.jmol.viewer.Viewer
setOrder(int) - Method in class org.jmol.modelset.Bond
setOrigin(String) - Method in class jspecview.source.JDXHeader
  Sets the origin of the JCAMP-DX spectrum
setOutputChannel(GenericBinaryDocument, OC) - Method in interface org.jmol.jvxl.api.MeshDataServer
setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.shapesurface.Isosurface
setOutputChannel(GenericOutputChannel) - Method in interface javajs.api.GenericBinaryDocument
setOutputChannel(GenericOutputChannel) - Method in class javajs.util.BinaryDocument
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.JvxlReader
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceReader
setOutputStream(OutputStream) - Method in class javajs.export.PDFCreator
setOwner(String) - Method in class jspecview.source.JDXHeader
  Sets the owner
setP(T3) - Method in class javajs.util.T3
setP(PanelData, ScriptToken, String) - Method in class jspecview.common.Parameters
setPanel(JPanel) - Method in class org.openscience.jmol.app.jsonkiosk.KioskFrame
setPanelVisible(boolean) - Method in interface jspecview.api.AppletFrame
setPanelVisible(boolean) - Method in class jspecview.appletjs.JSVApplet
setParallel() - Method in class org.jmol.viewer.ShapeManager
setParallel(boolean) - Method in class org.jmol.viewer.Viewer
setparam - Static variable in class org.jmol.script.T
setParameters(String, Object, BS, Viewer) - Method in class org.jmol.inchi.InchiJmol
setParameters(Spectrum) - Method in class jspecview.export.AMLExporter
setParameters(Spectrum) - Method in class jspecview.export.CMLExporter
setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
setParams(Object[], int[], BS) - Method in class org.jmol.shapebio.BioShape
setParams(String, JSViewer, Spectrum) - Method in class jspecview.dialog.JSVDialog
  required initializer; from JSViewer
setParams(Map) - Method in class javajs.img.GifEncoder
  we allow for animated GIF by being able to re-enter the code with different parameters held in params
setParams(Map) - Method in class javajs.img.ImageEncoder
setParams(Map) - Method in class javajs.img.Jpg64Encoder
setParams(Map) - Method in class javajs.img.JpgEncoder
setParams(Map) - Method in class javajs.img.PdfEncoder
setParams(Map) - Method in class javajs.img.PngEncoder
setParams(Map) - Method in class javajs.img.PpmEncoder
setParams(BytePoster, String, boolean, OutputStream) - Method in class javajs.util.OC
  Set up an output channel.
setParent(Object) - Method in class org.jmol.awtjs.swing.Component
setParentFrame(JFrame) - Method in class jspecview.common.JSViewer
setPartialCharge(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
setPartProperty() - Method in class org.jmol.adapter.smarter.XtalSymmetry
  create property_part for SHELX and CIF loaders
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
setPass2(boolean) - Method in class org.jmol.util.GData
setPath(JSVTreePath) - Method in interface jspecview.api.JSVTree
setPath(JSVTreePath) - Method in class jspecview.application.AwtTree
setPath(JSVTreePath) - Method in class jspecview.tree.SimpleTree
setPdbConectBonding(int, int, BS) - Method in class org.jmol.modelset.ModelSet
SETPEAK - Enum constant in enum class jspecview.common.ScriptToken
setPeakList(Lst, String, String) - Method in class jspecview.common.Spectrum
setPeakList(Parameters, int, ScaleData) - Method in class jspecview.common.PeakData
setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
setPeriodicity(P3[], float) - Method in class org.jmol.render.AxesRenderer
  Uccage only
setPeriodicity(P3[], float) - Method in class org.jmol.render.BbcageRenderer
  Uccage only
setPeriodicity(P3[], float) - Method in class org.jmol.render.UccageRenderer
setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
setPF(Point3fi) - Method in class org.jmol.util.Point3fi
setPhongExponent(int) - Method in class org.jmol.util.GData
  p in I = df * (N dot L) + sf * (R dot V)^p
setPicked(int, boolean) - Method in class org.jmol.viewer.Viewer
setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
setPixelRange(int, int) - Method in class jspecview.common.PeakInfo
setPlaneParameters(P4) - Method in class org.jmol.jvxl.data.VolumeData
setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
  Raw file data planes are passed to us here from VolumeFileReader
setPlanes(float[][]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Planes to use for holding raw file data.
setPlotColors(GenericColor[]) - Method in class jspecview.common.PanelData
setPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setPointer(int, int) - Static method in class org.jmol.viewer.JC
setPointGroup(Viewer, SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in interface org.jmol.api.SymmetryInterface
setPointGroup(Viewer, SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in class org.jmol.symmetry.Symmetry
setPoints(int) - Method in class org.jmol.shape.Axes
setPoints(ModelSet, int[], Point3fi[], TickInfo) - Method in class org.jmol.modelset.Measurement
setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
setPopulationDisplay(PopulationDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
setPopupMenu(boolean, boolean) - Method in class jspecview.common.JSViewer
setPosition(float, float, boolean, float[]) - Method in class org.jmol.modelset.Text
setPrecision() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  Called by PWMAT ALWAYS and CIFReader as well if a double-precision value for alpha is found.
setPrecision(float) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
setPrecision(float) - Method in class org.jmol.util.SimpleUnitCell
setPreferredScrollableViewportSize(Dimension) - Method in class org.jmol.awtjs.swing.JTable
setPreferredSize(int, int) - Method in interface jspecview.api.PlatformDialog
setPreferredSize(int, int) - Method in class jspecview.java.AwtDialog
setPreferredSize(int, int) - Method in class jspecview.js2d.JsDialog
setPreferredSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
setPreferredWidth(int) - Method in interface org.jmol.awtjs.swing.TableColumn
setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
setPreviewOptions(boolean) - Method in class org.jmol.dialog.FilePreview
setPrevNode(CLEG.ClegNode) - Method in class org.jmol.symmetry.CLEG.ClegData
setPrimitive(int) - Method in class org.jmol.smiles.SmilesBond
setPrint(PrintLayout, String) - Method in class jspecview.common.PanelData
setProcessingMenu(JComponent) - Method in class jspecview.application.ApplicationMenu
setProp(String, Object, BS) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setPropAS(String, Object, BS) - Method in class org.jmol.shape.AtomShape
setPropBSC(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
setProperties(Object) - Method in class org.jmol.shape.Shape
setProperties(Properties) - Method in class jspecview.app.JSVAppPro
setProperties(Properties) - Method in class jspecview.application.JSpecView
setProperties(Properties) - Method in interface org.jmol.api.JSVInterface
setProperties(Properties) - Method in class org.openscience.jmol.app.status.StatusListener
setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
setProperty(String, Object) - Method in class org.jmol.modelkit.ModelKit
  Modify the state by setting a property.
setProperty(String, Object, BS) - Method in class org.jmol.shape.Axes
setProperty(String, Object, BS) - Method in class org.jmol.shape.Balls
setProperty(String, Object, BS) - Method in class org.jmol.shape.Bbcage
setProperty(String, Object, BS) - Method in class org.jmol.shape.Echo
setProperty(String, Object, BS) - Method in class org.jmol.shape.Frank
setProperty(String, Object, BS) - Method in class org.jmol.shape.Halos
setProperty(String, Object, BS) - Method in class org.jmol.shape.Hover
setProperty(String, Object, BS) - Method in class org.jmol.shape.Labels
setProperty(String, Object, BS) - Method in class org.jmol.shape.Measures
setProperty(String, Object, BS) - Method in class org.jmol.shape.Shape
setProperty(String, Object, BS) - Method in class org.jmol.shape.Stars
setProperty(String, Object, BS) - Method in class org.jmol.shape.Sticks
setProperty(String, Object, BS) - Method in class org.jmol.shape.Uccage
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Backbone
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShape
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Trace
setProperty(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dipoles
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dots
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Ellipsoids
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Polyhedra
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Vectors
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Contact
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.LcaoCartoon
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.MolecularOrbital
setProperty(String, String) - Method in class jspecview.common.JSViewer
setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
setPropertyColorRangeData(float[], BS) - Method in class org.jmol.viewer.ColorManager
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
setPropFLS(String, Object) - Method in class org.jmol.shape.FontLineShape
setPropI(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
setPropMC(String, Object, BS) - Method in class org.jmol.shape.MeshCollection
setPropS(String, Object, BS) - Method in class org.jmol.shape.Shape
setPropTS(String, Object, BS) - Method in class org.jmol.shape.TextShape
setProteinStructureType(STR, int) - Method in class org.jmol.modelset.Group
setProteinStructureType(STR, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
setProteinType(BS, STR) - Method in class org.jmol.modelset.ModelSet
setProteinType(STR, BS) - Method in class org.jmol.viewer.Viewer
setPt2(double, double) - Method in class jspecview.common.Measurement
setPt2(Spectrum, boolean) - Method in class jspecview.common.Measurement
setRadius(float) - Method in class org.jmol.modelset.Atom
setRandom(boolean) - Method in class javajs.util.BinaryDocument
setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
setRastAB(int, int, int, int) - Method in class org.jmol.g3d.PrecisionRenderer
setRastABFloat(float, float, float, float) - Method in class org.jmol.g3d.PrecisionRenderer
setReader(CifReader) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
  filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb
setRecentMenu(Lst) - Method in class jspecview.application.ApplicationMenu
setRecentSimulation(String) - Method in class jspecview.common.JSViewer
setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setRef(Quat) - Method in class javajs.util.Quat
setRenderVars() - Method in class org.jmol.render.LabelsRenderer
setRequiredFile(String, String) - Method in interface org.jmol.jvxl.api.MeshDataServer
setRequiredFile(String, String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setRequiredFile(String, String) - Method in class org.jmol.shapesurface.Isosurface
setResno(int) - Method in class org.jmol.modelset.Group
setReturnLst(Lst) - Method in class org.jmol.symmetry.CLEG.ClegData
setReturnMap(Map) - Method in class org.jmol.symmetry.CLEG.ClegData
setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
setRhoStar(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setRightComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
setRingData(int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
setRingsClickable() - Method in class org.jmol.modelsetbio.NucleicMonomer
setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
setRingsVisible(boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
setRotation(M3) - Method in class org.jmol.viewer.TransformManager
setRotationMatrix(M3) - Method in class org.jmol.g3d.Graphics3D
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelSet
setRotationScale(M3) - Method in class javajs.util.M4
  Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.
setRotationX(float) - Method in class com.sparshui.common.messages.events.SpinEvent
setRotationY(float) - Method in class com.sparshui.common.messages.events.SpinEvent
setRotationZ(float) - Method in class com.sparshui.common.messages.events.SpinEvent
setRow(int, float, float, float) - Method in class javajs.util.M3
  Sets the specified row of this matrix3d to the three values provided.
setRow33(int, float[]) - Method in class javajs.util.M34
setRowA(int, float[]) - Method in class javajs.util.M3
  Sets the specified row of this matrix3d to the four values provided.
setRowA(int, float[]) - Method in class javajs.util.M4
  Sets the specified row of this matrix4f to the four values provided.
setRowSelectionAllowed(boolean) - Method in class org.jmol.awtjs.swing.JTable
setRowSelectionInterval(int, int) - Method in class org.jmol.awtjs.swing.JTable
setRowV(int, T3) - Method in class javajs.util.M3
  Sets the specified row of this matrix3d to the Vector provided.
setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
setRule6Full(boolean) - Method in class org.jmol.symmetry.CIPData
setScale() - Method in class org.jmol.viewer.ShapeManager
setScale(float) - Method in class javajs.util.M3
  Sets this Matrix3f to a scalar * Identity.
setScale(float) - Method in class org.jmol.modelset.Text
setScale(float, boolean) - Method in class org.jmol.shapespecial.Ellipsoid
setScale(int, int, int, boolean) - Method in class jspecview.common.ViewData
setScalePixelsPerMicron(float) - Method in class org.jmol.modelset.Text
setScreenDimension(int, int) - Method in interface javajs.api.JSInterface
setScreenDimension(int, int) - Method in class jspecview.appletjs.JSVApplet
setScreenDimension(int, int) - Method in class jspecview.common.JSViewer
setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
setScreenDimension(int, int) - Method in class org.jmol.util.GenericApplet
setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
setScript(String) - Method in class org.jmol.modelset.Text
setScriptArguments(Object, boolean) - Method in class org.jmol.script.ScriptParam
setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
setSelected(boolean) - Method in interface org.jmol.api.SC
setSelected(boolean) - Method in class org.jmol.awt.AwtSwingComponent
setSelected(boolean) - Method in class org.jmol.awtjs.swing.AbstractButton
setSelected(Object, boolean) - Method in interface jspecview.api.PlatformDialog
setSelected(Object, boolean) - Method in class jspecview.java.AwtDialog
setSelected(Object, boolean) - Method in class jspecview.js2d.JsDialog
setSelected(String, boolean) - Method in class jspecview.popup.JSVGenericPopup
setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
setSelected(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this check box's selection has been changed.
setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
setSelectedAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
setSelectedIndex(int) - Method in class org.jmol.awtjs.swing.JComboBox
setSelectedIndex(Object, int) - Method in interface jspecview.api.PlatformDialog
setSelectedIndex(Object, int) - Method in class jspecview.java.AwtDialog
setSelectedIndex(Object, int) - Method in class jspecview.js2d.JsDialog
setSelectedIndex(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this combo box's selected item has been changed.
setSelectedIntegral(double) - Method in class jspecview.common.PanelData
setSelectedIntegral(Measurement, double) - Method in class jspecview.common.IntegralData
setSelectedPanel(ScriptInterface, JSVPanel) - Method in interface jspecview.api.JSVTree
setSelectedPanel(ScriptInterface, JSVPanel) - Method in class jspecview.application.AwtTree
setSelectedPanel(ScriptInterface, JSVPanel) - Method in class jspecview.tree.SimpleTree
setSelectedPanel(JSViewer, JSVPanel, Lst) - Method in interface jspecview.api.JSVMainPanel
setSelectedPanel(JSViewer, JSVPanel, Lst) - Method in class jspecview.java.AwtMainPanel
setSelectedPanel(JSViewer, JSVPanel, Lst) - Method in class jspecview.js2d.JsMainPanel
setSelectedPeak(PeakInfo) - Method in class jspecview.common.Spectrum
setSelectionHalos(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
setSelectionHalosEnabled(boolean) - Method in class org.jmol.viewer.Viewer
setSelections(boolean, boolean, boolean, JSVPanel) - Method in class jspecview.application.ApplicationMenu
setSelectionSet(BS) - Method in class org.jmol.api.JmolViewer
setSelectionSet(BS) - Method in class org.jmol.viewer.Viewer
setSelectionSubset(BS) - Method in class org.jmol.viewer.SelectionManager
setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
setShapeId(int, int, boolean) - Method in class org.jmol.scriptext.ScriptExt
setShapeNameParameter(int) - Method in class org.jmol.script.ScriptEval
setShapeProperties(int, Object[]...) - Method in class org.jmol.viewer.ShapeManager
setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEval
setShapeProperty(int, String, Object) - Method in class org.jmol.scriptext.ScriptExt
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.script.ScriptEval
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.viewer.ShapeManager
setShapeSize(int, int, BS) - Method in class org.jmol.viewer.Viewer
setShapeSizeBs(int, int, BS) - Method in class org.jmol.script.ScriptEval
setShapeSizeBs(int, int, RadiusData, BS) - Method in class org.jmol.viewer.ShapeManager
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shape.Shape
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.Backbone
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.BioShapeCollection
setShapeTranslucency(int, String, String, float, BS) - Method in class org.jmol.script.ScriptEval
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
setShifts() - Method in class org.jmol.render.AxesRenderer
setShifts() - Method in class org.jmol.render.BbcageRenderer
setShifts() - Method in class org.jmol.render.UccageRenderer
setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
setShowWithin(Lst, float, boolean) - Method in class org.jmol.shape.Mesh
setSigma(String, Matrix) - Method in class org.jmol.symmetry.SymmetryOperation
  Sets sigma and the subsystem code for modulated CIF
setSimpleCage(SymmetryInterface) - Method in class org.jmol.modelset.Model
setSimulated(String) - Method in class jspecview.common.Spectrum
setSite(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
setSize(int, BS) - Method in class org.jmol.shape.AtomShape
setSize(int, BS) - Method in class org.jmol.shape.Balls
setSize(int, BS) - Method in class org.jmol.shape.Measures
setSize(int, BS) - Method in class org.jmol.shape.Shape
setSize(int, BS) - Method in class org.jmol.shape.Sticks
  sets the size of a bond, or sets the selectedBonds set
setSize(int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
setSize2(int, BS) - Method in class org.jmol.shape.AtomShape
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.AtomShape
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Balls
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Shape
setSizeRD(RadiusData, BS) - Method in class org.jmol.shapespecial.Dots
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shape.AtomShape
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shapespecial.Vectors
setSlab(int) - Method in interface org.jmol.api.JmolGraphicsInterface
setSlab(int) - Method in class org.jmol.export.Export3D
setSlab(int) - Method in class org.jmol.util.GData
  clipping from the front and the back
setSlabAndZShade(int, int, int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.export.Export3D
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.util.GData
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
  set internal slab or depth from screen-based slab or depth
setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.AdfReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.AmsReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.DgridReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  after the vectors intinfo and floatinfo are completed, we
setSmilesString(String) - Method in class org.jmol.viewer.Viewer
setSolutionColor(String) - Method in class jspecview.common.PanelData
setSortingStatus(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
setSourceEnabled(boolean) - Method in class jspecview.application.ApplicationMenu
setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
setSpaceGroup(int, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
  Set up all the model-related fields in association with a new space group.
setSpaceGroupName(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setSpaceGroupName(String) - Method in interface org.jmol.api.SymmetryInterface
setSpaceGroupName(String) - Method in class org.jmol.symmetry.Symmetry
setSpaceGroupTo(Object) - Method in interface org.jmol.api.SymmetryInterface
setSpaceGroupTo(Object) - Method in class org.jmol.symmetry.Symmetry
setSpecForIRMode(Spectrum) - Method in class jspecview.common.PanelData
setSpecShift(double) - Method in interface jspecview.api.AnnotationData
setSpecShift(double) - Method in class jspecview.common.IntegralData
setSpecShift(double) - Method in class jspecview.common.MeasurementData
setSpecShift(double) - Method in class jspecview.dialog.JSVDialog
setSpectrum(int, boolean) - Method in class jspecview.common.PanelData
setSpectrumNumber(int) - Method in interface jspecview.api.JSVAppletInterface
  Sets the spectrum to the specified block number
setSpectrumNumber(int) - Method in class jspecview.app.JSVApp
  Sets the spectrum to the specified block number
setSpectrumNumber(int) - Method in class jspecview.appletjs.JSVApplet
setSpectrumPeaks(int, String, String) - Method in class jspecview.source.JDXReader
setSpectrumPeaks(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
setSpectrumPeaks(int, String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
setSpecular(boolean) - Method in class org.jmol.util.GData
setSpecularExponent(int) - Method in class org.jmol.util.GData
  log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
setSpecularPercent(int) - Method in class org.jmol.util.GData
  sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
setSpecularPower(int) - Method in class org.jmol.util.GData
  fractional distance to white for specular dot
setSphereMatrix(T3, float, float, float, A4, M4) - Method in class org.jmol.export.__CartesianExporter
setSpin(String) - Method in class org.jmol.symmetry.SymmetryOperation
setSpin(String, int) - Method in class org.jmol.viewer.Viewer
setSpinAxisAngle(A4) - Method in interface org.jmol.api.SymmetryInterface
setSpinAxisAngle(A4) - Method in class org.jmol.symmetry.Symmetry
setSpinAxisAngle(A4) - Method in class org.jmol.symmetry.UnitCell
setSpinList(String) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
setSpinList(String) - Method in class org.jmol.symmetry.SpaceGroup
setSpinOff() - Method in class org.jmol.viewer.TransformManager
setSpinOn() - Method in class org.jmol.viewer.TransformManager
setSplitFrame(int, int) - Method in class org.jmol.viewer.AnimationManager
setSplitFrameMouse(int) - Method in class org.jmol.viewer.AnimationManager
  Adjust x-value of mouse action to be offset by the frame offset.
setState(boolean) - Method in interface jspecview.api.AnnotationData
setState(boolean) - Method in class jspecview.common.MeasurementData
setState(boolean) - Method in class jspecview.dialog.JSVDialog
setState(int) - Method in class com.sparshui.server.TouchPoint
setStatement(T[], int) - Method in class org.jmol.script.ScriptEval
  provides support for @x and @{....} in statements.
setStateScriptVersion(Viewer, String) - Static method in class org.jmol.script.ScriptManager
setStatic(int, int) - Method in interface org.jmol.api.JmolScriptEvaluator
setStatic(int, int) - Method in class org.jmol.script.ScriptEval
  set a static variable, with checking for range
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
setStatusAtomMoved(boolean, BS) - Method in class org.jmol.viewer.Viewer
setStatusAtomPicked(int, String, Map, boolean) - Method in class org.jmol.viewer.Viewer
setStatusDragDropped(int, int, int, String, String[]) - Method in interface javajs.api.JSInterface
setStatusDragDropped(int, int, int, String, String[]) - Method in class jspecview.appletjs.JSVApplet
setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.util.GenericApplet
setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.viewer.Viewer
  Allows a handler to set Jmol variable doDrop=false to cancel and also set the file type directly (Java) via the Jmol variable dropFileType (Java or JavaScript) if desired.
setStatusListener(JmolStatusListener) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setStatusListener(JSVInterface) - Method in class jspecview.application.JSpecView
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
setStatusPicked(int, T3, Map) - Method in class org.jmol.shape.MeshCollection
setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
  resizeCallback is called whenever the applet gets a resize notification from the browser jmolSetCallback("resizeCallback", "myResizeCallback") function myResizeCallback(width, height) {}
setStatusSelect(BS) - Method in class org.jmol.viewer.Viewer
  Make the SelectCallback call and reset the hasSelected value to false.
setStatusStructureModified(int, int, int, String, int, BS) - Method in class org.jmol.viewer.StatusManager
setStereo(boolean, Object) - Method in class org.jmol.viewer.Viewer
setStereo0D(int) - Method in interface org.iupac.InChIStructureProvider
setStereo0D(int) - Method in class org.jmol.inchi.InChIJNA
setStereo0D(int) - Method in class org.jmol.inchi.InChIJS
setStereoGraphics(boolean) - Method in interface org.jmol.api.JmolAppletInterface
setStereoGraphics(boolean) - Method in class org.jmol.util.GenericApplet
setStereoMode(int[], STER, float) - Method in class org.jmol.viewer.Viewer
setStrandCount() - Method in class org.jmol.renderbio.StrandsRenderer
setStream(BufferedInputStream, boolean) - Method in interface javajs.api.GenericBinaryDocument
setStream(BufferedInputStream, boolean) - Method in class javajs.util.BinaryDocument
setStream(OutputStream) - Method in class org.jmol.util.JSONWriter
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
setStreamData(DataInputStream, boolean) - Method in interface javajs.api.GenericBinaryDocument
setStreamData(DataInputStream, boolean) - Method in class javajs.util.BinaryDocument
setString(String) - Method in class javajs.util.CifDataParser
  sets global str and line to be parsed from the beginning \1 ....
setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
setStringProperty(String, String) - Method in class org.jmol.script.ScriptParam
setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
setStrokeBold(Object, boolean) - Method in class jspecview.common.PDFWriter
setStrokeBold(Object, boolean) - Method in class jspecview.java.AwtG2D
setStrokeBold(Object, boolean) - Method in class jspecview.js2d.JsG2D
setStrokeBold(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
setStrokeBold(Object, boolean) - Method in class org.jmol.awt.AwtG2D
setStrokeBold(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
setStrucNo(int) - Method in class org.jmol.modelset.Group
setStrucNo(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
setStrucNo(int) - Method in class org.jmol.modelsetbio.Monomer
setStructure(String, Translator) - Method in class org.jmol.popup.PopupResource
setStructureBS(int, int, STR, BS, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
  bits in the bitset determines the type
setStructureIndexes() - Method in class org.jmol.modelset.ModelSet
  ///////// state definition ///////////
setStructureList(float[], STR) - Method in class org.jmol.viewer.GlobalSettings
setStructureList(float[], STR) - Method in class org.jmol.viewer.Viewer
setStructureList(Map) - Method in class org.jmol.modelset.ModelSet
setStructureList(Map) - Method in class org.jmol.modelsetbio.AminoPolymer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.BackboneRenderer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.CartoonRenderer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.MeshRibbonRenderer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.RibbonsRenderer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.RocketsRenderer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.StrandsRenderer
setStrutPoint(Atom, Point3fi) - Method in class org.jmol.renderbio.TraceRenderer
setSubstituent(String) - Method in class jme.JME
setSurfaceInfo(P4, P3, int, String) - Method in class org.jmol.jvxl.data.JvxlData
setSurfaceInfoFromBitSet(BS, P4) - Method in class org.jmol.jvxl.data.JvxlData
setSurfaceInfoFromBitSetPts(BS, P4, P3) - Method in class org.jmol.jvxl.data.JvxlData
setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
  Sets the symbol of the atm.
setSymmetry(SymmetryInterface) - Method in class org.jmol.symmetry.CLEG.ClegData
setSymmetryFromAuditBlock(XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setSymmetryInfoFromFile(ModelSet, int, float[]) - Method in class org.jmol.symmetry.Symmetry
  Set space group and unit cell from the auxiliary info generated by XtalSymmetry specific to a given model.
setSymmetryMinMax(P3, P3, P3) - Static method in class org.jmol.symmetry.UnitCell
setSymmetryOperator(String) - Method in class org.jmol.adapter.readers.cif.CifReader
setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setSymop(int, boolean) - Method in class org.jmol.modelset.Atom
setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
setT(T3) - Method in class javajs.util.T3
  Sets the value of this tuple to the value of the Tuple3f argument.
setT(T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the value of the Tuple3d argument.
setT(T3i) - Method in class javajs.util.T3i
  Sets the value of this tuple to the value of tuple t1.
setTA(T3, float) - Method in class javajs.util.Quat
  q = (cos(theta/2), sin(theta/2) * n)
settable - Static variable in class org.jmol.script.T
setTableHeader(JTableHeader) - Method in class org.openscience.jmol.app.janocchio.TableSorter
setTableModel(TableModel) - Method in class org.openscience.jmol.app.janocchio.TableSorter
setTainted(boolean) - Method in class org.jmol.viewer.Viewer
setTaintedAll() - Method in class jspecview.common.PanelData
setTaintedAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
setTemplate(String, String) - Method in class jme.JME
setTempVertex(T3, T3, T3) - Static method in class org.jmol.export.___Exporter
setTensor(Tensor) - Method in class org.jmol.shapespecial.Ellipsoid
setTensors() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setText(Object, String) - Method in interface jspecview.api.PlatformDialog
setText(Object, String) - Method in class jspecview.java.AwtDialog
setText(Object, String) - Method in class jspecview.js2d.JsDialog
setText(String) - Method in class jme.JME
setText(String) - Method in interface org.jmol.api.JmolAbstractButton
setText(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
setText(String) - Method in interface org.jmol.api.SC
setText(String) - Method in class org.jmol.awt.AwtSwingComponent
setText(String) - Method in class org.jmol.awtjs.swing.Component
setText(String) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this component's text has been changed.
setText(String) - Method in interface org.jmol.console.GenericTextArea
setText(String) - Method in class org.jmol.modelset.Text
setText(String, String) - Method in class org.jmol.popup.GenericPopup
setTextPosition(int) - Method in class org.jmol.util.GData
setThreshold(double) - Method in class jspecview.dialog.JSVDialog
setTime(String) - Method in class jspecview.source.JDXHeader
  Sets the time the file was created
setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
setTimeout(Viewer, Map, String, int, String) - Static method in class org.jmol.thread.TimeoutThread
setTitle() - Method in class org.jmol.console.GenericConsole
setTitle() - Method in class org.jmol.console.JmolConsole
setTitle() - Method in class org.jmol.consolejs.AppletConsole
setTitle(Object) - Method in class org.jmol.shape.MeshCollection
setTitle(Object) - Method in class org.jmol.shapespecial.Draw
setTitle(String) - Method in interface jspecview.api.JSVViewPanel
setTitle(String) - Method in interface jspecview.api.PlatformDialog
setTitle(String) - Method in class jspecview.common.PanelData
setTitle(String) - Method in class jspecview.java.AwtMainPanel
setTitle(String) - Method in class jspecview.java.AwtPanel
setTitle(String) - Method in class jspecview.js2d.JsMainPanel
setTitle(String) - Method in class jspecview.js2d.JsPanel
setTitle(String) - Method in class jspecview.source.JDXHeader
  Sets the title of the spectrum
setTitle(String) - Method in interface org.jmol.api.js.JSConsole
setTitle(String) - Method in class org.jmol.awtjs.swing.JDialog
setToAA(A4) - Method in class javajs.util.M4
  Sets the rotational component (upper 3x3) of this matrix to a rotation given by an axis angle
setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
setToM3(M34) - Method in class javajs.util.M4
  Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are initialized as if this were an identity matrix (ie, affine matrix with no translational component).
setToolTipText(String) - Method in interface jspecview.api.JSVPanel
setToolTipText(String) - Method in class jspecview.common.PanelData
setToolTipText(String) - Method in class jspecview.js2d.JsPanel
setToolTipText(String) - Method in interface org.jmol.api.JmolAbstractButton
setTopoAtom(int, int, String, int, int) - Method in class org.jmol.smiles.SmilesAtom
setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, Node[], boolean) - Method in class org.jmol.smiles.SmilesStereo
setTorsionData(T3, T3, T3, T3, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
  calculate temporary points
setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
setTrajectoryBs(BS) - Method in class org.jmol.modelset.ModelSet
setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setTranslation(T3) - Method in class javajs.util.M4
  Modifies the translational components of this matrix to the values of the Vector3f argument; the other values of this matrix are not modified.
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setTranslucent(float, boolean) - Method in class org.jmol.modelset.Text
setTranslucentVertices(BS) - Method in class org.jmol.util.MeshSurface
  Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygons
setTransparentCursor(Object) - Method in class jspecview.java.AwtPlatform
setTransparentCursor(Object) - Method in class jspecview.js2d.JsPlatform
setTransparentCursor(Object) - Method in interface org.jmol.api.GenericPlatform
setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
setTransparentCursor(Object) - Method in class org.jmol.awtjs2d.Platform
setTreeNode(JSVTreeNode) - Method in class jspecview.common.PanelNode
setTurn() - Method in class org.jmol.shapebio.Rockets
setType(int) - Method in class org.jmol.util.Vibration
setType(String) - Method in class javajs.util.OC
setType(String) - Method in class org.jmol.util.Tensor
  Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.
setU(Atom, int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setUndoMax(int) - Method in class org.jmol.viewer.StateManager
setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setUnitCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
setUnitCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
setUnitCellAtomIndex(int) - Method in class org.jmol.viewer.AnimationManager
setUnitCellAtomIndex(int) - Method in class org.jmol.viewer.Viewer
setUnitCellFromParams(float[], boolean, float) - Method in interface org.jmol.api.SymmetryInterface
setUnitCellFromParams(float[], boolean, float) - Method in class org.jmol.symmetry.Symmetry
setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setUnits(String, boolean) - Method in class org.jmol.viewer.Viewer
setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
setup(int, float[], P3[], BS) - Method in class org.jmol.quantum.MepCalculation
setup(String, Map, Object) - Method in class org.jmol.adapter.readers.cif.BCIFReader
  binary must set up initially
setup(String, Map, Object) - Method in class org.jmol.adapter.readers.cif.MMTFReader
  standard set up
setup(String, Map, Object) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
setup(String, Map, Object) - Method in class org.jmol.adapter.readers.more.MdCrdReader
setup(String, Map, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
setup(String, Map, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setup(JSViewer, Spectrum, OC, int, int) - Method in class jspecview.export.AMLExporter
setup(JSViewer, Spectrum, OC, int, int) - Method in class jspecview.export.CMLExporter
setup(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
setupAC() - Method in class org.jmol.modelset.AtomCollection
setupArrays() - Method in class org.jmol.modelset.Model
setupASCR(String, Map, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setupBC() - Method in class org.jmol.modelset.BondCollection
setupCalculation(Map, boolean, VolumeData, BS, T3[], Atom[], int, int[][], float[], float[], boolean, float[][], T3[]) - Method in class org.jmol.quantum.MOCalculation
setupCalculation(VolumeData, BS, BS, BS[], T3[], int, boolean, T3[], float[], int) - Method in class org.jmol.quantum.NciCalculation
setupConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setupConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setupCoordinates(float[], float[], BS, T3[], Atom[], T3[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
setupDisplay() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setupDisplay() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setupDnD() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setupDnD() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setupLabels(Map) - Method in class org.jmol.console.GenericConsole
setupLabels0(Map) - Method in class org.jmol.console.GenericConsole
setupLabels0(Map) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setupPS(AlphaPolymer, STR, int, int) - Method in class org.jmol.modelsetbio.ProteinStructure
setupRR(BioShape, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
setupUI(boolean) - Method in class org.jmol.dialog.Dialog
setupUIManager() - Static method in class org.jmol.dialog.Dialog
  Setup the UIManager (for i18n)
setUseNumberLocalization(boolean) - Static method in class javajs.util.DF
setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
setUserStatusListener(JmolStatusListener) - Method in class org.openscience.jmol.app.status.StatusListener
setUserVariable(String, SV) - Method in class org.jmol.viewer.GlobalSettings
setUserYFactor(double) - Method in class jspecview.common.Spectrum
  Set by JSViewer
setV0() - Method in class org.jmol.util.Vibration
setVA(V3, float) - Method in class javajs.util.A4
  Sets the value of this AxisAngle4f to the specified axis and angle.
setValence(int) - Method in class org.jmol.modelset.Atom
setValence(int) - Method in class org.jmol.smiles.SmilesAtom
setValue(double) - Method in class jspecview.common.Measurement
setValueAt(Object, int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
setValues(LabelToken[], Map) - Static method in class org.jmol.modelset.LabelToken
setVariable(int, int, String, boolean) - Method in class org.jmol.script.ScriptEval
setVarName(String) - Method in class jspecview.source.JDXDataObject
  From ##VARNAME
setVectorAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
setVectorScale(float) - Method in class org.jmol.api.JmolViewer
setVectorScale(float) - Method in class org.jmol.viewer.Viewer
setVertexAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
  sets the period of vibration -- period > 0: sets the period and turns -- period invalid input: '<' 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Double.NaN: uses current setting (frame change)
setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
setViewer(JFrame, Viewer, Container) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
setViewer(PlatformViewer, Object) - Method in class jspecview.java.AwtPlatform
setViewer(PlatformViewer, Object) - Method in class jspecview.js2d.JsPlatform
setViewer(PlatformViewer, Object) - Method in interface org.jmol.api.GenericPlatform
setViewer(PlatformViewer, Object) - Method in class org.jmol.awt.Platform
setViewer(PlatformViewer, Object) - Method in class org.jmol.awtjs2d.Platform
setViewer(Viewer) - Method in class org.jmol.adapter.writers.MOLWriter
setViewer(Viewer) - Method in interface org.jmol.api.JmolJSpecView
setViewer(Viewer) - Method in interface org.jmol.api.JmolNMRInterface
setViewer(Viewer) - Method in interface org.jmol.api.JmolPropertyManager
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptEvaluator
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptManager
setViewer(Viewer) - Method in class org.jmol.console.GenericConsole
setViewer(Viewer) - Method in class org.jmol.jsv.JSV
setViewer(Viewer) - Method in class org.jmol.modelsetbio.BioResolver
setViewer(Viewer) - Method in class org.jmol.quantum.NMRCalculation
setViewer(Viewer) - Method in class org.jmol.script.ScriptEval
setViewer(Viewer) - Method in class org.jmol.script.ScriptManager
setViewer(Viewer) - Method in class org.jmol.viewer.PropertyManager
setViewer(Viewer) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setViewer(Viewer, String) - Method in interface org.jmol.api.SymmetryInterface
  for Viewer.getSymStatic only
setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
setViewer(Viewer, String) - Method in class org.jmol.symmetry.Symmetry
setViewer(Viewer, String) - Method in class org.jmol.thread.JmolThread
setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
setViewerG3dShapeID(Viewer, int) - Method in class org.jmol.render.ShapeRenderer
setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
setVisibilityInfo() - Method in class org.jmol.shape.Measures
setVisible(boolean) - Method in interface jspecview.api.JSVAppInterface
setVisible(boolean) - Method in interface jspecview.api.PlatformDialog
setVisible(boolean) - Method in class jspecview.app.JSVApp
setVisible(boolean) - Method in class jspecview.dialog.JSVDialog
setVisible(boolean) - Method in class jspecview.java.AwtDialog
setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
setVisible(boolean) - Method in interface org.jmol.api.js.JSConsole
setVisible(boolean) - Method in class org.jmol.awtjs.swing.Component
setVisible(boolean) - Method in class org.jmol.awtjs.swing.JDialog
setVisible(boolean) - Method in class org.jmol.console.AppletConsole
setVisible(boolean) - Method in class org.jmol.console.GenericConsole
setVisible(boolean) - Method in class org.jmol.console.JmolConsole
setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
setVisible(boolean) - Method in class org.jmol.consolejs.AppletConsole
setVisible(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
setVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
setVisible(boolean) - Method in interface org.openscience.jmol.app.JmolPlugin
setVisible(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this component's text has been changed.
setVolumeDataV(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
setVoxelDataAsArray(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
  for sparse data mapping, as for a plane
setWhiteSpace(boolean) - Method in class org.jmol.util.JSONWriter
setWidthHeight(boolean) - Method in class org.jmol.util.GData
setWidthHeightVar() - Method in class org.jmol.viewer.Viewer
setWindow(int, int, float) - Method in class org.jmol.modelset.Text
setWindowDimensions(float[]) - Method in class org.jmol.viewer.Viewer
setWindowParameters(int, int) - Method in class jspecview.common.PDFWriter
  /////// defer to JsG2D ///////
setWindowParameters(int, int) - Method in class jspecview.java.AwtG2D
setWindowParameters(int, int) - Method in class jspecview.js2d.JsG2D
setWindowParameters(int, int) - Method in interface org.jmol.api.GenericGraphics
setWindowParameters(int, int) - Method in class org.jmol.awt.AwtG2D
setWindowParameters(int, int) - Method in class org.jmol.awtjs2d.JsG2D
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
setWinParams(int, int, boolean) - Method in class org.jmol.util.GData
setWriteNullAsString(boolean) - Method in class org.jmol.util.JSONWriter
  Set option to write a null as the string "null" or just null itself.
setX(float) - Method in class com.sparshui.common.messages.events.TouchEvent
SETX - Enum constant in enum class jspecview.common.ScriptToken
setXFactor(double) - Method in class jspecview.source.JDXDataObject
  Sets the original xfactor, from JDXReader and XMLReader
setXLabel(String) - Method in class jspecview.source.JDXDataObject
setXPointers(Spectrum, double, Spectrum, double) - Method in class jspecview.common.PanelData
setXRangeForSubSpectrum(Coordinate[]) - Method in class jspecview.common.ViewData
setXRot(float) - Method in class javajs.util.M34
setXUnits(String) - Method in class jspecview.source.JDXDataObject
  Sets the units for the x axis
setXVal(double) - Method in class jspecview.common.Coordinate
  Sets the x value of the coordinate
setXYA(float[], int) - Method in class org.jmol.modelset.Text
setXYCoords(Coordinate[]) - Method in class jspecview.source.JDXDataObject
  Sets the array of coordinates
setXYZ(P3, boolean) - Method in class org.jmol.modelset.Text
setXYZ(T3) - Method in class org.jmol.util.ModulationSet
setXYZ(T3) - Method in class org.jmol.util.Vibration
setXYZBohr(T3[]) - Method in class org.jmol.quantum.QuantumCalculation
setXYZs(int, int, int, int) - Method in class org.jmol.modelset.Text
setY(float) - Method in class com.sparshui.common.messages.events.TouchEvent
setY2D(double) - Method in class jspecview.source.JDXDataObject
setY2DUnits(String) - Method in class jspecview.source.JDXDataObject
setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
setYFactor(double) - Method in class jspecview.source.JDXDataObject
  Sets the original y factor, from JDXReader and XMLReader
setYLabel(String) - Method in class jspecview.source.JDXDataObject
setYRot(float) - Method in class javajs.util.M34
setYStackOffsetPercent(int) - Method in class jspecview.common.PanelData
setYUnits(String) - Method in class jspecview.source.JDXDataObject
  Sets the units for the y axis
setYVal(double) - Method in class jspecview.common.Coordinate
  Sets the y value of the coordinate
setYVal2(double) - Method in class jspecview.common.Measurement
setZero() - Method in class javajs.util.M3
  Sets this matrix to all zeros.
setZero() - Method in class javajs.util.M4
  Sets this matrix to all zeros.
setZeroOffset(float) - Method in class org.jmol.shapespecial.Polyhedron
setZIndex(int) - Method in class org.jmol.awtjs.swing.JDialog
setZoom(double, double, double, double) - Method in class jspecview.common.PanelData
setZoomHeight(boolean, boolean) - Method in class org.jmol.viewer.TransformManager
setZPosition(int, int) - Static method in class org.jmol.viewer.JC
setZRot(float) - Method in class javajs.util.M34
setZs(int, int) - Method in class org.jmol.modelset.Text
sfIndex - Variable in class org.jmol.symmetry.SpaceGroup
  just while SpaceGroupFinder is sorting
sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
sg - Variable in class org.jmol.shapesurface.Isosurface
SG_AS_STRING - Static variable in class org.jmol.viewer.JC
SG_CALC_ONLY - Static variable in class org.jmol.viewer.JC
SG_CHECK_SUPERCELL - Static variable in class org.jmol.viewer.JC
SG_FROM_SCRATCH - Static variable in class org.jmol.viewer.JC
SG_IS_ASSIGN - Static variable in class org.jmol.viewer.JC
sgName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
SHADE_INDEX_LAST - Static variable in class org.jmol.util.Shader
SHADE_INDEX_NOISY_LIMIT - Static variable in class org.jmol.util.Shader
SHADE_INDEX_NORMAL - Static variable in class org.jmol.util.Shader
shader - Variable in class org.jmol.util.GData
Shader - Class in org.jmol.util
  All functions.
Shader() - Constructor for class org.jmol.util.Shader
shader_path - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
shape - Variable in class org.jmol.render.ShapeRenderer
shape - Static variable in class org.jmol.script.T
Shape - Class in org.jmol.shape
  Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
Shape() - Constructor for class org.jmol.shape.Shape
SHAPE_AXES - Static variable in class org.jmol.viewer.JC
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_BALLS - Static variable in class org.jmol.viewer.JC
  /////////////////////////////////////////////////////////////
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JC
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JC
SHAPE_CGO - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_CONTACT - Static variable in class org.jmol.viewer.JC
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JC
SHAPE_DOTS - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_DRAW - Static variable in class org.jmol.viewer.JC
SHAPE_ECHO - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JC
SHAPE_FRANK - Static variable in class org.jmol.viewer.JC
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_HALOS - Static variable in class org.jmol.viewer.JC
SHAPE_HOVER - Static variable in class org.jmol.viewer.JC
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JC
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_LABELS - Static variable in class org.jmol.viewer.JC
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JC
SHAPE_MAX - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JC
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_MIN_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_MO - Static variable in class org.jmol.viewer.JC
SHAPE_NBO - Static variable in class org.jmol.viewer.JC
SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JC
SHAPE_PMESH - Static variable in class org.jmol.viewer.JC
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JC
  ///////
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JC
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JC
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JC
SHAPE_STARS - Static variable in class org.jmol.viewer.JC
SHAPE_STICKS - Static variable in class org.jmol.viewer.JC
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JC
SHAPE_STRUTS - Static variable in class org.jmol.viewer.JC
SHAPE_TRACE - Static variable in class org.jmol.viewer.JC
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JC
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JC
shapeClassBases - Static variable in class org.jmol.viewer.JC
shapeCommand - Static variable in class org.jmol.script.T
shapeID - Variable in class org.jmol.render.ShapeRenderer
shapeID - Variable in class org.jmol.shape.Shape
shapely - Static variable in class org.jmol.script.T
SHAPELY - Enum constant in enum class org.jmol.c.PAL
SHAPELY - Static variable in class org.jmol.util.ColorEncoder
ShapeManager - Class in org.jmol.viewer
ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
ShapeRenderer - Class in org.jmol.render
ShapeRenderer() - Constructor for class org.jmol.render.ShapeRenderer
shapes - Variable in class org.jmol.viewer.ShapeManager
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JC
shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
sheet - Static variable in class org.jmol.script.T
Sheet - Class in org.jmol.modelsetbio
SHEET - Enum constant in enum class org.jmol.c.STR
sheetsmoothing - Static variable in class org.jmol.script.T
sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
ShelxReader - Class in org.jmol.adapter.readers.xtal
  A reader for SHELX output (RES) files.
ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
SHIFT - Static variable in class org.jmol.viewer.binding.Binding
SHIFT_MASK - Static variable in class org.jmol.awtjs.Event
shiftA - Variable in class org.jmol.render.AxesRenderer
shiftA - Variable in class org.jmol.render.BbcageRenderer
shiftA - Variable in class org.jmol.render.UccageRenderer
shiftB - Variable in class org.jmol.render.AxesRenderer
shiftB - Variable in class org.jmol.render.BbcageRenderer
shiftB - Variable in class org.jmol.render.UccageRenderer
shiftBits(BS, BS, boolean, int) - Static method in class org.jmol.util.BSUtil
  this one slides bits to higher positions based on a pattern.
shiftC - Variable in class org.jmol.render.AxesRenderer
shiftC - Variable in class org.jmol.render.BbcageRenderer
shiftC - Variable in class org.jmol.render.UccageRenderer
shifting - Variable in class org.jmol.render.AxesRenderer
shifting - Variable in class org.jmol.render.BbcageRenderer
shifting - Variable in class org.jmol.render.UccageRenderer
shiftPressed - Variable in class jspecview.common.PanelData
shiftSpectrum(int, double, double) - Method in class jspecview.common.PanelData
  shifts xyCoords for a spectrum by the specified amount
shiftToXY(double, double) - Method in class jme.JMEmol
  shift to an origin and return a dimension
shiftX(Coordinate[], double) - Static method in class jspecview.common.Coordinate
SHIFTX - Enum constant in enum class jspecview.common.ScriptToken
shiftY(int, int, int, int) - Method in class jspecview.common.IntegralData
shininess - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
shm - Variable in class org.jmol.viewer.Viewer
shouldApplySpectrumDisplaySettingsNow() - Method in class jspecview.application.PreferencesDialog
shouldDisplayXAxisIncreasing() - Method in class jspecview.source.JDXDataObject
  Determines if the plot should be displayed decreasing by default
show - Static variable in class org.jmol.script.T
show(int, int, boolean) - Method in class org.jmol.popup.GenericPopup
show(String[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
show(String[]) - Method in class org.jmol.console.ScriptEditor
show(Component, int, int) - Method in class org.jmol.awtjs.swing.JPopupMenu
show_alpha_checker - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
show_frame_rate - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
show_progress - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
showAnnotation(Annotation.AType, Boolean) - Method in class jspecview.common.PanelData
showAtomNumbers - Variable in class jme.JME
showAtomNumbers() - Method in class jme.JME
showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Show an atom set from the indexes array
showAuxiliaryInfo(Map) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
showaxes - Static variable in class org.jmol.script.T
showboundbox - Static variable in class org.jmol.script.T
showConsole(boolean) - Method in class org.jmol.viewer.Viewer
showContourLines - Variable in class org.jmol.shape.Mesh
showDialog(Annotation.AType) - Method in class jspecview.common.PanelData
showEditor(String[]) - Method in class org.jmol.viewer.Viewer
SHOWERRORS - Enum constant in enum class jspecview.common.ScriptToken
showFileOpenDialog(Object, Object[]) - Method in interface jspecview.api.JSVFileHelper
showFileOpenDialog(Object, Object[]) - Method in class jspecview.java.AwtFileHelper
showFileOpenDialog(Object, Object[]) - Method in class jspecview.js2d.JsFileHelper
showfrank - Static variable in class org.jmol.script.T
showFrankMenu() - Method in class org.jmol.popup.JmolGenericPopup
showFrankMenu() - Method in class org.jmol.popup.JmolPopup
showGrid - Variable in class jspecview.common.PrintLayout
  whether or not the grid should be printed
showHash(SB, String) - Method in class org.jmol.viewer.ChimeMessenger
  #xxxx command output
showHash(SB, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
showhiddenselectionhalos - Static variable in class org.jmol.script.T
showHover() - Method in class org.jmol.viewer.Viewer
showhydrogens - Static variable in class org.jmol.script.T
showHydrogens - Variable in class jme.JME
showInfo(JSAppletObject, boolean) - Method in interface javajs.api.js.J2SObjectInterface
SHOWINTEGRATION - Enum constant in enum class jspecview.common.ScriptToken
showkeystrokes - Static variable in class org.jmol.script.T
showmeasurements - Static variable in class org.jmol.script.T
SHOWMEASUREMENTS - Enum constant in enum class jspecview.common.ScriptToken
showMenu(int, int) - Method in interface jspecview.api.JSVPanel
showMenu(int, int) - Method in class jspecview.common.JSViewer
showMenu(int, int) - Method in class jspecview.java.AwtPanel
showMenu(int, int) - Method in class jspecview.js2d.JsPanel
showMenu(int, int) - Method in class org.jmol.modelkit.ModelKit
SHOWMENU - Enum constant in enum class jspecview.common.ScriptToken
showMessage(Object, String, String) - Method in class jspecview.dialog.DialogManager
showMessage(Object, String, String) - Method in class jspecview.java.AwtDialogManager
showMessage(Object, String, String) - Method in class jspecview.js2d.JsDialogManager
showMessage(String) - Method in class jspecview.common.JSViewer
showMessage(String, String) - Method in interface jspecview.api.JSVPanel
showMessage(String, String) - Method in class jspecview.java.AwtPanel
showMessage(String, String) - Method in class jspecview.js2d.JsPanel
showMessage(String, String, int) - Method in class jspecview.dialog.JSVDialog
showMessageDialog(Object, String, String, int) - Method in class jspecview.dialog.DialogManager
showMessageDialog(Object, String, String, int) - Method in class jspecview.java.AwtDialogManager
showMessageDialog(Object, String, String, int) - Method in class jspecview.js2d.JsDialogManager
showmodvecs - Static variable in class org.jmol.script.T
showmultiplebonds - Static variable in class org.jmol.script.T
shownavigationpointalways - Static variable in class org.jmol.script.T
showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
SHOWPEAKLIST - Enum constant in enum class jspecview.common.ScriptToken
showPoints - Variable in class org.jmol.shape.Mesh
showProperties(Object, Spectrum) - Method in class jspecview.dialog.DialogManager
showProperties(Object, Spectrum) - Method in class jspecview.java.AwtDialogManager
showProperties(Object, Spectrum) - Method in class jspecview.js2d.JsDialogManager
  Looks a lot like Swing, right? :)
showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Shows the properties in the propertiesPane of the AtomSetChooser window
SHOWPROPERTIES - Enum constant in enum class jspecview.common.ScriptToken
showscript - Static variable in class org.jmol.script.T
showSource(Object, Spectrum) - Method in class jspecview.dialog.DialogManager
SHOWSOURCE - Enum constant in enum class jspecview.common.ScriptToken
showSourceErrors(Object, JDXSource) - Method in class jspecview.dialog.DialogManager
showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
showString(String) - Method in class org.jmol.script.ScriptEval
  ///////////////// showing strings /////////////////
showString(String) - Method in class org.jmol.scriptext.ScriptExt
showString(String, boolean) - Method in class org.jmol.viewer.Viewer
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptError
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptEval
showSystemInfo() - Method in class org.jmol.viewer.Viewer
showTimeout(String) - Method in class org.jmol.viewer.Viewer
showTimeout(Map, String) - Static method in class org.jmol.thread.TimeoutThread
showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
showtiming - Static variable in class org.jmol.script.T
showTiming - Variable in class org.jmol.jvxl.readers.Parameters
showTiming - Variable in class org.jmol.viewer.GlobalSettings
showTitles - Variable in class jspecview.common.PrintLayout
  whether or not the title should be printed
showTrace - Variable in class org.jmol.util.Vibration
showTriangles - Variable in class org.jmol.shape.Mesh
showunitcell - Static variable in class org.jmol.script.T
showunitcelldetails - Static variable in class org.jmol.script.T
showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
showUrl(String) - Method in class org.jmol.api.JmolViewer
showUrl(String) - Method in class org.jmol.util.GenericApplet
showUrl(String) - Method in class org.jmol.viewer.Viewer
  syncCallback traps script synchronization messages and allows for cancellation (by returning "") or modification jmolSetCallback("syncCallback", "mySyncCallback") function mySyncCallback(app, script, appletName) { ...[modify script here]...
showUrl(String) - Method in class org.openscience.jmol.app.status.StatusListener
showXScale - Variable in class jspecview.common.PrintLayout
  whether or not the X-scale should be printed
showYScale - Variable in class jspecview.common.PrintLayout
  whether or not the Y-scale should be printed
si - Variable in class jspecview.application.AwtTree
si - Variable in class jspecview.common.JSViewer
si - Variable in class jspecview.tree.SimpleTree
siCheckCallbacks(String) - Method in interface jspecview.api.ScriptInterface
siCheckCallbacks(String) - Method in class jspecview.app.JSVApp
siCheckCallbacks(String) - Method in class jspecview.application.JSpecView
sidechain - Static variable in class org.jmol.script.T
SiestaReader - Class in org.jmol.adapter.readers.xtal
  BH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/
SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
siExecHidden(boolean) - Method in interface jspecview.api.ScriptInterface
siExecHidden(boolean) - Method in class jspecview.app.JSVApp
siExecHidden(boolean) - Method in class jspecview.application.JSpecView
siExecScriptComplete(String, boolean) - Method in interface jspecview.api.ScriptInterface
siExecScriptComplete(String, boolean) - Method in class jspecview.app.JSVApp
siExecScriptComplete(String, boolean) - Method in class jspecview.application.JSpecView
siExecSetCallback(ScriptToken, String) - Method in interface jspecview.api.ScriptInterface
siExecSetCallback(ScriptToken, String) - Method in class jspecview.app.JSVApp
siExecSetCallback(ScriptToken, String) - Method in class jspecview.application.JSpecView
siExecTest(String) - Method in interface jspecview.api.ScriptInterface
siExecTest(String) - Method in class jspecview.app.JSVApp
siExecTest(String) - Method in class jspecview.application.JSpecView
siGetNewJSVPanel(Spectrum) - Method in interface jspecview.api.ScriptInterface
siGetNewJSVPanel(Spectrum) - Method in class jspecview.app.JSVApp
siGetNewJSVPanel(Spectrum) - Method in class jspecview.application.JSpecView
siGetNewJSVPanel2(Lst) - Method in interface jspecview.api.ScriptInterface
siGetNewJSVPanel2(Lst) - Method in class jspecview.app.JSVApp
siGetNewJSVPanel2(Lst) - Method in class jspecview.application.JSpecView
sigma - Variable in class org.jmol.jvxl.readers.Parameters
sigma - Static variable in class org.jmol.script.T
sign - Static variable in class org.jmol.script.T
signFactor - Variable in class org.jmol.modelset.TickInfo
silent - Static variable in class org.jmol.script.T
siLoaded(String) - Method in interface jspecview.api.ScriptInterface
siLoaded(String) - Method in class jspecview.app.JSVApp
siLoaded(String) - Method in class jspecview.application.JSpecView
SILVER - Static variable in class org.jmol.util.C
SIMPLE_LINE - Static variable in class org.jmol.shapecgo.CGOMesh
simpleCage - Variable in class org.jmol.modelset.Model
SimpleEdge - Interface in org.jmol.util
  minimal bond interface for SMILES and CIP
simpleEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, Lst, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
SimpleMarchingCubesOld() - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
SimpleNode - Interface in org.jmol.util
  Just the bare minimum for CIP, and non-BioSMILES
SimpleTree - Class in jspecview.tree
SimpleTree(JSViewer) - Constructor for class jspecview.tree.SimpleTree
SimpleTreeEnumeration - Class in jspecview.tree
SimpleTreeEnumeration(SimpleTreeNode) - Constructor for class jspecview.tree.SimpleTreeEnumeration
SimpleTreeModel - Class in jspecview.tree
SimpleTreeModel(JSVTreeNode) - Constructor for class jspecview.tree.SimpleTreeModel
SimpleTreeNode - Class in jspecview.tree
SimpleTreeNode(String, PanelNode) - Constructor for class jspecview.tree.SimpleTreeNode
SimpleTreePath - Class in jspecview.tree
SimpleTreePath(Object[]) - Constructor for class jspecview.tree.SimpleTreePath
SimpleUnitCell - Class in org.jmol.util
  general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
SimpleUnitCell() - Constructor for class org.jmol.util.SimpleUnitCell
simplify_display_lists - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SIMULATION_PROTOCOL - Static variable in class jspecview.common.JSVFileManager
SIMULATION_PROTOCOL - Static variable in class org.jmol.viewer.FileManager
sin - Static variable in class org.jmol.script.T
sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
sinBeta - Variable in class org.jmol.util.SimpleUnitCell
siNewWindow(boolean, boolean) - Method in interface jspecview.api.ScriptInterface
siNewWindow(boolean, boolean) - Method in class jspecview.app.JSVApp
  Shows the applet in a Frame
siNewWindow(boolean, boolean) - Method in class jspecview.application.JSpecView
sinGamma - Variable in class org.jmol.util.SimpleUnitCell
SINGLE - Static variable in class org.jmol.viewer.binding.Binding
single_image - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SinglePointGesture - Class in org.jmol.multitouch.sparshui
  SINGLE_POINT_GESTURE only passes single-touch gestures.
SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
siNodeSet(PanelNode) - Method in interface jspecview.api.ScriptInterface
siNodeSet(PanelNode) - Method in class jspecview.app.JSVApp
siNodeSet(PanelNode) - Method in class jspecview.application.JSpecView
siOpenDataOrFile(Object, String, Lst, String, int, int, boolean, String, String) - Method in interface jspecview.api.ScriptInterface
siOpenDataOrFile(Object, String, Lst, String, int, int, boolean, String, String) - Method in class jspecview.app.JSVApp
siOpenDataOrFile(Object, String, Lst, String, int, int, boolean, String, String) - Method in class jspecview.application.JSpecView
siProcessCommand(String) - Method in interface jspecview.api.ScriptInterface
siProcessCommand(String) - Method in class jspecview.app.JSVApp
  overloaded in JSVAppletPro
siProcessCommand(String) - Method in class jspecview.app.JSVAppPro
siProcessCommand(String) - Method in class jspecview.application.JSpecView
siSendPanelChange() - Method in interface jspecview.api.ScriptInterface
siSendPanelChange() - Method in class jspecview.app.JSVApp
siSendPanelChange() - Method in class jspecview.application.JSpecView
siSetCurrentSource(JDXSource) - Method in interface jspecview.api.ScriptInterface
siSetCurrentSource(JDXSource) - Method in class jspecview.app.JSVApp
siSetCurrentSource(JDXSource) - Method in class jspecview.application.JSpecView
siSetLoaded(String, String) - Method in interface jspecview.api.ScriptInterface
siSetLoaded(String, String) - Method in class jspecview.app.JSVApp
siSetLoaded(String, String) - Method in class jspecview.application.JSpecView
siSetMenuEnables(PanelNode, boolean) - Method in interface jspecview.api.ScriptInterface
siSetMenuEnables(PanelNode, boolean) - Method in class jspecview.app.JSVApp
siSetMenuEnables(PanelNode, boolean) - Method in class jspecview.application.JSpecView
siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in interface jspecview.api.ScriptInterface
siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in class jspecview.app.JSVApp
siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in class jspecview.application.JSpecView
  Sets the display properties as specified from the preferences dialog or the properties file
siSetSelectedPanel(JSVPanel) - Method in interface jspecview.api.ScriptInterface
siSetSelectedPanel(JSVPanel) - Method in class jspecview.app.JSVApp
siSetSelectedPanel(JSVPanel) - Method in class jspecview.application.JSpecView
siSourceClosed(JDXSource) - Method in interface jspecview.api.ScriptInterface
siSourceClosed(JDXSource) - Method in class jspecview.app.JSVApp
siSourceClosed(JDXSource) - Method in class jspecview.application.JSpecView
  Closes the `JDXSource` specified by source
siSyncLoad(String) - Method in interface jspecview.api.ScriptInterface
siSyncLoad(String) - Method in class jspecview.app.JSVApp
  Loads a new file into the existing applet window
siSyncLoad(String) - Method in class jspecview.application.JSpecView
site - Static variable in class org.jmol.script.T
siUpdateBoolean(ScriptToken, boolean) - Method in interface jspecview.api.ScriptInterface
siUpdateBoolean(ScriptToken, boolean) - Method in class jspecview.app.JSVApp
siUpdateBoolean(ScriptToken, boolean) - Method in class jspecview.application.JSpecView
siUpdateRecentMenus(String) - Method in interface jspecview.api.ScriptInterface
siUpdateRecentMenus(String) - Method in class jspecview.app.JSVApp
siUpdateRecentMenus(String) - Method in class jspecview.application.JSpecView
siValidateAndRepaint(boolean) - Method in interface jspecview.api.ScriptInterface
siValidateAndRepaint(boolean) - Method in class jspecview.app.JSVApp
siValidateAndRepaint(boolean) - Method in class jspecview.application.JSpecView
sixdots - Static variable in class org.jmol.render.FontLineShapeRenderer
size - Static variable in class org.jmol.script.T
size() - Method in class javajs.util.BS
  Returns the number of bits of space actually in use by this `BitSet` to represent bit values.
skew() - Method in class org.jmol.util.Tensor
  a measure of asymmetry.
skipComments(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
skipComments(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
skipComments(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
skipData(int) - Method in class org.jmol.jvxl.readers.JvxlReader
skipData(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
skipData(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.JvxlReader
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
skipLoop(boolean) - Method in interface javajs.api.GenericCifDataParser
skipLoop(boolean) - Method in class javajs.util.CifDataParser
  Skips all associated loop data.
skipLoop(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
skipLoopKeyword() - Method in class org.jmol.adapter.readers.cif.CifReader
skipNextToken() - Method in interface javajs.api.GenericCifDataParser
skipNextToken() - Method in class javajs.util.CifDataParser
skipping - Variable in class org.jmol.adapter.readers.cif.CifReader
skipTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
skipTo(String, String) - Method in class org.jmol.jvxl.readers.JvxlReader
skipTo(String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
skipTo(String, String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
slab - Static variable in class org.jmol.script.T
slab - Variable in class org.jmol.util.GData
slabbingObject - Variable in class org.jmol.shape.Mesh
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSlicer
  "slabs" an isosurface into the first Brillouin zone moving points as necessary.
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSurface
slabbyatom - Static variable in class org.jmol.script.T
slabbymolecule - Static variable in class org.jmol.script.T
slabColix - Variable in class org.jmol.util.MeshSurface
slabenabled - Static variable in class org.jmol.script.T
slabEnabled - Variable in class org.jmol.viewer.TransformManager
slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
slabInternal(P4, boolean) - Method in class org.jmol.viewer.TransformManager
slabIsosurface(Lst) - Method in class org.jmol.jvxl.readers.SurfaceReader
slabMeshType - Variable in class org.jmol.util.MeshSurface
slabOptions - Variable in class org.jmol.util.MeshSurface
slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSlicer
slabPolygonsList(Lst, boolean) - Method in class org.jmol.util.MeshSurface
slabrange - Static variable in class org.jmol.script.T
slabReset() - Method in class org.jmol.viewer.TransformManager
slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
slabValue - Variable in class org.jmol.jvxl.data.JvxlData
slabValue - Variable in class org.jmol.viewer.TransformManager
slabXY - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
slabZ - Variable in class org.jmol.export.___Exporter
slaterArray - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
SlaterData - Class in org.jmol.quantum
SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
slaters - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
sleepTime - Variable in class org.jmol.thread.JmolThread
slen - Variable in class org.jmol.script.ScriptParam
slen - Variable in class org.jmol.scriptext.ScriptExt
slice_dynamic_grid - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
slice_dynamic_grid_resolution - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
slice_grid - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
slice_height_map - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
slice_height_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
slice_track_camera - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
slm - Variable in class org.jmol.viewer.Viewer
slop - Variable in class org.jmol.adapter.writers.XtlWriter
slop - Variable in class org.jmol.util.SimpleUnitCell
  initial value is set in subclass UnitCell
SLOP_PARAMS - Static variable in class org.jmol.util.SimpleUnitCell
SLOPDP - Static variable in class org.jmol.util.SimpleUnitCell
SLOPSP - Static variable in class org.jmol.util.SimpleUnitCell
  allowance for rounding in [0,1)
slow_idle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SLUUD - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Stereo labels for "unknown" and "undefined" are different, 'u' and '?', resp.
sm - Variable in class org.jmol.modelset.ModelSet
sm - Variable in class org.jmol.script.ScriptEval
sm - Variable in class org.jmol.viewer.Viewer
smallAtomWidthLabel - Variable in class jme.AtomDisplayLabel
smallmoleculemaxatoms - Static variable in class org.jmol.script.T
smartaromatic - Static variable in class org.jmol.script.T
SmarterJmolAdapter - Class in org.jmol.adapter.smarter
SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
smarts - Variable in class org.jmol.shapespecial.Polyhedron
smiles - Static variable in class org.jmol.script.T
smiles - Variable in class org.jmol.shapespecial.Polyhedron
smiles() - Method in class jme.JME
smiles() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
SMILES_2D - Static variable in class org.jmol.viewer.JC
SMILES_AROMATIC_DEFINED - Static variable in class org.jmol.viewer.JC
  AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.
SMILES_AROMATIC_DOUBLE - Static variable in class org.jmol.viewer.JC
  AROMATIC_DOUBLE allows a distinction between single and double, as for example is necessary to distinguish between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing)
SMILES_AROMATIC_MMFF94 - Static variable in class org.jmol.viewer.JC
  AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.
SMILES_AROMATIC_PLANAR - Static variable in class org.jmol.viewer.JC
  AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)
SMILES_AROMATIC_STRICT - Static variable in class org.jmol.viewer.JC
  AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds
SMILES_FIRST_MATCH_ONLY - Static variable in class org.jmol.viewer.JC
SMILES_GEN_ALL_COMPONENTS - Static variable in class org.jmol.viewer.JC
SMILES_GEN_ATOM_COMMENT - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_COMMENT - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_COV_CROSSLINK - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_HH_CROSSLINK - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_NOCOMMENTS - Static variable in class org.jmol.viewer.JC
SMILES_GEN_EXPLICIT_H_ALL - Static variable in class org.jmol.viewer.JC
SMILES_GEN_EXPLICIT_H2_ONLY - Static variable in class org.jmol.viewer.JC
SMILES_GEN_NO_BRANCHES - Static variable in class org.jmol.viewer.JC
SMILES_GEN_POLYHEDRAL - Static variable in class org.jmol.viewer.JC
SMILES_GEN_TOPOLOGY - Static variable in class org.jmol.viewer.JC
SMILES_GROUP_BY_MODEL - Static variable in class org.jmol.viewer.JC
SMILES_IGNORE_ATOM_CLASS - Static variable in class org.jmol.viewer.JC
SMILES_IGNORE_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
SMILES_INVERT_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
SMILES_MAP_UNIQUE - Static variable in class org.jmol.viewer.JC
SMILES_NO_AROMATIC - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_OPENSMARTS - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_OPENSMILES - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_SMARTS - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_SMILES - Static variable in class org.jmol.viewer.JC
smiles2dimageformat - Static variable in class org.jmol.script.T
SmilesAromatic - Class in org.jmol.smiles
SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
SmilesAtom - Class in org.jmol.smiles
  This class represents an atom in a `SmilesMolecule`.
SmilesAtom() - Constructor for class org.jmol.smiles.SmilesAtom
SmilesBond - Class in org.jmol.smiles
  Bond in a SmilesMolecule
SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
  SmilesBond constructor
SmilesExt - Class in org.jmol.scriptext
SmilesExt() - Constructor for class org.jmol.scriptext.SmilesExt
SmilesGenerator - Class in org.jmol.smiles
  Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
SmilesMatcher - Class in org.jmol.smiles
  Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
SmilesMatcherInterface - Interface in org.jmol.api
SmilesMeasure - Class in org.jmol.smiles
smilesOptions - Variable in class org.jmol.inchi.InchiJmol
SmilesParser - Class in org.jmol.smiles
  Parses a SMILES string or SMARTS pattern to create a `SmilesSearch`.
SmilesSearch - Class in org.jmol.smiles
  A class to build and carry out a SMILES or SMARTS match
SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
SmilesSearch.SmilesTarget - Class in org.jmol.smiles
SmilesStereo - Class in org.jmol.smiles
  This class relates to stereochemical issues
SmilesTarget() - Constructor for class org.jmol.smiles.SmilesSearch.SmilesTarget
smilesurlformat - Static variable in class org.jmol.script.T
smooth_color_triangle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
smooth_half_bonds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
SNon - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Ignore stereo [compatible with standard InChI]
solid - Static variable in class org.jmol.script.T
solidOnly - Variable in class org.jmol.export.___Exporter
solvent - Static variable in class org.jmol.script.T
solvent_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
solventprobe - Static variable in class org.jmol.script.T
solventproberadius - Static variable in class org.jmol.script.T
solvName - Variable in class jspecview.export.AMLExporter
solvName - Variable in class jspecview.export.CMLExporter
solvRef - Variable in class jspecview.export.AMLExporter
solvRef - Variable in class jspecview.export.CMLExporter
someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelSet
someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelSet
someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelSet
sort - Static variable in class org.jmol.g3d.Graphics3D
sort - Static variable in class org.jmol.script.T
Sort(int, String) - Constructor for class org.jmol.script.SV.Sort
sortAssemblyModels() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...
sortedItem(Lst, int) - Static method in class javajs.util.AU
sortMapArray(String) - Method in class org.jmol.script.SV
sortMOs() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.AdfReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.AmsReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.DgridReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  sorts coefficients by atomic number for speed later
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.AdfReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.AmsReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.CsfReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrReverse(int) - Method in class org.jmol.script.SV
SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
source - Variable in class jspecview.common.PanelNode
source - Variable in class jspecview.source.AnIMLReader
source - Variable in class jspecview.source.NMRMLReader
SOURCE - Enum constant in enum class jspecview.common.ExportType
sourceID - Variable in class jspecview.source.JDXDataObject
sourceLabel - Static variable in class jspecview.common.JSViewer
SourceReader - Interface in jspecview.api
SOUTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
SP - Static variable in class org.jmol.quantum.QS
SPACE_GROUP_LIST_BCS - Static variable in class org.jmol.viewer.JC
spacebeforesquare - Static variable in class org.jmol.script.T
spacefill - Static variable in class org.jmol.script.T
spacegroup - Static variable in class org.jmol.script.T
spaceGroup - Variable in class org.jmol.symmetry.Symmetry
SpaceGroup - Class in org.jmol.symmetry
  A general class to deal with Hermann-Mauguin or Hall names Bob Hanson 9/2006 references: International Tables for Crystallography Vol.
SpaceGroup(int, String, boolean) - Constructor for class org.jmol.symmetry.SpaceGroup
SpaceGroup.ParamCheck - Class in org.jmol.symmetry
SpaceGroupFinder - Class in org.jmol.symmetry
  A relatively simple space group finder given a unit cell.
SpaceGroupFinder() - Constructor for class org.jmol.symmetry.SpaceGroupFinder
span() - Method in class org.jmol.util.Tensor
  width of the signal; |e2 - e0|
spardirCache - Variable in class org.jmol.viewer.FileManager
SparseArray(String) - Constructor for class org.jmol.adapter.writers.QCJSONWriter.SparseArray
SparshClient - Interface in com.sparshui.client
  The Client interface must be implemented in all clients wishing to connect to the Sparsh-UI gesture server.
SpartanInputReader - Class in org.jmol.adapter.readers.spartan
SpartanInputReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanInputReader
SpartanReader - Class in org.jmol.adapter.readers.spartan
SpartanReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanReader
SpartanSmolReader - Class in org.jmol.adapter.readers.spartan
SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanSmolReader
spartanUtil() - Method in class org.jmol.viewer.FileManager
  An isolated class to retrieve Spartan file data from compound documents, zip files, and directories
SpartanUtil - Class in org.jmol.adapter.readers.spartan
  A class to isolate Spartan file reading methods from the rest of Jmol.
SpartanUtil() - Constructor for class org.jmol.adapter.readers.spartan.SpartanUtil
spec - Variable in class jspecview.common.MeasurementData
spec - Variable in class jspecview.dialog.JSVDialog
spec_alternate - Static variable in class org.jmol.script.T
spec_atom - Static variable in class org.jmol.script.T
spec_chain - Static variable in class org.jmol.script.T
spec_count - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spec_direct - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spec_direct_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spec_model - Static variable in class org.jmol.script.T
spec_model2 - Static variable in class org.jmol.script.T
spec_name_pattern - Static variable in class org.jmol.script.T
spec_power - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spec_reflect - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spec_resid - Static variable in class org.jmol.script.T
spec_seqcode - Static variable in class org.jmol.script.T
spec_seqcode_range - Static variable in class org.jmol.script.T
Special - Variable in class org.jmol.popup.JmolPopup
SPECIAL - Static variable in class org.jmol.shapecgo.CGOMesh
SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.C
specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
specialAtomNames - Static variable in class org.jmol.modelset.Group
SpecialGroup - Class in org.jmol.symmetry
SpecialGroupFactory - Class in org.jmol.symmetry
  A static singleton class to create plane, layer, rod, and frieze groups
SpecialGroupFactory() - Constructor for class org.jmol.symmetry.SpecialGroupFactory
specialLabel - Variable in class org.jmol.shape.Hover
specialposition - Static variable in class org.jmol.script.T
specialPrefix - Variable in class org.jmol.symmetry.SpaceGroup
spectraTree - Variable in class jspecview.common.JSViewer
spectrum - Variable in class jspecview.common.PeakInfo
Spectrum - Class in jspecview.common
  `JDXSpectrum` implements the Interface Spectrum for the display of JDX Files.
Spectrum() - Constructor for class jspecview.common.Spectrum
  Constructor
SPECTRUM - Enum constant in enum class jspecview.common.ScriptToken
Spectrum.IRMode - Enum Class in jspecview.common
SPECTRUMNUMBER - Enum constant in enum class jspecview.common.ScriptToken
spectypeInitials - Variable in class jspecview.export.AMLExporter
spectypeInitials - Variable in class jspecview.export.CMLExporter
specular - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
specular - Static variable in class org.jmol.script.T
specular_intensity - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
specularexponent - Static variable in class org.jmol.script.T
specularpercent - Static variable in class org.jmol.script.T
specularpower - Static variable in class org.jmol.script.T
sphere - Static variable in class org.jmol.script.T
SPHERE - Static variable in class org.jmol.shapecgo.CGOMesh
sphere_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_point_max_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_point_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_solvent - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphere_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
sphereMean(Quat[], float[], float) - Static method in class javajs.util.Quat
SphereRenderer - Class in org.jmol.g3d
  Implements high performance rendering of shaded spheres.
sphereShadeIndexes - Variable in class org.jmol.util.Shader
  /////////////////////////////////////////////////////////////
sphereShapeCache - Variable in class org.jmol.util.Shader
spheroid_fill - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spheroid_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spheroid_smooth - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
spin - Static variable in class org.jmol.script.T
SPIN_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
SPIN_EVENT - Static variable in class com.sparshui.GestureType
SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
SPIN_FRAME_ROTATION_MATRIX - Static variable in class org.jmol.viewer.JC
SPIN_GESTURE - Static variable in class com.sparshui.GestureType
SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
SPIN_ROTATION_AXIS_ANGLE_APPLIED - Static variable in class org.jmol.viewer.JC
SPIN_ROTATION_MATRIX_APPLIED - Static variable in class org.jmol.viewer.JC
spine - Static variable in class org.jmol.script.T
SpinEvent - Class in com.sparshui.common.messages.events
SpinEvent() - Constructor for class com.sparshui.common.messages.events.SpinEvent
SpinEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.SpinEvent
  Constructs a new SpinEvent from a serialized version - 4 bytes : rotationX - 4 bytes : rotationY - 4 bytes : rotationZ - 12 bytes total
SpinEvent(float, float, float) - Constructor for class com.sparshui.common.messages.events.SpinEvent
spinfps - Static variable in class org.jmol.script.T
spinFps - Variable in class org.jmol.viewer.TransformManager
spinFrameStr - Variable in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
  /////////////////// Magnetic and Spin Space Groups ///////////////
spinFrameToCartXYZ - Variable in class org.jmol.symmetry.Symmetry
spinIndex - Variable in class org.jmol.symmetry.SymmetryOperation
spinOn - Variable in class org.jmol.viewer.TransformManager
spinop - Static variable in class org.jmol.script.T
spinThread - Variable in class org.jmol.viewer.TransformManager
SpinThread - Class in org.jmol.thread
SpinThread() - Constructor for class org.jmol.thread.SpinThread
spinx - Static variable in class org.jmol.script.T
spinX - Variable in class org.jmol.viewer.TransformManager
spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
spiny - Static variable in class org.jmol.script.T
spinY - Variable in class org.jmol.viewer.TransformManager
spinz - Static variable in class org.jmol.script.T
spinZ - Variable in class org.jmol.viewer.TransformManager
splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
Splash - Class in org.openscience.jmol.app.jmolpanel
Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
SplashInterface - Interface in org.openscience.jmol.app
split - Static variable in class org.jmol.script.T
split(String, String) - Static method in class javajs.util.PT
  proper splitting, even for Java 1.3 -- if the text ends in the run, no new line is appended.
splitFrame - Variable in class org.jmol.viewer.AnimationManager
  left-right split-frame dual images; could be combined with stereo DTI
splitFrameCurrentlyRendering - Variable in class org.jmol.viewer.TransformManager
  right-hand split frame has fewer capabilities than right-hand
splitSpectra() - Method in class jspecview.common.JSViewer
splitStack(boolean) - Method in class jspecview.common.PanelData
sppa - Variable in class org.jmol.render.LabelsRenderer
sprintf(String, String, Object[]) - Static method in class javajs.util.PT
  sprintf emulation uses (almost) c++ standard string formats 's' string 'i' or 'd' integer, 'e' double, 'f' float, 'p' point3f 'q' quaternion/plane/axisangle with added "i" (equal to the insipid "d" -- digits?)
sprintf(String, SV) - Static method in class org.jmol.script.SV
sqrt - Static variable in class org.jmol.script.T
SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesStereo
squared - Static variable in class org.jmol.script.T
squareEuclideanDist(double, double, double, double) - Static method in class jme.JMEUtil
SQZ - Enum constant in enum class jspecview.common.ExportType
sr - Variable in class org.jmol.jvxl.data.VolumeData
SRac - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Use racemic stereo
SRel - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Use relative stereo
ss_helix_phi_exclude - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_helix_phi_include - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_helix_phi_target - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_helix_psi_exclude - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_helix_psi_include - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_helix_psi_target - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_strand_phi_exclude - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_strand_phi_include - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_strand_phi_target - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_strand_psi_exclude - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_strand_psi_include - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ss_strand_psi_target - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
ssbond - Static variable in class org.jmol.script.T
ssbondsbackbone - Static variable in class org.jmol.script.T
SSG_POINT_GROUP_AXES - Static variable in class org.jmol.viewer.JC
st - Variable in class org.jmol.script.ScriptParam
st - Variable in class org.jmol.scriptext.ScriptExt
STACKOFFSETY - Enum constant in enum class jspecview.common.ScriptToken
STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
standardGroupList - Static variable in class org.jmol.modelset.Group
standardizeTokens(String[], boolean) - Static method in class org.jmol.symmetry.CLEG
standardLevel - Static variable in class org.jmol.util.Geodesic
  3 levels, 0 through 3
star - Variable in class jme.JME
star - Static variable in class org.jmol.script.T
Stars - Class in org.jmol.shape
Stars() - Constructor for class org.jmol.shape.Stars
StarsRenderer - Class in org.jmol.render
StarsRenderer() - Constructor for class org.jmol.render.StarsRenderer
start() - Method in class jme.JME
start() - Method in class org.jmol.thread.JmolThread
start() - Method in class org.jmol.util.PatternMatcher.JSPattern
start() - Method in class org.openscience.jmol.app.InputScannerThread
start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
start(JFrame, Viewer, Map) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
start(JFrame, Viewer, Map) - Method in interface org.openscience.jmol.app.JmolPlugin
start(Viewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
start(Viewer) - Method in class org.jmol.console.AppletConsole
start(Viewer) - Method in class org.jmol.consolejs.AppletConsole
start(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
START - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
START_ELEMENT - Static variable in class jspecview.source.XMLParser
START_END_ELEMENT - Static variable in class jspecview.source.XMLParser
startChainID - Variable in class org.jmol.adapter.smarter.Structure
startCommandWatcher(boolean) - Method in interface org.jmol.api.JmolScriptManager
startCommandWatcher(boolean) - Method in class org.jmol.script.ScriptManager
startDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlHandler
startGestureServer() - Method in class com.sparshui.server.GestureServer
  two independent threads -- one accepting multiple clients, one not.
startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
startHoverWatcher(boolean) - Method in interface javajs.api.JSInterface
startHoverWatcher(boolean) - Method in class jspecview.appletjs.JSVApplet
startHoverWatcher(boolean) - Method in class org.jmol.util.GenericApplet
startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
startHoverWatcher(boolean) - Method in class org.jmol.viewer.Viewer
startIndex - Variable in class jspecview.export.AMLExporter
startIndex - Variable in class jspecview.export.CMLExporter
STARTINDEX - Enum constant in enum class jspecview.common.ScriptToken
startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
startJmol(JmolApp) - Static method in class org.openscience.jmol.app.Jmol
startLayout() - Method in interface jspecview.api.PlatformDialog
startLayout() - Method in class jspecview.java.AwtDialog
startLayout() - Method in class jspecview.js2d.JsDialog
startMinimization() - Method in class org.jmol.minimize.Minimizer
startNBO(String) - Method in class org.jmol.viewer.Viewer
startOpenTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
startPlugin(String) - Method in class org.jmol.viewer.Viewer
  startup -U nbo option
startPos - Variable in class javajs.img.PngEncoder
startRecording() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
startService(int, JsonNioClient, Viewer, String, int) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
startService(int, JsonNioClient, Viewer, String, int) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
startSimulator(Object) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
startSpinningAxis(T3, T3, boolean) - Method in class org.jmol.viewer.Viewer
startTime - Variable in class org.jmol.thread.JmolThread
startTimer(String) - Static method in class org.jmol.util.Logger
startTrace(int) - Method in class org.jmol.util.Vibration
startupDim - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
startupHeight - Variable in class org.openscience.jmol.app.JmolApp
startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
startupPinTip - Variable in class jspecview.common.PanelData
startupWidth - Variable in class org.openscience.jmol.app.JmolApp
startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
startViewer(JmolViewer, SplashInterface, boolean) - Method in class org.openscience.jmol.app.JmolApp
starwidth - Static variable in class org.jmol.script.T
state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
state - Variable in class jspecview.export.AMLExporter
state - Variable in class jspecview.export.CMLExporter
state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state - Variable in class org.jmol.jvxl.readers.Parameters
state - Static variable in class org.jmol.script.T
state_counter_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.JC
stateButton - Variable in class org.jmol.console.GenericConsole
stateChanged(ChangeEvent) - Method in class org.jmol.dialog.Dialog.QualityListener
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
StateCreator - Class in org.jmol.viewer
  StateCreator handles all aspects of working with the "state" as generally defined, including -- creating the state script -- general output, including logging -- handling undo/redo -- processing SYNC directives Called by reflection only; all state generation script here, for modularization in JavaScript
StateCreator() - Constructor for class org.jmol.viewer.StateCreator
StateManager - Class in org.jmol.viewer
statement - Variable in class org.jmol.script.ScriptContext
statementAsString(Viewer, T[], int, boolean) - Static method in class org.jmol.script.ScriptEval
StateScript - Class in org.jmol.modelset
stateScripts - Variable in class org.jmol.modelset.ModelSet
stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
static_singletons - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
staticCleanTransform(String) - Method in interface org.jmol.api.SymmetryInterface
staticCleanTransform(String) - Method in class org.jmol.symmetry.Symmetry
  Normalize the transform, changing for instance a+1/2,b,c to "a,b,c;1/2,0,0" From SpaceGroupFinder only.
staticConvertOperation(String, M34, String) - Method in interface org.jmol.api.SymmetryInterface
staticConvertOperation(String, M34, String) - Method in class org.jmol.symmetry.Symmetry
staticConvertOperation(String, M34, String) - Static method in class org.jmol.symmetry.SymmetryOperation
staticGetAtomSetCollection(AtomSetCollectionReader) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
staticGetAtomSetCollectionReader(String, String, Object, Map) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  The primary file or string reader -- returns just the reader now
staticGetMatrixTransform(String, Object) - Method in interface org.jmol.api.SymmetryInterface
staticGetMatrixTransform(String, Object) - Method in class org.jmol.symmetry.Symmetry
staticGetTransformABC(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
staticGetTransformABC(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
staticID - Static variable in class org.jmol.minimize.Minimizer
staticToRationalXYZ(P3, String) - Method in interface org.jmol.api.SymmetryInterface
staticToRationalXYZ(P3, String) - Method in class org.jmol.symmetry.Symmetry
staticTransformSpaceGroup(BS, String, Object, SB) - Method in interface org.jmol.api.SymmetryInterface
staticTransformSpaceGroup(BS, String, Object, SB) - Method in class org.jmol.symmetry.Symmetry
stats() - Method in class org.jmol.bspt.Bspf
stats() - Method in class org.jmol.bspt.Bspt
  prints some simple stats to stdout
status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
STATUS_COORD - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
STATUS_TEXT - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
STATUS_TIME - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
StatusBar - Class in org.openscience.jmol.app.jmolpanel
StatusBar(int) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
statusForm - Variable in class org.jmol.util.GenericApplet
statusList - Variable in class org.jmol.viewer.StatusManager
StatusListener - Class in org.openscience.jmol.app.status
StatusListener(Viewer, JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.status.StatusListener
StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.status.StatusListener
StatusManager - Class in org.jmol.viewer
  The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
statusreporting - Static variable in class org.jmol.script.T
statusText - Variable in class org.jmol.util.GenericApplet
statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
statusTextarea - Variable in class org.jmol.util.GenericApplet
stddev - Static variable in class org.jmol.script.T
stdinchi - Static variable in class org.jmol.script.T
stdinchikey - Static variable in class org.jmol.script.T
steepestDescentInitialize(int, double, double) - Method in class org.jmol.minimize.forcefield.ForceField
  /////////// calculation /////////////////
steepestDescentTakeNSteps(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
step - Static variable in class org.jmol.script.T
stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
stepMinimization() - Method in class org.jmol.minimize.Minimizer
stepPausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
stepPausedExecution() - Method in class org.jmol.script.ScriptEval
steps - Variable in class jspecview.common.ScaleData
  The step values for the X and Y scales
steps - Variable in class org.jmol.jvxl.readers.Parameters
STER - Enum Class in org.jmol.c
stereo - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stereo - Variable in class jme.JME
stereo - Static variable in class org.jmol.script.T
stereo - Variable in class org.jmol.smiles.SmilesAtom
stereo_angle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stereo_double_pump_mono - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stereo_dynamic_strength - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stereo_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stereo_shift - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stereodegrees - Static variable in class org.jmol.script.T
stereoTransformation(int[], int[]) - Static method in class jme.JMEUtil
stick_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_ball - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_ball_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_ball_ratio - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_debug - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_fixed_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_good_geometry - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_h_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_nub - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_overlap - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_round_nub - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stick_valence_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
Sticks - Class in org.jmol.shape
Sticks() - Constructor for class org.jmol.shape.Sticks
SticksRenderer - Class in org.jmol.render
SticksRenderer() - Constructor for class org.jmol.render.SticksRenderer
stm - Variable in class org.jmol.viewer.Viewer
stop - Static variable in class org.jmol.script.T
stop() - Method in class jme.JME
STOP - Static variable in class org.jmol.shapecgo.CGOMesh
stop_on_exceptions - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
stopAudio(String) - Method in class org.jmol.viewer.StatusManager
stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
stopMotion() - Method in class org.jmol.viewer.TransformManager
stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
stopped - Variable in class org.jmol.thread.JmolThread
stopScriptThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
stopScriptThreads() - Method in class org.jmol.script.ScriptEval
stopThread(boolean) - Method in class org.jmol.viewer.AnimationManager
store() - Method in class jspecview.application.DisplaySchemesProcessor
  Saves the display schemes to file in XML format
str - Variable in class javajs.util.CifDataParser
  working string (buffer)
str - Variable in class jme.AtomDisplayLabel
STR - Enum Class in org.jmol.c
straightness - Static variable in class org.jmol.script.T
STRAIGHTNESS - Enum constant in enum class org.jmol.c.PAL
strandcount - Static variable in class org.jmol.script.T
strandCount - Variable in class org.jmol.adapter.smarter.Structure
strandCount - Variable in class org.jmol.renderbio.StrandsRenderer
strandcountformeshribbon - Static variable in class org.jmol.script.T
strandcountforstrands - Static variable in class org.jmol.script.T
strandID - Variable in class org.jmol.adapter.smarter.Structure
strands - Static variable in class org.jmol.script.T
Strands - Class in org.jmol.shapebio
Strands() - Constructor for class org.jmol.shapebio.Strands
strandSeparation - Variable in class org.jmol.renderbio.StrandsRenderer
StrandsRenderer - Class in org.jmol.renderbio
StrandsRenderer() - Constructor for class org.jmol.renderbio.StrandsRenderer
stream - Variable in class javajs.util.BinaryDocument
StreamReader(BufferedInputStream, String) - Constructor for class javajs.util.Rdr.StreamReader
streamToBytes(InputStream) - Static method in class javajs.util.Rdr
  Read an InputStream in its entirety as a byte array, closing the stream.
streamToString(InputStream) - Static method in class javajs.util.Rdr
  Read an InputStream in its entirety as a string, closing the stream.
streamToUTF8String(BufferedInputStream) - Static method in class javajs.util.Rdr
  Read a UTF-8 stream fully, converting it to a String.
strFormat - Variable in class org.jmol.modelset.Measurement
strFormat - Variable in class org.jmol.modelset.MeasurementData
string - Static variable in class org.jmol.script.T
StringDataReader - Class in javajs.util
StringDataReader() - Constructor for class javajs.util.StringDataReader
StringDataReader(String) - Constructor for class javajs.util.StringDataReader
stringHeight(FontMetrics) - Static method in class jme.JMEUtil
  Provide the ideal height of a string consisting of usual upper case characters.
stringParameter(int) - Method in class org.jmol.script.ScriptParam
stringParameter(int) - Method in class org.jmol.scriptext.ScriptExt
stringParameterSet(int) - Method in class org.jmol.script.ScriptParam
strings - Variable in class org.jmol.shape.Labels
stringToByteArray(String) - Static method in class com.sparshui.common.utils.Converter
stringWidth(String) - Method in class org.jmol.util.Font
stripPath(String) - Static method in class org.jmol.viewer.FileManager
stripTypePrefix(String) - Static method in class org.jmol.viewer.FileManager
  Stip PDB::file://...
strJavaVendor - Static variable in class org.jmol.viewer.Viewer
strJavaVersion - Static variable in class org.jmol.viewer.Viewer
strListValue(T) - Static method in class org.jmol.script.SV
strMenuStructure - Variable in class org.jmol.popup.GenericPopup
strObFreq - Variable in class jspecview.source.AnIMLReader
strObFreq - Variable in class jspecview.source.NMRMLReader
stroke() - Method in class javajs.export.PDFCreator
strOSName - Static variable in class org.jmol.viewer.Viewer
strparam - Static variable in class org.jmol.script.T
strproperty - Static variable in class org.jmol.script.T
strSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
strucid - Static variable in class org.jmol.script.T
strucno - Static variable in class org.jmol.script.T
structure - Variable in class org.jmol.popup.PopupResource
structure - Static variable in class org.jmol.script.T
Structure - Class in org.jmol.adapter.smarter
Structure - Interface in org.jmol.modelset
Structure(int, STR, STR, String, String, int, BS[]) - Constructor for class org.jmol.adapter.smarter.Structure
STRUCTURE - Enum constant in enum class org.jmol.c.PAL
structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
structureID - Variable in class org.jmol.adapter.smarter.Structure
StructureIterator - Class in org.jmol.adapter.smarter
STRUCTUREMODIFIED - Enum constant in enum class org.jmol.c.CBK
structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
structureTainted - Variable in class org.jmol.modelset.Model
structureType - Variable in class org.jmol.adapter.smarter.Structure
structureTypes - Variable in class org.jmol.renderbio.BackboneRenderer
structureTypes - Variable in class org.jmol.renderbio.CartoonRenderer
structureTypes - Variable in class org.jmol.renderbio.MeshRibbonRenderer
structureTypes - Variable in class org.jmol.renderbio.RibbonsRenderer
structureTypes - Variable in class org.jmol.renderbio.RocketsRenderer
structureTypes - Variable in class org.jmol.renderbio.StrandsRenderer
structureTypes - Variable in class org.jmol.renderbio.TraceRenderer
strutdefaultradius - Static variable in class org.jmol.script.T
strutlengthmaximum - Static variable in class org.jmol.script.T
strutPoint - Variable in class org.jmol.modelset.Group
struts - Static variable in class org.jmol.script.T
strutsmultiple - Static variable in class org.jmol.script.T
strutspacing - Static variable in class org.jmol.script.T
sType - Variable in class com.sparshui.GestureType
sType - Variable in class org.jmol.minimize.MinAtom
sub - Static variable in class org.jmol.script.T
sub(double[], double[], V3d) - Static method in class org.jmol.minimize.Util
sub(M3) - Method in class javajs.util.M3
  Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
sub(M4) - Method in class javajs.util.M4
  Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
sub(Matrix) - Method in class javajs.util.Matrix
  subtract two matrices
sub(T3) - Method in class javajs.util.T3
  Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
sub(T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
sub2(T3d, T3d) - Method in class javajs.util.T3d
  Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
sub2(T3, T3) - Method in class javajs.util.T3
  Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
sub33(M34) - Method in class javajs.util.M34
sublistAt(Lst, int...) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
subscripts - Variable in class jme.AtomDisplayLabel
subset - Static variable in class org.jmol.script.T
SubSpecChangeEvent - Class in jspecview.common
SubSpecChangeEvent(int, String) - Constructor for class jspecview.common.SubSpecChangeEvent
substring(int) - Method in class javajs.util.SB
substring2(int, int) - Method in class javajs.util.SB
substructure - Static variable in class org.jmol.script.T
substructureType - Variable in class org.jmol.adapter.smarter.Structure
subsystem - Static variable in class org.jmol.script.T
subsystemCode - Variable in class org.jmol.symmetry.SymmetryOperation
subzones - Variable in class org.jmol.util.BZone
SUCF - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Use Chiral Flag in MOL/SD file record: if On – use Absolute stereo, Off – use Relative stereo
sum - Static variable in class org.jmol.script.T
sum2 - Static variable in class org.jmol.script.T
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shape.Mesh
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
sumVertexNormals2(Mesh, T3[], V3[]) - Static method in class org.jmol.shape.Mesh
supercell - Static variable in class org.jmol.script.T
superscripts - Variable in class jme.AtomDisplayLabel
suppress_hidden - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface - Static variable in class org.jmol.script.T
SURFACE - Enum constant in enum class org.jmol.c.PAL
surface_best - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_carve_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_carve_normal_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_carve_selection - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_carve_state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_cavity_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_cavity_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_cavity_radius - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_circumscribe - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_clear_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_clear_selection - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_clear_state - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_color_smoothing - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_color_smoothing_threshold - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_debug - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
surface_miserable - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_negative_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_negative_visible - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_normal - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_optimize_subsets - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_poor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_proximity - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_quality - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
surface_ramp_above_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_residue_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_solvent - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_trim_cutoff - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_trim_factor - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_type - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surface_use_shader - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
surfaceAtoms - Variable in class org.jmol.jvxl.readers.Parameters
surfaceAtoms - Variable in class org.jmol.util.MeshSurface
surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
surfacedistance - Static variable in class org.jmol.script.T
surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
SurfaceGenerator - Class in org.jmol.jvxl.readers
SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
SurfaceReader - Class in org.jmol.jvxl.readers
surfaceSet - Variable in class org.jmol.util.MeshSurface
SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
  Class that holds the surface status information that the surface tool needs.
SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
SurfaceTool - Class in org.openscience.jmol.app.surfacetool
SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
suspend_undo - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
suspend_undo_atom_count - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
suspend_updates - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SUU - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Always indicate unknown/undefined stereo
suvw - Variable in class org.jmol.symmetry.SymmetryOperation
suvwId - Variable in class org.jmol.symmetry.SymmetryOperation
  CIF space_group_symop_spin_operation_uvw_id was an idea Bob had to separate out the uvw part from the xyz part into separate CIF blocks.
SV - Class in org.jmol.script
  ScriptVariable class
SV() - Constructor for class org.jmol.script.SV
SV.Sort - Class in org.jmol.script
sValue(T) - Static method in class org.jmol.script.SV
SVG - Enum constant in enum class jspecview.common.ExportType
SVGExporter - Class in jspecview.export
  class `SVGExporter` contains static methods to export a Graph as as SVG.
SVGExporter() - Constructor for class jspecview.export.SVGExporter
SVGI - Enum constant in enum class jspecview.common.ExportType
swap(Object[], int, int) - Static method in class javajs.util.AU
swap(T[], int, int) - Static method in class jme.JMEUtil
swap_dsn6_bytes - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
swapBytesI(int) - Method in interface javajs.api.GenericBinaryDocument
swapBytesI(int) - Method in class javajs.util.BinaryDocument
swapBytesS(short) - Method in interface javajs.api.GenericBinaryDocument
swapBytesS(short) - Method in class javajs.util.BinaryDocument
swapInt(int[], int, int) - Static method in class javajs.util.AU
swapXZ() - Method in class org.jmol.jvxl.readers.JvxlReader
swapXZ() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
swapXZ() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
sweep_angle - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sweep_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sweep_phase - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
sweep_speed - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
SwingConstants - Class in org.jmol.awtjs.swing
SwingConstants() - Constructor for class org.jmol.awtjs.swing.SwingConstants
SwingController - Interface in org.jmol.awtjs.swing
  SwingController is an interface that org.jmol.awtjs.swing classes will need.
swipeCount - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
swipeCutoff - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
swipeDelayMs - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
swipeFactor - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
swipeStartTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
switchAtoms() - Method in class org.jmol.util.ContactPair
switchcmd - Static variable in class org.jmol.script.T
sX - Variable in class org.jmol.util.Point3fi
  screen X
sY - Variable in class org.jmol.util.Point3fi
  screen Y
sym - Variable in class org.jmol.symmetry.CLEG.ClegData
symbol - Static variable in class org.jmol.script.T
symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
symMatrix - Variable in class org.jmol.util.Tensor
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
symmetry - Static variable in class org.jmol.script.T
Symmetry - Class in org.jmol.symmetry
Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
SymmetryDesc - Class in org.jmol.symmetry
  A class to handle requests for information about space groups and symmetry operations.
SymmetryDesc() - Constructor for class org.jmol.symmetry.SymmetryDesc
symmetryhermannmauguin - Static variable in class org.jmol.script.T
SymmetryInterface - Interface in org.jmol.api
SymmetryOperation - Class in org.jmol.symmetry
symmetryOperations - Variable in class org.jmol.symmetry.SpaceGroup
symmform - Variable in class org.jmol.util.Vibration
symop - Static variable in class org.jmol.script.T
symopColixes - Variable in class org.jmol.shape.Mesh
symopNormixes - Variable in class org.jmol.shape.Mesh
symops - Variable in class org.jmol.adapter.readers.cif.CifReader
symops - Variable in class org.jmol.shape.Mesh
sync - Static variable in class org.jmol.script.T
SYNC - Enum constant in enum class org.jmol.c.CBK
SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
SYNCCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
syncFromJmol(JSViewer, String) - Static method in class jspecview.common.SyncManager
  incoming script processing of invalid input: '<'PeakAssignment file="" type="xxx"...> record from Jmol
syncID - Variable in class jspecview.common.JSViewer
SYNCID - Enum constant in enum class jspecview.common.ScriptToken
syncingScripts - Variable in class org.jmol.viewer.StatusManager
SyncManager - Class in jspecview.common
SyncManager() - Constructor for class jspecview.common.SyncManager
syncmouse - Static variable in class org.jmol.script.T
syncscript - Static variable in class org.jmol.script.T
syncScript(String) - Method in interface jspecview.api.JSVAppletInterface
  precede invalid input: '<'Peaks here with full name of Jmol applet (including syncID)
syncScript(String) - Method in class jspecview.app.JSVApp
syncScript(String) - Method in class jspecview.appletjs.JSVApplet
syncScript(String) - Method in class jspecview.application.JSpecView
syncScript(String) - Method in class jspecview.common.JSViewer
  / Jmol sychronization
syncScript(String) - Method in interface org.jmol.api.JmolSyncInterface
syncScript(String) - Method in class org.jmol.util.GenericApplet
syncScript(String) - Method in class org.openscience.jmol.app.status.StatusListener
syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
syncScript(Viewer, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
syncSend(String, Object, int) - Method in class org.jmol.viewer.StatusManager
syncToJmol(String) - Method in interface jspecview.api.ScriptInterface
syncToJmol(String) - Method in class jspecview.app.JSVApp
syncToJmol(String) - Method in class jspecview.application.JSpecView
syncToJmol(String) - Method in interface org.jmol.api.JSVInterface
syncToJmol(String) - Method in class org.openscience.jmol.app.status.StatusListener
syntaxError(String) - Method in class javajs.util.JSJSONParser
  Make a JSONException to signal a syntax error.
sZ - Variable in class org.jmol.util.Point3fi
  screen Z

## T

t(int) - Static method in class org.jmol.script.T
T - Class in org.jmol.script
  Script token class.
T() - Constructor for class org.jmol.script.T
T_SHAPED - Static variable in class org.jmol.smiles.SmilesStereo
T3 - Class in javajs.util
  A generic 3 element tuple that is represented by single precision floating point x,y and z coordinates.
T3() - Constructor for class javajs.util.T3
T3d - Class in javajs.util
  A generic 3 element tuple that is represented by double precision floating point x,y and z coordinates.
T3d() - Constructor for class javajs.util.T3d
  Constructs and initializes a Tuple3d to (0,0,0).
T3i - Class in javajs.util
  A 3-element tuple represented by signed integer x,y,z coordinates.
T3i() - Constructor for class javajs.util.T3i
  Constructs and initializes a Tuple3i to (0,0,0).
T4 - Class in javajs.util
  A generic 4 element tuple that is represented by single precision floating point x,y,z and w coordinates.
T4() - Constructor for class javajs.util.T4
  Constructs and initializes a Tuple4f to (0,0,0,0).
tableCellAlignLeft - Variable in class jspecview.java.AwtDialog
tableCellAlignLeft - Variable in class jspecview.js2d.JsDialog
TableCellRenderer - Interface in org.jmol.awtjs.swing
TableColumn - Interface in org.jmol.awtjs.swing
tableModel - Variable in class org.openscience.jmol.app.janocchio.TableSorter
TableSorter - Class in org.openscience.jmol.app.janocchio
TableSorter() - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
TableSorter(TableModel) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
TableSorter(TableModel, JTableHeader) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
taConvert(Spectrum, Spectrum.IRMode) - Static method in class jspecview.common.Spectrum
TAG_NONE - Static variable in class jspecview.source.XMLParser
tagName - Variable in class jspecview.source.AnIMLReader
tagName - Variable in class jspecview.source.NMRMLReader
tags - Static variable in class org.jmol.quantum.QS
tags2 - Static variable in class org.jmol.quantum.QS
TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_BONDINGRADIUS - Static variable in class org.jmol.modelset.AtomCollection
TAINT_CHAIN - Static variable in class org.jmol.modelset.AtomCollection
TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_RESNO - Static variable in class org.jmol.modelset.AtomCollection
TAINT_SEQID - Static variable in class org.jmol.modelset.AtomCollection
TAINT_SITE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
taintAtom(int, int) - Method in class org.jmol.modelset.AtomCollection
taintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
tainted - Variable in class org.jmol.modelset.AtomCollection
  // SETTABLE atomic properties ///////////////
tan - Static variable in class org.jmol.script.T
target - Variable in class org.jmol.modelset.Text
targetTime - Variable in class org.jmol.thread.JmolThread
TBI_AB - Static variable in class org.jmol.minimize.forcefield.ForceField
TBI_BC - Static variable in class org.jmol.minimize.forcefield.ForceField
TBI_CD - Static variable in class org.jmol.minimize.forcefield.ForceField
TEAL - Static variable in class org.jmol.util.C
techname - Variable in class jspecview.source.AnIMLReader
techname - Variable in class jspecview.source.NMRMLReader
temp - Static variable in class org.jmol.adapter.readers.cif.BCIFReader
TEMP - Enum constant in enum class org.jmol.c.PAL
TEMP - Enum constant in enum class org.jmol.c.VDW
TempArray - Class in org.jmol.util
TempArray() - Constructor for class org.jmol.util.TempArray
temperature - Static variable in class org.jmol.script.T
templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
tempP1 - Variable in class org.jmol.export.___Exporter
tempP2 - Variable in class org.jmol.export.___Exporter
tempP3 - Variable in class org.jmol.export.___Exporter
tempQ1 - Variable in class org.jmol.export._VrmlExporter
tempQ2 - Variable in class org.jmol.export._VrmlExporter
tempQ3 - Variable in class org.jmol.export._VrmlExporter
tempStatement - Variable in class org.jmol.script.ScriptEval
tempV1 - Variable in class org.jmol.export.___Exporter
tempV2 - Variable in class org.jmol.export.___Exporter
tensor - Static variable in class org.jmol.script.T
tensor - Variable in class org.jmol.shapespecial.Ellipsoid
Tensor - Class in org.jmol.util
Tensor() - Constructor for class org.jmol.util.Tensor
  Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods.
tensors - Variable in class org.jmol.adapter.smarter.Atom
tensScale - Static variable in class javajs.util.PT
terminateEmptyTag(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
terminateTag(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
test() - Static method in class javajs.util.Measure
test(String) - Static method in class javajs.util.DebugJS
  Insert a JavaScript debug statement
Test - Class in org.openscience.jmol.app.webexport
TEST - Enum constant in enum class jspecview.common.ScriptToken
test1 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
test2 - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
testAsync - Variable in class org.jmol.viewer.Viewer
testflag1 - Static variable in class org.jmol.script.T
testflag2 - Static variable in class org.jmol.script.T
testflag3 - Static variable in class org.jmol.script.T
testflag4 - Static variable in class org.jmol.script.T
testFlags - Variable in class org.jmol.jvxl.readers.Parameters
testRule6Full - Variable in class org.jmol.symmetry.CIPData
  A flag that, if set, returns rr for bicyclo[2.2.2]octane
TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
text - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
text - Variable in class jspecview.common.Annotation
text - Variable in class org.jmol.awtjs.swing.Component
text - Variable in class org.jmol.modelset.Measurement
text - Variable in class org.jmol.modelset.MeasurementData
text - Variable in class org.jmol.modelset.Text
text - Variable in class org.jmol.shape.Hover
Text - Class in org.jmol.modelset
Text() - Constructor for class org.jmol.modelset.Text
TEXT_ALIGN_CENTER - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_LEFT - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_NONE - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_RIGHT - Static variable in class org.jmol.viewer.JC
textAlign - Variable in class org.jmol.render.LabelsRenderer
TextShape - Class in org.jmol.shape
TextShape() - Constructor for class org.jmol.shape.TextShape
textUnformatted - Variable in class org.jmol.modelset.Text
texture_fonts - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
textY - Variable in class org.jmol.util.GData
thePlane - Variable in class org.jmol.jvxl.readers.Parameters
thePlane - Variable in class org.jmol.render.MeshRenderer
theta - Static variable in class org.jmol.script.T
theta0 - Variable in class org.jmol.minimize.MinAngle
theTok - Variable in class org.jmol.script.ScriptParam
theTok - Variable in class org.jmol.script.ScriptCompiler
theToken - Variable in class org.jmol.script.ScriptParam
theToken - Variable in class org.jmol.script.ScriptCompiler
this_ - Static variable in class org.jmol.script.T
THIS_MODEL_ONLY - Static variable in class org.jmol.viewer.JC
  specifically for ECHO and DRAW to have these specific for a given model and only appearing when there is only one model showing (see MODELKIT SET KEY ON)
thisAtom - Variable in class org.jmol.adapter.readers.xml.XmlReader
thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
thisBiomolecule - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
thisCommand - Variable in class org.jmol.script.ScriptEval
thisContext - Variable in class org.jmol.script.ScriptParam
thisContour - Variable in class org.jmol.jvxl.data.JvxlData
thisDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
thisID - Variable in class org.jmol.modelset.Measurement
thisID - Variable in class org.jmol.modelset.MeasurementData
thisID - Variable in class org.jmol.shape.Mesh
thisID - Variable in class org.jmol.shape.TextShape
thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
thisJsvp - Variable in class jspecview.popup.JSVGenericPopup
thisMesh - Variable in class org.jmol.shapesurface.Isosurface
thismodel - Static variable in class org.jmol.script.T
thisModelOnly - Variable in class org.jmol.modelset.Text
thisModelOnly - Variable in class org.jmol.shapespecial.DrawMesh
thisPopup - Variable in class org.jmol.popup.GenericPopup
thisSet - Variable in class org.jmol.jvxl.data.JvxlData
thisValue() - Method in class jspecview.source.XMLParser
  for value without surrounding tag
thisWidget - Variable in class jspecview.common.PanelData
thisx - Variable in class org.jmol.popup.GenericPopup
thisy - Variable in class org.jmol.popup.GenericPopup
throwcmd - Static variable in class org.jmol.script.T
tickA - Variable in class org.jmol.render.FontLineShapeRenderer
tickAs - Variable in class org.jmol.render.FontLineShapeRenderer
tickB - Variable in class org.jmol.render.FontLineShapeRenderer
tickBs - Variable in class org.jmol.render.FontLineShapeRenderer
tickEdges - Variable in class org.jmol.render.AxesRenderer
tickEdges - Variable in class org.jmol.render.BbcageRenderer
tickEdges - Variable in class org.jmol.render.UccageRenderer
tickInfo - Variable in class org.jmol.modelset.Measurement
tickInfo - Variable in class org.jmol.modelset.MeasurementData
tickInfo - Variable in class org.jmol.render.FontLineShapeRenderer
TickInfo - Class in org.jmol.modelset
TickInfo(P3) - Constructor for class org.jmol.modelset.TickInfo
tickInfos - Variable in class org.jmol.shape.FontLineShape
tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
tickParamAsStr(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
ticks - Variable in class org.jmol.modelset.TickInfo
ticks - Static variable in class org.jmol.script.T
time - Variable in class jspecview.export.AMLExporter
time - Variable in class jspecview.export.CMLExporter
time - Variable in class jspecview.source.JDXHeader
time - Variable in class org.jmol.viewer.MouseState
timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
timeout - Static variable in class org.jmol.script.T
timeouts - Variable in class org.jmol.viewer.Viewer
TimeoutThread - Class in org.jmol.thread
TimeoutThread(Viewer, String, int, String) - Constructor for class org.jmol.thread.TimeoutThread
times - Static variable in class org.jmol.script.T
timestimes - Static variable in class org.jmol.script.T
timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
TinkerReader - Class in org.jmol.adapter.readers.simple
  simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
TinkerReader() - Constructor for class org.jmol.adapter.readers.simple.TinkerReader
title - Variable in class jspecview.common.PrintLayout
title - Variable in class jspecview.dialog.JSVDialog
title - Variable in class jspecview.export.AMLExporter
title - Variable in class jspecview.export.CMLExporter
title - Variable in class jspecview.source.JDXHeader
title - Variable in class jspecview.source.AnIMLReader
title - Variable in class jspecview.source.NMRMLReader
title - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
title - Variable in class org.jmol.console.ScriptEditor
title - Variable in class org.jmol.jvxl.data.JvxlData
title - Variable in class org.jmol.jvxl.readers.Parameters
title - Static variable in class org.jmol.script.T
title - Variable in class org.jmol.shape.Mesh
title - Variable in class org.jmol.shape.MeshCollection
TITLEBOLDON - Enum constant in enum class jspecview.common.ScriptToken
titleColor - Variable in class jspecview.common.PanelData
titleColor - Variable in class org.jmol.shapespecial.DrawMesh
TITLECOLOR - Enum constant in enum class jspecview.common.ScriptToken
titleFontName - Variable in class jspecview.common.ColorParameters
TITLEFONTNAME - Enum constant in enum class jspecview.common.ScriptToken
titleformat - Static variable in class org.jmol.script.T
titleOn - Variable in class jspecview.common.PanelData
TITLEON - Enum constant in enum class jspecview.common.ScriptToken
TlsDataOnlyReader - Class in org.jmol.adapter.readers.more
TlsDataOnlyReader() - Constructor for class org.jmol.adapter.readers.more.TlsDataOnlyReader
tm - Variable in class org.jmol.export.___Exporter
tm - Variable in class org.jmol.render.ShapeRenderer
tm - Variable in class org.jmol.viewer.Viewer
tmpEnd - Variable in class jspecview.source.AnIMLReader
tmpEnd - Variable in class jspecview.source.NMRMLReader
to - Static variable in class org.jmol.script.T
TO_ABS - Enum constant in enum class jspecview.common.Spectrum.IRMode
TO_TRANS - Enum constant in enum class jspecview.common.Spectrum.IRMode
to3D(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
toArray() - Method in class org.jmol.script.SV
TOAU_ANGSTROMS - Static variable in class org.qcschema.QCSchemaUnits
TOAU_AU - Static variable in class org.qcschema.QCSchemaUnits
TOAU_BOHR - Static variable in class org.qcschema.QCSchemaUnits
TOAU_CM - Static variable in class org.qcschema.QCSchemaUnits
TOAU_CM_1 - Static variable in class org.qcschema.QCSchemaUnits
TOAU_EV - Static variable in class org.qcschema.QCSchemaUnits
TOAU_HARTREE - Static variable in class org.qcschema.QCSchemaUnits
TOAU_KCAL_MOL - Static variable in class org.qcschema.QCSchemaUnits
TOAU_KJ_MOL - Static variable in class org.qcschema.QCSchemaUnits
TOAU_M - Static variable in class org.qcschema.QCSchemaUnits
toAxisAngle4f() - Method in class javajs.util.Quat
toByteArray() - Method in class javajs.util.OC
toBytes(int, int) - Method in class javajs.util.SB
  simple byte conversion properly implementing UTF-8.
toCartesian(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
toCartesian(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
toCartesian(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
toCartesian(T3, boolean) - Method in class org.jmol.viewer.Viewer
  absolute or relative to origin of UNITCELL {x y z}
toCartesianSpin(T3) - Method in interface org.jmol.api.SymmetryInterface
toCartesianSpin(T3) - Method in class org.jmol.symmetry.Symmetry
toCartesianSpin(T3) - Method in class org.jmol.symmetry.UnitCell
toCartesianUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
toCDXML() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
toCSSString(GenericColor) - Static method in class javajs.util.CU
toExternalForm(URL) - Method in class javajs.util.AjaxURLStreamHandler
toFFGGGfromRGB(int) - Static method in class javajs.util.CU
  Return a greyscale rgb value 0-FF using NTSC color lightness algorithm
toFractional(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
toFractional(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
toFractional(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
toFractional(T3, boolean) - Method in class org.jmol.viewer.Viewer
toFractionalM(M4) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
toFractionalM(M4) - Method in class org.jmol.util.SimpleUnitCell
toFractionalSpin(T3) - Method in interface org.jmol.api.SymmetryInterface
toFractionalSpin(T3) - Method in class org.jmol.symmetry.Symmetry
toFractionalSpin(T3) - Method in class org.jmol.symmetry.UnitCell
toFractionalUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
toFromPrimitive(boolean, char, T3[], M3) - Method in interface org.jmol.api.SymmetryInterface
toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.Symmetry
toFront() - Method in class org.jmol.awtjs.swing.JDialog
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
TOGGLE - Enum constant in enum class jspecview.common.IntegralData.IntMode
TOGGLE - Enum constant in enum class jspecview.common.Spectrum.IRMode
toggleCoordinate() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that toggles the coordinate on a `JSVPanel`
toggleCoordinate() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that toggles the coordinate on a `JSVPanel`
toggleCoordinate() - Method in class jspecview.appletjs.JSVApplet
toggleGrid() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that toggles the grid on a `JSVPanel`
toggleGrid() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that toggles the grid on a `JSVPanel`
toggleGrid() - Method in class jspecview.appletjs.JSVApplet
toggleInPlace(BS, BS) - Static method in class org.jmol.util.BSUtil
  a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
toggleIntegration() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that toggles the integration graph of a `JSVPanel`.
toggleIntegration() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that toggles the integration graph of a `JSVPanel`.
toggleIntegration() - Method in class jspecview.appletjs.JSVApplet
togglelabel - Static variable in class org.jmol.script.T
toggleMode() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
togglePointsOnly() - Method in interface jspecview.api.JSVAppletInterface
  Method that can be called from another applet or from javascript that toggles the flag for points only on a `JSVPanel`
togglePointsOnly() - Method in class jspecview.app.JSVApp
  Method that can be called from another applet or from javascript that toggles the coordinate on a `JSVPanel`
togglePointsOnly() - Method in class jspecview.appletjs.JSVApplet
toHTML() - Method in class org.jmol.awtjs.swing.Component
toHTML() - Method in class org.jmol.awtjs.swing.JButton
toHTML() - Method in class org.jmol.awtjs.swing.JCheckBox
toHTML() - Method in class org.jmol.awtjs.swing.JComboBox
toHTML() - Method in class org.jmol.awtjs.swing.JContentPane
toHTML() - Method in class org.jmol.awtjs.swing.JDialog
toHTML() - Method in class org.jmol.awtjs.swing.JEditorPane
toHTML() - Method in class org.jmol.awtjs.swing.JLabel
toHTML() - Method in class org.jmol.awtjs.swing.JMenu
toHTML() - Method in class org.jmol.awtjs.swing.JMenuItem
toHTML() - Method in class org.jmol.awtjs.swing.JPanel
toHTML() - Method in class org.jmol.awtjs.swing.JPopupMenu
toHTML() - Method in class org.jmol.awtjs.swing.JScrollPane
toHTML() - Method in class org.jmol.awtjs.swing.JSplitPane
toHTML() - Method in class org.jmol.awtjs.swing.JTable
toHTML() - Method in class org.jmol.awtjs.swing.JTextField
toHTML() - Method in class org.jmol.awtjs.swing.JTextPane
toHTML(String) - Method in class org.jmol.awtjs.swing.Cell
toHTML(String) - Method in class org.jmol.awtjs.swing.Grid
toHTML(SB, String, BS) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
toJSON() - Method in interface javajs.api.JSONEncodable
toJSON() - Method in class javajs.util.A4
toJSON() - Method in class javajs.util.BS
toJSON() - Method in class javajs.util.T3
toJSON() - Method in class javajs.util.T4
toJSON() - Method in class org.jmol.script.SV
toJSON(String, Object) - Static method in class javajs.util.PT
toJSONBytes(Map) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
  Guaranteed to create a clean no-whitespace JSON stream terminated by a single \n.
tok - Variable in class org.jmol.script.T
tokAction - Variable in class org.jmol.modelset.MeasurementData
tokAt(int) - Method in class org.jmol.script.ScriptCompiler
tokAt(int) - Method in class org.jmol.script.ScriptParam
tokAt(int) - Method in class org.jmol.scriptext.ScriptExt
tokAttr(int, int) - Static method in class org.jmol.script.T
tokAttrOr(int, int, int) - Static method in class org.jmol.script.T
tokCommand - Variable in class org.jmol.script.ScriptCompiler
tokenAll - Static variable in class org.jmol.script.T
tokenAnd - Static variable in class org.jmol.script.T
tokenAndEquals - Variable in class org.jmol.script.ScriptCompiler
tokenAndFALSE - Static variable in class org.jmol.script.T
tokenAndSpec - Static variable in class org.jmol.script.T
tokenArrayClose - Static variable in class org.jmol.script.T
tokenArrayOpen - Static variable in class org.jmol.script.T
tokenArraySquare - Static variable in class org.jmol.script.T
tokenAttr(T, int) - Static method in class org.jmol.script.ScriptCompiler
tokenColon - Static variable in class org.jmol.script.T
tokenComma - Static variable in class org.jmol.script.T
tokenCommand - Variable in class org.jmol.script.ScriptCompiler
tokenConnected - Static variable in class org.jmol.script.T
tokenCoordinateBegin - Static variable in class org.jmol.script.T
tokenCoordinateEnd - Static variable in class org.jmol.script.T
tokenDefineString - Static variable in class org.jmol.script.T
tokenDivide - Static variable in class org.jmol.script.T
tokenEquals - Static variable in class org.jmol.script.T
tokenExpressionBegin - Static variable in class org.jmol.script.T
tokenExpressionEnd - Static variable in class org.jmol.script.T
tokenIf - Static variable in class org.jmol.script.T
tokenize(String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
  Take the given string and chop it up into a series of strings on whitespace boundries.
tokenLeftBrace - Static variable in class org.jmol.script.T
tokenLeftParen - Static variable in class org.jmol.script.T
tokenLength - Static variable in class org.jmol.script.T
tokenMinus - Static variable in class org.jmol.script.T
tokenMul3 - Static variable in class org.jmol.script.T
tokenOff - Static variable in class org.jmol.script.T
tokenOn - Static variable in class org.jmol.script.T
tokenOpIf - Static variable in class org.jmol.script.T
tokenOr - Static variable in class org.jmol.script.T
tokenOrTRUE - Static variable in class org.jmol.script.T
tokenPlus - Static variable in class org.jmol.script.T
tokenRightBrace - Static variable in class org.jmol.script.T
tokenRightParen - Static variable in class org.jmol.script.T
tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  /////////////////////////////////////////////////////////////
tokens - Variable in class org.jmol.symmetry.CLEG.ClegData
tokenScript - Static variable in class org.jmol.script.T
tokenSet - Static variable in class org.jmol.script.T
tokenSetArray - Static variable in class org.jmol.script.T
tokenSetCmd - Static variable in class org.jmol.script.T
tokenSetProperty - Static variable in class org.jmol.script.T
tokenSetVar - Static variable in class org.jmol.script.T
tokenSpaceBeforeSquare - Static variable in class org.jmol.script.T
tokenSwitch - Static variable in class org.jmol.script.T
tokenTimes - Static variable in class org.jmol.script.T
toLABnorm(int) - Method in class javajs.img.GifEncoder
  ////////////////////// CIE Lab / XYZ / sRGB conversion methods /////////
toMap(byte[]) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
toMOL() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
toOABC(P3[], T3) - Static method in class org.jmol.util.BoxInfo
  Delivers [center a b c] for generation of unit cells from a boundbox
toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
top - Static variable in class org.jmol.script.T
topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
toPeak(int) - Method in class jspecview.common.PanelData
topMargin - Static variable in class jspecview.common.PanelData
toPNG(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
TopoCifParser - Class in org.jmol.adapter.readers.cif
  see https://github.com/COMCIFS/TopoCif Basic idea: We have TLinks, TNodes, and TAtoms TLinks each have two TNodes and may also be associated with bridging TAtom sets.
TopoCifParser() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser
toPoint4f() - Method in class javajs.util.Quat
  Quaternions are saved as {q1, q2, q3, q0} While this may seem odd, it is so that for any point4 -- planes, axisangles, and quaternions -- we can use the first three coordinates to determine the relavent axis the fourth then gives us offset to {0,0,0} (plane), rotation angle (axisangle), and cos(theta/2) (quaternion).
toRadians - Static variable in class org.jmol.util.SimpleUnitCell
toReadable(String, Object) - Static method in class org.jmol.util.Escape
  Used only for getProperty("readable",...)
toRGB(P3) - Method in class javajs.img.GifEncoder
toRGB3f(int, float[]) - Static method in class javajs.util.CU
toRGBHexString(GenericColor) - Static method in class javajs.util.CU
torsion - Static variable in class org.jmol.script.T
toStdAmino3(String) - Method in class org.jmol.modelsetbio.BioResolver
toString() - Method in class com.sparshui.common.Location
toString() - Method in class com.sparshui.common.messages.events.DragEvent
toString() - Method in class com.sparshui.common.messages.events.FlickEvent
toString() - Method in class com.sparshui.common.messages.events.RotateEvent
toString() - Method in class com.sparshui.common.messages.events.SpinEvent
toString() - Method in class com.sparshui.common.messages.events.TouchEvent
toString() - Method in class com.sparshui.common.messages.events.ZoomEvent
toString() - Method in enum class io.github.dan2097.jnainchi.InchiFlag
toString() - Method in class javajs.util.A4
  Returns a string that contains the values of this AxisAngle4f.
toString() - Method in class javajs.util.BArray
toString() - Method in class javajs.util.BS
  Returns a string representation of this bit set.
toString() - Method in class javajs.util.M3
  Returns a string that contains the values of this Matrix3f.
toString() - Method in class javajs.util.M4
  Returns a string that contains the values of this Matrix4f.
toString() - Method in class javajs.util.Matrix
toString() - Method in class javajs.util.OC
toString() - Method in class javajs.util.Quat
  Java axisAngle / plane / Point4f format all have the format {x y z w} so we go with that here as well
toString() - Method in class javajs.util.SB
toString() - Method in class javajs.util.T3
  Returns a string that contains the values of this Tuple3f.
toString() - Method in class javajs.util.T3d
  Returns a string that contains the values of this Tuple3d.
toString() - Method in class javajs.util.T3i
  Returns a string that contains the values of this Tuple3i.
toString() - Method in class javajs.util.T4
  Returns a string that contains the values of this Tuple4f.
toString() - Method in class jspecview.common.Annotation
  Overrides Objects toString() method
toString() - Method in class jspecview.common.Coordinate
  Overides Objects toString() method
toString() - Method in class jspecview.common.Measurement
  Overrides Objects toString() method
toString() - Method in class jspecview.common.PanelNode
toString() - Method in class jspecview.common.PeakInfo
toString() - Method in class jspecview.common.PeakPickEvent
toString() - Method in class jspecview.common.Spectrum
toString() - Method in class jspecview.common.SubSpecChangeEvent
toString() - Method in class jspecview.java.AwtColor
toString() - Method in class jspecview.java.AwtPanel
  ////////
toString() - Method in class jspecview.js2d.JsPanel
toString() - Method in class jspecview.tree.SimpleTreeNode
toString() - Method in class org.jmol.adapter.smarter.Bond
toString() - Method in class org.jmol.adapter.writers.CIFWriter
toString() - Method in class org.jmol.adapter.writers.CMLWriter
toString() - Method in class org.jmol.adapter.writers.PDBWriter
toString() - Method in class org.jmol.adapter.writers.PWMATWriter
toString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
toString() - Method in class org.jmol.adapter.writers.QCJSONWriter
toString() - Method in class org.jmol.adapter.writers.XSFWriter
toString() - Method in class org.jmol.atomdata.RadiusData
toString() - Method in class org.jmol.awtjs.swing.Color
toString() - Method in class org.jmol.minimize.MinAtom
toString() - Method in class org.jmol.minimize.Minimizer
toString() - Method in class org.jmol.minimize.MinObject
toString() - Method in class org.jmol.modelset.Atom
toString() - Method in class org.jmol.modelset.Bond
toString() - Method in class org.jmol.modelset.Group
toString() - Method in class org.jmol.modelset.Measurement
toString() - Method in class org.jmol.modelset.Orientation
toString() - Method in class org.jmol.modelset.StateScript
toString() - Method in class org.jmol.modelset.Text
toString() - Method in class org.jmol.modelsetbio.BasePair
toString() - Method in class org.jmol.modelsetbio.BioPolymer
toString() - Method in class org.jmol.modelsetbio.Monomer
toString() - Method in class org.jmol.modelsetbio.ProteinStructure
toString() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
toString() - Method in class org.jmol.quantum.NMRNoeMatrix
toString() - Method in class org.jmol.quantum.SlaterData
toString() - Method in class org.jmol.script.ScriptEval
toString() - Method in exception class org.jmol.script.ScriptException
toString() - Method in class org.jmol.script.ScriptFunction
toString() - Method in class org.jmol.script.SV
toString() - Method in class org.jmol.script.T
toString() - Method in class org.jmol.smiles.SmilesAtom
toString() - Method in class org.jmol.smiles.SmilesBond
toString() - Method in class org.jmol.smiles.SmilesMeasure
toString() - Method in class org.jmol.smiles.SmilesSearch
toString() - Method in class org.jmol.symmetry.CLEG.ClegNode
toString() - Method in class org.jmol.symmetry.HallInfo
toString() - Method in class org.jmol.symmetry.SpaceGroup
toString() - Method in class org.jmol.symmetry.SymmetryOperation
toString() - Method in class org.jmol.thread.JmolThread
toString() - Method in class org.jmol.thread.TimeoutThread
toString() - Method in class org.jmol.util.BoxInfo
toString() - Method in class org.jmol.util.ContactPair
toString() - Method in class org.jmol.util.Font
toString() - Method in class org.jmol.util.Modulation
toString() - Method in class org.jmol.util.Rgb16
toString() - Method in class org.jmol.util.SimpleUnitCell
toString() - Method in class org.jmol.util.Tensor
toString() - Method in class org.openscience.jmol.app.janocchio.Measure
toString2() - Method in class org.jmol.script.T
  /////command sets ///////
toStringNormRow() - Method in class org.jmol.quantum.NMRNoeMatrix
toSupercell(P3) - Method in interface org.jmol.api.SymmetryInterface
toSupercell(P3) - Method in class org.jmol.symmetry.Symmetry
toSupercell(P3) - Method in class org.jmol.util.SimpleUnitCell
  convenience return only after changing fpt
toTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
toTrm(String, M4) - Static method in class org.jmol.symmetry.UnitCell
TOUCH_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
TOUCH_EVENT - Static variable in class com.sparshui.GestureType
TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
TOUCH_GESTURE - Static variable in class com.sparshui.GestureType
TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
TouchData() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
TouchDataComparator() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator.TouchDataComparator
TouchEvent - Class in com.sparshui.common.messages.events
TouchEvent() - Constructor for class com.sparshui.common.messages.events.TouchEvent
TouchEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.TouchEvent
  Constructs a new TouchEvent from a serialized version - 4 bytes : id - 4 bytes : x - 4 bytes : y - 4 bytes : state - 8 bytes : time - 24 bytes total
TouchEvent(int, float, float, int) - Constructor for class com.sparshui.common.messages.events.TouchEvent
TouchEvent(TouchPoint) - Constructor for class com.sparshui.common.messages.events.TouchEvent
TouchHandler() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
TouchPoint - Class in com.sparshui.server
  Represents a touch point.
TouchPoint(int, Location, long) - Constructor for class com.sparshui.server.TouchPoint
TouchPoint(TouchPoint) - Constructor for class com.sparshui.server.TouchPoint
  Copy constructor
TouchState - Class in com.sparshui.common
  Defines the types of touches that can ocurr in sparsh-UI: Birth, Move, and Death.
TouchState() - Constructor for class com.sparshui.common.TouchState
toUnicode(String) - Method in interface javajs.api.GenericCifDataParser
toUnicode(String) - Method in class javajs.util.CifDataParser
  Only translating the basic Greek set here, not all the other stuff.
toUnicode(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  There is no need to convert to unicode in CIF 2.0.
toUnitCell(P3, P3) - Method in class org.jmol.viewer.Viewer
  Returns the relative to origin without regard to offset created using the UNITCELL command.
toUnitCell(T3, T3) - Method in interface org.jmol.api.SymmetryInterface
toUnitCell(T3, T3) - Method in class org.jmol.symmetry.Symmetry
toUnitCellRnd(T3, T3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
toUnitCellRnd(T3, T3) - Method in class org.jmol.symmetry.UnitCell
  when offset is null, use the current cell, otherwise use the original unit cell
toUnits(float, String, boolean) - Static method in class org.jmol.modelset.Measurement
toUserUnits(double) - Method in class org.jmol.minimize.forcefield.ForceField
toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
tQuiet - Variable in class org.jmol.script.ScriptEval
trace - Static variable in class org.jmol.script.T
trace() - Method in class javajs.util.Matrix
  Matrix trace.
Trace - Class in org.jmol.shapebio
Trace() - Constructor for class org.jmol.shapebio.Trace
trace_atoms_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
tracealpha - Static variable in class org.jmol.script.T
tracePt - Variable in class org.jmol.util.Vibration
TraceRenderer - Class in org.jmol.renderbio
TraceRenderer() - Constructor for class org.jmol.renderbio.TraceRenderer
traceX - Variable in class org.jmol.modelset.Measurement
traceY - Variable in class org.jmol.modelset.Measurement
trajectory - Variable in class org.jmol.modelset.AtomCollection
trajectory - Static variable in class org.jmol.script.T
Trajectory - Class in org.jmol.modelset
Trajectory() - Constructor for class org.jmol.modelset.Trajectory
trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
transform - Static variable in class org.jmol.script.T
transform(T4) - Method in class javajs.util.M4
  Transform the vector vec using this Matrix4f and place the result back into vec.
transform(V3, V3) - Method in class org.jmol.jvxl.data.VolumeData
transform2(T3, T3) - Method in class javajs.util.Quat
transform2(T4, T4) - Method in class javajs.util.M4
  Transform the vector vec using this Matrix4f and place the result into vecOut.
transformAtomsToUnitCell(SymmetryInterface, T3[], String) - Method in class org.jmol.modelkit.ModelKit
  Transform the atoms to fractional coordinate, set the unit cell to a new cell, and then transform them back to Cartesians.
transformedVectors - Variable in class org.jmol.render.MeshRenderer
transformedVectors - Variable in class org.jmol.util.GData
TransformManager - Class in org.jmol.viewer
TransformManager() - Constructor for class org.jmol.viewer.TransformManager
TransformManager4D - Class in org.jmol.viewer
TransformManager4D() - Constructor for class org.jmol.viewer.TransformManager4D
transformPoints(Lst, M4, P3) - Static method in class javajs.util.Measure
transformPoints(Lst, M4, P3) - Static method in class org.jmol.script.ScriptParam
transformPt(T3) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPt2D(T3) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY
transformPt3f(T3, P3) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY
transformPt3fSafe(T3, P3) - Method in class org.jmol.viewer.TransformManager
transformPtNoClip(T3, T3) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY
transformPtSafe(T3) - Method in class org.jmol.viewer.TransformManager
transformPtScr(T3, P3i) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY
transformPtScrSafe(T3, P3i) - Method in class org.jmol.viewer.TransformManager
transformPtScrT3(T3, T3) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY
transformPtVib(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
  RENDERERS ONLY
transformPtVibSafe(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
transformUnitCell(M4) - Method in class org.jmol.symmetry.Symmetry
  Transform the unit cell based on the calculated transformation matrix.
transformXYZ(M4, BS) - Method in class org.jmol.atomdata.AtomData
  allow for transformed XYZ
translate - Static variable in class org.jmol.script.T
translate(char, float, char, BS) - Method in class org.jmol.viewer.Viewer
translate(String) - Method in interface org.jmol.api.Translator
translate(String) - Method in class org.jmol.i18n.GT
  used in custom menu translation only
translate(String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
translateModel(int, T3) - Method in class org.jmol.modelset.ModelSet
  move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE
translateScale(float, float, float) - Method in class javajs.export.PDFCreator
translateScale(Object, double, double, double) - Method in class jspecview.common.PDFWriter
translateScale(Object, double, double, double) - Method in class jspecview.java.AwtG2D
translateScale(Object, double, double, double) - Method in class jspecview.js2d.JsG2D
translateScale(Object, double, double, double) - Method in interface org.jmol.api.GenericGraphics
translateScale(Object, double, double, double) - Method in class org.jmol.awt.AwtG2D
translateScale(Object, double, double, double) - Method in class org.jmol.awtjs2d.JsG2D
translateSelected - Static variable in class org.jmol.script.T
translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
translation - Static variable in class org.jmol.script.T
translations - Variable in class org.jmol.modelset.ModelSet
Translator - Interface in org.jmol.api
translucency - Variable in class org.jmol.jvxl.data.JvxlData
translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
translucent - Static variable in class org.jmol.script.T
TRANSLUCENT_MASK - Static variable in class org.jmol.util.C
TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.C
TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.C
translucentAllowed - Variable in class org.jmol.shape.Shape
translucentCoverOnly - Variable in class org.jmol.util.GData
translucentLevel - Variable in class org.jmol.shape.Shape
transparency - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
transparency_global_sort - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
transparency_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
transparency_picking_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
TRANSPARENT - Static variable in class org.jmol.util.C
TRANSPARENT_LEVEL - Static variable in class org.jmol.util.C
transpose() - Method in class javajs.util.M3
  Sets the value of this matrix to its transpose.
transpose() - Method in class javajs.util.M4
  Sets the value of this matrix to its transpose.
transpose() - Method in class javajs.util.Matrix
  Matrix transpose.
transpose33() - Method in class javajs.util.M34
transposeM(M3) - Method in class javajs.util.M3
  Sets the value of this matrix to the transpose of the argument matrix
treeNode - Variable in class jspecview.common.PanelNode
triangle_max_passes - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
TriangleData - Class in org.jmol.util
  An adaptation of Marching Cubes that allows for indicating edges on triangles.
TriangleData() - Constructor for class org.jmol.util.TriangleData
triangleHeight(double, double, double) - Static method in class jme.JMEUtil
  Compute the height of a triangle knowing the length of each side.
TriangleRenderer - Class in org.jmol.g3d
  renders triangles
TriangleRenderer() - Constructor for class org.jmol.g3d.TriangleRenderer
triangles - Static variable in class org.jmol.script.T
triangles - Variable in class org.jmol.shapespecial.Polyhedron
triangleTable2 - Static variable in class org.jmol.util.TriangleData
  The new triangle table developed specifically for Jmol.
triangulateFaces(int[][], P3[], int[][]) - Method in class org.jmol.util.MeshCapper
  generic entry for a set of faces
triangulatePolygon(P3[], int) - Method in class org.jmol.util.MeshCapper
  generic entry for a polygon
Triangulator - Class in org.jmol.util
Triangulator() - Constructor for class org.jmol.util.Triangulator
TRICOLOR_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
trigger(Map, String) - Static method in class org.jmol.thread.TimeoutThread
triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
TRIGONAL_PYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
trim - Static variable in class org.jmol.script.T
trim(String, String) - Static method in class javajs.util.PT
trim_dots - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
trimGUI(String) - Method in class org.jmol.console.GenericConsole
trimQuotes(String) - Static method in class javajs.util.PT
trMat - Variable in class org.jmol.symmetry.CLEG.ClegData
trycmd - Static variable in class org.jmol.script.T
tryPt - Variable in class org.jmol.viewer.Viewer
TURN - Enum constant in enum class org.jmol.c.STR
tv(int, int, Object) - Static method in class org.jmol.script.T
twelfthify(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
twelfthify(P3) - Method in class org.jmol.util.SimpleUnitCell
twelfthsOf(float) - Method in class org.jmol.util.SimpleUnitCell
twistedsheets - Static variable in class org.jmol.script.T
twistedSheets - Variable in class org.jmol.modelsetbio.BioPolymer
two_sided_lighting - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
twoDEditorAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
TwoDEditorAction(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
twoDEditorActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
twodots - Static variable in class org.jmol.render.FontLineShapeRenderer
twoPI - Static variable in class org.jmol.util.Vibration
TwoPointGesture - Class in org.jmol.multitouch.sparshui
  TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
Txt - Class in org.jmol.util
Txt() - Constructor for class org.jmol.util.Txt
txt1 - Variable in class jspecview.dialog.JSVDialog
txt2 - Variable in class jspecview.dialog.JSVDialog
txt3 - Variable in class jspecview.dialog.JSVDialog
type - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
type - Variable in class jspecview.dialog.JSVDialog
type - Variable in class jspecview.source.JDXSource
type - Variable in class org.jmol.minimize.MinObject
type - Variable in class org.jmol.minimize.MMConstraint
type - Variable in class org.jmol.modelset.TickInfo
type - Variable in class org.jmol.modelsetbio.BioPolymer
type - Static variable in class org.jmol.script.T
type - Variable in class org.jmol.util.Tensor
TYPE - Enum constant in enum class org.jmol.c.PAL
TYPE_ADP - Static variable in class org.jmol.util.Tensor
TYPE_AMINO - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_ANGLE - Static variable in class org.jmol.minimize.MMConstraint
TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
TYPE_ATROPISOMER - Static variable in class org.jmol.util.Edge
TYPE_ATROPISOMER_REV - Static variable in class org.jmol.util.Edge
TYPE_BIO_CROSSLINK - Static variable in class org.jmol.smiles.SmilesBond
TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
TYPE_BLOCK - Static variable in class jspecview.source.JDXSource
TYPE_BUTTON - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_CHARGE - Static variable in class org.jmol.util.Tensor
TYPE_CHECKBOX - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_CSA - Static variable in class org.jmol.util.Tensor
TYPE_DIHEDRAL - Static variable in class org.jmol.minimize.MMConstraint
TYPE_DISP_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_DISP_LEGENDRE - Static variable in class org.jmol.util.Modulation
TYPE_DISP_SAWTOOTH - Static variable in class org.jmol.util.Modulation
TYPE_DISTANCE - Static variable in class org.jmol.minimize.MMConstraint
TYPE_EFG - Static variable in class org.jmol.util.Tensor
TYPE_FRIEZE - Static variable in class org.jmol.symmetry.SpaceGroup
TYPE_INVALID - Static variable in class org.jmol.symmetry.SpaceGroup
TYPE_ISC - Static variable in class org.jmol.util.Tensor
TYPE_ISO - Static variable in class org.jmol.util.Tensor
TYPE_LAYER - Static variable in class org.jmol.symmetry.SpaceGroup
TYPE_MENU - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_MS - Static variable in class org.jmol.util.Tensor
TYPE_NOBONDING - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
TYPE_NTUPLE - Static variable in class jspecview.source.JDXSource
TYPE_NUCLEIC - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_OCC_CRENEL - Static variable in class org.jmol.util.Modulation
TYPE_OCC_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_OTHER - Static variable in class org.jmol.util.Tensor
TYPE_PLANE - Static variable in class org.jmol.symmetry.SpaceGroup
TYPE_QUADRUPOLE - Static variable in class org.jmol.util.Tensor
TYPE_RADIO - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_RAMAN - Static variable in class org.jmol.util.Tensor
TYPE_REFERENCE - Static variable in class org.jmol.symmetry.CLEG.ClegNode
TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
TYPE_ROD - Static variable in class org.jmol.symmetry.SpaceGroup
TYPE_SEPARATOR - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_SIMPLE - Static variable in class jspecview.source.JDXSource
TYPE_SPACE - Static variable in class org.jmol.symmetry.SpaceGroup
TYPE_SPIN - Static variable in class org.jmol.util.Vibration
TYPE_SPIN_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_SPIN_SAWTOOTH - Static variable in class org.jmol.util.Modulation
TYPE_TLS_R - Static variable in class org.jmol.util.Tensor
TYPE_TLS_U - Static variable in class org.jmol.util.Tensor
TYPE_U_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_U_LEGENDRE - Static variable in class org.jmol.util.Modulation
TYPE_UNKNOWN - Static variable in class jspecview.source.JDXSource
TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
TYPE_VIBRATION - Static variable in class org.jmol.util.Vibration
TYPE_VIEW - Static variable in class jspecview.source.JDXSource
TYPE_WYCKOFF - Static variable in class org.jmol.util.Vibration
typeName - Variable in class org.jmol.script.ScriptFunction
TYPES - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
typeSymbol - Variable in class org.jmol.adapter.smarter.Atom

## U

U_LIST - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
uABsM(String) - Static method in class org.jmol.util.Escape
uc - Variable in class org.jmol.adapter.writers.CIFWriter
UC_MOREINFO - Static variable in class org.jmol.viewer.JC
UC_TOLERANCE2 - Static variable in class org.jmol.viewer.JC
  used to compare two atom *fractional* positions in order to see if they are at the same position.
Uccage - Class in org.jmol.shape
Uccage() - Constructor for class org.jmol.shape.Uccage
UccageRenderer - Class in org.jmol.render
UccageRenderer() - Constructor for class org.jmol.render.UccageRenderer
uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
ucItems - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
unaryMinus - Static variable in class org.jmol.script.T
unbind - Static variable in class org.jmol.script.T
unbindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
unbindName(int, String) - Method in class org.jmol.viewer.binding.Binding
unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
  called from org.jmol.modelsetbio.resolver when adding hydrogens.
undo - Static variable in class org.jmol.script.T
undoauto - Static variable in class org.jmol.script.T
undomax - Static variable in class org.jmol.script.T
undomove - Static variable in class org.jmol.script.T
undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.Viewer
unescape(String) - Static method in class javajs.util.BS
unescapeMatrix(String) - Static method in class org.jmol.util.Escape
unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.SV
unescapeString(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
unescapeStringArray(String) - Static method in class org.jmol.util.Escape
unescapeUnicode(String) - Static method in class org.jmol.util.Escape
uniqueID - Variable in class org.jmol.adapter.smarter.Bond
unitAxisVectors - Static variable in class org.jmol.viewer.JC
unitcell - Static variable in class org.jmol.script.T
unitCell - Variable in class org.jmol.shape.Mesh
unitCell - Variable in class org.jmol.symmetry.Symmetry
UnitCell - Class in org.jmol.symmetry
  a class pseudoprivate to the org.jmol.symmetry and org.jmol.applet.smarter.FileSymmetry to be accessed generally only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
UNITCELL_PREFIX - Static variable in class org.jmol.viewer.JC
unitcellcolor - Static variable in class org.jmol.script.T
unitCellEquals(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
unitCellEquals(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
UnitCellIterator - Class in org.jmol.symmetry
UnitCellIterator() - Constructor for class org.jmol.symmetry.UnitCellIterator
unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
unitCellParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
unitCellParams - Variable in class org.jmol.util.SimpleUnitCell
unitCells - Variable in class org.jmol.modelset.ModelSet
unitCubePoints - Static variable in class org.jmol.util.BoxInfo
unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
UNITID_ATOM - Static variable in class org.jmol.viewer.JC
UNITID_INSCODE - Static variable in class org.jmol.viewer.JC
UNITID_MODEL - Static variable in class org.jmol.viewer.JC
UNITID_RESIDUE - Static variable in class org.jmol.viewer.JC
UNITID_TRIM - Static variable in class org.jmol.viewer.JC
unitize(T3) - Method in interface org.jmol.api.SymmetryInterface
unitize(T3) - Method in class org.jmol.symmetry.Symmetry
unitizeDim(int, T3) - Method in class org.jmol.util.SimpleUnitCell
  Used for just about everything; via UnitCell including SpaceGroup.getSiteMultiplicity, Symmetry.getInvariantSymops, Symmetry.removeDuplicates, Symmetry.unitize, Symmetry.toUnitCell, SymmetryDesc.getTransform.
unitizeDimRnd(int, T3, float) - Static method in class org.jmol.util.SimpleUnitCell
  Only used for getting equivalent points and checking for duplicates.
unitizeX(float, float) - Static method in class org.jmol.util.SimpleUnitCell
unitizeXRnd(float, float) - Static method in class org.jmol.util.SimpleUnitCell
  Slightly higher precision -- only used for cmdAssignSpaceGroup checking for duplicates
units - Variable in class jspecview.common.MeasurementData
units - Variable in class org.jmol.minimize.Minimizer
units - Variable in class org.jmol.modelset.Measurement
units - Variable in class org.jmol.modelset.MeasurementData
UNITS_ANGSTROMS - Static variable in class org.qcschema.QCSchemaUnits
UNITS_AU - Static variable in class org.qcschema.QCSchemaUnits
UNITS_BOHR - Static variable in class org.qcschema.QCSchemaUnits
UNITS_CM - Static variable in class org.qcschema.QCSchemaUnits
UNITS_CM_1 - Static variable in class org.qcschema.QCSchemaUnits
UNITS_EV - Static variable in class org.qcschema.QCSchemaUnits
UNITS_FRACTIONAL - Static variable in class org.qcschema.QCSchemaUnits
UNITS_HARTREE - Static variable in class org.qcschema.QCSchemaUnits
UNITS_KCAL_MOL - Static variable in class org.qcschema.QCSchemaUnits
UNITS_KJ_MOL - Static variable in class org.qcschema.QCSchemaUnits
UNITS_M - Static variable in class org.qcschema.QCSchemaUnits
unitsColor - Variable in class jspecview.common.PanelData
UNITSCOLOR - Enum constant in enum class jspecview.common.ScriptToken
unitsDrawn - Variable in class jspecview.common.PanelData
unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
unitx - Static variable in class org.jmol.script.T
unitxyz - Static variable in class org.jmol.script.T
unity - Static variable in class org.jmol.script.T
unitz - Static variable in class org.jmol.script.T
UNK - Enum constant in enum class jspecview.common.ExportType
UNKNOWN - Enum constant in enum class jspecview.common.ScriptToken
UNKNOWN - Enum constant in enum class org.jmol.c.HB
UNKNOWN - Enum constant in enum class org.jmol.c.PAL
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.C
unpack(byte[], int, int) - Static method in class javajs.util.MessagePackReader
  mmtf type 14 and 15 Unpack an array of int8 or int16 to int32.
unpack16Deltaf(byte[], int, float) - Static method in class javajs.util.MessagePackReader
  mmtf type 10 Decode an array of int16 using run-length decoding of a difference array.
unpackf(byte[], int, int, float) - Static method in class javajs.util.MessagePackReader
  mmtf type 12 and 13 Unpack an array of int8 or int16 to int32 and divide to give a float32.
unquoted(String) - Method in class javajs.util.CifDataParser
  In CIF 2.0, this method turns a String into an Integer or Float In CIF 1.0 (here) just return the unchanged value.
unquoted(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Handle unquoted value as Integer or Float if we can.
unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
unsetProperty(String) - Method in class org.jmol.viewer.Viewer
unsetStrutPoint() - Method in class org.jmol.modelset.Group
unTaintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
untransformedPoint - Variable in class org.jmol.viewer.TransformManager
unTransformPoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
unused_boolean_def_true - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
unwrapCdata(String) - Static method in class org.jmol.jvxl.readers.XmlReader
uP(String) - Static method in class org.jmol.util.Escape
UP - Static variable in class org.jmol.viewer.binding.Binding
update() - Method in interface javajs.api.JSInterface
update() - Method in class jspecview.appletjs.JSVApplet
update() - Method in class org.jmol.util.GenericApplet
update(double, double, double) - Method in class jspecview.common.IntegralData
  minY is ignored
update(Location, long, int) - Method in class com.sparshui.server.TouchPoint
  Update this touch point with a new location and state.
update(TouchPoint) - Method in class com.sparshui.server.Group
  Update the given touch point that belongs to this group.
update(Graphics) - Method in class jme.JME
update(Graphics) - Method in class jspecview.java.AwtPanel
update(String) - Method in class org.jmol.viewer.ChimeMessenger
  called upon script exit and file opening
update(String) - Method in interface org.jmol.viewer.JmolChimeMessenger
update(LineEvent) - Method in class org.jmol.util.JmolAudio
update(Coordinate, double, int) - Method in class jspecview.dialog.JSVDialog
update(Parameters) - Method in class jspecview.common.IntegralData
update(CLEG.ClegData) - Method in class org.jmol.symmetry.CLEG.ClegNode
UPDATE - Enum constant in enum class jspecview.common.IntegralData.IntMode
UPDATE_ALL - Static variable in class org.jmol.popup.JmolPopup
UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolPopup
UPDATE_NEVER - Static variable in class jspecview.popup.JSVGenericPopup
UPDATE_NEVER - Static variable in class org.jmol.popup.JmolPopup
UPDATE_SHOW - Static variable in class org.jmol.popup.JmolPopup
updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
updateAllXtalMenuOptions() - Method in class org.jmol.modelkit.ModelKitPopup
updateAtomXYZ(boolean) - Method in class org.jmol.minimize.Minimizer
updateAwtMenus(String) - Method in class org.jmol.awt.AwtJmolPopup
updateAwtMenus(String) - Method in class org.jmol.awt.AwtModelKitPopup
updateBasisFromSite(int) - Method in class org.jmol.modelset.ModelSet
updateButton(SC, String, String) - Method in class org.jmol.popup.GenericPopup
updateCheckBoxesForModelKit(String) - Method in class org.jmol.modelkit.ModelKitPopup
updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateConsoleFont() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
updateControlPressed(int) - Method in class jspecview.common.PanelData
updateCoordinates(M4, BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
  bs will be null if this is a set from the new isosurface MOVE [mat4] command
updateElementsComputedMenu(BS) - Method in class org.jmol.popup.JmolPopup
updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
updateFileMenu() - Method in class org.jmol.popup.JmolPopup
updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolPopup
updateFontSize() - Method in class org.jmol.console.JmolConsole
updateFontSize() - Method in class org.jmol.console.ScriptEditor
updateFontSize() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateHeteroComputedMenu(Map) - Method in class org.jmol.popup.JmolPopup
updateInvalidatedVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
updateJS() - Method in class jspecview.common.JSViewer
  for JavaScript only; this is the call to draw the spectrum
updateJS() - Method in class org.jmol.viewer.Viewer
  for JavaScript only
updateJS(int, int) - Method in class jspecview.app.JSVApp
updateLabels() - Method in class org.jmol.console.GenericConsole
updateLabels() - Method in class org.jmol.console.JmolConsole
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
updateMark(int) - Method in class jme.JME
updateMenu() - Method in class org.jmol.modelkit.ModelKit
updateMenus() - Method in class org.jmol.popup.JmolPopup
  ////// protected methods //////////
updateMode - Variable in class jspecview.popup.JSVGenericPopup
updateMode - Variable in class org.jmol.popup.JmolPopup
updateModel(int) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateOffsetsForAlternativeLocations(Atom[], BS) - Method in class org.jmol.modelsetbio.Monomer
updateOperatorMenu() - Method in class org.jmol.modelkit.ModelKitPopup
updatePDBResidueComputedMenus() - Method in class org.jmol.popup.JmolPopup
updatePointGroup() - Method in interface org.jmol.api.SymmetryInterface
updatePointGroup() - Method in class org.jmol.symmetry.Symmetry
updateRecentMenus(Lst) - Method in class jspecview.application.ApplicationMenu
updateSceneComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Update screen informations
updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
updateSignedAppletItems() - Method in class org.jmol.popup.GenericPopup
updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
updateSpecialMenuItem(SC) - Method in class org.jmol.popup.JmolPopup
updateSpectraMenu() - Method in class org.jmol.popup.JmolPopup
updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
updateSurfMoComputedMenu(Map) - Method in class org.jmol.popup.JmolPopup
updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolPopup
updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateTables() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
updateTables() - Method in class org.openscience.jmol.app.janocchio.NoeTable
updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
updateTokens(CLEG.ClegNode) - Method in class org.jmol.symmetry.CLEG.ClegData
  fill in the blanks to create a CLEG string when joined.
updatingForShow - Variable in class org.jmol.popup.GenericPopup
url - Static variable in class org.jmol.script.T
URL_CACHE - Static variable in class javajs.util.OC
URL_LOCAL - Static variable in class javajs.util.OC
URL_LOCAL - Static variable in class jspecview.common.JSVFileManager
urlPrefixes - Static variable in class javajs.util.OC
urlTypeIndex(String) - Static method in class javajs.util.OC
urlTypeIndex(String) - Static method in class jspecview.common.JSVFileManager
use_display_lists - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
USE_PALETTE - Static variable in class org.jmol.util.C
use_shaders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
useAuthorChainID - Variable in class org.jmol.adapter.readers.cif.CifReader
useColix - Variable in class org.jmol.shape.Mesh
useDirLastExported - Variable in class jspecview.java.AwtFileHelper
useDirLastOpened - Variable in class jspecview.java.AwtFileHelper
useFileModelNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
useminimizationthread - Static variable in class org.jmol.script.T
useMinimizationThread() - Method in class org.jmol.viewer.Viewer
usenumberlocalization - Static variable in class org.jmol.script.T
usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
user - Static variable in class org.jmol.script.T
USER - Enum constant in enum class org.jmol.c.VDW
USER - Static variable in class org.jmol.util.ColorEncoder
userAction(int, Object[]) - Method in class org.jmol.viewer.ActionManager
  If the user has created a function to handle this action, run it and cancel action processing if that function returns an explicit FALSE;
userActionEnabled(int) - Method in class org.jmol.viewer.ActionManager
usercolorscheme - Static variable in class org.jmol.script.T
userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
useScriptQueue - Variable in class org.jmol.viewer.GlobalSettings
useTable - Variable in class org.jmol.export._VrmlExporter
useThreads(boolean) - Method in class org.jmol.script.ScriptEval
useTimeout - Variable in class org.jmol.thread.JmolThread
UTF_16BE - Enum constant in enum class javajs.util.Encoding
UTF_16LE - Enum constant in enum class javajs.util.Encoding
UTF_32BE - Enum constant in enum class javajs.util.Encoding
UTF_32LE - Enum constant in enum class javajs.util.Encoding
UTF8 - Enum constant in enum class javajs.util.Encoding
Util - Class in org.jmol.minimize
Util() - Constructor for class org.jmol.minimize.Util
uvw - Variable in class org.jmol.modelset.Model
uvw0 - Variable in class org.jmol.modelset.Model

## V

v0 - Variable in class org.jmol.util.Vibration
v1 - Variable in class org.jmol.modelset.BondCollection
v2 - Variable in class org.jmol.modelset.BondCollection
V3 - Class in javajs.util
  A 3-element vector that is represented by single precision floating point x,y,z coordinates.
V3() - Constructor for class javajs.util.V3
V3000Rdr - Class in org.jmol.adapter.readers.molxyz
  A reader for Accelrys V3000 files.
V3000Rdr() - Constructor for class org.jmol.adapter.readers.molxyz.V3000Rdr
V3d - Class in javajs.util
  A 3 element vector that is represented by double precision floating point x,y,z coordinates.
V3d() - Constructor for class javajs.util.V3d
vAB - Variable in class org.jmol.shape.Mesh
val - Static variable in class org.jmol.script.T
valence - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
valence - Static variable in class org.jmol.script.T
valence_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
valence_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
validate() - Method in interface jspecview.api.AppletFrame
validate() - Method in class jspecview.appletjs.JSVApplet
validate() - Method in class org.jmol.awtjs.swing.JDialog
validate_object_names - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
validateContent(int) - Method in interface jspecview.api.AppletFrame
validateContent(int) - Method in class jspecview.appletjs.JSVApplet
validateModel(int, boolean) - Method in class org.jmol.bspt.Bspf
validation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
validation - Static variable in class org.jmol.script.T
valign - Variable in class org.jmol.modelset.Text
value - Variable in class jspecview.common.Measurement
value - Variable in class org.jmol.atomdata.RadiusData
value - Variable in class org.jmol.minimize.MMConstraint
value - Variable in class org.jmol.modelset.Measurement
value - Variable in class org.jmol.script.T
value() - Element in annotation interface javajs.J2SIgnoreImport
value() - Element in annotation interface javajs.J2SRequireImport
valueChanged() - Method in class jspecview.tree.SimpleTree
valueChanged(ListSelectionEvent) - Method in class jspecview.java.AwtDialogManager
  ListSelectionListener callback
valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
valueExtended - Variable in class org.jmol.atomdata.RadiusData
valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
valueOf(String) - Static method in enum class io.github.dan2097.jnainchi.InchiFlag
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class javajs.util.Encoding
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.Annotation.AType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.ExportType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.IntegralData.IntMode
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.PanelData.LinkMode
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.ScriptToken
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.Spectrum.IRMode
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.atomdata.RadiusData.EnumType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.CBK
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.FIL
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.HB
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.PAL
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.STER
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.STR
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.VDW
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
  Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.viewer.Viewer.ACCESS
  Returns the enum constant of this class with the specified name.
values - Variable in class org.jmol.atomdata.RadiusData
values() - Static method in enum class io.github.dan2097.jnainchi.InchiFlag
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class javajs.util.Encoding
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.Annotation.AType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.ExportType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.IntegralData.IntMode
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.PanelData.LinkMode
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.ScriptToken
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.Spectrum.IRMode
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.atomdata.RadiusData.EnumType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.CBK
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.FIL
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.HB
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.PAL
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.STER
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.STR
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.VDW
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
  Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.viewer.Viewer.ACCESS
  Returns an array containing the constants of this enum class, in the order they are declared.
vanderwaals - Static variable in class org.jmol.script.T
vanderwaalsMars - Static variable in class org.jmol.util.Elements
  Default table of van der Waals Radii.
var - Static variable in class org.jmol.script.T
varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
variable - Static variable in class org.jmol.script.T
VARIABLE - Enum constant in enum class org.jmol.c.PAL
variables - Static variable in class org.jmol.script.T
varray - Static variable in class org.jmol.script.T
vars - Variable in class org.jmol.script.ScriptContext
VaspChgcarReader - Class in org.jmol.adapter.readers.xtal
  http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
VaspChgcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspChgcarReader
VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
  http://cms.mpi.univie.ac.at/vasp/
VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
VaspPoscarReader - Class in org.jmol.adapter.readers.xtal
  adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
VaspPoscarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspPoscarReader
vAtoms - Variable in class org.jmol.adapter.readers.simple.InputReader
vBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
vBiomolecules - Variable in class org.jmol.adapter.readers.cif.MMCifReader
vc - Variable in class org.jmol.util.MeshSurface
  vertex count
vContours - Variable in class org.jmol.jvxl.data.JvxlData
vcs - Variable in class org.jmol.util.MeshSurface
  vertex color index "colix" array
VDW - Enum Class in org.jmol.c
vdwKey - Variable in class org.jmol.minimize.MinAtom
VdwPROBE - Static variable in class org.jmol.util.Elements
vdws - Variable in class org.jmol.util.ContactPair
vdwType - Variable in class org.jmol.atomdata.RadiusData
vdwVolume - Variable in class org.jmol.util.ContactPair
vector - Static variable in class org.jmol.script.T
vector - Variable in class org.jmol.shapespecial.Dipole
vector12ths - Variable in class org.jmol.symmetry.HallInfo
vectorCode - Variable in class org.jmol.symmetry.HallInfo
vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
Vectors - Class in org.jmol.shapespecial
Vectors() - Constructor for class org.jmol.shapespecial.Vectors
vectorscale - Static variable in class org.jmol.script.T
vectorscentered - Static variable in class org.jmol.script.T
vectorSpinOnly - Variable in class org.jmol.viewer.TransformManager
VectorsRenderer - Class in org.jmol.renderspecial
VectorsRenderer() - Constructor for class org.jmol.renderspecial.VectorsRenderer
vectorsymmetry - Static variable in class org.jmol.script.T
vectorT - Variable in class org.jmol.render.FontLineShapeRenderer
vectorT2 - Variable in class org.jmol.render.FontLineShapeRenderer
vectorT3 - Variable in class org.jmol.render.FontLineShapeRenderer
vectorTemp - Variable in class org.jmol.viewer.TransformManager
vectortrail - Static variable in class org.jmol.script.T
vendor - Variable in class jspecview.export.AMLExporter
vendor - Variable in class jspecview.export.CMLExporter
vendor - Variable in class jspecview.source.AnIMLReader
vendor - Variable in class jspecview.source.NMRMLReader
version - Variable in class org.jmol.jvxl.data.JvxlData
version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
version - Static variable in class org.jmol.viewer.JC
version - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
version - Static variable in class org.qcschema.QCSchemaUnits
VERSION - Enum constant in enum class jspecview.common.ScriptToken
VERSION - Static variable in class jspecview.common.JSVersion
VERSION - Static variable in class org.openscience.jmol.app.janocchio.Nmr
VERSION - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
VERSION_SHORT - Static variable in class jspecview.common.JSVersion
versionInt - Static variable in class jspecview.common.JSVersion
versionInt - Static variable in class org.jmol.viewer.JC
VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
vertexColors - Variable in class org.jmol.jvxl.data.JvxlData
vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
vertexCount - Variable in class org.jmol.render.MeshRenderer
vertexCount0 - Variable in class org.jmol.util.MeshSurface
vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
VertexDataServer - Interface in org.jmol.jvxl.api
vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
vertexSets - Variable in class org.jmol.util.MeshSurface
vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
vertexSource - Variable in class org.jmol.util.MeshSurface
vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
vertexValues - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
vertices - Variable in class org.jmol.render.MeshRenderer
vertices - Static variable in class org.jmol.script.T
vertices - Variable in class org.jmol.shapespecial.Polyhedron
vf - Variable in class org.jmol.shape.Shape
  shape visibility flag
vF - Static variable in class org.jmol.script.SV
vib - Variable in class org.jmol.adapter.smarter.Atom
vib - Variable in class org.jmol.modelset.AtomCollection
vib - Variable in class org.jmol.util.ModulationSet
  vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
vibration - Static variable in class org.jmol.script.T
Vibration - Class in org.jmol.util
  A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
Vibration() - Constructor for class org.jmol.util.Vibration
vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
vibrationOn - Variable in class org.jmol.viewer.TransformManager
vibrationperiod - Static variable in class org.jmol.script.T
vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
vibrations - Variable in class org.jmol.modelset.AtomCollection
vibrationscale - Static variable in class org.jmol.script.T
vibrationSteps - Variable in class org.jmol.modelset.ModelSet
vibrationThread - Variable in class org.jmol.viewer.TransformManager
VibrationThread - Class in org.jmol.thread
VibrationThread() - Constructor for class org.jmol.thread.VibrationThread
vibScale - Variable in class org.jmol.adapter.smarter.AtomSetCollection
vibsFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
vibx - Static variable in class org.jmol.script.T
vibxyz - Static variable in class org.jmol.script.T
viby - Static variable in class org.jmol.script.T
vibz - Static variable in class org.jmol.script.T
VIEW - Enum constant in enum class jspecview.common.ScriptToken
ViewCoupleTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
ViewData - Class in jspecview.common
  Stores information that `GraphSet` needs to display a view with one or more spectra.
ViewData(Lst, double, double, boolean) - Constructor for class jspecview.common.ViewData
ViewData(Lst, double, double, int[], int[], boolean, boolean) - Constructor for class jspecview.common.ViewData
viewer - Variable in class jspecview.appletjs.JSVApplet
viewer - Variable in class org.jmol.util.GenericApplet
viewer - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
Viewer - Class in org.jmol.viewer
Viewer() - Constructor for class org.jmol.viewer.Viewer
Viewer(Map) - Constructor for class org.jmol.viewer.Viewer
  new way...
Viewer.ACCESS - Enum Class in org.jmol.viewer
viewerOptions - Variable in class jspecview.appletjs.JSVApplet
viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
ViewNoeTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
viewOffset - Variable in class jspecview.common.Parameters
viewpoint - Variable in class org.jmol.export.__CartesianExporter
Views - Enum constant in enum class jspecview.common.Annotation.AType
ViewsDialog - Class in jspecview.dialog
  Dialog for managing overlaying spectra and closing files
ViewsDialog() - Constructor for class jspecview.dialog.ViewsDialog
viewSelected() - Method in class jspecview.dialog.ViewsDialog
virtual_trackball - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
VIS_BACKBONE_FLAG - Static variable in class org.jmol.viewer.JC
VIS_BALLS_FLAG - Static variable in class org.jmol.viewer.JC
VIS_BOND_FLAG - Static variable in class org.jmol.viewer.JC
VIS_CARTOON_FLAG - Static variable in class org.jmol.viewer.JC
VIS_LABEL_FLAG - Static variable in class org.jmol.viewer.JC
visibilityFlags - Variable in class org.jmol.shape.Mesh
visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedron
visible - Variable in class org.jmol.modelset.Text
visible - Static variable in class org.jmol.script.T
visible - Variable in class org.jmol.shape.Mesh
visible - Variable in class org.jmol.shapespecial.Ellipsoid
Visible - Class in jspecview.common
  Visible class - for prediction of colour from visible spectrum see Robert J.
Visible() - Constructor for class jspecview.common.Visible
VisibleInterface - Interface in jspecview.api
visualrange - Static variable in class org.jmol.script.T
visualRangeAngstroms - Variable in class org.jmol.viewer.TransformManager
VK_ALT - Static variable in class org.jmol.awtjs.Event
VK_BACK_SPACE - Static variable in class org.jmol.awtjs.Event
VK_CONTROL - Static variable in class org.jmol.awtjs.Event
VK_DELETE - Static variable in class org.jmol.awtjs.Event
VK_DOWN - Static variable in class org.jmol.awtjs.Event
VK_ESCAPE - Static variable in class org.jmol.awtjs.Event
VK_LEFT - Static variable in class org.jmol.awtjs.Event
VK_META - Static variable in class org.jmol.awtjs.Event
VK_PAGE_DOWN - Static variable in class org.jmol.awtjs.Event
VK_PAGE_UP - Static variable in class org.jmol.awtjs.Event
VK_PERIOD - Static variable in class org.jmol.awtjs.Event
VK_RIGHT - Static variable in class org.jmol.awtjs.Event
VK_SHIFT - Static variable in class org.jmol.awtjs.Event
VK_SPACE - Static variable in class org.jmol.awtjs.Event
VK_UP - Static variable in class org.jmol.awtjs.Event
vNaN - Static variable in class org.jmol.script.SV
vNorm - Variable in class org.jmol.symmetry.CIPData
vOcc - Variable in class org.jmol.util.ModulationSet
  the current value of the occupancy modulation
volume - Variable in class org.jmol.quantum.QuantumCalculation
volume - Static variable in class org.jmol.script.T
volume - Variable in class org.jmol.util.BZone
volume - Variable in class org.jmol.util.ContactPair
volume - Variable in class org.jmol.util.SimpleUnitCell
volume_bit_depth - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
volume_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
volume_data_range - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
volume_layers - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
volumeData - Variable in class org.jmol.jvxl.readers.Parameters
VolumeData - Class in org.jmol.jvxl.data
VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
volumeDataTemp - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
volumeRender - Variable in class org.jmol.render.MeshRenderer
volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
volumeRender(boolean) - Method in class org.jmol.export.Export3D
volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
volumeRender4(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
volumeRender4(int, int, int, int) - Method in class org.jmol.export.Export3D
volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
volumeRenderPointSize - Variable in class org.jmol.shape.Mesh
volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
voxelData - Variable in class org.jmol.quantum.QuantumCalculation
VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
voxelDataTemp - Variable in class org.jmol.quantum.QuantumCalculation
voxelPtToXYZ(int, int, int, T3) - Method in class org.jmol.jvxl.data.VolumeData
voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
vs - Variable in class org.jmol.util.MeshSurface
  vertices
vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
vT - Static variable in class org.jmol.script.SV
vTemp - Variable in class org.jmol.renderspecial.DrawRenderer
vTemp - Variable in class org.jmol.shape.Mesh
vTemp - Variable in class org.jmol.symmetry.CIPData
vTemp2 - Variable in class org.jmol.renderspecial.DrawRenderer
vvert - Variable in class org.jmol.render.AxesRenderer
vvert - Variable in class org.jmol.render.BbcageRenderer
vvert - Variable in class org.jmol.render.UccageRenderer
vvs - Variable in class org.jmol.util.MeshSurface
  vertex values
vwr - Variable in class jspecview.app.JSVApp
vwr - Variable in class jspecview.application.AppToolBar
vwr - Variable in class jspecview.application.AwtTree
vwr - Variable in class jspecview.dialog.DialogManager
vwr - Variable in class jspecview.dialog.JSVDialog
vwr - Variable in class jspecview.export.AMLExporter
vwr - Variable in class jspecview.export.CMLExporter
vwr - Variable in class jspecview.export.SVGExporter
vwr - Variable in class jspecview.popup.JSVGenericPopup
vwr - Variable in class jspecview.tree.SimpleTree
vwr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
vwr - Variable in class org.jmol.adapter.writers.CIFWriter
vwr - Variable in class org.jmol.adapter.writers.CMLWriter
vwr - Variable in class org.jmol.console.GenericConsole
vwr - Variable in class org.jmol.console.ImageDialog
vwr - Variable in class org.jmol.dialog.Dialog
vwr - Variable in class org.jmol.export.___Exporter
vwr - Variable in class org.jmol.minimize.Minimizer
vwr - Variable in class org.jmol.modelkit.ModelKit
vwr - Variable in class org.jmol.modelset.AtomCollection
vwr - Variable in class org.jmol.popup.JmolGenericPopup
vwr - Variable in class org.jmol.render.ShapeRenderer
vwr - Variable in class org.jmol.script.ScriptError
vwr - Variable in class org.jmol.script.ScriptCompiler
vwr - Variable in class org.jmol.scriptext.ScriptExt
vwr - Variable in class org.jmol.shape.Shape
vwr - Variable in class org.jmol.thread.JmolThread
vwr - Variable in class org.jmol.util.GData
vwr - Variable in class org.jmol.util.MeshSurface
vwr - Variable in class org.jmol.viewer.ActionManager
vwr - Variable in class org.jmol.viewer.AnimationManager
vwr - Variable in class org.jmol.viewer.FileManager
vwr - Variable in class org.jmol.viewer.OutputManagerAwt
vwr - Variable in class org.jmol.viewer.OutputManagerJS
vwr - Variable in class org.jmol.viewer.ShapeManager
vwr - Variable in class org.jmol.viewer.StateManager
vwr - Variable in class org.jmol.viewer.StatusManager
vwr - Variable in class org.jmol.viewer.TransformManager
vwr - Variable in class org.molecularplayground.MPJmolApp
vwr - Variable in class org.openscience.jmol.app.JmolData
vwr - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
vwr - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
vwr - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
vwrFrame - Variable in class org.jmol.console.JmolConsole
vwrOptions - Variable in class org.jmol.util.GenericApplet
vwrOptions - Variable in class org.jmol.viewer.Viewer
vwrOptions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel

## W

w - Variable in class javajs.util.T4
  The w coordinate.
w - Static variable in class org.jmol.script.T
waitForDisplay(Object, Object) - Method in class jspecview.java.AwtPlatform
waitForDisplay(Object, Object) - Method in class jspecview.js2d.JsPlatform
waitForDisplay(Object, Object) - Method in interface org.jmol.api.GenericPlatform
  can be ignored (return false) if platform cannot save images
waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
waitForDisplay(Object, Object) - Method in class org.jmol.awtjs2d.Platform
waitformoveto - Static variable in class org.jmol.script.T
waitForMoveTo - Variable in class org.jmol.viewer.GlobalSettings
waitForQueue() - Method in interface org.jmol.api.JmolScriptManager
waitForQueue() - Method in class org.jmol.script.ScriptManager
warn(String) - Method in interface org.jmol.adapter.readers.xml.CDXMLParser.CDXReaderI
warn(String) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
warn(String) - Method in class org.jmol.util.DefaultLogger
warn(String) - Static method in class org.jmol.util.Logger
  Writes a log at WARN level.
warn(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at WARN level.
warnAtom(int) - Method in class org.jmol.viewer.Viewer
warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
  Writes a log at WARN level with detail on exception.
warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at WARN level with detail on exception.
warning(int, String, String) - Method in class org.jmol.script.ScriptError
warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
WARNING_MESSAGE - Static variable in class jspecview.dialog.DialogManager
WarnOnEmptyStructure - Enum constant in enum class io.github.dan2097.jnainchi.InchiFlag
  Warn and produce empty InChI for empty structure NOTE: This option doesn't currently work due to an InChI library bug
warnSkippingOperation(String) - Method in class org.jmol.adapter.readers.xtal.FSGOutputReader
warnSkippingOperation(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
wasClicked(int, int) - Method in class org.jmol.shape.Frank
wasClicked(int, int) - Method in class org.jmol.shape.Shape
wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
wasmInchiHack(String) - Method in class org.jmol.viewer.Viewer
  WASM inchi must be initialized asynchronously
wasPerspective - Variable in class org.jmol.export._PovrayExporter
wasPerspective - Variable in class org.jmol.export._TachyonExporter
wasRotating() - Method in class org.jmol.modelkit.ModelKit
wasSpinOn - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
wasUnquoted - Variable in class javajs.util.CifDataParser
  whether we are processing an unquoted value or key
wasX - Variable in class org.jmol.script.ScriptMathProcessor
WB - Static variable in class org.jmol.util.ColorEncoder
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
WebExport - Class in org.openscience.jmol.app.webexport
webme - Variable in class jme.JME
WebMOReader - Class in org.jmol.adapter.readers.quantum
  A molecular orbital reader for WebMO files.
WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
WEST - Static variable in class org.jmol.awtjs.swing.BorderLayout
WEST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
WHEEL - Static variable in class org.jmol.viewer.binding.Binding
wheeled(long, int, int) - Method in class jspecview.app.GenericMouse
WHEELED - Static variable in class org.jmol.awtjs.Event
when - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
whilecmd - Static variable in class org.jmol.script.T
WHITE - Static variable in class jspecview.common.ColorParameters
WHITE - Static variable in class org.jmol.util.C
why - Variable in class org.jmol.script.ScriptContext
width - Variable in class javajs.img.ImageEncoder
width - Variable in class org.jmol.awtjs.swing.Component
width - Variable in class org.jmol.awtjs.swing.Dimension
width - Variable in class org.jmol.render.FontLineShapeRenderer
width - Variable in class org.jmol.render.MeshRenderer
width - Static variable in class org.jmol.script.T
width - Variable in class org.jmol.shape.Mesh
width - Variable in class org.jmol.util.GData
width - Variable in class org.jmol.util.Rectangle
width - Variable in class org.jmol.viewer.TransformManager
WIDTHSCALE - Static variable in class org.jmol.shapecgo.CGOMesh
Wien2kReader - Class in org.jmol.adapter.readers.xtal
  A reader for Wein2k DFT files.
Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
wigner - Static variable in class org.jmol.script.T
wildcard - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
window - Static variable in class org.jmol.script.T
WINDOW - Enum constant in enum class jspecview.common.ScriptToken
windowActivated(WindowEvent) - Method in class jspecview.java.AwtDialogManager
  / required but unused
windowActivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowActivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowcentered - Static variable in class org.jmol.script.T
windowCentered - Variable in class org.jmol.viewer.TransformManager
  //////// rotation center ////////////
windowClosed(WindowEvent) - Method in class jspecview.java.AwtDialogManager
windowClosed(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowClosed(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowClosing(WindowEvent) - Method in class jspecview.java.AwtDialogManager
  WindowListener callback
windowClosing(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowClosing(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowClosing(HTMLElement) - Method in interface org.jmol.awtjs.swing.SwingController
  Called by clicking the [x] in the corner of the dialog; send a notification back to the manager via processWindowClosing(key) var id = $("div.JDialog:has(#" + element.id + ")")[0].id var dialog = Jmol.Swing.htDialogs[id]; dialog.manager.processWindowClosing(dialog.registryKey);
windowClosing_actionPerformed() - Method in class jspecview.application.MainFrame
windowDeactivated(WindowEvent) - Method in class jspecview.java.AwtDialogManager
windowDeactivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowDeactivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowDeiconified(WindowEvent) - Method in class jspecview.java.AwtDialogManager
windowDeiconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowDeiconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowHeight - Variable in class org.jmol.modelset.Text
windowHeight - Variable in class org.jmol.util.GData
windowIconified(WindowEvent) - Method in class jspecview.java.AwtDialogManager
windowIconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowIconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowIconified_actionPerformed() - Method in class jspecview.application.MainFrame
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowName - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
windowOpened(WindowEvent) - Method in class jspecview.java.AwtDialogManager
windowOpened(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowOpened(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowWidth - Variable in class org.jmol.modelset.Text
windowWidth - Variable in class org.jmol.util.GData
wingVectors - Variable in class org.jmol.modelsetbio.BioPolymer
wingVectors - Variable in class org.jmol.renderbio.BackboneRenderer
wingVectors - Variable in class org.jmol.renderbio.CartoonRenderer
wingVectors - Variable in class org.jmol.renderbio.MeshRibbonRenderer
wingVectors - Variable in class org.jmol.renderbio.RibbonsRenderer
wingVectors - Variable in class org.jmol.renderbio.RocketsRenderer
wingVectors - Variable in class org.jmol.renderbio.StrandsRenderer
wingVectors - Variable in class org.jmol.renderbio.TraceRenderer
wingVectors - Variable in class org.jmol.shapebio.BioShape
wireframe - Static variable in class org.jmol.script.T
wireframeOnly - Variable in class org.jmol.renderbio.BackboneRenderer
wireframeOnly - Variable in class org.jmol.renderbio.CartoonRenderer
wireframeOnly - Variable in class org.jmol.renderbio.MeshRibbonRenderer
wireframeOnly - Variable in class org.jmol.renderbio.RibbonsRenderer
wireframeOnly - Variable in class org.jmol.renderbio.RocketsRenderer
wireframeOnly - Variable in class org.jmol.renderbio.StrandsRenderer
wireframeOnly - Variable in class org.jmol.renderbio.TraceRenderer
wireframerotation - Static variable in class org.jmol.script.T
within - Static variable in class org.jmol.script.T
within(float, P3, Lst) - Static method in class org.jmol.util.BZone
withinDistPoints(float, P3, P3[], P3[], BS, Object[]) - Static method in class org.jmol.bspt.PointIterator
  carry out various functions of the within() script function
wizard_prompt_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
words - Variable in class org.jmol.popup.PopupResource
wrap(String, SB) - Static method in class org.jmol.symmetry.WyckoffFinder
  Just wrap the coordinate with parentheses.
wrap_output - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
wrapCdata(Object) - Static method in class javajs.util.XmlUtil
  wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
wrapCData(String) - Static method in class org.jmol.adapter.writers.CDXMLWriter
  wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManagerAwt
wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManagerJS
write - Static variable in class org.jmol.script.T
write(byte[], int, int) - Method in interface javajs.api.GenericOutputChannel
write(byte[], int, int) - Method in class javajs.util.OC
write(int) - Method in class javajs.util.OC
  Deprecated.
write(BS) - Method in class org.jmol.adapter.writers.CDXMLWriter
write(BS) - Method in class org.jmol.adapter.writers.CIFWriter
write(BS) - Method in class org.jmol.adapter.writers.CMLWriter
write(BS) - Method in class org.jmol.adapter.writers.PDBWriter
write(BS) - Method in class org.jmol.adapter.writers.PWMATWriter
write(BS) - Method in class org.jmol.adapter.writers.QCJSONWriter
write(BS) - Method in class org.jmol.adapter.writers.XSFWriter
write(BS) - Method in interface org.jmol.api.JmolWriter
write(JSViewer, Lst, boolean) - Method in interface jspecview.api.ExportInterface
  from EXPORT command
write(JSViewer, Lst, boolean) - Method in class jspecview.export.Exporter
WRITE - Enum constant in enum class jspecview.common.ScriptToken
writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
writeArray(Object) - Method in class org.jmol.util.JSONWriter
writeAtoms(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeAtomSite(SB) - Method in class org.jmol.adapter.writers.CIFWriter
writeAtomSite(SB) - Method in class org.jmol.adapter.writers.FSG2SCIFConverter
writeBinaryFile(String, byte[]) - Method in class org.jmol.viewer.Viewer
writeBonds(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeBoolean(Boolean) - Method in class org.jmol.util.JSONWriter
writeByte(int) - Method in class javajs.img.PngEncoder
  Write a single byte into the pngBytes array at a given position.
writeByteAsInt(int) - Method in interface javajs.api.GenericOutputChannel
writeByteAsInt(int) - Method in class javajs.util.OC
writeBytes(byte[]) - Method in class javajs.img.PngEncoder
  Write an array of bytes into the pngBytes array.
writeChecked(SB, String) - Method in class org.jmol.adapter.writers.CIFWriter
  see https://github.com/rcsb/ciftools-java/blob/master/src/main/java/org/rcsb/cif/text/TextCifWriter.java
writeCRC() - Method in class javajs.img.PngEncoder
writeFile(String, Object, String) - Method in class org.jmol.viewer.Viewer
writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
writeFloat(float) - Method in class javajs.util.OC
writeForm(String) - Method in class jspecview.export.AMLExporter
writeForm(String) - Method in class jspecview.export.CMLExporter
writeForm(String) - Method in class jspecview.export.SVGExporter
writeHeader(SB) - Method in class org.jmol.adapter.writers.CIFWriter
writeHeader(SB) - Method in class org.jmol.adapter.writers.FSG2SCIFConverter
writeInt(int) - Method in interface javajs.api.GenericOutputChannel
writeInt(int) - Method in class javajs.util.OC
writeInt2(int) - Method in class javajs.img.PngEncoder
  Write a two-byte integer into the pngBytes array at a given position.
writeInt4(int) - Method in class javajs.img.PngEncoder
  Write a four-byte integer into the pngBytes array at a given position.
writeJob(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeJobMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeJobs() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeJSON() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeList(List) - Method in class org.jmol.util.JSONWriter
writeLong(long) - Method in interface javajs.api.GenericOutputChannel
writeLong(long) - Method in class javajs.util.OC
writeMagic() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeMap(Map) - Method in class org.jmol.util.JSONWriter
writemi - Variable in class jme.JME
writeMOBases() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeModel(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeModelMetadata(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeModels() - Method in class org.jmol.adapter.writers.QCJSONWriter
writemol - Variable in class jme.JME
writeMultiline(SB, String) - Method in class org.jmol.adapter.writers.CIFWriter
WriteNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
writeNamfisFiles(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
writeNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
writeNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
writeNull() - Method in class org.jmol.util.JSONWriter
writeNumber(Number) - Method in class org.jmol.util.JSONWriter
writeObject(Object) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeObject(Object) - Method in class org.jmol.util.JSONWriter
writeOperations(SB) - Method in class org.jmol.adapter.writers.CIFWriter
writeOperations(SB) - Method in class org.jmol.adapter.writers.FSG2SCIFConverter
writeParams(SB) - Method in class org.jmol.adapter.writers.CIFWriter
writeSchemaMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeShort(short) - Method in interface javajs.api.GenericOutputChannel
writeShort(short) - Method in class javajs.util.OC
writesmi - Variable in class jme.JME
writeStatus(String) - Method in interface jspecview.api.JSVAppletInterface
  Writes a message to the status label
writeStatus(String) - Method in interface jspecview.api.ScriptInterface
writeStatus(String) - Method in class jspecview.app.JSVApp
  Writes a message to the status label
writeStatus(String) - Method in class jspecview.appletjs.JSVApplet
writeStatus(String) - Method in class jspecview.application.JSpecView
  Writes a message to the status bar
writeString(String) - Method in class javajs.img.PngEncoder
  Write a string into the pngBytes array at a given position.
writeString(String) - Method in class org.jmol.util.JSONWriter
writeString(String, SB) - Method in class org.jmol.util.JSONWriter
writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
writeTopology(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeVibrations(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
wyckoff - Static variable in class org.jmol.script.T
WYCKOFF_RET_ALL_ARRAY - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_CENTERING - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_CENTERING_STRING - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_COORD - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_COORDS - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_COORDS_ALL - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_GENERAL - Static variable in class org.jmol.symmetry.WyckoffFinder
WYCKOFF_RET_LABEL - Static variable in class org.jmol.symmetry.WyckoffFinder
  positive numbers will be label characters or '*'
WYCKOFF_RET_WITH_MULT - Static variable in class org.jmol.symmetry.WyckoffFinder
WyckoffFinder - Class in org.jmol.symmetry
  A class to calculate, store, and retrieve Wyckoff information as per BCS nph-trgen at https://www.cryst.ehu.es/cgi-bin/cryst/programs//nph-trgen?gnum=146invalid input: '&what'=wposinvalid input: '&trmat'=2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3cinvalid input: '&unconv'=R%203%20:Rinvalid input: '&from'=ita For the 611 standard setting in ITA GENPOS, we are just reading the json file and loading its information.
WyckoffFinder() - Constructor for class org.jmol.symmetry.WyckoffFinder
wyckoffm - Static variable in class org.jmol.script.T

## X

x - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
x - Variable in class javajs.util.T3
x - Variable in class javajs.util.T3d
  The x coordinate.
x - Variable in class javajs.util.T3i
  The x coordinate.
x - Variable in class org.jmol.quantum.SlaterData
x - Static variable in class org.jmol.script.T
x - Variable in class org.jmol.util.Rectangle
x - Variable in class org.jmol.viewer.MouseState
X - Variable in class org.jmol.quantum.QuantumCalculation
X - Static variable in class org.jmol.util.BoxInfo
X2 - Variable in class org.jmol.quantum.QuantumCalculation
xaxisData - Variable in class jspecview.source.AnIMLReader
xaxisData - Variable in class jspecview.source.NMRMLReader
xAxisLeftToRight - Variable in class jspecview.common.PanelData
xBohr - Variable in class org.jmol.quantum.QuantumCalculation
xButton - Variable in class jme.JME
XcrysdenReader - Class in org.jmol.adapter.readers.xtal
XcrysdenReader() - Constructor for class org.jmol.adapter.readers.xtal.XcrysdenReader
xFactor - Variable in class jspecview.source.JDXDataObject
  Also used in JDXExport
xFactor - Variable in class jspecview.source.AnIMLReader
xFactor - Variable in class jspecview.source.NMRMLReader
xGT - Static variable in class org.jmol.util.GData
xLabel - Variable in class jspecview.source.JDXDataObject
xLast - Variable in class org.jmol.util.GData
xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
xLT - Static variable in class org.jmol.util.GData
xMax - Variable in class org.jmol.quantum.QuantumCalculation
xMin - Variable in class org.jmol.quantum.QuantumCalculation
XmlArgusReader - Class in org.jmol.adapter.readers.xml
  A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
XmlCdxReader - Class in org.jmol.adapter.readers.xml
  A reader for CambridgeSoft CDXML files.
XmlCdxReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCdxReader
XmlChem3dReader - Class in org.jmol.adapter.readers.xml
  An chem3d c3xml reader
XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
XmlCmlReader - Class in org.jmol.adapter.readers.xml
  A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
xmlData - Variable in class org.jmol.jvxl.data.VolumeData
XmlHandler - Class in org.jmol.adapter.readers.xml
  a SAX handler -- Java only
XmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlHandler
XmlMagResReader - Class in org.jmol.adapter.readers.xml
XmlMagResReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMagResReader
XmlMolproReader - Class in org.jmol.adapter.readers.xml
  A Molpro 2005 reader
XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
XmlMOReader - Class in org.jmol.adapter.readers.xml
  An abstract class accessing MOReader -- currently just for XmlMolproReader only.
XmlMOReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMOReader
XmlNmrmlReader - Class in org.jmol.adapter.readers.xml
  A reader for the structure part of an nmrML file
XmlNmrmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlNmrmlReader
XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
  An Odyssey xodydata reader
XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
XMLParser - Class in jspecview.source
XMLParser(BufferedReader) - Constructor for class jspecview.source.XMLParser
XmlQEReader - Class in org.jmol.adapter.readers.xml
  QuantumEspresso XML reader
XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
XmlReader - Class in org.jmol.adapter.readers.xml
  A generic XML reader template -- by itself, does nothing.
XmlReader - Class in org.jmol.jvxl.readers
XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
XmlReader(BufferedReader) - Constructor for class org.jmol.jvxl.readers.XmlReader
XmlUtil - Class in javajs.util
  A very simplistic XML generator
XmlUtil() - Constructor for class javajs.util.XmlUtil
XmlVaspReader - Class in org.jmol.adapter.readers.xml
  Vasp vasprun.xml reader
XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
XmlXsdReader - Class in org.jmol.adapter.readers.xml
  An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
xor(BS) - Method in class javajs.util.BS
  Performs a logical XOR of this bit set with the bit set argument.
xPixelClicked - Variable in class jspecview.common.PanelData
XSCALEON - Enum constant in enum class jspecview.common.ScriptToken
XSFWriter - Class in org.jmol.adapter.writers
  An XCrysDen XSF writer.
XSFWriter() - Constructor for class org.jmol.adapter.writers.XSFWriter
xtalSymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
XtalSymmetry - Class in org.jmol.adapter.smarter
  A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
XtalSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry
XtalSymmetry.FileSymmetry - Class in org.jmol.adapter.smarter
  A class only used by adapter.smarter.XtalSymmetry while building the file-based model.
XtlWriter - Class in org.jmol.adapter.writers
XtlWriter() - Constructor for class org.jmol.adapter.writers.XtlWriter
xUnitExponent - Variable in class jspecview.export.AMLExporter
xUnitExponent - Variable in class jspecview.export.CMLExporter
xUnitFactor - Variable in class jspecview.export.AMLExporter
xUnitFactor - Variable in class jspecview.export.CMLExporter
xUnitLabel - Variable in class jspecview.export.AMLExporter
xUnitLabel - Variable in class jspecview.export.CMLExporter
xUnits - Variable in class jspecview.export.AMLExporter
xUnits - Variable in class jspecview.export.CMLExporter
xUnits - Variable in class jspecview.source.JDXDataObject
xUnits - Variable in class jspecview.source.AnIMLReader
xUnits - Variable in class jspecview.source.NMRMLReader
XUNITSON - Enum constant in enum class jspecview.common.ScriptToken
xVdwClash - Variable in class org.jmol.util.ContactPair
xWhenPressed - Variable in class jspecview.app.GenericMouse
xy - Variable in class org.jmol.render.LabelsRenderer
xy - Variable in class org.jmol.shape.Hover
XY - Enum constant in enum class jspecview.common.ExportType
XY_RANGE - Static variable in class org.jmol.viewer.ActionManager
XY_ZTOP - Static variable in class org.jmol.viewer.JC
xyCoords - Variable in class jspecview.export.AMLExporter
xyCoords - Variable in class jspecview.export.CMLExporter
xyCoords - Variable in class jspecview.source.JDXDataObject
  array of x,y coordinates
xyData - Variable in class jspecview.dialog.JSVDialog
xypParameter(int) - Method in class org.jmol.script.ScriptParam
xyz - Variable in class org.jmol.atomdata.AtomData
xyz - Variable in class org.jmol.modelset.Text
xyz - Static variable in class org.jmol.script.T
xyz - Variable in class org.jmol.symmetry.SymmetryOperation
XYZ - Static variable in class org.jmol.util.BoxInfo
xyzIsSlabbedInternal(T3) - Method in class org.jmol.viewer.TransformManager
xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
xyzpParameter(int) - Method in class org.jmol.script.ScriptParam
XyzReader - Class in org.jmol.adapter.readers.molxyz
  Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
xyzToLab(P3, P3) - Method in class javajs.img.GifEncoder
xyzToRgb(P3, P3) - Method in class javajs.img.GifEncoder
xyzToVoxelPt(float, float, float, T3i) - Method in class org.jmol.jvxl.data.VolumeData

## Y

y - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
y - Variable in class javajs.util.T3
y - Variable in class javajs.util.T3d
  The y coordinate.
y - Variable in class javajs.util.T3i
  The y coordinate.
y - Variable in class org.jmol.quantum.SlaterData
y - Static variable in class org.jmol.script.T
y - Variable in class org.jmol.util.Rectangle
y - Variable in class org.jmol.viewer.MouseState
Y - Variable in class org.jmol.quantum.QuantumCalculation
Y - Static variable in class org.jmol.util.BoxInfo
Y2 - Variable in class org.jmol.quantum.QuantumCalculation
y2DUnits - Variable in class jspecview.source.JDXDataObject
yaxisData - Variable in class jspecview.source.AnIMLReader
yaxisData - Variable in class jspecview.source.NMRMLReader
yBohr - Variable in class org.jmol.quantum.QuantumCalculation
YELLOW - Static variable in class org.jmol.util.C
yFactor - Variable in class jspecview.source.JDXDataObject
  Also used in JDXExport
yFactor - Variable in class jspecview.source.AnIMLReader
yFactor - Variable in class jspecview.source.NMRMLReader
yGT - Static variable in class org.jmol.util.GData
yLabel - Variable in class jspecview.source.JDXDataObject
yLast - Variable in class org.jmol.util.GData
yLT - Static variable in class org.jmol.util.GData
yMax - Variable in class org.jmol.quantum.QuantumCalculation
yMin - Variable in class org.jmol.quantum.QuantumCalculation
YSCALE - Enum constant in enum class jspecview.common.ScriptToken
YSCALEON - Enum constant in enum class jspecview.common.ScriptToken
yUnitLabel - Variable in class jspecview.export.AMLExporter
yUnitLabel - Variable in class jspecview.export.CMLExporter
yUnits - Variable in class jspecview.export.AMLExporter
yUnits - Variable in class jspecview.export.CMLExporter
yUnits - Variable in class jspecview.source.JDXDataObject
yUnits - Variable in class jspecview.source.AnIMLReader
yUnits - Variable in class jspecview.source.NMRMLReader
YUNITSON - Enum constant in enum class jspecview.common.ScriptToken
yWhenPressed - Variable in class jspecview.app.GenericMouse
yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader

## Z

z - Variable in class javajs.util.T3
z - Variable in class javajs.util.T3d
  The z coordinate.
z - Variable in class javajs.util.T3i
  The z coordinate.
z - Variable in class org.jmol.modelset.Text
z - Variable in class org.jmol.quantum.SlaterData
z - Static variable in class org.jmol.script.T
Z - Variable in class org.jmol.quantum.QuantumCalculation
Z - Static variable in class org.jmol.util.BoxInfo
Z2 - Variable in class org.jmol.quantum.QuantumCalculation
zap - Static variable in class org.jmol.script.T
zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
zap() - Method in class org.jmol.console.GenericConsole
zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
ZAP_TITLE - Static variable in class org.jmol.viewer.JC
ZAPPED - Enum constant in enum class org.jmol.c.FIL
zBohr - Variable in class org.jmol.quantum.QuantumCalculation
zbuf - Variable in class org.jmol.g3d.Graphics3D
zbufT - Variable in class org.jmol.g3d.Graphics3D
zdepth - Static variable in class org.jmol.script.T
zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
zDepthValue - Variable in class org.jmol.viewer.TransformManager
zerobasedxyzrasmol - Static variable in class org.jmol.script.T
zeroFontId - Variable in class org.jmol.shape.Labels
zeta - Variable in class org.jmol.quantum.SlaterData
zGT - Static variable in class org.jmol.util.GData
ZInputStream - Interface in javajs.api
ZipData - Class in javajs.util
ZipData(int) - Constructor for class javajs.util.ZipData
ZipTools - Class in javajs.util
  Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
ZipTools() - Constructor for class javajs.util.ZipTools
zLT - Static variable in class org.jmol.util.GData
zMargin - Variable in class org.jmol.g3d.Graphics3D
zMax - Variable in class org.jmol.quantum.QuantumCalculation
zMin - Variable in class org.jmol.quantum.QuantumCalculation
zmPct - Variable in class org.jmol.viewer.TransformManager
  zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled
zoom - Static variable in class org.jmol.script.T
ZOOM - Enum constant in enum class jspecview.common.ScriptToken
ZOOM_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
ZOOM_EVENT - Static variable in class com.sparshui.GestureType
ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
ZOOM_GESTURE - Static variable in class com.sparshui.GestureType
ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
zoomBoxColor - Variable in class jspecview.common.PanelData
ZOOMBOXCOLOR - Enum constant in enum class jspecview.common.ScriptToken
zoomBoxColor2 - Variable in class jspecview.common.PanelData
ZOOMBOXCOLOR2 - Enum constant in enum class jspecview.common.ScriptToken
zoomBy(int) - Method in class org.jmol.viewer.TransformManager
  standard response to user mouse vertical shift-drag
zoomByFactor(float, int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
zoomByFactor(float, int, int) - Method in class org.jmol.navigate.Navigator
zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
zoomenabled - Static variable in class org.jmol.script.T
zoomEnabled - Variable in class org.jmol.viewer.TransformManager
ZoomEvent - Class in com.sparshui.common.messages.events
ZoomEvent - Class in jspecview.common
ZoomEvent() - Constructor for class com.sparshui.common.messages.events.ZoomEvent
ZoomEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.ZoomEvent
  Constructs a ZoomEvent from a serialized version of ZoomEvent.
ZoomEvent(float, Location, long) - Constructor for class com.sparshui.common.messages.events.ZoomEvent
zoomFactor - Variable in class org.jmol.viewer.TransformManager
zoomheight - Static variable in class org.jmol.script.T
zoomlarge - Static variable in class org.jmol.script.T
zoomTo - Static variable in class org.jmol.script.T
zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
zoomTrigger - Variable in class org.jmol.viewer.ActionManager
zshade - Static variable in class org.jmol.script.T
zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
zshadepower - Static variable in class org.jmol.script.T
zslab - Static variable in class org.jmol.script.T
zSlab - Variable in class org.jmol.modelset.Text
zSlab - Variable in class org.jmol.render.LabelsRenderer
zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
zSlabPoint - Variable in class org.jmol.viewer.TransformManager
zSlabValue - Variable in class org.jmol.viewer.TransformManager
zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager

## _

__ - Static variable in class org.jmol.script.T
___Exporter - Class in org.jmol.export
___Exporter() - Constructor for class org.jmol.export.___Exporter
__CartesianExporter - Class in org.jmol.export
__CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.AdfReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.AmsReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.DgridReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
_active - Variable in class com.sparshui.inputdevice.JmolTouchSimulator
_args - Static variable in class org.jmol.script.T
_atomPickedCallback(int, int) - Method in interface org.jmol.api.js.JSmolAppletObject
_IdtfExporter - Class in org.jmol.export
_IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
_in - Variable in class com.sparshui.common.ClientProtocol
_MayaExporter - Class in org.jmol.export
_MayaExporter() - Constructor for class org.jmol.export._MayaExporter
_ObjExporter - Class in org.jmol.export
  Class to export Wavefront OBJ files.
_ObjExporter() - Constructor for class org.jmol.export._ObjExporter
_offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_out - Variable in class com.sparshui.common.ClientProtocol
_PovrayExporter - Class in org.jmol.export
_PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
_refresh() - Method in interface org.jmol.api.js.JSmolAppletObject
_search(String) - Method in interface jspecview.api.js.JSVAppletObject
_showStatus(String, String) - Method in interface jspecview.api.js.JSVAppletObject
_showTooltip(String, int, int) - Method in interface jspecview.api.js.JSVAppletObject
_socket - Variable in class com.sparshui.common.ClientProtocol
_StlExporter - Class in org.jmol.export
  STereoLithography file format exporter for 3D printing.
_StlExporter() - Constructor for class org.jmol.export._StlExporter
_TachyonExporter - Class in org.jmol.export
_TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
_updateView(Object, String) - Method in interface jspecview.api.js.JSVAppletObject
_VrmlExporter - Class in org.jmol.export
  A basic VRML generator.
_VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
_X3dExporter - Class in org.jmol.export
_X3dExporter() - Constructor for class org.jmol.export._X3dExporter

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