Class Summary | |
---|---|
AboutDialog | |
AboutDialog.PageLoader | temporary class that loads synchronously (although later than the request so that a cursor change can be done). |
AdfReader | A reader for ADF output. |
AlphaMonomer | |
AlphaPolymer | |
AminoMonomer | |
AminoPolymer | |
ApbsReader | |
AppletWrapper | |
ArrayListTransferHandler | |
ArrayListTransferHandler.ArrayListTransferable | |
ArrayUtil | |
Atom | |
Atom | |
AtomCollection | |
AtomData | |
AtomDataReader | |
AtomDataServer | |
AtomIndexIterator | |
AtomIteratorWithinModel | |
AtomIteratorWithinSet | |
AtomSetChooser | A JFrame that allows for choosing an Atomset to view. |
AtomSetChooser.AtomSet | Objects in the AtomSetChooser tree |
AtomSetCollection | |
AtomSetCollectionReader | |
AtomShape | |
Awt3D |
Implementation of Platform3D when using AWT on 1.1 JVMs. |
Axes | |
AxesGenerator | |
AxesRenderer | |
Backbone | |
BackboneGenerator | |
BackboneRenderer | |
Balls | |
BallsGenerator | |
BallsRenderer | |
Base64 | |
Bbcage | |
BbcageGenerator | |
BbcageRenderer | |
BinaryDocument | |
BioPolymer | |
BioShape | |
BioShapeCollection | Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set. |
BioShapeRenderer | |
BitSetUtil | |
Bond | |
Bond | |
BondCollection | |
BondIterator | |
BondIteratorSelected | |
Bond.BondSet | |
BoxInfo | |
Bspf |
A Binary Space Partitioning Forest
This is simply an array of Binary Space Partitioning Trees identified by indexes |
Bspt |
a Binary Space Partitioning Tree The tree partitions n-dimensional space (in our case 3) into little boxes, facilitating searches for things which are *nearby*. |
Calculation | |
Calculations | |
CalculationsUFF | |
CalculationsUFF.AngleCalc | |
CalculationsUFF.DistanceCalc | |
CalculationsUFF.ESCalc | |
CalculationsUFF.OOPCalc | |
CalculationsUFF.PairCalc | |
CalculationsUFF.TorsionCalc | |
CalculationsUFF.VDWCalc | |
CarbohydrateMonomer | |
CarbohydratePolymer | |
Cartoon | |
CartoonGenerator | |
CartoonRenderer | |
Chain | |
CifReader | A true line-free CIF file reader for CIF and mmCIF files. |
CifReader.RidiculousFileFormatTokenizer | A special tokenizer class for dealing with quoted strings in CIF files. |
Circle3D |
Implements flat circle drawing/filling routines. |
ClassPreloader | |
Colix3D |
Implements a color index model using a colix as a COLor IndeX. |
ColorEncoder | |
ColorManager | |
CommandHistory | Implements a queue for a bash-like command history. |
Compiler | |
Compiler.FlowContext | |
CompoundDocument | |
CompoundDocument.CmpDocDirectoryEntry | |
CompoundDocument.CmpDocHeader | |
Console | |
ConsoleDocument | |
ConsoleTextArea | |
ConsoleTextPane | |
Console.ControlEnterTextArea | |
CsfReader | CSF file reader based on CIF idea -- fluid property fields. note that, like CIF, the order of fields is totally unpredictable in addition, ID numbers are not sequential, requiring atomNames first crack at this 2006/04/13 added DGAUSS, MOPAC, EHT orbital/basis reading 2007/04/09 streamlined CSF dataset reading capabilities 2007/04/09 |
CubeIterator |
Iterator used for finding all points within a box or a hemi-box
Obtain a CubeIterator by calling Bspt.allocateCubeIterator(). |
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. |
CubeReader | |
Cylinder3D |
Draws shaded cylinders in 3D. |
DataManager | |
DCT | |
DefaultLogger | Default implementation of the logger. |
Dialog | |
Dialog.ExportChoiceListener | |
Dialog.QualityListener | |
Dialog.TypeFilter | |
Dipole | |
Dipoles | |
DipolesGenerator | |
DipolesRenderer | |
DisplayPanel | |
DisplayPanel.CheckBoxMenuItemAction | Action calling evalStringQuiet(<action> + CheckBoxState) |
DisplayPanel.DefineCenterAction | |
DisplayPanel.HomeAction | |
DisplayPanel.MoveToAction | Action calling moveTo() |
DisplayPanel.SetStatusAction | Action calling setStatus() |
Dots | |
DotsGenerator | |
DotsRenderer | |
Draw | |
DrawGenerator | |
DrawMesh | |
DrawRenderer | |
Echo | |
EchoGenerator | |
EchoRenderer | |
Eigen | Eigenvalues and eigenvectors of a real 3x3 symmetric matrix.
adapted by Bob Hanson from http://math.nist.gov/javanumerics/jama/ (public domain)
If A is symmetric, then A = V*D*V' where the eigenvalue matrix D is diagonal and the eigenvector matrix V is orthogonal. |
Element | the internal tree is made up of elements ... either Node or Leaf |
Ellipsoids | |
EllipsoidsGenerator | |
EllipsoidsRenderer | |
Ellipsoids.Ellipsoid | |
EnterListener | |
EnvelopeCalculation | |
Escape | For defining the state, mostly |
Eval | |
Eval.Context | |
Eval.Rpn | |
Eval.ScriptException | |
Export3D | Provides high-level graphics primitives for 3D graphics export. |
FFParam | |
FileChooser | JFileChooser with possibility to fix size and location |
FileDropper | A simple Dropping class to allow files to be dragged onto a target. |
FileManager | |
FileManager.DOMOpenThread | |
FileManager.FileOpenThread | |
FileManager.FilesOpenThread | |
FilePreview | File previsualisation before opening |
FilePreview.JmolPanel | |
FileReader | |
FileTyper | |
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. |
Font3D |
Provides font support using a byte fid (Font ID) as an index into font table. |
FontLineShape | |
FontLineShapeRenderer | |
ForceField | |
ForceFieldUFF | |
FrameExportJmolAdapter | |
FrameExportJmolAdapter.AtomIterator | |
FrameExportJmolAdapter.BondIterator | |
FrameRenderer | |
Frank | |
FrankGenerator | |
FrankRenderer | |
Function | |
GamessReader | |
GamessUKReader | |
GamessUSReader | |
GaussianReader | Reader for Gaussian 94/98/03 output files. |
Geodesic | Consolidated Geodesic from dotsRenderer 3/19/07 Bob Hanson Constructs a canonical geodesic sphere of unit radius. |
GeoSurface | |
GeoSurfaceGenerator | |
GeoSurfaceRenderer | |
GhemicalMMReader | Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files. |
GifEncoder | |
GifEncoder.AdaptiveColorCollection | |
GifEncoder.ColorItem | |
GifEncoder.ColorVector | |
GifEncoder.ColorVector.CountComparator | |
GraphCharacteristics | |
GraphControlData | |
Graphics3D | Provides high-level graphics primitives for 3D visualization. |
Group | |
GT | |
GT.Language | |
GuiMap | |
GuiMap | |
GuiMap.GetKey | |
GuiMap.GetKey | |
GuiMap.KeyJCheckBox | |
GuiMap.KeyJCheckBoxMenuItem | |
GuiMap.KeyJMenu | |
GuiMap.KeyJMenu | |
GuiMap.KeyJMenuItem | |
GuiMap.KeyJMenuItem | |
GuiMap.KeyJRadioButtonMenuItem | |
HallInfo | |
HallInfo.RotationTerm | |
Halos | |
HalosGenerator | |
HalosRenderer | |
Helix | |
HelpDialog | |
HelpDialog.PageLoader | temporary class that loads synchronously (although later than the request so that a cursor change can be done). |
Hermite3D |
Implementation of hermite curves for drawing smoothed curves that pass through specified points. |
HinReader |
Support for .hin, HyperChem's native file format.
http://www.hyper.com
Record format is:
atom 1 - C ** - -0.06040 0.00000 0.00000 0.00000 3 2 a 6 a 38 s
...
atom 67 - H ** - 0.17710 -7.10260 -3.74840 2.24660 1 34 s
endmol 1
interesting fields are partialCharge, x, y, z, bondCountbonds are atom number and s/d/t/a for single/double/triple/aromatic |
HistoryFile | The history file contains data from previous uses of Jmol. |
Hover | |
HoverRenderer | |
Huffman | |
ImageCreator | |
ImageEncoder | |
ImageSelection | This class is used to transfer an Image into the clipboard. |
Int2IntHash | |
Int2IntHash.Entry | |
Interface | |
InvalidSmilesException | Exception thrown for invalid SMILES String |
IsoFxyReader | |
IsoMepReader | |
IsoMOReader | |
IsoPlaneReader | |
Isosurface | |
IsosurfaceGenerator | |
IsosurfaceMesh | |
IsosurfaceRenderer | |
IsoShapeReader | |
IsoSolventReader | |
JaguarReader | Jaguar reader tested for the two samples files in CVS. |
JaguarReader | |
JmeReader | |
Jmol | |
Jmol | |
JmolAdapter | The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering. |
JmolAdapter.AtomIterator |
AtomIterator is used to enumerate all the clientAtom
objects in a specified frame.
|
JmolAdapter.BondIterator | BondIterator is used to enumerate all the bonds |
JmolAdapter.StructureIterator | StructureIterator is used to enumerate Structures Helix, Sheet, Turn |
JmolAppletInterface | This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet. |
JmolAppletRegistry | |
JmolBioResolver | |
JmolConstants | |
JmolDialogInterface | |
JmolExportInterface | |
JmolFileReaderInterface | |
JmolImageCreatorInterface | |
JmolInstance | |
JmolPopup | |
JmolPopupAwt | |
JmolPopupSwing | |
JmolPopup.CheckboxMenuItemListener | |
JmolPopup.MenuItemListener | |
JmolRendererInterface | |
JmolResourceHandler | Provides access to resources (for example, strings and images). |
JmolSelectionListener | listen to atom selections in a Jmol Viewer |
JmolSimpleViewer | This is the high-level API for the JmolViewer for simple access. |
JmolStatusListener | |
JmolViewer | This is the high-level API for the JmolViewer for simple access. |
Jmol.AboutAction | |
Jmol.ActionChangedListener | |
Jmol.AppCloser | To shutdown when run as an application. |
Jmol.AtomSetChooserAction | |
Jmol.CloseAction | |
Jmol.ConsoleAction | |
Jmol.CopyImageAction | An Action to copy the current image into the clipboard. |
Jmol.CopyScriptAction | |
Jmol.ExecuteScriptAction | |
Jmol.ExitAction | Really lame implementation of an exit command |
Jmol.ExportAction | |
Jmol.MyStatusListener | |
Jmol.MyStatusListener | |
Jmol.NewAction | |
Jmol.NewwinAction | |
Jmol.OpenAction | |
Jmol.OpenUrlAction | |
Jmol.PasteClipboardAction | |
Jmol.PovrayAction | |
Jmol.PrintAction | |
Jmol.RecentFilesAction | |
Jmol.ScriptWindowAction | |
Jmol.ToWebAction | |
Jmol.UguideAction | |
Jmol.ViewMeasurementTableAction | |
Jmol.WhatsNewAction | |
Jmol.WriteAction | |
JpegEncoder | |
JpegInfo | |
Jvm12 | |
Jvxl | |
JvxlData | |
JvxlReader | |
Labels | |
LabelsGenerator | |
LabelsRenderer | |
LcaoCartoon | |
LcaoCartoonGenerator | |
LcaoCartoonRenderer | |
Leaf | A leaf of Point3f objects in the bsp tree |
LimitedLineReader | |
LimitedLineReader | |
Line3D |
Implements 3D line drawing routines. |
Logger | Logger mechanism. |
LoggerInterface | Interface used for the logging mechanism. |
LogPanel | |
LoopedStreams | |
MarchingCubes | |
MarchingSquares | |
MarchingSquares.ContourVertex | |
MarchingSquares.PlanarSquare | |
Measure | |
Measurement | |
MeasurementPending | |
MeasurementTable | |
MeasurementTable.MeasurementListWindowListener | |
MeasurementTable.MeasurementTableModel | |
Measures | |
MeasuresGenerator | |
MeasuresRenderer | |
MepCalculation | |
MepCalculationInterface | |
Mesh | |
MeshCollection | |
MeshData | |
MeshDataServer | |
MeshFileCollection | |
MeshRenderer | |
MeshRibbon | |
MeshRibbonGenerator | |
MeshRibbonRenderer | |
MinAtom | |
MinBond | |
Minimizer | |
MinimizerInterface | |
Minimizer.MinimizationThread | |
Model | |
ModelCollection | |
ModelCollection.StateScript | |
ModelCollection.Structure | |
ModelLoader | |
ModelManager | |
ModelSet | |
Mol2Reader | A minimal multi-file reader for TRIPOS SYBYL mol2 files. |
MoldenReader | A molecular structure and orbital reader for MolDen files. |
MolecularOrbital | |
MolecularOrbitalGenerator | |
MolecularOrbitalRenderer | |
Molecule | |
Molecules | |
MolReader | A reader for MDLI mol and sdf files. |
MonitorInputStream | |
MonitorInputStream | |
Monomer | |
MopacData | |
MopacDataReader | |
MopacGraphfReader | Reads Mopac 2007 GRAPHF output files |
MopacReader | Reads Mopac 93, 97 or 2002 output files, but was tested only for Mopac 93 files yet. |
MouseManager | |
MouseManager10 | |
MouseManager11 | |
MouseManager14 | |
MouseManager.HoverWatcher | |
MouseWrapper11 | |
MouseWrapper14 | |
MOCalculation | |
MOCalculationInterface | |
Node | Nodes of the bspt. |
Normix3D |
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
A 'normix' is a normal index, represented as a short |
NucleicMonomer | |
NucleicPolymer | |
NumericDataUtils | |
NWChemReader | A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory. |
Object2d | |
Object2dShape | |
OdysseyReader | |
OdysseyXMLReader | |
Orbitals | |
Parameters | |
Parser | |
PatternMatcher | A class to match a SMILES pattern with a Jmol molecule. |
PdbReader | PDB file reader. |
PhosphorusMonomer | |
PhosphorusPolymer | |
PickingManager | |
Platform3D |
Specifies the API to an underlying int[] buffer of ARGB values that can be converted into an Image object and a short[] for z-buffer depth. |
Platform3D.ClearingThread | |
PltFormattedReader | |
Pmesh | |
PmeshGenerator | |
PmeshRenderer | |
Pmesh.PmeshBinaryDocument | |
PngEncoder | PngEncoder takes a Java Image object and creates a byte string which can be saved as a PNG file. |
Point3fi | |
PointGroup | |
PointGroup.Operation | |
Polyhedra | |
PolyhedraGenerator | |
PolyhedraRenderer | |
Polyhedra.Polyhedron | |
Polymer | |
PopInJmol | |
PopupResourceBundle | |
PovrayDialog | A dialog for controling the creation of a povray input file from a Chemframe and a display. |
PovrayDialog.PovrayWindowListener | Listener for responding to dialog window events. |
PovraySaver | |
PpmEncoder | |
PqrReader | PQR file reader. |
PreferencesDialog | |
PreferencesDialog.PrefsAction | |
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. |
QchemReader |
A reader for Q-Chem 2.1
Q-Chem is a quantum chemistry program developed
by Q-Chem, Inc. (http://www.q-chem.com/)
Molecular coordinates and normal coordinates of vibrations are read. |
Quadric | |
QuantumCalculation | |
Quaternion | |
RecentFilesDialog | Manages a list of recently opened files. |
RepaintManager | |
RepaintManager.AnimationThread | |
Resolver | |
Resolver | |
Rgb16 | |
Ribbons | |
RibbonsGenerator | |
RibbonsRenderer | |
Rockets | |
RocketsGenerator | |
RocketsRenderer | |
Rotation | |
SaisieDlg | |
ScriptButtons | |
ScriptManager | |
ScriptManager.CommandWatcher | |
ScriptManager.ScriptQueueRunnable | |
ScriptWindow | |
ScriptWindow.ExecuteCommandThread | |
SelectionManager | |
Shade3D |
Implements the shading of RGB values to support shadow and lighting highlights. |
Shape | After code reorganization of 11/2006 (BH) Shape now encompasses: AtomShape | Balls, Dots, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface Dipoles, Measures FontLineShape | Axes, Bbcage, Frank, Uccage MeshCollection | | Draw MeshFileCollection (adds parser code) | | Pmesh IsosurfaceMeshCollection (adds JVXL code) | Isosurface |________ LcaoCartoon, MolecularOrbital BioShapeCollection | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Sticks | Hsticks, Sssticks TextShape | Echo, Hover |
ShapeRenderer | |
Sheet | |
ShelxReader | A reader for SHELX output (RES) files. |
SmarterJmolAdapter | |
SmarterJmolAdapter.AtomIterator | |
SmarterJmolAdapter.BondIterator | |
SmarterJmolAdapter.StructureIterator | |
SmilesAtom |
This class represents an atom in a SmilesMolecule . |
SmilesBond | Bond in a SmilesMolecule |
SmilesMatcherInterface | |
SmilesMolecule | Molecule created from a SMILES String |
SmilesParser |
Parses a SMILES String to create a SmilesMolecule .
|
SpaceGroup | |
SpartanArchive | |
SpartanReader | |
SpartanSmolReader | |
Sphere3D |
Implements high performance rendering of shaded spheres. |
Splash | |
Splash.WindowListener | |
Stars | |
StarsGenerator | |
StarsRenderer | |
StateManager | |
StateManager.Connection | |
StateManager.Connections | |
StateManager.GlobalSettings | |
StateManager.Orientation | |
StatusBar | |
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. atomPicked fileLoaded fileLoadError frameChanged measureCompleted measurePending measurePicked newOrientation scriptEcho scriptError scriptMessage scriptStarted scriptStatus scriptTerminated userAction viewerRefreshed Bob Hanson hansonr@stolaf.edu 2/2006 |
Sticks | |
SticksGenerator | |
SticksRenderer | |
Strands | |
StrandsGenerator | |
StrandsRenderer | |
StringDataUtils | Copyright (c) 2005, Shravan Sadasivan & Richard Spinney Department of Chemisty - The Ohio State University |
Structure | |
SurfaceGenerator | |
Swing3D |
Implementation of Platform3D when using Swing on JVMs >= 1.2 Uses the BufferedImage classe to turn an int[] into an Image that can be drawn. |
Symmetry | |
SymmetryInfo | |
SymmetryInterface | |
SymmetryOperation | |
TempArray | |
Test | |
Text | |
Text3D |
implementation for text rendering
uses java fonts by rendering into an offscreen buffer. strings are rasterized and stored as a bitmap in an int[]. |
TextFormat | |
TextShape | |
TickerThread | |
Token | |
Token.Token2 | |
Trace | |
TraceGenerator | |
TraceRenderer | |
TransformManager | |
TransformManager10 | |
TransformManager11 | |
TransformManager.SpinThread | |
TransformManager.VibrationThread | |
Translation | |
Triangle3D |
renders triangles
currently only renders flat triangles will probably need performance tuning |
Turn | |
Uccage | |
UccageGenerator | |
UccageRenderer | |
UnitCell | |
UnitCell.Data | |
Util | |
V3000Reader | A reader for MDL V3000 files |
Vectors | |
VectorsGenerator | |
VectorsRenderer | |
VertexDataServer | |
Viewer | |
Visua | |
VolumeData | |
VolumeDataInterface | |
VolumeDataReader | |
VolumeFileReader | |
VoxelReader | |
WebExport | |
WebMaker | |
WebMOReader | A molecular orbital reader for WebMO files. |
WebPanel | |
WebPanel.InstanceCellRenderer | |
WhatsNewDialog | |
WhatsNewDialog.PageLoader | temporary class that loads synchronously (although later than the request so that a cursor change can be done). |
WrappedApplet | |
WrappedAppletLoader | |
XmlArgusReader | A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers. |
XmlArgusReader.ArgusHandler | |
XmlChem3dReader | An chem3d c3xml reader |
XmlChem3dReader.Chem3dHandler | |
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. |
XmlCmlReader.CmlHandler | |
XmlMolproReader | A Molpro 2005 reader |
XmlMolproReader.MolproHandler | |
XmlOdysseyReader | An Odyssey xodydata reader |
XmlOdysseyReader.OdysseyHandler | |
XmlReader | A generic XML reader template -- by itself, does nothing. |
XmlReader.DummyResolver | |
XmlReader.JmolXmlHandler | |
XplorReader | |
XyzReader | Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetry() 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 |
ZipUtil | |
ZoneVisu | |
_Exporter | |
_MayaExporter | |
_PovrayExporter | |
_VrmlExporter |