# All Classes and Interfaces

Class
Description
___Exporter
__CartesianExporter
_IdtfExporter
_MayaExporter
_ObjExporter
Class to export Wavefront OBJ files.
_PovrayExporter
_StlExporter
STereoLithography file format exporter for 3D printing.
_TachyonExporter
_VrmlExporter
A basic VRML generator.
_X3dExporter
A4
A 4 element axis angle represented by single precision floating point x,y,z,angle components.
AbinitReader
AboutDialog
The `About Dialog` class is the help | about window for JSpecView.
AboutDialog
AbstractButton
AbstractTableModel
ActionManager
ActionManagerMT
AdfReader
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
AFLOWReader
A reader for various AFLOW file types.
AimsReader
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).
AjaxURLConnection
A method to allow a JavaScript Ajax
AjaxURLStreamHandler
A method to allow a JavaScript AJAX adapter to deliver web content to JSmol.
AjaxURLStreamHandlerFactory
For handling URL file IO via AJAX in JavaScript version
AlchemyReader
TRIPOS simple Alchemy reader.
AlphaMonomer
AlphaPolymer
AminoMonomer
AminoPolymer
AMLExporter
class `AnIMLExporter` contains static methods to export a Graph as as AnIML.
AmpacReader
A reader for AMPAC output.
AmsReader
A reader for AMS output subclassing the older AdfReader.
AnimationManager
AnimationThread
AnIMLReader
Representation of a XML Source.
Annotation
The `Annotation` class stores the spectral x and pixel y values of an annotation text along with its text
Annotation
Annotation.AType
AnnotationData
AnnotationParser
A parser for output from 3DNA web service.
AppConsole
AppletConsole
AppletConsole
An interface to Jmol.Console.
AppletFrame
ApplicationMenu
The Main Class or Entry point of the JSpecView Application.
AppToolBar
ArrayDataReader
ArrayDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with String[] arrays without any further adaptation.
ASimpleJvxlWriter
Atom
Atom
AtomCollection
AtomData
AtomDataServer
AtomDisplayLabel
AtomIndexIterator
note: YOU MUST RELEASE THE ITERATOR
AtomIteratorWithinModel
AtomIteratorWithinModelSet
AtomSetChooser
A JFrame that allows for choosing an Atomset to view.
AtomSetCollection
AtomSetCollectionReader
AtomSetObject
AtomShape
AtomType
AU
AviCreator
AwtClipboard
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtClipboard
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtColor
AwtColor
AwtDialog
AwtDialog extends JDialog, interpreting DialogManager's requests in terms of Swing and AWT.
AwtDialogFileFilter
A implementation of the `FileFilter` that filters out all files except those with extensions that are added.
AwtDialogManager
just a class I made to separate the construction of the AnnotationDialogs from their use
AwtFileDropper
AwtFileHelper
AwtG2D
generic 2D drawing methods -- AWT version
AwtG2D
generic 2D drawing methods -- AWT version
AwtJmolPopup
AwtMainPanel
AwtModelKitPopup
AwtPanel
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
AwtParameters
AwtPlatform
AwtPopup
AwtPopupHelper
all popup-related awt/swing class references are in this file.
AwtPrintDialog
Dialog to set print preferences for JSpecview.
AwtSwingComponent
A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.
AwtTree
AwtTreeNode
AwtTreePath
Axes
AxesRenderer
Backbone
BackboneRenderer
Balls
BallsRenderer
BannerFrame
A simple class that throws up a white rectangle that has a single centered label.
BArray
Base64
BasePair
BasisFunctionReader
Bbcage
BbcageRenderer
BC
byte converter
BCIFReader
A very simple Binary CIF file reader extention of MMCifReader extends CifReader.
BilbaoReader
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.
BinaryDcdReader
DCD binary trajectory file reader.
BinaryDocument
Binding
BioExt
BioMeshRenderer
BioModel
BioModelSet
BioPolymer
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.
BioResolver
a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
BioShape
BioShapeCollection
When a Cartoon is instantiated with a call to setSize(), it creates an BioShapeCollection for each BioPolymer in the model set.
BMPDecoder
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
Bond
Bond
BondCollection
BondIterator
BondSet
BorderLayout
BoxInfo
The BoxInfo class holds critical information about boundboxes.
BrukerReader
A class to read Bruker ZIP files and directories.
BS
a fast 32-bit BitSet optimized for Java2Script -- about 25 times faster than java.util.BitSet
Bspf
A Binary Space Partitioning Forest
Bspt
a Binary Space Partitioning Tree
BSUtil
ButtonGroup
BytePoster
BZip2Constants
Base class for both the compress and decompress classes.
BZone
A class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells.
C
Note: Color table is now in javajs/util/CU.java
CarbohydrateMonomer
CarbohydratePolymer
Cartoon
CartoonRenderer
CastepReader
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.
CBK
CBZip2InputStream
An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStreamFactory
CDXMLParser
A reader for CambridgeSoft CDXML files.
CDXMLParser.CDXReaderI
CDXMLWriter
Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the basic necessities for XmlCDXReader.
CDXReader
A reader for ChemDraw binary CDX files.
Cell
CgdReader
A reader for TOPOS systre file Crystal Graph Data format.
CGO
PyMOL Compiled Graphic Object (CGO) meshes
CGOMesh
CGORenderer
Something like a PyMOL Compiled Graphical Object, but more interesting!
Chain
A Model is a collection of Chains of Groups of Atoms.
ChimeMessenger
A legacy Chime-compatible messenger.
Cif2DataParser
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
Cif2Reader
Preliminary Cif2 reader.
CifDataParser
A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
CifReader
A true line-free CIF file reader for CIF files.
CIFWriter
A basic CIF writer only.
CIPChirality
A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
CIPData
A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.
CIPDataSmiles
A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
CIPDataTracker
An optional class to track digraph paths to decisions.
CircleRenderer
Implements flat circle drawing/filling routines.
CLEG
A holding class for ClegData and ClegNode, which are called by org.jmol.modelkit.Modelkit to process CLEG strings.
CLEG.ClegData
running data items for assignSpaceGroup iteration
CLEG.ClegNode
ClientProtocol
The abstract class for the client protocol that defines members common to both the server-side and client-side protocols.
ClientServerConnection
Represents the connection to the GestureServer.
ClientToServerProtocol
ClientToServerProtocol implements the Client side protocol.
CmdExt
CmdfReader
A reader for CrystalMaker CMDF binary/text files.
CMLExporter
class `CMLExporter` contains static methods to export a Graph as as CIML.
CMLWriter
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
Color
ColoredAnnotation
ColoredAnnotation is a label on the spectrum; not an integralRegion
ColorEncoder
ColorManager
ColorParameters
This a representation of the Display Scheme for the spectral display.
ColumnSelectionModel
CommandHistory
CommandHistory keeps a command history and responds to key events
CommandHistory
Implements a queue for a bash-like command history.
CommandWatcherThread
Component
CompoundDocument
ConnectionType
ConsoleTextArea
Contact
ContactPair
ContactRenderer
Container
Converter
Contains conversion methods that are needed by several elements of the Gesture Server.
Coordinate
The `Coordinate` class stores the x and y values of a coordinate.
CoupleColourSelectionPanel
CoupleParameterSelectionPanel
CoupleTable
CreditsDialog
CrystalReader
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
CsfReader
CSF file reader based on CIF idea -- fluid property fields.
CU
ColorUtility
CubeIterator
Iterator used for finding all points within a box or a hemi-box
CubeReader
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.
DataAdder
DataAdder11H
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributions
DataAdder13I
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributions
DataAdder7F
adds 7 spherical F orbital contributions
DataAdder9G
change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributions
DataAdderF
adds 10 cartesian F orbital contributions
DataAdderG
change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributions
DataAdderH
change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributions
DataAdderI
change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributions
DataManager
DataReader
Just a simple abstract class to join a String reader and a String[] reader under the same BufferedReader umbrella.
DebugJS
A class to insert a JavaScript debug statement for Firefox or Chrome debugger
DefaultLogger
Default implementation of the logger.
DF
created to remove ambiguities and make a simpler DecimalFormat
DgridReader
A reader for Dgrid BASISFILE data.
Dialog
Dialog.TypeFilter
DialogManager
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.
DialogParams
DialogParams handles all the platform-independent needs of AwtAnnotationDialog and subclasses of it.
Dimension
Dipole
Dipoles
DipolesRenderer
DisplayPanel
DisplaySchemesProcessor
`DisplaySchemesProcessor` loads and saves the display schemes of Jspecview.
DmolReader
Document
DOMReader
Dots
DotsRenderer
DragBinding
DragEvent
Draw
Draw.EnumDrawType
DrawMesh
DrawRenderer
DSSP
DSSR0
The original non-JSON parser for output from 3DNA web service.
DSSR1
A parser for output from 3DNA web service.
Echo
EchoRenderer
Edge
Eigen
Eigenvalues and eigenvectors of a real matrix.
EigenInterface
Elements
Ellipsoid
Ellipsoids
EllipsoidsRenderer
Encoding
EnvelopeCalculation
Escape
EspressoReader
Event
This interface must be implemented by all user-defined events.
Event
EventManager
EventType
This is an enumeration of all event types currently available.
Export3D
Exporter
ExportInterface
ExportInterface
ExportType
FAHReader
FoldingAtHome json reader.
FFParam
FIL
FileChooser
JFileChooser with possibility to fix size and location
FileDropper
A simple Dropping class to allow files to be dragged onto a target.
FileDropperJmol
A simple Dropping class to allow files to be dragged onto a target.
FileManager
FilePreview
File previsualisation before opening
FileReader
FilesReader
open a set of models residing in different files
FlickEvent
FlowLayout
FoldingXyzReader
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.
Font
Provides font support using a int fid (Font ID) as an index into font table.
FontLineShape
FontLineShapeRenderer
FontManager
A generic interface for font queries.
ForceField
ForceFieldMMFF
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
ForceFieldReader
ForceFieldUFF
FrameCounter
FrameDeltaDisplay
Frank
FrankRenderer
FSG2SCIFConverter
This class, a subclass of CIFWriter, should only be initialized dynamically and by CIFWriter.
FSGOutputReader
A reader for JSON output from the FINDSPINGROUP program.
G3DRenderer
GamessReader
GamessUKReader
GamessUSReader
GaussianDialog
GaussianFchkReader
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
GaussianReader
Reader for Gaussian 94/98/03/09 output files.
GaussianWfnReader
Reader for Gaussian Wfn files -- not implemented yet
GData
GenericApplet
A collection of all methods necessary for initialization of and communication with the applet.
GenericBinaryDocument
GenericBinaryDocumentReader
GenericCifDataParser
GenericColor
GenericColor allows both java.awt.Color and javajs.awt.Color to be handled by methods that need not distinguish between them.
GenericConsole
GenericConsoleTextArea
GenericFileInterface
GenericGraphics
GenericImageDialog
GenericImageEncoder
GenericLineReader
GenericMenuInterface
GenericMouse
GenericMouseInterface
GenericOutputChannel
GenericPlatform
GenericPopup
The overall parent of all popup classes in Jmol and JSmol.
GenericTextArea
GenericZipInputStream
GenericZipTools
Class abandoned as unnecessary in SwingJS
GenNBOReader
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
Geodesic
J2SRequireImport is needed because we use ArrayUtil in a static method
GeoSurface
GeoSurfaceRenderer
Gesture
Defines the interface that all user-defined gestures must implement.
GestureServer
The main gesture server class.
GestureType
This class is a place for the enum GestureType to stand.
GhemicalMMReader
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GifEncoder
GifEncoder extensively adapted for Jmol by Bob Hanson Color quantization roughly follows the GIMP method "dither Floyd-Steinberg (normal)" but with some twists.
GlobalSettings
Graphics3D
Provides high-level graphics primitives for 3D visualization for the software renderers.
Grid
GridBagConstraints
GridBagLayout
GromacsReader
Group
Represents a group of touch points for the gesture server.
Group
The essential container for every atom.
GT
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
GuiMap
GulpReader
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
HallInfo
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
An interface to receive the decoded matrices from Hall notation.
Halos
HalosRenderer
HB
Enum for hydrogen bonding donor/acceptor type
HBond
Helix
HelpDialog
HermiteRenderer
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
HistoryFile
The history file contains data from previous uses of Jmol.
Hover
HoverRenderer
HoverWatcherThread
HTMLElement
HTMLWindowEvent
The window.Event in HTML5 See SwingController.
HyperChemReader
Support for .hin, HyperChem's native file format.
ImageDialog
ImageEncoder
Generic abstract image creator: (1) set parameters (2) encode the image bytes, if necessary (3) generate the image
InchiFlag
InchiJmol
InChIJNA
Interface with inchi.c via JNA (see JNA-InChI github project).
InChIJS
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.
InChIStructureProvider
InchiUtils
periodic table daata from inchi C util.c
InputDeviceConnection
Represents a connection to the input device.
InputReader
InputScannerThread
Insets
Int2IntHash
Integral
IntegralData
from IntegralGraph a data structure for integration settings
IntegralData.IntMode
IntegrationDialog
Dialog for managing the integral listing for a Spectrum within a GraphSet
Interface
Interface
InvalidSmilesException
Exception thrown for invalid SMILES String
IsoExt
Isosurface
IsosurfaceMesh
IsosurfaceRenderer
J2SIgnoreImport
J2SObjectInterface
methods in j2s JavaScript accessed in Jmol
J2SRequireImport
JaguarReader
Jaguar reader tested for the two samples files in CVS.
JanaReader
A reader for Jana M50+M40 file pairs.
JButton
JC
JcampdxReader
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= <Models> acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...
JCheckBox
JCheckBoxMenuItem
JComboBox<T>
JComponent
JContentPane
JDialog
There is really no need here for awt.Dialog.
JDXDataObject
spectrum data AS READ FROM FILE
JDXDecompressor
JDXDecompressor contains static methods to decompress the data part of JCAMP-DX spectra that have been compressed using DIF, FIX, SQZ or PAC formats.
JDXDecompressorTest
JDXExporter
class `JDXExporter` contains methods for exporting a JCAMP-DX Spectrum in one of the compression formats DIF, FIX, PAC, SQZ or as x, y values.
JDXHeader
could be a spectrum or a source
JDXHeader.DataLDRTable
JDXMOLParser
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
JDXReader
`JDXFileReader` reads JDX data, including complex BLOCK files that contain NTUPLE blocks or nested BLOCK data.
JDXSource
`JDXSource` is representation of all the data in the JCAMP-DX file or source.
JDXSourceStreamTokenizer
JEditorPane
A simple implementation of a Swing JTextPane.
JLabel
JME
JMEmol
JMenu
JMenuItem
JmeReader
JMEUtil
JMEUtil.GWT
Do nothing , support for JSME code splitting.
JMEUtil.JSME_RunAsyncCallback
JMEUtil.RunAsyncCallback
A callback meant to be used by
JMEUtil.RunWhenDataReadyCallback
Jmol
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
Jmol
JmolAbstractButton
JmolAdapter
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapterAtomIterator
JmolAdapterBondIterator
JmolAdapterStructureIterator
JmolAnnotationParser
JmolApp
JmolAppAPI
JmolAppConsoleInterface
JmolAppletInterface
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAsyncException
JmolAudio
JmolAudioPlayer
JmolBinding
JmolButton
JmolCallbackListener
JmolChimeMessenger
JmolConsole
JmolData
JmolDataManager
JmolDataReader
JmolData file reader, for a modified PDB format This class also holds pseudo-static methods for spin
JmolDialogInterface
JmolDropEditor
JmolEnvCalc
JmolFilesReaderInterface
JmolFrame
JmolFrame
JmolGenericPopup
An abstract popup class that is instantiated for a given platform and context as one of:
JmolGestureServerInterface
JmolGraphicsInterface
JmolInChI
JmolJDXMOLParser
JmolJDXMOLReader
JmolJME
ONLY for legacy Jmol, not for JmolD (which uses jme.jmeJmol
JmolJniClientAdapter
JmolJSpecView
JmolLabel
JmolMeasurementClient
JmolModulationSet
JmolMolecule
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
JmolMovieCreatorInterface
JmolMultiTouchAdapter
JmolMultiTouchClient
JmolMultiTouchClientAdapter
JmolNavigatorInterface
JmolNMRInterface
JmolPanel
JmolPanel.ActionChangedListener
JmolParallelProcessor
JmolPdfCreatorInterface
JmolPlugin
JmolPopup
An abstract popup class that is instantiated for a given platform and context as one of:
JmolPropertyManager
JmolRendererInterface
JmolRepaintManager
JmolResourceHandler
Provides access to resources (for example, strings and images).
JmolSceneGenerator
JmolScriptEditorInterface
JmolScriptEvaluator
JmolScriptFunction
JmolScriptManager
JmolSelectionListener
listen to atom selections in a Jmol Viewer
JmolSparshClientAdapter
JmolStateCreator
JmolStatusListener
JmolSyncInterface
JmolThread
JmolToggleButton
JmolToJSmolInterface
methods in JSmol JavaScript accessed in Jmol
JmolTouchSimulator
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.
JmolTouchSimulatorInterface
JmolUtil
JmolViewer
JmolViewer is the main API for the Viewer class.
JmolWriter
JmolZipUtilities
JPanel
Jpg64Encoder
JpgEncoder
JpegEncoder - The JPEG main program which performs a jpeg compression of an image.
JPopupMenu
JRadioButtonMenuItem
JSAppletObject
JSConsole
JScrollPane
JsDialog
just a class I made to separate the construction of the AnnotationDialogs from their use
JsDialogManager
A DialogManager for JavaScript.
JSExporter
A class to output WebGL graphics.
JsFileHelper
JSFunction
A flag that this object is really a JavaScript function that, for example, might be called from setTimeout().
JsG2D
generic 2D drawing methods for JSpecView -- JavaScript version
JsG2D
generic 2D drawing methods -- JavaScript version
JSInterface
called by JSmol JavaScript methods using this._applet.xxxx()
JSJmolPopup
JSJSONParser
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
JsMainPanel
JSModelKitPopup
JSmolAppletObject
JSONEncodable
JSONException
JsonNioClient
a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
JsonNioClient.TouchHandler
JsonNioServer
JsonNioService
A class for interacting with Jmol over local sockets.
JSONReader
JSONWriter
JsPanel
The JavaScript extension of a JSVPanel.
JsParameters
JSpecView
The Main Class or Entry point of the JSpecView Application.
JsPlatform
JavaScript 2D canvas version requires Ajax-based URL stream processing.
JSplitPane
JsPopup
JSPopupHelper
For menus, popup-related awt/swing class references are in this file.
JSV
JSVApp
JSpecView Applet class.
JSVAppInterface
JSVApplet
Entry point for the web.
JSVAppletInterface
JSVAppletObject
JSVAppletPro
A signed applet that has an Advanced...
JSVAppPro
JSVDialog
JSVersion
JSVException
JSVException is the base class from which all exceptions in JSpecView is inherited.
JSVExporter
JSVFileDropper
JSVFileHelper
JSVFileManager
JSVGenericPopup
JSViewer
This class encapsulates all general functionality of applet and app.
JSVInterface
and interface for JSpecView for the Jmol application
JSVMainPanel
JSVPanel
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
JSVPdfWriter
JSVPopupResourceBundle
JSVPrintDialog
JSVToJSmolInterface
JSVTree
JSVTreeNode
JSVTreePath
JSVViewPanel
JSVZipFileSequentialReader
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()
JSVZipInterface
JSVZipReader
JSVZipUtil
JTable
JTextField
JTextPane
A simple implementation of a Swing JTextPane.
Jvxl
JvxlCoder
JvxlData
JvxlReader
JvxlWrite
JvxlXmlReader
KeyJCheckBox
KeyJCheckBoxMenuItem
KeyJMenu
KeyJMenuItem
KeyJRadioButtonMenuItem
KioskFrame
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
Labels
LabelSetter
LabelsRenderer
LabelToken
Language
LayoutManager
LcaoCartoon
LcaoCartoonRenderer
LimitedLineReader
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.
ListDataReader
VectorDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with Vector<String> arrays without any further adaptation.
ListSelectionModel
LoadMeasureThread
LoadMeasureThreadJSON
Location
Represents a 2D location with float values.
Logger
Logger mechanism.
LoggerInterface
Interface used for the logging mechanism.
LoopedStreams
Lst<V>
created to remove ambiguities in add and remove
M3
A single precision floating point 3 by 3 matrix.
M34
A base class for both M3 and M4 to conserve code size.
M4
A single precision floating point 4 by 4 matrix.
MagresReader
MainFrame
The Main Class or Entry point of the JSpecView Application.
MainPopupResourceBundle
MarchingCubes
MarchingSquares
MathExt
Matrix
streamlined and refined for Jmol by Bob Hanson from http://math.nist.gov/javanumerics/jama/ Jama = Java Matrix class.
MdCrdReader
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
MdTopReader
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
Measure
Measure
MeasureCouple
MeasureDist
Calculates the difference between calculated and experimental values for coloring table
Measurement
The `Measurement` class stores an annotation that is a measurement
Measurement
MeasurementData
MeasurementData
MeasurementPending
MeasurementsDialog
Dialog for managing the measurement list for a Spectrum within a GraphSet
MeasurementTable
MeasureNoe
Measures
MeasuresRenderer
MepCalculation
Mesh
MeshCapper
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.
MeshCollection
MeshData
MeshDataServer
MeshRenderer
an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
MeshRibbon
MeshRibbonRenderer
MeshSlicer
MeshSurface
MessagePackReader
A simple MessagePack reader.
MinAngle
MinAtom
MinBond
MinimizationThread
Minimizer
MinObject
MinPosition
not implemented -- would be a force toward a given position in space
MinTorsion
MlpCalculation
MMCifReader
mmCIF files are recognized prior to class creation.
MMCifValidationParser
MMConstraint
MMTFReader
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.
MOCalculation
Model
ModelKit
An abstract popup class that is instantiated for a given platform and context as one of:
ModelKitPopup
An abstract popup class that is instantiated for a given platform and context as one of:
ModelKitPopupResourceBundle
ModelLoader
ModelSet
Modulation
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
ModulationSet
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
Mol2Reader
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol3DReader
3D only
MoldenReader
A molecular structure and orbital reader for MolDen files.
MolecularOrbital
MolecularOrbitalRenderer
MolReader
A reader for MDLI mol and sdf files.
MOLWriter
Monomer
A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
MopacArchiveReader
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
MopacGraphfReader
Reads Mopac 2007 GRAPHF output files
MopacReader
Reads Mopac 93, 6, 7, 2002, or 2009 output files
MOReader
General methods for reading molecular orbital data, including embedded output from the NBO program.
Mouse
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
MouseState
MoveToThread
MPJmolApp
MSCifParser
MSInterface
Modulated Structure Reader Interface
MSRdr
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
MyFileFilter
NamfisReader
NamfisSaver
Navigator
Navigator is a user input mechanism that utilizes the keypad to drive through the model.
NBO
NBOParser
NBORenderer
NciCalculation
NetworkConfiguration
Defines the port the server will be listening for connections on.
Nmr
NMR_DisplayPanel
NMR_JmolPanel
NMR_Viewer
Implements some lost interfaces.
NmrApplet
NMRCalculation
NmrGuiMap
NMRMLReader
Representation of an nmrML Source.
NmrMolecule
NMRNoeMatrix
Class for calculating NOE intensities by full matrix relaxation approach.
NMRNoeMatrix.NOEParams
NmrPlugin
NmrReader
NmrResourceHandler
Provides access to resources (for example, strings and images).
NmrSaver
Node
NoeColourSelectionPanel
NoeParameterSelectionPanel
NoeTable
Normix
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
NucleicMonomer
NucleicPolymer
NucleicRenderer
extends CartoonRenderer for nucleics
NWChemReader
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
OC
A generic output method.
OdysseyReader
OptimadeReader
A (preliminary) reader for OPTIMADE resources.
Orbitals
OrcaReader
Reads ORCA input and output files
OrcaReader
Reads ORCA input and output files
Orientation
OutputManagerAwt
OutputManagerJS
OverlayLegendDialog
Dialog for showing the legend or key for overlaid plots in a `JSVPanel`.
P2nReader
P2N file reader.
P3
A 3 element point that is represented by single precision floating point x,y,z coordinates.
P3i
A 3 element point that is represented by signed integer x,y,z coordinates.
P4
A 4 element point that is represented by single precision floating point x,y,z,w coordinates.
PAL
Enum for animation mode.
PanelData
JSVPanel class draws a plot from the data contained a instance of one or more `GraphSet` objects.
PanelData.LinkMode
PanelListener
PanelNode
Parameters
Parameters
Parser
PatternMatcher
PatternMatcher.JSPattern
Super-simplified for JavaScript
PdbReader
PDB file reader.
PDBWriter
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
PDFCreator
PdfEncoder
A relatively primitive PDF generator that just makes a document with an image in it.
PDFWriter
A class that creates the PDF document specific to JSpecView using javajs.export.PDFCreator.
PeakData
a data structure for peak lists
PeakInfo
PeakListDialog
Dialog for managing the peak listing for a Spectrum within a GraphSet
PeakPickEvent
PeriodicVolumeFileReader
PfaatBinding
PhosphorusMonomer
PhosphorusPolymer
Platform
Platform
WebGL interface
Platform
JavaScript 2D canvas version requires Ajax-based URL stream processing.
PlatformDialog
PlatformViewer
Plot3D
Plot3DRenderer
PLYWriter
A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
Pmesh
PmeshRenderer
PMeshWriter
A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
PngEncoder
Modified by Bob Hanson hansonr@stolaf.edu to be a subclass of ImageEncoder and to use javajs.util.OutputChannel instead of just returning bytes.
PO
Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.
Point3fi
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)
PointIterator
Polyhedra
PolyhedraRenderer
Polyhedron
PopulationDisplay
PopupHelper
PopupResource
PovrayDialog
A dialog for controling the creation of a povray input file from a Chemframe and a display.
PpmEncoder
see http://netpbm.sourceforge.net/doc/ppm.html
PqrReader
PQR file reader.
PrecisionRenderer
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.
PreferencesDialog
Dialog to change the preferences for the application.
PreferencesDialog
PrintLayout
`PrintLayout` class stores all the information needed from the `PrintLayoutDialog`
PropertyManager
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
ProteinStructure
PsiReader
Reader for Psi3 output files.
PT
a combination of Parsing and Text-related utility classes
PWmatReader
crude PWmat atom.config reader http://pwmatus.com/manual
PWMATWriter
A writer for PWMAT atom.config files.
PymolAtomReader
PyMOLReader
PyMOL PSE (binary Python session) file reader.
PyMOLSettings
QchemReader
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QCJSONReader
A molecular structure and orbital reader for MolDen files.
QCJSONWriter
A very experimental class for writing QCJSON files.
QCSchemaUnits
A general Java class for working with QCShema units and array types.
QS
Constants and static methods for quantum shells.
QuantumCalculation
QuantumPlaneCalculation
Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
Quat
RadiusData
RadiusData.EnumType
RasmolBinding
Rdr
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.StreamReader
Rectangle
RelativeDragEvent
RepaintManager
RepaintManager
Resolver
Rgb16
Ribbons
RibbonsRenderer
RocketRenderer
Rockets
RocketsRenderer
RotateEvent
SB
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
SC
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.
ScaleData
Stores information about scale and range that `JSVPanel` needs to to display a graph with a single plot.
ScriptCompiler
ScriptContext
ScriptEditor
ScriptError
Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
ScriptEval
ScriptException
ScriptExt
ScriptFunction
ScriptInterface
ScriptInterruption
ScriptManager
ScriptMathProcessor
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
ScriptParallelProcessor
ScriptParam
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
ScriptProcessRunnable
ScriptQueueThread
ScriptToken
ScriptToken takes care of script command processing
ScriptTokenizer
SelectionManager
ServerToClientProtocol
Represents the server to client connection.
Shader
All functions.
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
ShapeManager
ShapeRenderer
Sheet
ShelxReader
A reader for SHELX output (RES) files.
SiestaReader
BH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/
SimpleEdge
minimal bond interface for SMILES and CIP
SimpleMarchingCubes
SimpleMarchingCubesOld
SimpleNode
Just the bare minimum for CIP, and non-BioSMILES
SimpleTree
SimpleTreeEnumeration
SimpleTreeModel
SimpleTreeNode
SimpleTreePath
SimpleUnitCell
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
SinglePointGesture
SINGLE_POINT_GESTURE only passes single-touch gestures.
SlaterData
SmarterJmolAdapter
SmilesAromatic
SmilesAtom
This class represents an atom in a `SmilesMolecule`.
SmilesBond
Bond in a SmilesMolecule
SmilesExt
SmilesGenerator
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
SmilesMatcher
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
SmilesMatcherInterface
SmilesMeasure
SmilesParser
Parses a SMILES string or SMARTS pattern to create a `SmilesSearch`.
SmilesSearch
A class to build and carry out a SMILES or SMARTS match
SmilesSearch.SmilesTarget
SmilesStereo
This class relates to stereochemical issues
SourceReader
SpaceGroup
A general class to deal with Hermann-Mauguin or Hall names Bob Hanson 9/2006 references: International Tables for Crystallography Vol.
SpaceGroup.ParamCheck
SpaceGroupFinder
A relatively simple space group finder given a unit cell.
SparshClient
The Client interface must be implemented in all clients wishing to connect to the Sparsh-UI gesture server.
SpartanInputReader
SpartanReader
SpartanSmolReader
SpartanUtil
A class to isolate Spartan file reading methods from the rest of Jmol.
SpecialGroup
SpecialGroupFactory
A static singleton class to create plane, layer, rod, and frieze groups
Spectrum
`JDXSpectrum` implements the Interface Spectrum for the display of JDX Files.
Spectrum.IRMode
SphereRenderer
Implements high performance rendering of shaded spheres.
SpinEvent
SpinThread
Splash
SplashInterface
Stars
StarsRenderer
StateCreator
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
StateManager
StateScript
StatusBar
StatusListener
StatusManager
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.
STER
Sticks
SticksRenderer
STR
Strands
StrandsRenderer
StringDataReader
Structure
Structure
StructureIterator
SubSpecChangeEvent
SurfaceGenerator
SurfaceReader
SurfaceStatus
Class that holds the surface status information that the surface tool needs.
SurfaceTool
SV
ScriptVariable class
SVGExporter
class `SVGExporter` contains static methods to export a Graph as as SVG.
SwingConstants
SwingController
SwingController is an interface that org.jmol.awtjs.swing classes will need.
Symmetry
SymmetryDesc
A class to handle requests for information about space groups and symmetry operations.
SymmetryInterface
SymmetryOperation
SyncManager
T
Script token class.
T3
A generic 3 element tuple that is represented by single precision floating point x,y and z coordinates.
T3d
A generic 3 element tuple that is represented by double precision floating point x,y and z coordinates.
T3i
A 3-element tuple represented by signed integer x,y,z coordinates.
T4
A generic 4 element tuple that is represented by single precision floating point x,y,z and w coordinates.
TableCellRenderer
TableColumn
TableSorter
TempArray
Tensor
Test
Text
TextShape
TickInfo
TimeoutThread
TinkerReader
simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
TlsDataOnlyReader
TopoCifParser
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.
TouchEvent
TouchPoint
Represents a touch point.
TouchState
Defines the types of touches that can ocurr in sparsh-UI: Birth, Move, and Death.
Trace
TraceRenderer
Trajectory
TransformManager
TransformManager4D
Translator
TriangleData
An adaptation of Marching Cubes that allows for indicating edges on triangles.
TriangleRenderer
renders triangles
Triangulator
TwoPointGesture
TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
Txt
Uccage
UccageRenderer
UnitCell
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.
UnitCellIterator
Util
V3
A 3-element vector that is represented by single precision floating point x,y,z coordinates.
V3000Rdr
A reader for Accelrys V3000 files.
V3d
A 3 element vector that is represented by double precision floating point x,y,z coordinates.
VaspChgcarReader
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
VaspOutcarReader
http://cms.mpi.univie.ac.at/vasp/
VaspPoscarReader
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
VDW
Vectors
VectorsRenderer
VertexDataServer
Vibration
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
VibrationThread
ViewData
Stores information that `GraphSet` needs to display a view with one or more spectra.
Viewer
Viewer.ACCESS
ViewsDialog
Dialog for managing overlaying spectra and closing files
Visible
Visible class - for prediction of colour from visible spectrum see Robert J.
VisibleInterface
VolumeData
VoxelDataCreator
WebExport
WebMOReader
A molecular orbital reader for WebMO files.
WhatsNewDialog
Wien2kReader
A reader for Wein2k DFT files.
WyckoffFinder
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.
XcrysdenReader
XmlArgusReader
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlCdxReader
A reader for CambridgeSoft CDXML files.
XmlChem3dReader
An chem3d c3xml reader
XmlCmlReader
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.
XmlHandler
a SAX handler -- Java only
XmlMagResReader
XmlMolproReader
A Molpro 2005 reader
XmlMOReader
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
XmlNmrmlReader
A reader for the structure part of an nmrML file
XmlOdysseyReader
An Odyssey xodydata reader
XMLParser
XmlQEReader
QuantumEspresso XML reader
XmlReader
A generic XML reader template -- by itself, does nothing.
XmlReader
XmlUtil
A very simplistic XML generator
XmlVaspReader
Vasp vasprun.xml reader
XmlXsdReader
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
XSFWriter
An XCrysDen XSF writer.
XtalSymmetry
A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
XtalSymmetry.FileSymmetry
A class only used by adapter.smarter.XtalSymmetry while building the file-based model.
XtlWriter
XyzReader
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
ZInputStream
ZipData
ZipTools
Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
ZoomEvent
ZoomEvent