# Serialized Form

## Package com.sparshui.common

### Class com.sparshui.common.Location

class Location extends Object implements Serializable

serialVersionUID:
  -3472243250219991476L

#### Serialized Fields

##### _x

    float _x

##### _y

    float _y

## Package com.sparshui.common.messages.events

### Class com.sparshui.common.messages.events.DragEvent

class DragEvent extends Object implements Serializable

serialVersionUID:
  -2305607021385835330L

#### Serialized Fields

##### _dx

    float _dx

##### _dy

    float _dy

##### _nPoints

    byte _nPoints

##### _time

    long _time

### Class com.sparshui.common.messages.events.FlickEvent

class FlickEvent extends Object implements Serializable

serialVersionUID:
  -2305607021385835330L

#### Serialized Fields

##### speedLevel

    float speedLevel

##### xDirection

    float xDirection

##### yDirection

    float yDirection

### Class com.sparshui.common.messages.events.RelativeDragEvent

class RelativeDragEvent extends Object implements Serializable

serialVersionUID:
  7743528698376037703L

#### Serialized Fields

##### _changeInX

    float _changeInX

##### _changeInY

    float _changeInY

### Class com.sparshui.common.messages.events.RotateEvent

class RotateEvent extends Object implements Serializable

serialVersionUID:
  -5467788080845086125L

#### Serialized Fields

##### _center

    Location _center

##### _rotation

    float _rotation

Rotation of this component in radians

##### _time

    long _time

### Class com.sparshui.common.messages.events.SpinEvent

class SpinEvent extends Object implements Serializable

serialVersionUID:
  6394319277586792988L

#### Serialized Fields

##### _rotationX

    float _rotationX

##### _rotationY

    float _rotationY

##### _rotationZ

    float _rotationZ

### Class com.sparshui.common.messages.events.TouchEvent

class TouchEvent extends Object implements Serializable

serialVersionUID:
  370824346017492361L

#### Serialized Fields

##### _id

    int _id

##### _state

    int _state

##### _time

    long _time

##### _x

    float _x

##### _y

    float _y

### Class com.sparshui.common.messages.events.ZoomEvent

class ZoomEvent extends Object implements Serializable

serialVersionUID:
  -4658011539863774168L

#### Serialized Fields

##### _center

    Location _center

##### _scale

    float _scale

##### _time

    long _time

## Package javajs.util

### Class javajs.util.A4

class A4 extends P3 implements Serializable

#### Serialized Fields

##### angle

    float angle

The angle.

### Exception Class javajs.util.JSONException

class JSONException extends RuntimeException implements Serializable

### Class javajs.util.Lst

class Lst extends ArrayList<V> implements Serializable

### Class javajs.util.M3

class M3 extends M34 implements Serializable

### Class javajs.util.P3

class P3 extends T3 implements Serializable

### Class javajs.util.P3i

class P3i extends T3i implements Serializable

### Class javajs.util.P4

class P4 extends T4 implements Serializable

### Class javajs.util.T3

class T3 extends Object implements Serializable

#### Serialized Fields

##### x

    float x

##### y

    float y

##### z

    float z

### Class javajs.util.T3d

class T3d extends Object implements Serializable

#### Serialized Fields

##### x

    double x

The x coordinate.

##### y

    double y

The y coordinate.

##### z

    double z

The z coordinate.

### Class javajs.util.T3i

class T3i extends Object implements Serializable

#### Serialized Fields

##### x

    int x

The x coordinate.

##### y

    int y

The y coordinate.

##### z

    int z

The z coordinate.

### Class javajs.util.T4

class T4 extends T3 implements Serializable

#### Serialized Fields

##### w

    float w

The w coordinate.

### Class javajs.util.V3

class V3 extends T3 implements Serializable

### Class javajs.util.V3d

class V3d extends T3d implements Serializable

## Package jme

### Class jme.JME

class JME extends JPanel implements Serializable

#### Serialized Fields

##### aboutBox

    jme.MultiBox aboutBox

##### aboutBoxPoint

    Point aboutBoxPoint

##### action

    int action

##### active_an

    int active_an

##### actualMolecule

    int actualMolecule

##### afterClear

    boolean afterClear

##### allHs

    boolean allHs

##### any

    JButton any

##### anyBond

    JButton anyBond

##### anyec

    JButton anyec

##### apointx

    int[] apointx

##### apointy

    int[] apointy

##### application

    boolean application

##### aromatic

    JButton aromatic

##### aromaticBond

    JButton aromaticBond

##### arrowWidth

    int arrowWidth

##### atomBgColors

    String atomBgColors

##### atomColors

    String atomColors

##### atomicSymbol

    JTextField atomicSymbol

##### atomxBox

    jme.MultiBox atomxBox

##### atomxBoxPoint

    Point atomxBoxPoint

##### autoez

    boolean autoez

##### autonumber

    boolean autonumber

##### bpointx

    int[] bpointx

##### bpointy

    int[] bpointy

##### br

    JButton br

##### bwMode

    boolean bwMode

##### c

    JButton c

##### canonize

    boolean canonize

##### canvasBg

    Color canvasBg

##### chargeImage

    Image chargeImage

##### choiced

    JComboBox<String> choiced

##### choiceh

    JComboBox<String> choiceh

##### cl

    JButton cl

##### clearImage

    Image clearImage

##### currentMark

    int currentMark

##### deleteImage

    Image deleteImage

##### deleterImage

    Image deleterImage

##### depict

    boolean depict

##### depictBorder

    boolean depictBorder

##### depictcgi

    String depictcgi

##### depictScale

    double depictScale

##### depictservlet

    String depictservlet

##### dimension

    Dimension dimension

##### doMenu

    boolean doMenu

##### doTags

    boolean doTags

##### dyMode

    boolean dyMode

##### embedded

    boolean embedded

##### endImage

    Image endImage

##### f

    JButton f

##### font

    Font font

##### fontBold

    Font fontBold

##### fontBoldMet

    FontMetrics fontBoldMet

##### fontMet

    FontMetrics fontMet

##### fontSize

    int fontSize

##### fontSmall

    Font fontSmall

##### fontSmallMet

    FontMetrics fontSmallMet

##### halogen

    JButton halogen

##### i

    JButton i

##### infoArea

    BufferedImage infoArea

##### infoImage

    Image infoImage

##### infoText

    String infoText

##### jmeh

    boolean jmeh

##### jmeString

    String jmeString

##### keepHydrogens

    boolean keepHydrogens

##### lastAction

    int lastAction

##### leftMenu

    BufferedImage leftMenu

##### markUsed

    boolean markUsed

##### mol

    JMEmol mol

##### molecularArea

    BufferedImage molecularArea

##### mols

    JMEmol[] mols

##### molStack

    List<JMEmol> molStack

##### molString

    String molString

##### molText

    String molText

##### mouseShift

    boolean mouseShift

##### movePossible

    boolean movePossible

##### multipart

    boolean multipart

##### myFrame

    JFrame myFrame

##### n

    JButton n

##### newMolecule

    boolean newMolecule

##### nmols

    int nmols

##### nocenter

    boolean nocenter

##### nonaromatic

    JButton nonaromatic

##### nonring

    JButton nonring

##### nonringBond

    JButton nonringBond

##### number

    boolean number

##### o

    JButton o

##### p

    JButton p

##### point

    Point point

##### polarnitro

    boolean polarnitro

##### psColor

    Color[] psColor

##### query

    boolean query

##### queryBox

    jme.QueryBox queryBox

##### rButton

    boolean rButton

##### reaction

    boolean reaction

##### relativeStereo

    boolean relativeStereo

##### revertStereo

    boolean revertStereo

##### ring

    JButton ring

##### ringBond

    JButton ringBond

##### rtemplatesImage

    Image rtemplatesImage

##### runsmi

    boolean runsmi

##### s

    JButton s

##### saved

    int saved

##### sd

    int sd

##### sdBond

    JButton sdBond

##### showAtomNumbers

    boolean showAtomNumbers

##### showHydrogens

    boolean showHydrogens

##### smartsImage

    Image smartsImage

##### smiImage

    Image smiImage

##### smiles

    String smiles

##### smilesBox

    jme.MultiBox smilesBox

##### smilesBoxPoint

    Point smilesBoxPoint

##### smitImage

    Image smitImage

##### smol

    JMEmol smol

##### stackPointer

    int stackPointer

##### star

    boolean star

##### stereo

    boolean stereo

##### stereoImage

    Image stereoImage

##### stereoxImage

    Image stereoxImage

##### template

    String template

##### templatesImage

    Image templatesImage

##### tmol

    JMEmol tmol

##### topMenu

    BufferedImage topMenu

##### undoImage

    Image undoImage

##### webme

    boolean webme

##### writemi

    boolean writemi

##### writemol

    boolean writemol

##### writesmi

    boolean writesmi

##### xButton

    boolean xButton

##### xold

    int xold

##### yold

    int yold

## Package jspecview.application

### Class jspecview.application.AboutDialog

class AboutDialog extends JDialog implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### p

    JPanel p

##### txt

    JTextArea txt

### Class jspecview.application.ApplicationMenu

class ApplicationMenu extends JMenuBar implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### closeAllMenuItem

    JMenuItem closeAllMenuItem

##### closeMenuItem

    JMenuItem closeMenuItem

##### coordsCheckBoxMenuItem

    JCheckBoxMenuItem coordsCheckBoxMenuItem

##### displayMenu

    JMenu displayMenu

##### errorLogMenuItem

    JMenuItem errorLogMenuItem

##### exportAsMenu

    JMenu exportAsMenu

##### gridCheckBoxMenuItem

    JCheckBoxMenuItem gridCheckBoxMenuItem

##### integrationMenuItem

    JMenuItem integrationMenuItem

##### jsvViewer

    JSViewer jsvViewer

##### mainFrame

    MainFrame mainFrame

##### openRecentMenu

    JMenu openRecentMenu

##### pointsOnlyCheckBoxMenuItem

    JCheckBoxMenuItem pointsOnlyCheckBoxMenuItem

##### printMenuItem

    JMenuItem printMenuItem

##### processingMenu

    JMenu processingMenu

##### revPlotCheckBoxMenuItem

    JCheckBoxMenuItem revPlotCheckBoxMenuItem

##### saveAsJDXMenu

    JMenu saveAsJDXMenu

##### saveAsMenu

    JMenu saveAsMenu

##### scaleXCheckBoxMenuItem

    JCheckBoxMenuItem scaleXCheckBoxMenuItem

##### scaleYCheckBoxMenuItem

    JCheckBoxMenuItem scaleYCheckBoxMenuItem

##### sidePanelCheckBoxMenuItem

    JCheckBoxMenuItem sidePanelCheckBoxMenuItem

##### solutionColorMenuItem

    JMenuItem solutionColorMenuItem

##### sourceMenuItem

    JMenuItem sourceMenuItem

##### statusCheckBoxMenuItem

    JCheckBoxMenuItem statusCheckBoxMenuItem

##### toolbarCheckBoxMenuItem

    JCheckBoxMenuItem toolbarCheckBoxMenuItem

##### transmittanceMenuItem

    JMenuItem transmittanceMenuItem

### Class jspecview.application.AppToolBar

class AppToolBar extends JToolBar implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### coordsToggleButton

    JToggleButton coordsToggleButton

##### errorLogButton

    JButton errorLogButton

##### errorLogIcon

    ImageIcon errorLogIcon

##### errorLogRedIcon

    ImageIcon errorLogRedIcon

##### errorLogYellowIcon

    ImageIcon errorLogYellowIcon

##### gridToggleButton

    JToggleButton gridToggleButton

##### mainFrame

    MainFrame mainFrame

##### revPlotToggleButton

    JToggleButton revPlotToggleButton

##### spectraButton

    JButton spectraButton

##### vwr

    JSViewer vwr

### Class jspecview.application.AwtTree

class AwtTree extends JTree implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### rootNode

    JSVTreeNode rootNode

##### si

    ScriptInterface si

##### spectraTreeModel

    DefaultTreeModel spectraTreeModel

##### vwr

    JSViewer vwr

### Class jspecview.application.AwtTreeNode

class AwtTreeNode extends DefaultMutableTreeNode implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### index

    int index

##### panelNode

    PanelNode panelNode

### Class jspecview.application.AwtTreePath

class AwtTreePath extends TreePath implements Serializable

### Class jspecview.application.MainFrame

class MainFrame extends JFrame implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### appMenu

    ApplicationMenu appMenu

##### commandHistory

    CommandHistory commandHistory

##### commandInput

    JTextField commandInput

##### dsp

    DisplaySchemesProcessor dsp

##### isAwake

    boolean isAwake

##### isHidden

    boolean isHidden

##### jmolDimensionNew

    Dimension jmolDimensionNew

##### jmolDimensionOld

    Dimension jmolDimensionOld

##### jmolDisplay

    Component jmolDisplay

##### jmolFrameHeight

    int jmolFrameHeight

##### jmolFrameWidth

    int jmolFrameWidth

##### jmolPanel

    JPanel jmolPanel

##### jsv

    JSpecView jsv

##### mainborderLayout

    BorderLayout mainborderLayout

##### mainPanel

    Component mainPanel

##### mainSplitPane

    JSplitPane mainSplitPane

##### mainSplitPosition

    int mainSplitPosition

##### nullPanel

    JPanel nullPanel

##### recentFilePaths

    Lst<String> recentFilePaths

##### showExitDialog

    boolean showExitDialog

##### sidePanelOn

    boolean sidePanelOn

##### sideSplitPane

    JSplitPane sideSplitPane

##### spectraTreeScrollPane

    JScrollPane spectraTreeScrollPane

##### splitPosition

    int splitPosition

##### statusbarOn

    boolean statusbarOn

##### statusLabel

    JLabel statusLabel

##### statusPanel

    JPanel statusPanel

##### tempDS

    String tempDS

##### toolBar

    AppToolBar toolBar

##### toolbarOn

    boolean toolbarOn

##### tree

    AwtTree tree

##### vwr

    JSViewer vwr

### Class jspecview.application.PreferencesDialog

class PreferencesDialog extends JDialog implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### absTransPanel

    JPanel absTransPanel

##### absTransTitledBorder

    TitledBorder absTransTitledBorder

##### applicationPanel

    JPanel applicationPanel

##### AtoTRadioButton

    JRadioButton AtoTRadioButton

##### AutoConvertCheckBox

    JCheckBox AutoConvertCheckBox

##### autoIntegrateCheckBox

    JCheckBox autoIntegrateCheckBox

##### borderLayout6

    BorderLayout borderLayout6

##### buttonPanel

    JPanel buttonPanel

##### cancelButton

    JButton cancelButton

##### clearRecentButton

    JButton clearRecentButton

##### colorButton1

    JButton colorButton1

##### colorButton2

    JButton colorButton2

##### colorButton3

    JButton colorButton3

##### colorButton4

    JButton colorButton4

##### colorButton5

    JButton colorButton5

##### colorButton6

    JButton colorButton6

##### colorButton7

    JButton colorButton7

##### colorButton8

    JButton colorButton8

##### colorPanel

    JPanel colorPanel

##### colorPanel1

    JPanel colorPanel1

##### colorSchemePanel

    JPanel colorSchemePanel

##### confirmExitCheckBox

    JCheckBox confirmExitCheckBox

##### contentBorderLayout

    BorderLayout contentBorderLayout

##### contentpanel

    JPanel contentpanel

##### contentTitledBorder

    TitledBorder contentTitledBorder

##### conversionButtonGroup

    ButtonGroup conversionButtonGroup

##### coordinatesCheckBox

    JCheckBox coordinatesCheckBox

##### currentColorButton

    JButton currentColorButton

##### currentDS

    ColorParameters currentDS

##### customButton

    JButton customButton

##### defaultColorCheckBox

    JCheckBox defaultColorCheckBox

##### defaultDSName

    String defaultDSName

##### defaultFontCheckBox

    JCheckBox defaultFontCheckBox

##### deleteButton

    JButton deleteButton

##### displayFontPanel

    JPanel displayFontPanel

##### displayPanel

    JPanel displayPanel

##### dsp

    DisplaySchemesProcessor dsp

##### elementLabel

    JLabel elementLabel

##### elementList

    JList<String> elementList

##### elementPanel

    JPanel elementPanel

##### elModel

    DefaultListModel<String> elModel

##### exportDirCheckBox

    JCheckBox exportDirCheckBox

##### fontComboBox

    JComboBox<String> fontComboBox

##### fontTitledBorder

    TitledBorder fontTitledBorder

##### generalPanel

    JPanel generalPanel

##### gridBagLayout1

    GridBagLayout gridBagLayout1

##### gridBagLayout2

    GridBagLayout gridBagLayout2

##### gridBagLayout3

    GridBagLayout gridBagLayout3

##### gridBagLayout4

    GridBagLayout gridBagLayout4

##### gridBagLayout5

    GridBagLayout gridBagLayout5

##### gridBagLayout6

    GridBagLayout gridBagLayout6

##### gridBagLayout7

    GridBagLayout gridBagLayout7

##### gridCheckBox

    JCheckBox gridCheckBox

##### gridLayout1

    GridLayout gridLayout1

##### gridLayout2

    GridLayout gridLayout2

##### integFactorTextField

    JTextField integFactorTextField

##### integOffsetTextField

    JTextField integOffsetTextField

##### integratinTitledBorder

    TitledBorder integratinTitledBorder

##### integrationPanel

    JPanel integrationPanel

##### isSpectrumDisplayApplyNowEnabled

    boolean isSpectrumDisplayApplyNowEnabled

##### jLabel1

    JLabel jLabel1

##### jLabel2

    JLabel jLabel2

##### jLabel3

    JLabel jLabel3

##### jLabel4

    JLabel jLabel4

##### jLabel5

    JLabel jLabel5

##### jLabel6

    JLabel jLabel6

##### jLabel7

    JLabel jLabel7

##### jLabel8

    JLabel jLabel8

##### jLabel9

    JLabel jLabel9

##### legendCheckBox

    JCheckBox legendCheckBox

##### listScrollPane

    JScrollPane listScrollPane

##### minYTextField

    JTextField minYTextField

##### okButton

    JButton okButton

##### openedDirCheckBox

    JCheckBox openedDirCheckBox

##### overlayCheckBox

    JCheckBox overlayCheckBox

##### panel

    JPanel panel

##### plotColorButton

    JButton plotColorButton

##### preferences

    Properties preferences

##### preferencesTabbedPane

    JTabbedPane preferencesTabbedPane

##### previewPanel

    AwtPanel previewPanel

##### procColorButton1

    JButton procColorButton1

##### procColorButton2

    JButton procColorButton2

##### procColorButton3

    JButton procColorButton3

##### procColorButton4

    JButton procColorButton4

##### procColorButton5

    JButton procColorButton5

##### procColorButton6

    JButton procColorButton6

##### procColorButton7

    JButton procColorButton7

##### procColorButton8

    JButton procColorButton8

##### processingCustomButton

    JButton processingCustomButton

##### processingPanel

    JPanel processingPanel

##### saveButton

    JButton saveButton

##### scaleXCheckBox

    JCheckBox scaleXCheckBox

##### scaleYCheckBox

    JCheckBox scaleYCheckBox

##### schemeComboBox

    JComboBox<String> schemeComboBox

##### separateWindowCheckBox

    JCheckBox separateWindowCheckBox

##### sidePanelCheckBox

    JCheckBox sidePanelCheckBox

##### spectrumDisplayApplyNowCheckBox

    JCheckBox spectrumDisplayApplyNowCheckBox

##### spectrumPanel

    JPanel spectrumPanel

##### statusBarCheckBox

    JCheckBox statusBarCheckBox

##### svgForInkscapeCheckBox

    JCheckBox svgForInkscapeCheckBox

##### toolbarCheckBox

    JCheckBox toolbarCheckBox

##### topPanel

    JPanel topPanel

##### TtoARadioButton

    JRadioButton TtoARadioButton

##### uiPanel

    JPanel uiPanel

## Package jspecview.common

### Class jspecview.common.IntegralData

class IntegralData extends MeasurementData implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### haveRegions

    boolean haveRegions

##### integralTotal

    double integralTotal

##### intRange

    double intRange

##### normalizationFactor

    double normalizationFactor

##### offset

    double offset

##### percentMinY

    double percentMinY

##### percentOffset

    double percentOffset

##### percentRange

    double percentRange

##### xyCoords

    Coordinate[] xyCoords

### Class jspecview.common.MeasurementData

class MeasurementData extends Lst<Measurement> implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### isON

    boolean isON

##### key

    String key

##### myParams

    Parameters myParams

##### precision

    int precision

##### spec

    Spectrum spec

##### type

    Annotation.AType type

##### units

    String units

### Class jspecview.common.PeakData

class PeakData extends MeasurementData implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### maxY

    double maxY

##### minY

    double minY

##### thresh

    double thresh

### Class jspecview.common.PeakPickEvent

class PeakPickEvent extends EventObject implements Serializable

#### Serialized Fields

##### coord

    Coordinate coord

##### peakInfo

    PeakInfo peakInfo

## Package jspecview.exception

### Exception Class jspecview.exception.JSVException

class JSVException extends Exception implements Serializable

## Package jspecview.java

### Class jspecview.java.AwtColor

class AwtColor extends Color implements Serializable

#### Serialized Fields

##### opacity

    int opacity

### Class jspecview.java.AwtDialog

class AwtDialog extends JDialog implements Serializable

#### Serialized Fields

##### buttonInsets

    Insets buttonInsets

##### dataTable

    JTable dataTable

##### defaultHeight

    int defaultHeight

##### haveColors

    boolean haveColors

##### haveTwoPanels

    boolean haveTwoPanels

##### iRow

    int iRow

##### leftPanel

    JPanel leftPanel

##### mainSplitPane

    JSplitPane mainSplitPane

##### manager

    DialogManager manager

##### optionKey

    String optionKey

##### options

    Map<String,Object> options

##### panelInsets

    Insets panelInsets

##### registryKey

    String registryKey

##### rightPanel

    JPanel rightPanel

##### selectedRow

    int selectedRow

##### tableCellAlignLeft

    boolean tableCellAlignLeft

##### tableModel

    jspecview.java.DialogTableModel tableModel

##### thisPanel

    JPanel thisPanel

##### type

    Annotation.AType type

### Class jspecview.java.AwtMainPanel

class AwtMainPanel extends JPanel implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### currentPanelIndex

    int currentPanelIndex

##### mainSelectedPanel

    JSVPanel mainSelectedPanel

### Class jspecview.java.AwtPanel

class AwtPanel extends JPanel implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### apiPlatform

    GenericPlatform apiPlatform

##### bgcolor

    GenericColor bgcolor

##### mouse

    GenericMouseInterface mouse

##### pd

    PanelData pd

##### vwr

    JSViewer vwr

### Class jspecview.java.AwtPrintDialog

class AwtPrintDialog extends JDialog implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### cancelButton

    JButton cancelButton

##### centerRadioButton

    JRadioButton centerRadioButton

##### chooseFontRadioButton

    JRadioButton chooseFontRadioButton

##### defaultFontRadioButton

    JRadioButton defaultFontRadioButton

##### fitToPageRadioButton

    JRadioButton fitToPageRadioButton

##### fontButtonGroup

    ButtonGroup fontButtonGroup

##### gridCheckBox

    JCheckBox gridCheckBox

##### landscapeRadioButton

    JRadioButton landscapeRadioButton

##### layoutButtonGroup

    ButtonGroup layoutButtonGroup

##### pdfButton

    JButton pdfButton

##### pl

    PrintLayout pl

##### plNew

    PrintLayout plNew

##### portraitRadioButton

    JRadioButton portraitRadioButton

##### positionButtonGroup

    ButtonGroup positionButtonGroup

##### previewButton

    JButton previewButton

##### printButton

    JButton printButton

##### scaleXCheckBox

    JCheckBox scaleXCheckBox

##### scaleYCheckBox

    JCheckBox scaleYCheckBox

##### titleCheckBox

    JCheckBox titleCheckBox

##### topLeftRadioButton

    JRadioButton topLeftRadioButton

## Package org.jmol.adapter.smarter

### Class org.jmol.adapter.smarter.Atom

class Atom extends P3 implements Serializable

#### Serialized Fields

##### altLoc

    char altLoc

##### anisoBorU

    float[] anisoBorU

##### atomName

    String atomName

##### atomSerial

    int atomSerial

##### atomSetIndex

    int atomSetIndex

##### atomSite

    int atomSite

##### bfactor

    float bfactor

##### bondingRadius

    float bondingRadius

##### bsSymmetry

    BS bsSymmetry

##### chainID

    int chainID

##### elementNumber

    short elementNumber

##### elementSymbol

    String elementSymbol

##### foccupancy

    float foccupancy

##### formalCharge

    int formalCharge

##### group3

    String group3

##### index

    int index

##### insertionCode

    char insertionCode

##### isHetero

    boolean isHetero

##### part

    int part

##### partialCharge

    float partialCharge

##### radius

    float radius

##### seqIdOrWyckoffCode

    int seqIdOrWyckoffCode

##### sequenceNumber

    int sequenceNumber

##### tensors

    Lst<Object> tensors

##### typeSymbol

    String typeSymbol

##### vib

    V3 vib

## Package org.jmol.awt

### Class org.jmol.awt.AwtColor

class AwtColor extends Color implements Serializable

#### Serialized Fields

##### opacity

    int opacity

## Package org.jmol.console

### Class org.jmol.console.ImageDialog

class ImageDialog extends JDialog implements Serializable

#### Serialized Fields

##### canvas

    org.jmol.console.ImageDialog.ImageCanvas canvas

##### console

    JmolAppConsoleInterface console

##### image

    Image image

##### imageMap

    Map<String, GenericImageDialog> imageMap

##### menubar

    JMenuBar menubar

##### title

    String title

##### vwr

    Viewer vwr

### Class org.jmol.console.JmolButton

class JmolButton extends JButton implements Serializable

### Class org.jmol.console.JmolLabel

class JmolLabel extends JLabel implements Serializable

### Class org.jmol.console.JmolToggleButton

class JmolToggleButton extends JToggleButton implements Serializable

### Class org.jmol.console.KeyJCheckBox

class KeyJCheckBox extends JCheckBox implements Serializable

#### Serialized Fields

##### key

    String key

### Class org.jmol.console.KeyJCheckBoxMenuItem

class KeyJCheckBoxMenuItem extends JCheckBoxMenuItem implements Serializable

#### Serialized Fields

##### key

    String key

### Class org.jmol.console.KeyJMenu

class KeyJMenu extends JMenu implements Serializable

#### Serialized Fields

##### itemKeys

    String[] itemKeys

##### key

    String key

### Class org.jmol.console.KeyJMenuItem

class KeyJMenuItem extends JMenuItem implements Serializable

#### Serialized Fields

##### key

    String key

### Class org.jmol.console.KeyJRadioButtonMenuItem

class KeyJRadioButtonMenuItem extends JRadioButtonMenuItem implements Serializable

#### Serialized Fields

##### key

    String key

### Class org.jmol.console.ScriptEditor

class ScriptEditor extends JDialog implements Serializable

#### Serialized Fields

##### attEcho

    SimpleAttributeSet attEcho

##### attError

    SimpleAttributeSet attError

##### attHighlight

    SimpleAttributeSet attHighlight

##### buttonPanel

    JPanel buttonPanel

##### checkButton

    JButton checkButton

##### clearButton

    JButton clearButton

##### closeButton

    JButton closeButton

##### consoleButton

    JButton consoleButton

##### editor

    org.jmol.console.ScriptEditor.EditorTextPane editor

##### filename

    String filename

##### fontButton

    JButton fontButton

##### fontSize

    int fontSize

##### haltButton

    JButton haltButton

##### jmolConsole

    JmolConsole jmolConsole

##### lastIndices

    int lastIndices

##### loadButton

    JButton loadButton

##### map

    Map<String,Object> map

##### noPrefs

    boolean noPrefs

##### openButton

    JButton openButton

##### parsedContext

    ScriptContext parsedContext

##### parsedData

    String parsedData

##### pauseButton

    JButton pauseButton

##### resumeButton

    JButton resumeButton

##### runButton

    JButton runButton

##### saveAsButton

    JButton saveAsButton

##### saveButton

    JButton saveButton

##### state

    int state

##### stateButton

    JButton stateButton

##### stepButton

    JButton stepButton

##### title

    String title

##### topButton

    JButton topButton

##### vwr

    Viewer vwr

##### zipFileName

    String zipFileName

## Package org.jmol.dialog

### Class org.jmol.dialog.Dialog

class Dialog extends JPanel implements Serializable

#### Serialized Fields

##### cb

    JComboBox<String> cb

##### choice

    String choice

##### dialogType

    String dialogType

##### extension

    String extension

##### extensions

    String[] extensions

##### imageChoices

    String[] imageChoices

##### imageExtensions

    String[] imageExtensions

##### imageType

    String imageType

##### initialFile

    File initialFile

##### inputFileName

    String inputFileName

##### openPreview

    FilePreview openPreview

##### outputFileName

    String outputFileName

##### qPanelJPEG

    JPanel qPanelJPEG

##### qPanelPNG

    JPanel qPanelPNG

##### qSliderJPEG

    JSlider qSliderJPEG

##### qSliderPNG

    JSlider qSliderPNG

##### qualityJ

    int qualityJ

##### qualityP

    int qualityP

##### vwr

    Viewer vwr

### Class org.jmol.dialog.FileChooser

class FileChooser extends JFileChooser implements Serializable

#### Serialized Fields

##### dialog

    JDialog dialog

##### dialogLocation

    Point dialogLocation

##### dialogSize

    Dimension dialogSize

### Class org.jmol.dialog.FilePreview

class FilePreview extends JPanel implements Serializable

#### Serialized Fields

##### active

    JCheckBox active

##### append

    JCheckBox append

##### cartoons

    JCheckBox cartoons

##### chooser

    JFileChooser chooser

##### display

    org.jmol.dialog.FilePreview.FPPanel display

##### vwr

    Viewer vwr

## Package org.jmol.modelset

### Class org.jmol.modelset.Atom

class Atom extends Point3fi implements Serializable

#### Serialized Fields

##### altloc

    char altloc

##### atomID

    byte atomID

##### atomNumberFlags

    short atomNumberFlags

atomNumberFlags encodes atomic number (a), isotope number(i) as: iiii iiii iaaa aaaa

##### atomSite

    int atomSite

##### atomSymmetry

    BS atomSymmetry

##### bonds

    Bond[] bonds

MAY BE NULL

##### clickabilityFlags

    int clickabilityFlags

##### colixAtom

    short colixAtom

##### formalChargeAndFlags

    int formalChargeAndFlags

##### group

    Group group

##### madAtom

    short madAtom

##### nBackbonesDisplayed

    int nBackbonesDisplayed

##### nBondsDisplayed

    int nBondsDisplayed

##### paletteID

    byte paletteID

##### shapeVisibilityFlags

    int shapeVisibilityFlags

##### userDefinedVanDerWaalRadius

    float userDefinedVanDerWaalRadius

##### valence

    byte valence

## Package org.jmol.script

### Exception Class org.jmol.script.ScriptException

class ScriptException extends Exception implements Serializable

#### Serialized Fields

##### eval

    ScriptEval eval

##### isError

    boolean isError

##### message

    String message

##### untranslated

    String untranslated

### Exception Class org.jmol.script.ScriptInterruption

class ScriptInterruption extends ScriptException implements Serializable

## Package org.jmol.smiles

### Exception Class org.jmol.smiles.InvalidSmilesException

class InvalidSmilesException extends Exception implements Serializable

### Class org.jmol.smiles.SmilesAtom

class SmilesAtom extends P3 implements Serializable

#### Serialized Fields

##### aromaticAmbiguous

    boolean aromaticAmbiguous

##### atomClass

    float atomClass

##### atomicMass

    int atomicMass

##### atomNumber

    int atomNumber

##### atomSite

    int atomSite

##### atomType

    String atomType

##### bioAtomName

    String bioAtomName

##### bioType

    char bioType

##### bondCount

    int bondCount

##### bonds

    SmilesBond[] bonds

##### charge

    int charge

##### cipChirality

    int cipChirality

##### component

    int component

##### connectivity

    int connectivity

##### covalentHydrogenCount

    int covalentHydrogenCount

##### degree

    int degree

##### elementDefined

    boolean elementDefined

##### elementNumber

    int elementNumber

##### explicitHydrogenCount

    int explicitHydrogenCount

##### hasDoubleBond

    boolean hasDoubleBond

##### hasSubpattern

    boolean hasSubpattern

##### hasSymbol

    boolean hasSymbol

##### implicitHydrogenCount

    int implicitHydrogenCount

##### index

    int index

##### iNested

    int iNested

##### insCode

    char insCode

##### isAND

    boolean isAND

##### isAromatic

    boolean isAromatic

##### isBioAtom

    boolean isBioAtom

##### isBioAtomWild

    boolean isBioAtomWild

##### isBioResidue

    boolean isBioResidue

##### isFirst

    boolean isFirst

true if this atom is the first SMILES atom or first after a . with no connector

##### isLeadAtom

    boolean isLeadAtom

##### isTopoAtom

    boolean isTopoAtom

##### jmolIndex

    int jmolIndex

##### mapIndex

    int mapIndex

##### matchingComponent

    int matchingComponent

##### matchingIndex

    int matchingIndex

##### matchingNode

    Node matchingNode

##### missingHydrogenCount

    int missingHydrogenCount

##### nonhydrogenDegree

    int nonhydrogenDegree

##### not

    boolean not

##### notBondedIndex

    int notBondedIndex

##### notCrossLinked

    boolean notCrossLinked

##### nSubAtoms

    int nSubAtoms

##### parent

    SmilesAtom parent

##### pattern

    String pattern

##### patternIndex

    int patternIndex

##### primitiveType

    int primitiveType

##### referance

    String referance

##### residueChar

    String residueChar

##### residueName

    String residueName

##### residueNumber

    int residueNumber

##### ringConnectivity

    int ringConnectivity

##### ringMembership

    int ringMembership

##### ringSize

    int ringSize

##### selected

    boolean selected

##### stereo

    SmilesStereo stereo

##### subAtoms

    SmilesAtom[] subAtoms

##### symbol

    String symbol

##### valence

    int valence

## Package org.jmol.util

### Class org.jmol.util.ModulationSet

class ModulationSet extends Vibration implements Serializable

#### Serialized Fields

##### axesLengths

    float[] axesLengths

unit cell axes -- used in Modulation for calculating magnetic modulations

##### enabled

    boolean enabled

indicates state of modulated or unmodulated

##### fileOcc

    double fileOcc

##### gammaE

    M3 gammaE

##### gammaIinv

    Matrix gammaIinv

##### htUij

    Map<String,Float> htUij

current value of anisotropic parameter modulation

##### id

    String id

an identifier for this modulation

##### iop

    int iop

the symmetry operation used to generate this atom

##### isCommensurate

    boolean isCommensurate

commensurate modulations cannot be "undone" and they cannot be turned off

##### isQ

    boolean isQ

##### isSubsystem

    boolean isSubsystem

subsystems can deliver their own unique unit cell; they are commensurate

##### modCalc

    ModulationSet modCalc

modCalc is used for calculations independent of what the current setting is

##### mods

    Lst<Modulation> mods

the list of all modulations associated with this atom

##### mxyz

    V3 mxyz

the modulated magnetic spin

##### nOps

    int nOps

the number of operators in this space group -- needed for occupancy calculation

##### occAbsolute

    boolean occAbsolute

for Crenels (simple occupational modulation or Legendre displacement modulation, the value determined here is absolute (0 or 1), not an adjustment; set in calculate() by one of the modulations

##### occParams

    double[] occParams

##### occSiteMultiplicity

    double occSiteMultiplicity

##### ptTemp

    P3 ptTemp

##### qtOffset

    P3 qtOffset

##### r0

    P3 r0

the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself

##### rI

    Matrix rI

##### rsvs

    Matrix rsvs

the matrix representation for this atom's symmetry operation

##### scale

    float scale

an adjustable scaling factor, as for vibrations

##### sigma

    Matrix sigma

##### spinOp

    float spinOp

the spin operation for this atom: +1/0/-1

##### strop

    String strop

a string description of the atom's symmetry operator

##### symmetry

    SymmetryInterface symmetry

the space group appropriate to this atom

##### tau

    Matrix tau

##### tFactorInv

    Matrix tFactorInv

##### v0

    V3 v0

##### vib

    Vibration vib

vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.

##### vOcc

    float vOcc

the current value of the occupancy modulation

### Class org.jmol.util.Point3fi

class Point3fi extends P3 implements Serializable

#### Serialized Fields

##### i

    int i

index in full collection

##### mi

    short mi

model index -- may be to a trajectory

##### sD

    int sD

screen diameter

##### sX

    int sX

screen X

##### sY

    int sY

screen Y

##### sZ

    int sZ

screen Z

### Class org.jmol.util.Vibration

class Vibration extends V3 implements Serializable

#### Serialized Fields

##### isFractional

    boolean isFractional

##### isFrom000

    boolean isFrom000

##### magMoment

    float magMoment

##### matInv

    M3 matInv

##### matTemp

    M3 matTemp

##### modDim

    int modDim

modDim will be > 0 for modulation

##### modScale

    float modScale

##### showTrace

    boolean showTrace

##### symmform

    String symmform

##### trace

    P3[] trace

##### tracePt

    int tracePt

##### v0

    V3 v0

## Package org.jmol.viewer

### Exception Class org.jmol.viewer.JmolAsyncException

class JmolAsyncException extends IOException implements Serializable

#### Serialized Fields

##### fileName

    String fileName

## Package org.openscience.jmol.app

### Class org.openscience.jmol.app.Jmol

class Jmol extends JmolPanel implements Serializable

## Package org.openscience.jmol.app.janocchio

### Class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel

class CoupleColourSelectionPanel extends JPanel implements Serializable

#### Serialized Fields

##### coupleTable

    CoupleTable coupleTable

##### jLabel1

    JLabel jLabel1

##### jLabel2

    JLabel jLabel2

##### redField

    JTextField redField

##### redLabel

    JLabel redLabel

##### setAllButton

    JButton setAllButton

##### yellowField

    JTextField yellowField

##### yellowLabel

    JLabel yellowLabel

### Class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel

class CoupleParameterSelectionPanel extends JPanel implements Serializable

#### Serialized Fields

##### chButtonGroup

    ButtonGroup chButtonGroup

##### coupleTable

    CoupleTable coupleTable

##### eq0RadioButton

    JRadioButton eq0RadioButton

##### eq1RadioButton

    JRadioButton eq1RadioButton

##### eq2RadioButton

    JRadioButton eq2RadioButton

##### eq3RadioButton

    JRadioButton eq3RadioButton

##### jLabel1

    JLabel jLabel1

##### jLabel2

    JLabel jLabel2

##### jLabel3

    JLabel jLabel3

##### jLabel4

    JLabel jLabel4

##### titleLabel

    JLabel titleLabel

### Class org.openscience.jmol.app.janocchio.CoupleTable

class CoupleTable extends JTabbedPane implements Serializable

#### Serialized Fields

##### calcProps

    NmrMolecule calcProps

##### CHequation

    String CHequation

##### colorCellRenderer

    org.openscience.jmol.app.janocchio.NMRTableCellRenderer colorCellRenderer

##### coupleAddAllButton

    JButton coupleAddAllButton

##### coupleColourSelectionPanel

    CoupleColourSelectionPanel coupleColourSelectionPanel

##### coupledeleteAllButton

    JButton coupledeleteAllButton

##### coupledeleteButton

    JButton coupledeleteButton

##### coupleSelection

    ListSelectionModel coupleSelection

##### coupleTable

    JTable coupleTable

##### coupleTableModel

    org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel coupleTableModel

##### degtorad

    double degtorad

##### expCouples

    String[][] expCouples

##### frameDeltaDisplay

    FrameDeltaDisplay frameDeltaDisplay

##### labelArray

    String[] labelArray

##### molCDKuptodate

    boolean molCDKuptodate

##### natomsPerModel

    int natomsPerModel

##### nmrPanel

    NMR_JmolPanel nmrPanel

##### redValue

    double redValue

##### selectedCoupleRow

    int[] selectedCoupleRow

##### viewer

    NMR_Viewer viewer

##### yellowValue

    double yellowValue

### Class org.openscience.jmol.app.janocchio.FrameCounter

class FrameCounter extends JPanel implements Serializable

#### Serialized Fields

##### field

    JTextField field

##### frameCount

    int frameCount

##### frameNumber

    int frameNumber

##### label

    JLabel label

##### viewer

    NMR_Viewer viewer

### Class org.openscience.jmol.app.janocchio.FrameDeltaDisplay

class FrameDeltaDisplay extends JPanel implements Serializable

#### Serialized Fields

##### coupleWeight

    double coupleWeight

##### coupleWeightField

    JTextField coupleWeightField

##### frameDeltaCouple

    double frameDeltaCouple

##### frameDeltaNoe

    double frameDeltaNoe

##### label

    JLabel label

##### noeWeight

    double noeWeight

##### noeWeightField

    JTextField noeWeightField

##### totalfield

    JTextField totalfield

##### viewer

    NMR_Viewer viewer

### Class org.openscience.jmol.app.janocchio.LabelSetter

class LabelSetter extends JPanel implements Serializable

#### Serialized Fields

##### coupleTable

    CoupleTable coupleTable

##### field

    JTextField field

##### label

    JLabel label

##### labelArray

    String[] labelArray

##### minindex

    int minindex

##### noeTable

    NoeTable noeTable

##### selectedAtomIndex

    int selectedAtomIndex

##### viewer

    NMR_Viewer viewer

### Class org.openscience.jmol.app.janocchio.NamfisReader

class NamfisReader extends JPanel implements Serializable

### Class org.openscience.jmol.app.janocchio.NamfisSaver

class NamfisSaver extends JPanel implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_DisplayPanel

class NMR_DisplayPanel extends DisplayPanel implements Serializable

#### Serialized Fields

##### frameDeltaDisplay

    FrameDeltaDisplay frameDeltaDisplay

##### guimap

    NmrGuiMap guimap

##### populationDisplay

    PopulationDisplay populationDisplay

##### status

    StatusBar status

##### viewer

    NMR_Viewer viewer

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel

class NMR_JmolPanel extends JmolPanel implements Serializable

#### Serialized Fields

##### coupleTable

    CoupleTable coupleTable

##### exportChooser

    JFileChooser exportChooser

##### frameCounter

    FrameCounter frameCounter

##### frameDeltaDisplay

    FrameDeltaDisplay frameDeltaDisplay

##### htMessageCallbacks

    Map<String,Thread> htMessageCallbacks

##### isApplet

    boolean isApplet

##### labelSetter

    LabelSetter labelSetter

##### mainSplitPane

    JSplitPane mainSplitPane

##### nmrApplet

    NmrApplet nmrApplet

##### nmrDisplay

    NMR_DisplayPanel nmrDisplay

##### nmrguimap

    NmrGuiMap nmrguimap

##### noeTable

    NoeTable noeTable

##### openChooser

    FileChooser openChooser

##### populationDisplay

    PopulationDisplay populationDisplay

##### readNamfisChooser

    JFileChooser readNamfisChooser

##### readNmrChooser

    JFileChooser readNmrChooser

##### saveNamfisChooser

    JFileChooser saveNamfisChooser

##### saveNmrChooser

    JFileChooser saveNmrChooser

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction

class DetachAppletAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction

class JumpBestFrameAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction

class LabelNmrAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction

class ReadNamfisAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction

class ReadNmrAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction

class ReattachAppletAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction

class ViewCoupleTableAction extends org.openscience.jmol.app.janocchio.NMR_JmolPanel.MoleculeDependentAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction

class ViewNoeTableAction extends org.openscience.jmol.app.janocchio.NMR_JmolPanel.MoleculeDependentAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction

class WriteNamfisAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.janocchio.NmrReader

class NmrReader extends JPanel implements Serializable

### Class org.openscience.jmol.app.janocchio.NmrSaver

class NmrSaver extends JPanel implements Serializable

### Class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel

class NoeColourSelectionPanel extends JPanel implements Serializable

#### Serialized Fields

##### jLabel1

    JLabel jLabel1

##### jLabel2

    JLabel jLabel2

##### jLabel3

    JLabel jLabel3

##### jLabel4

    JLabel jLabel4

##### jLabel5

    JLabel jLabel5

##### noeTable

    NoeTable noeTable

##### redField

    JTextField redField

##### redLabel

    JLabel redLabel

##### setAllButton

    JButton setAllButton

##### yellowField

    JTextField yellowField

##### yellowLabel

    JLabel yellowLabel

### Class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel

class NoeParameterSelectionPanel extends JPanel implements Serializable

#### Serialized Fields

##### cutoffField

    JTextField cutoffField

##### cutoffLabel

    JLabel cutoffLabel

##### freqField

    JTextField freqField

##### freqLabel

    JLabel freqLabel

##### noesyComboBox

    JComboBox<String> noesyComboBox

##### noesyLabel

    JLabel noesyLabel

##### noeTable

    NoeTable noeTable

##### refSingleComboBox

    JComboBox<String> refSingleComboBox

##### refSingleLabel

    JLabel refSingleLabel

##### rhoStarField

    JTextField rhoStarField

##### rhoStarLabel

    JLabel rhoStarLabel

##### setAllButton

    JButton setAllButton

##### tauField

    JTextField tauField

##### tauLabel

    JLabel tauLabel

##### titleLabel

    JLabel titleLabel

##### tMixField

    JTextField tMixField

##### tMixLabel

    JLabel tMixLabel

### Class org.openscience.jmol.app.janocchio.NoeTable

class NoeTable extends JTabbedPane implements Serializable

#### Serialized Fields

##### calcProps

    NmrMolecule calcProps

##### colorCellRenderer

    org.openscience.jmol.app.janocchio.NMRTableCellRenderer colorCellRenderer

##### cutoff

    double cutoff

##### expDists

    String[][] expDists

##### expNoes

    String[][] expNoes

##### expOrDistButton

    JComboBox<String> expOrDistButton

##### frameDeltaDisplay

    FrameDeltaDisplay frameDeltaDisplay

##### freq

    double freq

##### labelArray

    String[] labelArray

##### lexpNoes

    boolean lexpNoes

##### lrefSingle

    boolean lrefSingle

##### molCDKuptodate

    boolean molCDKuptodate

##### natomsPerModel

    int natomsPerModel

##### nmrPanel

    NMR_JmolPanel nmrPanel

##### noeColourSelectionPanel

    NoeColourSelectionPanel noeColourSelectionPanel

##### noedeleteAllButton

    JButton noedeleteAllButton

##### noedeleteButton

    JButton noedeleteButton

##### noeExprefValue

    double noeExprefValue

##### noeNPrefIndices

    int[] noeNPrefIndices

##### noeNPrefValue

    double noeNPrefValue

##### noeParameterSelectionPanel

    NoeParameterSelectionPanel noeParameterSelectionPanel

##### noeSelection

    ListSelectionModel noeSelection

##### noesetRefButton

    JButton noesetRefButton

##### noesy

    boolean noesy

##### noeTable

    JTable noeTable

##### noeTableModel

    org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel noeTableModel

##### redValue

    double redValue

##### rhoStar

    double rhoStar

##### selectedNoeRow

    int[] selectedNoeRow

##### tau

    double tau

##### tMix

    double tMix

##### viewer

    NMR_Viewer viewer

##### yellowValue

    double yellowValue

### Class org.openscience.jmol.app.janocchio.PopulationDisplay

class PopulationDisplay extends JPanel implements Serializable

#### Serialized Fields

##### field

    JTextField field

##### frameNumber

    int frameNumber

##### imaxp

    int imaxp

##### label

    JLabel label

##### maxp

    double maxp

##### population

    double[] population

##### populationFrames

    JCheckBox populationFrames

##### storedFrameNumber

    int storedFrameNumber

##### viewer

    NMR_Viewer viewer

### Class org.openscience.jmol.app.janocchio.TableSorter

class TableSorter extends AbstractTableModel implements Serializable

#### Serialized Fields

##### columnComparators

    Map columnComparators

##### modelToView

    int[] modelToView

##### mouseListener

    MouseListener mouseListener

##### sortingColumns

    List sortingColumns

##### tableHeader

    JTableHeader tableHeader

##### tableModel

    TableModel tableModel

##### tableModelListener

    TableModelListener tableModelListener

##### viewToModel

    org.openscience.jmol.app.janocchio.TableSorter.Row[] viewToModel

## Package org.openscience.jmol.app.jmolpanel

### Class org.openscience.jmol.app.jmolpanel.AboutDialog

class AboutDialog extends JDialog implements Serializable

#### Serialized Fields

##### vwr

    JmolViewer vwr

### Class org.openscience.jmol.app.jmolpanel.AtomSetChooser

class AtomSetChooser extends JFrame implements Serializable

#### Serialized Fields

##### amplitudeSlider

    JSlider amplitudeSlider

##### animThread

    Thread animThread

##### currentIndex

    int currentIndex

##### fpsSlider

    JSlider fpsSlider

##### indexes

    int[] indexes

Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.

##### infoLabel

    JLabel infoLabel

##### periodSlider

    JSlider periodSlider

##### propertiesTextArea

    JTextArea propertiesTextArea

##### radiusSlider

    JSlider radiusSlider

##### radiusValue

    int radiusValue

##### repeatCheckBox

    JCheckBox repeatCheckBox

##### saveChooser

    JFileChooser saveChooser

##### scaleSlider

    JSlider scaleSlider

##### selectSlider

    JSlider selectSlider

##### tree

    JTree tree

##### treeModel

    DefaultTreeModel treeModel

##### vwr

    Viewer vwr

### Class org.openscience.jmol.app.jmolpanel.CreditsDialog

class CreditsDialog extends HelpDialog implements Serializable

### Class org.openscience.jmol.app.jmolpanel.DisplayPanel

class DisplayPanel extends JPanel implements Serializable

#### Serialized Fields

##### axesAction

    Action axesAction

##### bottomAction

    Action bottomAction

##### boundboxAction

    Action boundboxAction

##### buttonModelkit

    AbstractButton buttonModelkit

##### buttonRotate

    AbstractButton buttonRotate

##### defineCenterAction

    org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction defineCenterAction

##### deleteAction

    Action deleteAction

##### dimSize

    Dimension dimSize

##### displaySpeed

    String displaySpeed

##### frame

    JFrame frame

##### frontAction

    Action frontAction

##### haveDisplay

    boolean haveDisplay

##### homeAction

    org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction homeAction

##### hydrogensAction

    Action hydrogensAction

##### jmolPanel

    JmolPanel jmolPanel

##### lastMotionEventNumber

    int lastMotionEventNumber

##### leftAction

    Action leftAction

##### measurementsAction

    Action measurementsAction

##### perspectiveAction

    Action perspectiveAction

##### rectClip

    Rectangle rectClip

##### rightAction

    Action rightAction

##### showPaintTime

    boolean showPaintTime

##### startupDim

    Dimension startupDim

##### timeBegin

    long timeBegin

##### toolbarButtonGroup

    ButtonGroup toolbarButtonGroup

##### topAction

    Action topAction

##### vwr

    Viewer vwr

##### xlateAction

    Action xlateAction

##### zoomAction

    Action zoomAction

### Class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction

class CheckBoxMenuItemAction extends AbstractAction implements Serializable

#### Serialized Fields

##### action

    String action

### Class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction

class MoveToAction extends AbstractAction implements Serializable

#### Serialized Fields

##### action

    String action

### Class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction

class SetStatusAction extends AbstractAction implements Serializable

#### Serialized Fields

##### statusText

    String statusText

### Class org.openscience.jmol.app.jmolpanel.GaussianDialog

class GaussianDialog extends JDialog implements Serializable

#### Serialized Fields

##### basisBox

    JComboBox<String> basisBox

##### charge

    String charge

##### chargeSpinner

    JSpinner chargeSpinner

##### check

    String check

##### checkField

    JTextField checkField

##### closeButton

    JButton closeButton

##### container

    JPanel container

##### dfBox

    JComboBox<String> dfBox

##### editArea

    JTextPane editArea

##### editPane

    JScrollPane editPane

##### file

    String file

##### fileButton

    JButton fileButton

##### fileChooser

    JFileChooser fileChooser

##### fileField

    JTextField fileField

##### iscroll

    int iscroll

##### mem

    String mem

##### memBox

    JComboBox<String> memBox

##### meth

    String meth

##### methBox

    JComboBox<String> methBox

##### mult

    String mult

##### multSpinner

    JSpinner multSpinner

##### optsField

    JTextField optsField

##### proc

    String proc

##### procSpinner

    JSpinner procSpinner

##### refreshButton

    JButton refreshButton

##### route

    String route

##### saveButton

    JButton saveButton

##### select

    String select

##### selectField

    JTextField selectField

##### vwr

    Viewer vwr

### Class org.openscience.jmol.app.jmolpanel.HelpDialog

class HelpDialog extends JDialog implements Serializable

#### Serialized Fields

##### html

    JEditorPane html

### Class org.openscience.jmol.app.jmolpanel.JmolJME

class JmolJME extends JME implements Serializable

#### Serialized Fields

##### allowClean

    boolean allowClean

debug flag; set to false to see an actual 2D structure before SMILES-based cleaning.

##### cleaning

    boolean cleaning

##### fileName

    String fileName

##### headless

    boolean headless

allows working headlessly if no frame is defined; set false if a frame is present

##### parentWindow

    Container parentWindow

##### vwr

    Viewer vwr

### Class org.openscience.jmol.app.jmolpanel.JmolPanel

class JmolPanel extends JPanel implements Serializable

#### Serialized Fields

##### appletContext

    String appletContext

##### atomSetChooser

    AtomSetChooser atomSetChooser

##### clientService

    JsonNioServer clientService

##### commands

    Map<String,Action> commands

##### copyImageAction

    JmolPanel.CopyImageAction copyImageAction

##### copyScriptAction

    JmolPanel.CopyScriptAction copyScriptAction

##### display

    DisplayPanel display

##### executeScriptAction

    JmolPanel.ExecuteScriptAction executeScriptAction

##### exportAction

    JmolPanel.ExportAction exportAction

##### frame

    JFrame frame

##### gaussianDialog

    GaussianDialog gaussianDialog

##### guimap

    GuiMap guimap

##### imageType

    String imageType

##### isPlugin

    boolean isPlugin

##### javaConsoleframe

    JFrame javaConsoleframe

##### jmolApp

    JmolApp jmolApp

##### jmolJME

    JmolJME jmolJME

##### measurementTable

    MeasurementTable measurementTable

##### menubar

    JMenuBar menubar

##### menuItems

    Map<String, JMenuItem> menuItems

##### modelAdapter

    JmolAdapter modelAdapter

##### myStatusListener

    StatusListener myStatusListener

##### nboOptions

    Map<String,Object> nboOptions

##### pasteClipboardAction

    JmolPanel.PasteClipboardAction pasteClipboardAction

##### pcs

    PropertyChangeSupport pcs

##### pluginMenu

    JMenu pluginMenu

##### plugins

    Map<String, JmolPlugin> plugins

##### pluginsSet

    boolean pluginsSet

##### povrayAction

    JmolPanel.PovrayAction povrayAction

##### preferencesDialog

    PreferencesDialog preferencesDialog

##### printAction

    JmolPanel.PrintAction printAction

##### qualityJPG

    int qualityJPG

##### qualityPNG

    int qualityPNG

##### recentFiles

    org.openscience.jmol.app.jmolpanel.RecentFilesDialog recentFiles

##### serverService

    JsonNioServer serverService

##### splash

    SplashInterface splash

##### startupHeight

    int startupHeight

##### startupWidth

    int startupWidth

##### status

    StatusBar status

##### surfaceTool

    SurfaceTool surfaceTool

##### surfaceToolAction

    JmolPanel.SurfaceToolAction surfaceToolAction

##### toolbar

    JToolBar toolbar

##### touchHandler

    JsonNioClient.TouchHandler touchHandler

##### toWebAction

    JmolPanel.ToWebAction toWebAction

##### twoDEditorAction

    JmolPanel.TwoDEditorAction twoDEditorAction

##### viewMeasurementTableAction

    JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction

##### vwr

    Viewer vwr

##### vwrOptions

    Map<String,Object> vwrOptions

##### webExport

    WebExport webExport

##### windowName

    String windowName

##### writeAction

    JmolPanel.WriteAction writeAction

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction

class AboutAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton

class AnimButton extends JmolButton implements Serializable

#### Serialized Fields

##### lastPressTime

    long lastPressTime

##### script

    String script

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction

class AtomSetChooserAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction

class CloseAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction

class ConsoleAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction

class CopyImageAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction

class CopyScriptAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction

class CreditsAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction

class ExecuteScriptAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction

class ExitAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction

class ExportAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction

class GaussianAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction

class NewAction extends AbstractAction implements Serializable

#### Serialized Fields

##### script

    String script

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction

class NewwinAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction

class OpenAction extends JmolPanel.NewAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction

class OpenMolAction extends JmolPanel.NewAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction

class OpenPdbAction extends JmolPanel.NewAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction

class OpenUrlAction extends JmolPanel.NewAction implements Serializable

#### Serialized Fields

##### prompt

    String prompt

##### title

    String title

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction

class PasteClipboardAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction

class PovrayAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction

class PrintAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction

class RecentFilesAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction

class ResizeAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction

class ScriptEditorAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction

class ScriptWindowAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction

class SurfaceToolAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction

class ToWebAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction

class TwoDEditorAction extends AbstractAction implements Serializable

#### Serialized Fields

##### jmolPanel

    JmolPanel jmolPanel

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction

class UguideAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction

class ViewMeasurementTableAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction

class WhatsNewAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction

class WriteAction extends AbstractAction implements Serializable

### Class org.openscience.jmol.app.jmolpanel.MeasurementTable

class MeasurementTable extends JDialog implements Serializable

#### Serialized Fields

##### container

    JPanel container

##### deleteAllButton

    JButton deleteAllButton

##### deleteButton

    JButton deleteButton

##### measurementTable

    JTable measurementTable

##### measurementTableModel

    org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel measurementTableModel

##### selectedMeasurementRow

    int selectedMeasurementRow

##### stringClass

    Class<? extends String> stringClass

##### vwr

    Viewer vwr

### Class org.openscience.jmol.app.jmolpanel.PovrayDialog

class PovrayDialog extends JDialog implements Serializable

#### Serialized Fields

##### allFramesCheck

    JCheckBox allFramesCheck

##### antiAliasCheck

    JCheckBox antiAliasCheck

##### displayWhileRenderingCheck

    JCheckBox displayWhileRenderingCheck

##### goButton

    JButton goButton

##### imageSizeHeight

    JLabel imageSizeHeight

##### imageSizeRatioBox

    JCheckBox imageSizeRatioBox

##### imageSizeRatioCombo

    JComboBox<String> imageSizeRatioCombo

##### imageSizeTextHeight

    JFormattedTextField imageSizeTextHeight

##### imageSizeTextWidth

    JFormattedTextField imageSizeTextWidth

##### imageSizeWidth

    JLabel imageSizeWidth

##### mosaicPreviewCheck

    JCheckBox mosaicPreviewCheck

##### mosaicPreviewComboEnd

    JComboBox<String> mosaicPreviewComboEnd

##### mosaicPreviewComboStart

    JComboBox<String> mosaicPreviewComboStart

##### mosaicPreviewEnd

    JLabel mosaicPreviewEnd

##### mosaicPreviewStart

    JLabel mosaicPreviewStart

##### outputAlphaCheck

    JCheckBox outputAlphaCheck

##### outputExtension

    String outputExtension

##### outputFileType

    String outputFileType

##### outputFormatCheck

    JCheckBox outputFormatCheck

##### outputFormatCombo

    JComboBox<String> outputFormatCombo

##### outputHeight

    int outputHeight

##### outputWidth

    int outputWidth

##### povrayPathButton

    JButton povrayPathButton

##### povrayPathLabel

    JTextField povrayPathLabel

##### runPovCheck

    JCheckBox runPovCheck

##### saveField

    JTextField saveField

##### savePathLabel

    JTextField savePathLabel

### Class org.openscience.jmol.app.jmolpanel.PreferencesDialog

class PreferencesDialog extends JDialog implements Serializable

#### Serialized Fields

##### abNo

    JRadioButton abNo

##### abYes

    JRadioButton abYes

##### actions

    List<Action> actions

##### antialiasDisplay

    boolean antialiasDisplay

##### applyButton

    JButton applyButton

##### autoBond

    boolean autoBond

##### axesOrientationRasmol

    boolean axesOrientationRasmol

##### bButton

    JButton bButton

##### bdSlider

    JSlider bdSlider

##### bondingVersion

    int bondingVersion

##### bondTolerance

    float bondTolerance

##### btSlider

    JSlider btSlider

##### bwSlider

    JSlider bwSlider

##### cancelButton

    JButton cancelButton

##### cbAntialias

    JCheckBox cbAntialias

##### cbAxesOrientationRasmol

    JCheckBox cbAxesOrientationRasmol

##### cbClearHistory

    JCheckBox cbClearHistory

##### cbMeasureAngstroms

    JCheckBox cbMeasureAngstroms

##### cbOpenFilePreview

    JCheckBox cbOpenFilePreview

##### cbPerspectiveDepth

    JCheckBox cbPerspectiveDepth

##### cbShowAxes

    JCheckBox cbShowAxes

##### cbShowBoundingBox

    JCheckBox cbShowBoundingBox

##### cH

    JCheckBox cH

##### checkBoxListener

    ItemListener checkBoxListener

##### clearHistory

    boolean clearHistory

##### cM

    JCheckBox cM

##### commands

    Map<String,Action> commands

##### currentProperties

    Properties currentProperties

##### eButton

    JButton eButton

##### fontScale

    int fontScale

##### guimap

    GuiMap guimap

##### jmol

    JmolPanel jmol

##### jmolDefaultProperties

    Properties jmolDefaultProperties

##### jmolDefaultsButton

    JButton jmolDefaultsButton

##### marBond

    short marBond

##### measureAngstroms

    boolean measureAngstroms

##### minBondDistance

    float minBondDistance

##### okButton

    JButton okButton

##### openFilePreview

    boolean openFilePreview

##### pButton

    JButton pButton

##### percentVdwAtom

    int percentVdwAtom

##### perspectiveDepth

    boolean perspectiveDepth

##### prefsAction

    org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction prefsAction

##### rasmolDefaultsButton

    JButton rasmolDefaultsButton

##### showAxes

    boolean showAxes

##### showBoundingBox

    boolean showBoundingBox

##### showHydrogens

    boolean showHydrogens

##### showMeasurements

    boolean showMeasurements

##### tButton

    JButton tButton

##### vButton

    JButton vButton

##### vdwPercentSlider

    JSlider vdwPercentSlider

##### vwr

    Viewer vwr

### Class org.openscience.jmol.app.jmolpanel.Splash

class Splash extends Window implements Serializable

#### Serialized Fields

##### imgHeight

    int imgHeight

##### imgWidth

    int imgWidth

##### splashImage

    Image splashImage

##### status

    String status

##### statusTop

    int statusTop

##### textY

    int textY

### Class org.openscience.jmol.app.jmolpanel.StatusBar

class StatusBar extends JPanel implements Serializable

#### Serialized Fields

##### status

    JLabel[] status

### Class org.openscience.jmol.app.jmolpanel.WhatsNewDialog

class WhatsNewDialog extends HelpDialog implements Serializable

## Package org.openscience.jmol.app.jmolpanel.console

### Class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea

class ConsoleTextArea extends JTextArea implements Serializable

## Package org.openscience.jmol.app.jsonkiosk

### Class org.openscience.jmol.app.jsonkiosk.BannerFrame

class BannerFrame extends JFrame implements Serializable

#### Serialized Fields

##### bannerLabel

    JLabel bannerLabel

### Class org.openscience.jmol.app.jsonkiosk.KioskFrame

class KioskFrame extends JFrame implements Serializable

## Package org.openscience.jmol.app.webexport

### Class org.openscience.jmol.app.webexport.Orbitals

class Orbitals extends JPanel implements Serializable

### Class org.openscience.jmol.app.webexport.Test

class Test extends JPanel implements Serializable

serialVersionUID:
  1L

#### Serialized Fields

##### appletPath

    JTextField appletPath

##### arrayListHandler

    org.openscience.jmol.app.webexport.ArrayListTransferHandler arrayListHandler

##### fc

    JFileChooser fc

##### FileButton

    JButton FileButton

##### movetoTime

    JButton movetoTime

##### PathButton

    JButton PathButton

##### StateButton

    JButton StateButton

##### StringtoScriptButton

    JButton StringtoScriptButton

##### vwr

    Viewer vwr

### Class org.openscience.jmol.app.webexport.WebExport

class WebExport extends JPanel implements Serializable