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A

a - Variable in class org.jmol.minimize.forcefield.Calculation
 
a - Variable in class org.jmol.symmetry.UnitCell
 
A0 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
a1 - Variable in class org.jmol.g3d.Hermite3D
 
a2 - Variable in class org.jmol.g3d.Hermite3D
 
a_ - Variable in class org.jmol.symmetry.UnitCell.Data
 
a_count - Variable in class org.jmol.export.image.GifEncoder
 
aa - Variable in class org.jmol.modelset.Measurement
 
aa - Variable in class org.jmol.shapebio.BioShapeRenderer
 
aaMoveTo - Variable in class org.jmol.viewer.TransformManager
 
AANscale(double[], int[], int) - Static method in class org.jmol.util.DCT
 
AANscaleFactor - Static variable in class org.jmol.util.DCT
 
aaStep - Variable in class org.jmol.viewer.TransformManager
 
aaStepCenter - Variable in class org.jmol.viewer.TransformManager
 
aaStepNavCenter - Variable in class org.jmol.viewer.TransformManager
 
aaT - Variable in class org.jmol.shape.MeasuresRenderer
 
aaTest1 - Variable in class org.jmol.viewer.TransformManager
 
aatoken - Variable in class org.jmol.viewer.Eval
 
aatoken - Variable in class org.jmol.viewer.Eval.Context
 
aatoken - Variable in class org.jmol.viewer.Function
 
aatokenCompiled - Variable in class org.jmol.viewer.Compiler
 
aaTotal - Variable in class org.jmol.viewer.TransformManager
 
abNo - Variable in class org.openscience.jmol.app.PreferencesDialog
 
aboutAction - Static variable in class org.openscience.jmol.app.Jmol
 
aboutComputedMenuBaseCount - Variable in class org.jmol.popup.JmolPopup
 
AboutDialog - Class in org.openscience.jmol.app
 
AboutDialog(JFrame) - Constructor for class org.openscience.jmol.app.AboutDialog
 
AboutDialog.PageLoader - Class in org.openscience.jmol.app
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
AboutDialog.PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.AboutDialog.PageLoader
 
absolute - Static variable in class org.jmol.viewer.Token
 
ABSOLUTE_MIN_MESH_SIZE - Static variable in class org.jmol.shapebio.BioShapeRenderer
 
abYes - Variable in class org.openscience.jmol.app.PreferencesDialog
 
AC_matrix - Variable in class org.jmol.util.Huffman
 
AC_matrix0 - Variable in class org.jmol.util.Huffman
 
AC_matrix1 - Variable in class org.jmol.util.Huffman
 
acc - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
accept(File) - Method in class org.jmol.export.dialog.Dialog.TypeFilter
 
acceptsStringParameter(String) - Static method in class org.jmol.viewer.PropertyManager
 
accum - Variable in class org.jmol.export.image.GifEncoder
 
accumulate - Variable in class org.jmol.export.image.ImageEncoder
 
accumulator - Variable in class org.jmol.export.image.ImageEncoder
 
ACtableNumber - Variable in class org.jmol.util.JpegInfo
 
action - Variable in class org.openscience.jmol.app.DisplayPanel.CheckBoxMenuItemAction
 
action - Variable in class org.openscience.jmol.app.DisplayPanel.MoveToAction
 
actionPerformed(ActionEvent) - Method in class org.jmol.applet.Console
 
actionPerformed(ActionEvent) - Method in class org.jmol.popup.JmolPopup.MenuItemListener
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.AtomSetChooser
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.DisplayPanel.CheckBoxMenuItemAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.DisplayPanel.DefineCenterAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.DisplayPanel.HomeAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.DisplayPanel.MoveToAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.DisplayPanel.SetStatusAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.AboutAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.AtomSetChooserAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.CloseAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ConsoleAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.CopyImageAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.CopyScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ExecuteScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ExitAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ExportAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.NewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.NewwinAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.OpenAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.OpenUrlAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.PasteClipboardAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.PovrayAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.PrintAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.RecentFilesAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ScriptWindowAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ToWebAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.UguideAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.ViewMeasurementTableAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.WhatsNewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.Jmol.WriteAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.PreferencesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.PreferencesDialog.PrefsAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.ScriptWindow
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Molecules
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Orbitals
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
activate() - Method in class org.openscience.jmol.app.MeasurementTable
 
active - Variable in class org.jmol.export.dialog.FilePreview
 
adapterModelCount - Variable in class org.jmol.modelset.ModelLoader
 
adapterName - Variable in class org.jmol.api.JmolAdapter
 
adapterTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
 
add(float) - Method in class org.jmol.util.Quaternion
 
add - Static variable in class org.jmol.viewer.Token
 
addAllPixels - Variable in class org.jmol.g3d.Graphics3D
 
addAllPixels - Variable in class org.jmol.g3d.Sphere3D
 
addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtom(int, BitSet, int, Object, short, String, int, int, float, Object[], int, float, float, float, float, boolean, int, char, String, int, char, float, float, float, char, Object, float) - Method in class org.jmol.modelset.ModelLoader
 
addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAttr() - Method in class org.jmol.export._MayaExporter
 
addAxis(int, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
addBioPolymerToModel(Polymer, Model) - Method in class org.jmol.modelset.ModelCollection
 
addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addBond(SmilesBond) - Method in class org.jmol.smiles.SmilesAtom
Add a bond to the atom.
addBonds(String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
addBonds(String, int) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
addBondToAtom(Atom, Bond) - Method in class org.jmol.modelset.BondCollection
 
addBoundBoxPoint(Point3f) - Method in class org.jmol.modelset.BoxInfo
 
addBundle(String) - Method in class org.jmol.i18n.GT
 
addBundles(String, String, String, String) - Method in class org.jmol.i18n.GT
 
addCheckboxMenuItem(Object, String, String, String) - Method in class org.jmol.popup.JmolPopup
 
addCheckboxMenuItem(Object, String, String, String, boolean) - Method in class org.jmol.popup.JmolPopup
 
addCheckboxMenuItem(Object, String, String, String, boolean) - Method in class org.jmol.popup.JmolPopupAwt
 
addCheckboxMenuItem(Object, String, String, String, boolean) - Method in class org.jmol.popup.JmolPopupSwing
 
addCommand(String) - Method in class org.jmol.util.CommandHistory
Adds any number of lines to the command history
addCommand(String) - Method in class org.jmol.viewer.Viewer
Adds one or more commands to the command history
addCommandLine(String) - Method in class org.jmol.util.CommandHistory
Adds a single line to the bottom of the list, resets list position.
addConnect() - Method in class org.jmol.export._MayaExporter
 
addConnection(int[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addConstraint(Object[]) - Method in class org.jmol.minimize.Minimizer
 
addConsumer(ImageConsumer) - Method in class org.jmol.g3d.Awt3D
 
addContextVariable(String) - Method in class org.jmol.viewer.Compiler
 
addContourVertex(int, int, int, Point3i, Point3f, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addCount - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
addCurrentItem(StringBuffer, char, int, String, String, String, String) - Static method in class org.jmol.popup.JmolPopup
 
addData(int, int) - Method in class org.jmol.quantum.MOCalculation
 
addData10F(int) - Method in class org.jmol.quantum.MOCalculation
 
addData5D(int) - Method in class org.jmol.quantum.MOCalculation
 
addData6D(int) - Method in class org.jmol.quantum.MOCalculation
 
addData7F(int) - Method in class org.jmol.quantum.MOCalculation
 
addDataP(int) - Method in class org.jmol.quantum.MOCalculation
 
addDataS(int) - Method in class org.jmol.quantum.MOCalculation
 
addDataSP(int) - Method in class org.jmol.quantum.MOCalculation
 
addDirectory(String, String) - Method in class org.jmol.viewer.FileManager
 
addDisplayedBackbone(int, boolean) - Method in class org.jmol.modelset.Atom
 
addDisplayedBond(int, boolean) - Method in class org.jmol.modelset.Atom
 
addEdgeMask(int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
addFile(String) - Method in class org.openscience.jmol.app.RecentFilesDialog
Adds this file to the history.
addFileList(String, String) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
addForce(Vector3d, int, double) - Method in class org.jmol.minimize.forcefield.Calculations
 
addFunction(Function) - Method in class org.jmol.viewer.Compiler
 
addGroup(Chain, Group) - Method in class org.jmol.modelset.ModelLoader
 
addGroup3Name(String) - Static method in class org.jmol.modelset.Group
 
addHelpItems(JMenu, String, String) - Method in class org.jmol.applet.Console
 
addHelpMenuBar(JMenuBar) - Method in class org.jmol.applet.Console
 
addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.Jmol
 
addHetero(String, String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
addHydrogenBond(Atom, Atom, short, BitSet, BitSet) - Method in class org.jmol.modelset.BondCollection
These are not actual hydrogen bonds.
addHydrogenBond(Atom, Atom, short, BitSet, BitSet) - Method in class org.jmol.modelset.Model
 
addHydrogens - Variable in class org.jmol.jvxl.readers.Parameters
 
addIncompleteFaces(int[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
addIndex - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
addInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
addItems(String[][]) - Method in class org.jmol.popup.PopupResourceBundle
 
addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addListener(JmolSelectionListener) - Method in class org.jmol.viewer.SelectionManager
 
addLoadScript(String) - Method in class org.jmol.viewer.FileManager
 
addLoadScript(String) - Method in class org.jmol.viewer.Viewer
 
addMacrosMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.Jmol
 
addMenuItem(Object, String) - Method in class org.jmol.popup.JmolPopup
 
addMenuItem(Object, String, String, String) - Method in class org.jmol.popup.JmolPopup
 
addMenuItem(Object, String, String, String) - Method in class org.jmol.popup.JmolPopupAwt
 
addMenuItem(Object, String, String, String) - Method in class org.jmol.popup.JmolPopupSwing
 
addMenuItems(String, String, Object, PopupResourceBundle, boolean, boolean) - Method in class org.jmol.popup.JmolPopup
 
addMenuSeparator(Object) - Method in class org.jmol.popup.JmolPopup
 
addMenuSeparator(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
addMenuSeparator(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
addMenuSubMenu(Object, Object) - Method in class org.jmol.popup.JmolPopup
 
addMenuSubMenu(Object, Object) - Method in class org.jmol.popup.JmolPopupAwt
 
addMenuSubMenu(Object, Object) - Method in class org.jmol.popup.JmolPopupSwing
 
addMOData(int, Vector[], Hashtable[]) - Method in class org.jmol.adapter.readers.more.GaussianReader
 
addMOData(int, Vector[], Hashtable[]) - Method in class org.jmol.adapter.readers.more.PsiReader
 
addMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
Note that this method does not check to see that there are no overlapping protein structures.
addNeighboringVertexes(short[], short, short) - Static method in class org.jmol.geodesic.Geodesic
 
addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondWithMappedSerialNumbers(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNextToken() - Method in class org.jmol.viewer.Compiler
 
addNextTokenIf(int) - Method in class org.jmol.viewer.Compiler
 
addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.Jmol
 
addOp(Token) - Method in class org.jmol.viewer.Eval.Rpn
 
addOperation(SymmetryOperation) - Method in class org.jmol.symmetry.SpaceGroup
 
addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
addPixelT(int, int, int, int[], int[], int[], int[], int, boolean, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
addPoint(int, Point3f, boolean) - Method in class org.jmol.modelset.MeasurementPending
 
addPoint(Point3f, int) - Method in class org.jmol.shapespecial.Draw
 
addPrimitiveLatticeVector(int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addProperties(Properties) - Method in class org.jmol.export.dialog.HistoryFile
Adds the given properties to the history.
addProperty(String, String) - Method in class org.jmol.export.dialog.HistoryFile
Adds the given property to the history.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.openscience.jmol.app.FileDropper
 
addQuad(int, int, int, int) - Method in class org.jmol.shape.Mesh
 
addRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
addRgb(int, int) - Method in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
addScript(String) - Method in class org.jmol.viewer.ScriptManager
 
addScript(String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
 
addScript(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
 
addSecondaryStructure(byte, char, int, char, int) - Method in class org.jmol.modelset.Model
 
addSecondaryStructure(byte, char, int, char, int) - Method in class org.jmol.modelset.Polymer
 
addSecondaryStructure(byte, char, int, char, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSecondaryStructure(byte, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
addSites(Hashtable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSlater(int, int, int, int, int, float, float) - Method in class org.jmol.adapter.readers.more.MopacDataReader
 
addSpaceGroupOperation(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addSpaceGroupOperation(String) - Method in interface org.jmol.api.SymmetryInterface
 
addSpaceGroupOperation(String) - Method in class org.jmol.symmetry.Symmetry
 
addStateScript(String, BitSet, BitSet, BitSet, String, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addStateScript(String, BitSet, BitSet, BitSet, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addStructure(String, String) - Method in class org.jmol.popup.PopupResourceBundle
 
addStructuresFromTags(byte[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSubstituteTokenIf(int, Token) - Method in class org.jmol.viewer.Compiler
 
addSymmetry(String) - Method in class org.jmol.symmetry.SpaceGroup
 
addSymmetry(String, Matrix4f) - Method in class org.jmol.symmetry.SpaceGroup
 
addToBonds(Bond, Bond[]) - Method in class org.jmol.modelset.BondCollection
 
addToken(String, Token) - Static method in class org.jmol.viewer.Token
 
addTokenToPostfix(int, Object) - Method in class org.jmol.viewer.Compiler
 
addTokenToPostfix(int, int, Object) - Method in class org.jmol.viewer.Compiler
 
addTokenToPostfix(Token) - Method in class org.jmol.viewer.Compiler
 
addTokenToPrefix(Token) - Method in class org.jmol.viewer.Compiler
 
addToMeasurement(int, Point3f, boolean) - Method in class org.jmol.viewer.MouseManager
 
addToMenu(Object, MenuItem) - Method in class org.jmol.popup.JmolPopupAwt
 
addToMenu(Object, JComponent) - Method in class org.jmol.popup.JmolPopupSwing
 
addTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addTriangle(int, int, int) - Method in class org.jmol.shape.Mesh
 
addTriangleCheck(int, int, int, int, boolean) - Method in interface org.jmol.jvxl.api.MeshDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int) - Method in class org.jmol.jvxl.data.MeshData
 
addTriangleCheck(int, int, int, int, boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
addTriangleCheck(int, int, int, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
 
addTriangleCheck(int, int, int, int) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
addTuple(int, Point3f) - Method in class org.jmol.bspt.Bspf
 
addTuple(Point3f) - Method in class org.jmol.bspt.Bspt
Iterate through all of your data points, calling addTuple
addTuple(int, Point3f) - Method in class org.jmol.bspt.Element
 
addTuple(int, Point3f) - Method in class org.jmol.bspt.Leaf
 
addTuple(int, Point3f) - Method in class org.jmol.bspt.Node
 
addVariable(String, boolean) - Method in class org.jmol.viewer.Function
 
addVertexCopy(Point3f, float, int) - Method in interface org.jmol.jvxl.api.MeshDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(Point3f, float, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(Point3f, float, int) - Method in class org.jmol.jvxl.data.MeshData
 
addVertexCopy(Point3f) - Method in class org.jmol.jvxl.data.MeshData
 
addVertexCopy(Point3f, float, int) - Method in class org.jmol.jvxl.readers.VoxelReader
 
addVertexCopy(Point3f) - Method in class org.jmol.shape.Mesh
 
addVertexCopy(Point3f, float, int) - Method in class org.jmol.shapesurface.Isosurface
 
addVertexCopy(Point3f, float, int, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
addVertexCopy(Point3f, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
addVibrationVector(float, float, float) - Method in class org.jmol.adapter.smarter.Atom
 
addWindowBorder(String, Point) - Method in class org.jmol.export.dialog.HistoryFile
Adds the window border to the history.
addWindowInfo(String, Component, Point) - Method in class org.jmol.export.dialog.HistoryFile
Adds the window informations to the history.
addWindowPosition(String, Point) - Method in class org.jmol.export.dialog.HistoryFile
Adds the window position to the history.
addWindowSize(String, Dimension) - Method in class org.jmol.export.dialog.HistoryFile
Adds the window size to the history.
addWindowVisibility(String, boolean) - Method in class org.jmol.export.dialog.HistoryFile
Adds the window visibility to the history.
addX(Token) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(Object) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(boolean) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(int) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(float) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(String) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(String[]) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(Point3f) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(Point4f) - Method in class org.jmol.viewer.Eval.Rpn
 
addX(BitSet) - Method in class org.jmol.viewer.Eval.Rpn
 
addZoomTranslationNavigationText(StringBuffer) - Method in class org.jmol.viewer.TransformManager
 
AdfReader - Class in org.jmol.adapter.readers.more
A reader for ADF output.
AdfReader() - Constructor for class org.jmol.adapter.readers.more.AdfReader
 
adfRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
adjustForWindow - Variable in class org.jmol.shape.Object2d
 
adjustTemporaryScreenPoint() - Method in class org.jmol.viewer.TransformManager
adjusts the temporary point for perspective and offsets
adjustTemporaryScreenPoint() - Method in class org.jmol.viewer.TransformManager10
 
adjustTemporaryScreenPoint() - Method in class org.jmol.viewer.TransformManager11
 
adjustVertex(int[], float) - Method in class org.jmol.g3d.Triangle3D
 
aDOMNode - Variable in class org.jmol.viewer.FileManager.DOMOpenThread
 
aDOMOpenThread - Variable in class org.jmol.viewer.FileManager
 
ADP_TYPE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
adpmax - Static variable in class org.jmol.viewer.Token
 
adpmin - Static variable in class org.jmol.viewer.Token
 
adpMode - Variable in class org.jmol.atomdata.AtomData
 
Ah - Variable in class org.jmol.util.JpegInfo
 
Al - Variable in class org.jmol.util.JpegInfo
 
align - Variable in class org.jmol.shape.Object2d
 
align1 - Variable in class org.jmol.shapespecial.Polyhedra
 
align2 - Variable in class org.jmol.shapespecial.Polyhedra
 
ALIGN_CENTER - Static variable in class org.jmol.shape.Object2d
 
ALIGN_FLAGS - Static variable in class org.jmol.shape.Labels
 
ALIGN_LEFT - Static variable in class org.jmol.shape.Object2d
 
ALIGN_NONE - Static variable in class org.jmol.shape.Object2d
 
ALIGN_RIGHT - Static variable in class org.jmol.shape.Object2d
 
alignZX(Point3f, Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager11
brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
all - Static variable in class org.jmol.viewer.Token
 
allCarbohydrates - Static variable in class org.jmol.viewer.JmolConstants
 
allFramesCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
alloc(Component, Viewer) - Static method in class org.jmol.viewer.MouseWrapper11
 
alloc(Component, Viewer) - Static method in class org.jmol.viewer.MouseWrapper14
 
allocateBioPolymer(Group[], int, boolean) - Static method in class org.jmol.modelsetbio.BioPolymer
 
allocateBitmap(int) - Static method in class org.jmol.geodesic.EnvelopeCalculation
 
allocateBuffers(int, int, boolean) - Method in class org.jmol.g3d.Platform3D
 
allocateColix(int) - Static method in class org.jmol.g3d.Colix3D
 
allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
 
allocateImage() - Method in class org.jmol.g3d.Awt3D
 
allocateImage() - Method in class org.jmol.g3d.Platform3D
 
allocateImage() - Method in class org.jmol.g3d.Swing3D
 
allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Awt3D
 
allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Platform3D
 
allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Swing3D
 
allocateRenderer(int, Graphics3D) - Method in class org.jmol.viewer.FrameRenderer
 
allocateShape(int) - Method in class org.jmol.modelset.ModelSet
 
allocateSimpleViewer(Component, JmolAdapter) - Static method in class org.jmol.api.JmolSimpleViewer
This is the main access point for creating an application or applet viewer.
allocateSwing3D() - Static method in class org.jmol.g3d.Platform3D
 
allocateTBuffers(boolean) - Method in class org.jmol.g3d.Platform3D
 
allocateViewer(Component, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
This is the main access point for creating an application or applet viewer.
allocateViewer(Component, JmolAdapter) - Static method in class org.jmol.viewer.Viewer
NOTE: for APPLICATION AND APPLET call setModeMouse(JmolConstants.MOUSE_NONE); before setting viewer=null in order to remove references to display window in listeners and hoverWatcher This is the main access point for creating an application or applet viewer.
allocateXmlReader14() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
allocateXmlReaderAelfred2() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
allocDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
allocFont3D(int, int, int, float, float) - Static method in class org.jmol.g3d.Font3D
 
allocMesh(String) - Method in class org.jmol.shape.MeshCollection
 
allocMesh(String) - Method in class org.jmol.shapespecial.Draw
 
allocMesh(String) - Method in class org.jmol.shapesurface.Isosurface
 
allocRaster(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
allocTempBytes(int) - Method in class org.jmol.util.TempArray
 
allocTempBytes(int) - Method in class org.jmol.viewer.Viewer
 
allocTempPoints(int) - Method in class org.jmol.util.TempArray
 
allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
 
allocTempScreens(int) - Method in class org.jmol.util.TempArray
 
allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
 
allocVertexColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
allowEmbeddedScripts - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowMapData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
allowMesh - Variable in class org.jmol.shape.MeshCollection
 
allowNegative - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
allowRotateSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
allowRotateSelected() - Method in class org.jmol.viewer.Viewer
 
allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
 
allPositive - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
alpha - Variable in class org.jmol.symmetry.UnitCell
 
ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JmolConstants
 
ALPHA_SHIFT - Static variable in class org.jmol.g3d.Graphics3D
 
AlphaMonomer - Class in org.jmol.modelsetbio
 
AlphaMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.AlphaMonomer
 
alphaOffsets - Static variable in class org.jmol.modelsetbio.AlphaMonomer
 
alphaOffsets - Static variable in class org.jmol.modelsetbio.CarbohydrateMonomer
 
AlphaPolymer - Class in org.jmol.modelsetbio
 
AlphaPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.AlphaPolymer
 
alphaPolymer - Variable in class org.jmol.modelsetbio.Sheet
 
ALT - Static variable in class org.jmol.viewer.MouseManager
 
ALT_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ALT_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
ALT_SHIFT_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
altArgbsCpk - Variable in class org.jmol.viewer.ColorManager
 
altArgbsCpk - Static variable in class org.jmol.viewer.JmolConstants
 
altElementCounts - Variable in class org.jmol.modelset.Molecule
 
altElementIndexFromNumber(int) - Static method in class org.jmol.viewer.JmolConstants
 
altElementMax - Variable in class org.jmol.modelset.Molecule
 
altElementMax - Static variable in class org.jmol.viewer.JmolConstants
length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementNameFromIndex(int) - Static method in class org.jmol.viewer.JmolConstants
 
altElementNames - Static variable in class org.jmol.viewer.JmolConstants
 
altElementNumberFromIndex(int) - Static method in class org.jmol.viewer.JmolConstants
 
altElementNumbers - Static variable in class org.jmol.viewer.JmolConstants
 
altElementSymbolFromIndex(int) - Static method in class org.jmol.viewer.JmolConstants
 
altElementSymbols - Static variable in class org.jmol.viewer.JmolConstants
 
alternateLocationID - Variable in class org.jmol.adapter.smarter.Atom
 
alternateLocationID - Variable in class org.jmol.modelset.Atom
 
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.viewer.JmolConstants
 
altloc - Static variable in class org.jmol.viewer.Token
 
altlocs - Variable in class org.jmol.popup.JmolPopup
 
ambient - Static variable in class org.jmol.viewer.Token
 
AMBIENT_FRACTION - Static variable in class org.jmol.g3d.Shade3D
 
AMBIENT_PERCENT - Static variable in class org.jmol.g3d.Shade3D
 
ambientPercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ambiguityType - Variable in class org.jmol.symmetry.SpaceGroup
 
AMINO - Static variable in class org.jmol.util.ColorEncoder
 
amino - Static variable in class org.jmol.viewer.Token
 
AminoMonomer - Class in org.jmol.modelsetbio
 
AminoMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.AminoMonomer
 
AminoPolymer - Class in org.jmol.modelsetbio
 
AminoPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.AminoPolymer
 
AMPLITUDE_MAX - Static variable in class org.openscience.jmol.app.AtomSetChooser
Maximum value for vibration scale.
AMPLITUDE_PRECISION - Static variable in class org.openscience.jmol.app.AtomSetChooser
Precision of the vibration scale slider
AMPLITUDE_VALUE - Static variable in class org.openscience.jmol.app.AtomSetChooser
Initial value of vibration scale.
amplitudeSlider - Variable in class org.openscience.jmol.app.AtomSetChooser
 
anaglyphChannelBytes - Variable in class org.jmol.g3d.Graphics3D
 
anaglyphLength - Variable in class org.jmol.g3d.Graphics3D
 
andNot(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
angle - Static variable in class org.jmol.viewer.Token
 
angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
angles - Variable in class org.jmol.minimize.forcefield.Calculations
 
angles - Variable in class org.jmol.minimize.Minimizer
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.Parameters
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JmolConstants
 
animation() - Method in class org.jmol.viewer.Eval
 
animation - Static variable in class org.jmol.viewer.Token
 
ANIMATION_LOOP - Static variable in class org.jmol.viewer.RepaintManager
 
ANIMATION_ONCE - Static variable in class org.jmol.viewer.RepaintManager
 
ANIMATION_PALINDROME - Static variable in class org.jmol.viewer.RepaintManager
 
animationDirection() - Method in class org.jmol.viewer.Eval
 
animationDirection - Variable in class org.jmol.viewer.RepaintManager
 
animationFps - Variable in class org.jmol.viewer.RepaintManager
 
animationFps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
animationMode() - Method in class org.jmol.viewer.Eval
 
animationOn - Variable in class org.jmol.viewer.RepaintManager
 
animationOn(boolean) - Method in class org.jmol.viewer.RepaintManager
 
animationPaused - Variable in class org.jmol.viewer.RepaintManager
 
animationReplayMode - Variable in class org.jmol.viewer.RepaintManager
 
animationThread - Variable in class org.jmol.viewer.RepaintManager
 
animThread - Variable in class org.openscience.jmol.app.AtomSetChooser
 
anionLookupTable - Static variable in class org.jmol.viewer.JmolConstants
 
aniosU - Variable in class org.jmol.jvxl.readers.Parameters
 
ANISO_B11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_B33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_Beta_33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_LABEL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_MMCIF_U33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U11 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U12 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U13 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U22 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U23 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ANISO_U33 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
anisoB - Variable in class org.jmol.jvxl.readers.Parameters
 
anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
 
anisotropy - Variable in class org.jmol.jvxl.readers.Parameters
 
anisotropy - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
anisou() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
Annuler - Variable in class org.jmol.jcamp.SaisieDlg
 
antecedent(double) - Method in class org.jmol.jcamp.ZoneVisu
 
antialias - Variable in class org.jmol.shape.MeshRenderer
 
antialias - Variable in class org.jmol.viewer.TransformManager
 
antialias2 - Variable in class org.jmol.g3d.Graphics3D
 
antiAliasCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
antialiasDisplay - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
antialiasDisplay - Variable in class org.jmol.viewer.Viewer
 
antialiasEnabled - Variable in class org.jmol.g3d.Graphics3D
 
antialiasImages - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
antialiasThisFrame - Variable in class org.jmol.g3d.Graphics3D
 
antialiasTranslucent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
anum - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
ApbsReader - Class in org.jmol.jvxl.readers
 
ApbsReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.ApbsReader
 
apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
 
append - Variable in class org.jmol.export.dialog.FilePreview
 
appendAtomSetCollection(Vector) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Appends an AtomSetCollection
appendCmd(StringBuffer, String) - Static method in class org.jmol.shape.Shape
 
appendCmd(StringBuffer, String) - Static method in class org.jmol.viewer.StateManager
 
appendLogData(String) - Method in class org.jmol.minimize.forcefield.Calculations
 
appendNew - Variable in class org.jmol.modelset.ModelLoader
 
appendNew - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
appendNewline() - Method in class org.openscience.jmol.app.ConsoleDocument
 
appendNewline() - Method in class org.openscience.jmol.app.ConsoleTextPane
 
appletCodeBase - Variable in class org.jmol.viewer.FileManager
 
appletCodeBase - Variable in class org.jmol.viewer.Viewer
 
appletContext - Variable in class org.jmol.applet.Jvm12
 
appletContext - Variable in class org.openscience.jmol.app.Jmol
 
appletDocumentBase - Variable in class org.jmol.viewer.FileManager
 
appletDocumentBase - Variable in class org.jmol.viewer.Viewer
 
appletInfoDivs - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
AppletOnly - Variable in class org.jmol.popup.JmolPopup
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Molecules
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Test
 
appletProxy - Variable in class org.jmol.viewer.FileManager
 
appletProxy - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
appletSizeSpinnerH - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletSizeSpinnerP - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletSizeSpinnerW - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletWrapper - Variable in class org.jmol.applet.Jmol
 
AppletWrapper - Class in org.jmol.appletwrapper
 
AppletWrapper(String, String, int, String[]) - Constructor for class org.jmol.appletwrapper.AppletWrapper
 
appletWrapper - Variable in class org.jmol.appletwrapper.ClassPreloader
 
appletWrapper - Variable in class org.jmol.appletwrapper.TickerThread
 
appletWrapper - Variable in class org.jmol.appletwrapper.WrappedAppletLoader
 
applyAllSymmetry(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applyBlueAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
applyColorScale() - Method in class org.jmol.jvxl.readers.VoxelReader
 
applyColorTranslucencyLevel(short, float) - Static method in class org.jmol.g3d.Graphics3D
 
applyCustomAnaglyph(int[]) - Method in class org.jmol.g3d.Graphics3D
 
applyCyanAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyGreenAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyLeftMouse(int) - Method in class org.jmol.viewer.MouseManager10
 
applyMouseStyle(String, boolean, boolean) - Method in class org.jmol.viewer.PickingManager
 
applyRotation(Matrix3f, boolean, BitSet) - Method in class org.jmol.viewer.TransformManager
 
applySymmetry() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
applySymmetry() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
applySymmetry() - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
applySymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry(Vector, boolean, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymmetryToBonds - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
areAxesTainted() - Method in class org.jmol.viewer.Viewer
 
argbCurrent - Variable in class org.jmol.g3d.Graphics3D
 
argbEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
argbNoisyDn - Variable in class org.jmol.g3d.Graphics3D
 
argbNoisyUp - Variable in class org.jmol.g3d.Graphics3D
 
argbs - Static variable in class org.jmol.g3d.Colix3D
 
argbsAmino - Static variable in class org.jmol.util.ColorEncoder
 
argbsAmino - Static variable in class org.jmol.viewer.JmolConstants
 
argbsChainAtom - Static variable in class org.jmol.viewer.JmolConstants
some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainHetero - Static variable in class org.jmol.viewer.JmolConstants
 
argbsCpk - Static variable in class org.jmol.util.ColorEncoder
 
argbsCpk - Variable in class org.jmol.viewer.ColorManager
 
argbsCpk - Static variable in class org.jmol.viewer.JmolConstants
Default table of CPK atom colors.
argbsCpkRasmol - Static variable in class org.jmol.viewer.JmolConstants
 
argbsFormalCharge - Static variable in class org.jmol.viewer.JmolConstants
 
argbsGreyscale - Static variable in class org.jmol.g3d.Colix3D
 
argbShapelyBackbone - Static variable in class org.jmol.viewer.JmolConstants
 
argbShapelyDefault - Static variable in class org.jmol.viewer.JmolConstants
 
argbShapelySpecial - Static variable in class org.jmol.viewer.JmolConstants
 
argbsHbondType - Static variable in class org.jmol.viewer.JmolConstants
 
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JmolConstants
 
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JmolConstants
 
argbsRoygb - Static variable in class org.jmol.util.ColorEncoder
 
argbsRoygbScale - Static variable in class org.jmol.viewer.JmolConstants
 
argbsRwb - Static variable in class org.jmol.util.ColorEncoder
 
argbsRwbScale - Static variable in class org.jmol.viewer.JmolConstants
 
argbsShapely - Static variable in class org.jmol.util.ColorEncoder
 
argbsShapely - Static variable in class org.jmol.viewer.JmolConstants
 
argbsStructure - Static variable in class org.jmol.viewer.JmolConstants
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
argusImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
array - Static variable in class org.jmol.viewer.Token
 
arrayCopy(int[], int, int, boolean) - Static method in class org.jmol.util.ArrayUtil
 
arrayListHandler - Variable in class org.openscience.jmol.app.webexport.Test
 
ArrayListTransferHandler - Class in org.openscience.jmol.app.webexport
 
ArrayListTransferHandler(WebPanel) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
ArrayListTransferHandler.ArrayListTransferable - Class in org.openscience.jmol.app.webexport
 
ArrayListTransferHandler.ArrayListTransferable(ArrayList) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
arrayPairs - Static variable in class org.jmol.viewer.Token
 
ArrayUtil - Class in org.jmol.util
 
ArrayUtil() - Constructor for class org.jmol.util.ArrayUtil
 
arrowHeadBase - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
arrowHeadFaces - Static variable in class org.jmol.shapebio.RocketsRenderer
 
arrowHeadOffset - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
arrowHeadOffset - Static variable in class org.jmol.shapespecial.VectorsRenderer
 
arrowHeadTip - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
arrowHeadWidthFactor - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
as5D - Variable in class org.jmol.quantum.MOCalculation
 
ascent - Variable in class org.jmol.g3d.Text3D
 
ascent - Variable in class org.jmol.shape.LabelsRenderer
 
ascent - Variable in class org.jmol.shape.Text
 
ashades - Static variable in class org.jmol.g3d.Colix3D
 
ashadesGreyscale - Static variable in class org.jmol.g3d.Colix3D
 
aspectRatio - Variable in class org.jmol.shapebio.BioShapeRenderer
 
asPopup - Variable in class org.jmol.popup.JmolPopup
 
assignAromaticBonds() - Method in class org.jmol.modelset.BondCollection
 
assignAromaticBonds(boolean, BitSet) - Method in class org.jmol.modelset.BondCollection
algorithm discussed above.
assignAromaticBonds(boolean) - Method in class org.jmol.modelset.ModelSet
 
assignAromaticBonds() - Method in class org.jmol.viewer.Viewer
 
assignAromaticDouble(Bond) - Method in class org.jmol.modelset.BondCollection
try to assign AROMATICDOUBLE to this bond.
assignAromaticDouble(Atom) - Method in class org.jmol.modelset.BondCollection
N atoms with 3 bonds cannot also have a double bond; other atoms need one and only one double bond; the rest must be single bonds.
assignAromaticNandO(BitSet) - Method in class org.jmol.modelset.BondCollection
 
assignAromaticSingle(Bond) - Method in class org.jmol.modelset.BondCollection
try to assign AROMATICSINGLE to this bond.
assignAromaticSingle(Atom, int) - Method in class org.jmol.modelset.BondCollection
N atoms with 3 bonds cannot also have a double bond; other atoms needs all single bonds, because the bond leading up to it is double.
assignAromaticSingleHetero(Atom) - Method in class org.jmol.modelset.BondCollection
 
assignBitsetVariable(String, BitSet) - Method in class org.jmol.viewer.Eval
 
assocCutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
assocCutoff - Variable in class org.jmol.jvxl.readers.VoxelReader
 
assocGridPointMap - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
assocGridPointNormals - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
associatedAtoms - Variable in class org.jmol.modelset.Bond.BondSet
 
associateNormals - Variable in class org.jmol.shapesurface.Isosurface
 
assumeAtomRecord() - Method in class org.jmol.adapter.readers.more.ShelxReader
 
astrType - Static variable in class org.jmol.viewer.Token
 
asVector - Variable in class org.jmol.viewer.Eval.Rpn
 
ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atokenInfix - Variable in class org.jmol.viewer.Compiler
 
atom() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
Atom - Class in org.jmol.adapter.smarter
 
Atom() - Constructor for class org.jmol.adapter.smarter.Atom
 
atom - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atom - Variable in class org.jmol.minimize.MinAtom
 
Atom - Class in org.jmol.modelset
 
Atom(Point3f) - Constructor for class org.jmol.modelset.Atom
 
Atom(Viewer, int, int, BitSet, int, short, int, int, float, float, float, boolean, char, char, float) - Constructor for class org.jmol.modelset.Atom
 
atom - Variable in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
atom1 - Variable in class org.jmol.modelset.Bond
 
atom1 - Variable in class org.jmol.smiles.SmilesBond
 
atom2 - Variable in class org.jmol.modelset.Bond
 
atom2 - Variable in class org.jmol.smiles.SmilesBond
 
ATOM_COUNT_MAX - Static variable in class org.jmol.symmetry.PointGroup
 
ATOM_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.ModelLoader
 
ATOM_IN_MODEL - Static variable in class org.jmol.viewer.JmolConstants
 
ATOM_SLABBED - Static variable in class org.jmol.viewer.JmolConstants
 
ATOM_TYPE_OXIDATION_NUMBER - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
ATOM_TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomA - Variable in class org.jmol.shape.MeasuresRenderer
 
atomA - Variable in class org.jmol.shape.SticksRenderer
 
atomArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomB - Variable in class org.jmol.shape.MeasuresRenderer
 
atomB - Variable in class org.jmol.shape.SticksRenderer
 
atomC - Variable in class org.jmol.shape.MeasuresRenderer
 
atomCenterOrCoordinateParameter(int) - Method in class org.jmol.viewer.Eval
 
AtomCollection - Class in org.jmol.modelset
 
AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
 
atomCoordAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
 
atomCoordBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
atomCount - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.CubeReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.GamessReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.GaussianReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.JaguarReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
atomCount - Variable in class org.jmol.adapter.readers.more.MopacGraphfReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.OdysseyReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.QchemReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
atomCount - Variable in class org.jmol.adapter.readers.more.SpartanReader
 
atomCount - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
atomCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atomCount - Variable in class org.jmol.atomdata.AtomData
 
atomCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
atomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
atomCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
atomCount - Variable in class org.jmol.minimize.forcefield.ForceField
 
atomCount - Variable in class org.jmol.minimize.Minimizer
 
atomCount - Variable in class org.jmol.modelset.AtomCollection
 
atomCount - Variable in class org.jmol.modelset.Model
 
atomCount - Variable in class org.jmol.popup.JmolPopup
 
atomCount - Variable in class org.jmol.shape.AtomShape
 
atomCount - Variable in class org.jmol.shape.Measures
 
atomCount - Variable in class org.jmol.smiles.PatternMatcher
 
atomCountFull - Variable in class org.jmol.minimize.Minimizer
 
atomD - Variable in class org.jmol.shape.MeasuresRenderer
 
AtomData - Class in org.jmol.atomdata
 
AtomData() - Constructor for class org.jmol.atomdata.AtomData
 
atomData - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
atomData - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
AtomDataReader - Class in org.jmol.jvxl.readers
 
AtomDataReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.AtomDataReader
 
AtomDataServer - Interface in org.jmol.atomdata
 
atomDataServer - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
atomExpression - Static variable in class org.jmol.viewer.PropertyManager
 
atomExpressionCommand - Static variable in class org.jmol.viewer.Token
 
atomFieldMap - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
atomFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomFields - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
atomFormats - Variable in class org.jmol.shape.Hover
 
atomicAndIsotopeNumber - Variable in class org.jmol.modelset.Atom
 
atomicMass - Variable in class org.jmol.smiles.SmilesAtom
 
atomicNumber - Variable in class org.jmol.atomdata.AtomData
 
atomicNumbers - Variable in class org.jmol.adapter.readers.more.CsfReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.more.MopacGraphfReader
 
atomID - Static variable in class org.jmol.viewer.Token
 
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_BACKBONE_MIN - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C5 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C5M - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C6 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C7 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_C8 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N3 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N6 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N7 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_N9 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O1P - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O2P - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_O6 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_OP1 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_OP2 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_S4 - Static variable in class org.jmol.viewer.JmolConstants
 
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JmolConstants
 
atomIdNames - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomIndex - Variable in class org.jmol.adapter.readers.more.HinReader
 
atomIndex - Variable in class org.jmol.adapter.smarter.Atom
 
atomIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
atomIndex - Variable in class org.jmol.modelset.Atom
 
atomIndex - Variable in class org.jmol.modelset.AtomIteratorWithinSet
 
atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
 
atomIndex - Variable in class org.jmol.shape.Hover
 
atomIndex - Variable in class org.jmol.shape.Mesh
 
atomIndex - Variable in class org.jmol.shapesurface.Isosurface
 
atomIndex - Static variable in class org.jmol.viewer.Token
 
atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex1 - Variable in class org.jmol.shapespecial.Dipoles
 
atomIndex1 - Variable in class org.jmol.viewer.StateManager.Connection
 
atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex2 - Variable in class org.jmol.shapespecial.Dipoles
 
atomIndex2 - Variable in class org.jmol.viewer.StateManager.Connection
 
atomIndexes - Variable in class org.jmol.minimize.MinBond
 
AtomIndexIterator - Interface in org.jmol.modelset
 
AtomIteratorWithinModel - Class in org.jmol.modelset
 
AtomIteratorWithinModel() - Constructor for class org.jmol.modelset.AtomIteratorWithinModel
 
AtomIteratorWithinSet - Class in org.jmol.modelset
 
AtomIteratorWithinSet() - Constructor for class org.jmol.modelset.AtomIteratorWithinSet
 
atomLabels - Variable in class org.jmol.shape.Labels
 
atomList - Variable in class org.jmol.modelset.Molecule
 
atomMap - Variable in class org.jmol.minimize.Minimizer
 
atomName - Variable in class org.jmol.adapter.smarter.Atom
 
atomName1 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atomName2 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atomNames - Variable in class org.jmol.adapter.readers.more.GamessReader
 
atomNames - Variable in class org.jmol.adapter.readers.more.PsiReader
 
atomNames - Variable in class org.jmol.modelset.AtomCollection
 
atomNo - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomno - Static variable in class org.jmol.viewer.Token
 
atomPicked(int, Point3f, int) - Method in class org.jmol.viewer.PickingManager
 
atomPicked(int, Point3f, int) - Method in class org.jmol.viewer.Viewer
 
atomPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
atomProp - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomProperty(Atom, int, boolean) - Method in class org.jmol.viewer.Eval
 
atomproperty - Static variable in class org.jmol.viewer.Token
 
atomRadius - Variable in class org.jmol.atomdata.AtomData
 
atomRadius - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atoms - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atoms - Variable in class org.jmol.minimize.forcefield.Calculations
 
atoms - Variable in class org.jmol.minimize.forcefield.ForceField
 
atoms - Variable in class org.jmol.minimize.Minimizer
 
atoms - Variable in class org.jmol.modelset.AtomCollection
 
atoms - Variable in class org.jmol.shape.AtomShape
 
atoms - Variable in class org.jmol.shape.Measures
 
atoms - Variable in class org.jmol.shapebio.BioShapeCollection
 
atoms - Variable in class org.jmol.shapespecial.Dipole
 
atoms - Variable in class org.jmol.smiles.SmilesMolecule
 
atoms - Variable in class org.jmol.symmetry.PointGroup
 
atoms - Static variable in class org.jmol.viewer.Token
 
atomsCount - Variable in class org.jmol.smiles.SmilesMolecule
 
atomSerial - Variable in class org.jmol.adapter.smarter.Atom
 
atomSerials - Variable in class org.jmol.modelset.AtomCollection
 
atomSet - Variable in class org.jmol.quantum.QuantumCalculation
 
atomSetAtomCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetBondCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetChooser - Class in org.openscience.jmol.app
A JFrame that allows for choosing an Atomset to view.
AtomSetChooser(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.AtomSetChooser
 
atomSetChooser - Variable in class org.openscience.jmol.app.Jmol
 
AtomSetChooser.AtomSet - Class in org.openscience.jmol.app
Objects in the AtomSetChooser tree
AtomSetChooser.AtomSet(int, String) - Constructor for class org.openscience.jmol.app.AtomSetChooser.AtomSet
 
atomsetchooserAction - Static variable in class org.openscience.jmol.app.Jmol
 
atomSetCollection - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
AtomSetCollection - Class in org.jmol.adapter.smarter
 
AtomSetCollection(String) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetCollection(AtomSetCollection[]) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
Creates an AtomSetCollection based on an array of AtomSetCollection
AtomSetCollection(Vector) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
Creates an AtomSetCollection based on a Vector of AtomSetCollection or Vector (from zipped zip files)
atomSetCollection - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
atomSetCollection - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
atomSetCollection - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
atomSetCollectionAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetCollectionProperties - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetCollectionReader - Class in org.jmol.adapter.smarter
 
AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
 
atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
 
atomSetIndex - Variable in class org.openscience.jmol.app.AtomSetChooser.AtomSet
The index of that AtomSet
atomSetName - Variable in class org.openscience.jmol.app.AtomSetChooser.AtomSet
The name of the AtomSet
atomSetNames - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetProperties - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomShape - Class in org.jmol.shape
 
AtomShape() - Constructor for class org.jmol.shape.AtomShape
 
atomSite - Variable in class org.jmol.adapter.smarter.Atom
 
atomSite - Variable in class org.jmol.modelset.Atom
 
atomsPicked(BitSet, int) - Method in class org.jmol.viewer.PickingManager
 
atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSymmetry - Variable in class org.jmol.modelset.Atom
 
atomTest - Variable in class org.jmol.symmetry.SymmetryOperation
 
atomTypeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomTypes - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
atomTypes - Static variable in class org.jmol.minimize.Minimizer
 
atomX - Static variable in class org.jmol.viewer.Token
 
atomXyz - Variable in class org.jmol.atomdata.AtomData
 
atomXyz - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomY - Static variable in class org.jmol.viewer.Token
 
atomZ - Static variable in class org.jmol.viewer.Token
 
attEcho - Variable in class org.openscience.jmol.app.ConsoleDocument
 
attError - Variable in class org.openscience.jmol.app.ConsoleDocument
 
attPrompt - Variable in class org.openscience.jmol.app.ConsoleDocument
 
attributesCommand - Variable in class org.jmol.applet.Console
 
atts - Variable in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
attStatus - Variable in class org.openscience.jmol.app.ConsoleDocument
 
attUserInput - Variable in class org.openscience.jmol.app.ConsoleDocument
 
augmentGroup3List(Object, String, boolean) - Method in class org.jmol.popup.JmolPopup
 
AUTH_ATOM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
autoBond(BitSet, BitSet, BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
autoBond(short, BitSet, BitSet, BitSet, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
autoBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
autoBond - Variable in class org.openscience.jmol.app.PreferencesDialog
 
autoExit - Variable in class org.jmol.viewer.Viewer
 
autoFps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
autoHbond(BitSet, BitSet, BitSet) - Method in class org.jmol.modelset.BondCollection
 
autoHbond(BitSet, BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
 
autoHbond(BitSet) - Method in class org.jmol.viewer.Viewer
 
autoHbond(BitSet, BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
 
autoScaleOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
auxiliaryInfo - Variable in class org.jmol.modelset.Model
 
availableProcessorsForNewerJvm() - Method in class org.jmol.popup.JmolPopup
 
availableProcessorsForNewerJvm() - Method in class org.jmol.popup.JmolPopupSwing
 
average - Static variable in class org.jmol.viewer.Token
 
averageAtomPoint - Variable in class org.jmol.modelset.ModelCollection
 
averageBufferPixel(int[], int[], int, int) - Static method in class org.jmol.g3d.Graphics3D
 
Awt3D - Class in org.jmol.g3d
Implementation of Platform3D when using AWT on 1.1 JVMs.
Awt3D(Component) - Constructor for class org.jmol.g3d.Awt3D
 
awtComponent - Variable in class org.jmol.applet.Jvm12
 
awtPopup - Variable in class org.jmol.popup.JmolPopupAwt
 
ax - Variable in class org.jmol.g3d.Triangle3D
 
ax - Variable in class org.jmol.jcamp.ZoneVisu
 
axE - Variable in class org.jmol.g3d.Triangle3D
 
Axes - Class in org.jmol.shape
 
Axes() - Constructor for class org.jmol.shape.Axes
 
axes - Variable in class org.jmol.shapespecial.DrawMesh
 
axes - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
axes - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
axes - Variable in class org.jmol.symmetry.PointGroup
 
axes(int) - Method in class org.jmol.viewer.Eval
 
axes - Static variable in class org.jmol.viewer.Token
 
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
AXES_MODE_BOUNDBOX - Static variable in class org.jmol.viewer.JmolConstants
axes modes
AXES_MODE_MOLECULAR - Static variable in class org.jmol.viewer.JmolConstants
 
AXES_MODE_UNITCELL - Static variable in class org.jmol.viewer.JmolConstants
 
axesAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
axesAreTainted - Variable in class org.jmol.viewer.Viewer
 
AxesGenerator - Class in org.jmol.export
 
AxesGenerator() - Constructor for class org.jmol.export.AxesGenerator
 
axesMaxN - Static variable in class org.jmol.symmetry.PointGroup
 
axesMode - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
axesOrientationRasmol - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
axesOrientationRasmol - Variable in class org.openscience.jmol.app.PreferencesDialog
 
AxesRenderer - Class in org.jmol.shape
 
AxesRenderer() - Constructor for class org.jmol.shape.AxesRenderer
 
axesScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
axis - Variable in class org.jmol.shapespecial.DrawMesh
 
axis - Static variable in class org.jmol.viewer.Token
 
axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisangle - Static variable in class org.jmol.viewer.Token
 
axisangleT - Variable in class org.jmol.viewer.TransformManager
 
axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisChoice - Variable in class org.jmol.symmetry.SpaceGroup
 
axisLabels - Static variable in class org.jmol.shape.AxesRenderer
 
axisPoints - Variable in class org.jmol.shape.Axes
 
axisPoints - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
axisScreens - Variable in class org.jmol.shape.AxesRenderer
 
axisType - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisXY - Variable in class org.jmol.shape.Axes
 
axW - Variable in class org.jmol.g3d.Triangle3D
 
ay - Variable in class org.jmol.g3d.Triangle3D
 
ay - Variable in class org.jmol.jcamp.ZoneVisu
 
az - Variable in class org.jmol.g3d.Triangle3D
 
azE - Variable in class org.jmol.g3d.Triangle3D
 
azW - Variable in class org.jmol.g3d.Triangle3D
 

B

b - Variable in class org.jmol.minimize.forcefield.Calculation
 
b - Variable in class org.jmol.symmetry.UnitCell
 
b1 - Variable in class org.jmol.g3d.Hermite3D
 
b2 - Variable in class org.jmol.g3d.Hermite3D
 
b_ - Variable in class org.jmol.symmetry.UnitCell.Data
 
B_ISO - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
babel - Static variable in class org.jmol.viewer.Token
 
back - Static variable in class org.jmol.viewer.Token
 
Backbone - Class in org.jmol.shapebio
 
Backbone() - Constructor for class org.jmol.shapebio.Backbone
 
backbone - Static variable in class org.jmol.viewer.Token
 
BackboneGenerator - Class in org.jmol.export
 
BackboneGenerator() - Constructor for class org.jmol.export.BackboneGenerator
 
BackboneRenderer - Class in org.jmol.shapebio
 
BackboneRenderer() - Constructor for class org.jmol.shapebio.BackboneRenderer
 
background(int) - Method in class org.jmol.viewer.Eval
 
background - Static variable in class org.jmol.viewer.Token
 
backgroundColix - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
backgroundImage - Variable in class org.jmol.g3d.Graphics3D
 
backgroundImageFileName - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
backgroundModelIndex - Variable in class org.jmol.viewer.RepaintManager
 
backgroundTransparent - Static variable in class org.jmol.g3d.Swing3D
 
BACKLIT - Static variable in class org.jmol.viewer.JmolConstants
 
backlit - Static variable in class org.jmol.viewer.Token
 
BallandStick - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
Balls - Class in org.jmol.shape
 
Balls() - Constructor for class org.jmol.shape.Balls
 
BallsGenerator - Class in org.jmol.export
 
BallsGenerator() - Constructor for class org.jmol.export.BallsGenerator
 
BallsRenderer - Class in org.jmol.shape
 
BallsRenderer() - Constructor for class org.jmol.shape.BallsRenderer
 
Base64 - Class in org.jmol.util
 
Base64() - Constructor for class org.jmol.util.Base64
 
base64 - Static variable in class org.jmol.util.Base64
 
baseAtomIndex - Variable in class org.jmol.adapter.readers.more.HinReader
 
baseAtomIndex - Variable in class org.jmol.adapter.readers.more.MopacReader
 
baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseFont3d - Variable in class org.jmol.shape.Frank
 
baseGroupIndex - Variable in class org.jmol.modelset.ModelCollection
 
baseModelCount - Variable in class org.jmol.modelset.ModelLoader
 
baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseOffset - Variable in class org.jmol.shapebio.StrandsRenderer
 
baseTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
 
Bbcage - Class in org.jmol.shape
 
Bbcage() - Constructor for class org.jmol.shape.Bbcage
 
BbcageGenerator - Class in org.jmol.export
 
BbcageGenerator() - Constructor for class org.jmol.export.BbcageGenerator
 
BbcageRenderer - Class in org.jmol.shape
 
BbcageRenderer() - Constructor for class org.jmol.shape.BbcageRenderer
 
bbCenter - Variable in class org.jmol.modelset.BoxInfo
 
bbCorner0 - Variable in class org.jmol.modelset.BoxInfo
 
bbCorner1 - Variable in class org.jmol.modelset.BoxInfo
 
bboxAtoms - Variable in class org.jmol.modelset.ModelCollection
 
bboxModels - Variable in class org.jmol.modelset.ModelCollection
 
bButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
bbVector - Variable in class org.jmol.modelset.BoxInfo
 
bbVertices - Variable in class org.jmol.modelset.BoxInfo
 
bdSlider - Variable in class org.openscience.jmol.app.PreferencesDialog
 
BEG_ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
BEG_INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
BEG_SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
beginRendering(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
 
beta - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
beta - Variable in class org.jmol.symmetry.UnitCell
 
bfactor - Variable in class org.jmol.adapter.smarter.Atom
 
bfactor100Hi - Variable in class org.jmol.modelset.AtomCollection
 
bfactor100Lo - Variable in class org.jmol.modelset.AtomCollection
 
bfactor100s - Variable in class org.jmol.modelset.AtomCollection
 
bfactorMax - Variable in class org.jmol.shapebio.BioShape
 
bfactorMin - Variable in class org.jmol.shapebio.BioShape
 
bfxn_ang - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
bgcolix - Variable in class org.jmol.shape.Object2d
 
bgcolixes - Variable in class org.jmol.shape.Labels
 
bgcolor - Variable in class org.jmol.appletwrapper.AppletWrapper
 
bgcolor - Variable in class org.jmol.g3d.Graphics3D
 
BGYOR - Static variable in class org.jmol.util.ColorEncoder
 
BinaryDocument - Class in org.jmol.util
 
BinaryDocument() - Constructor for class org.jmol.util.BinaryDocument
 
biomolecules - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
biomts - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
BioPolymer - Class in org.jmol.modelsetbio
 
BioPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.BioPolymer
 
bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
 
bioPolymer - Variable in class org.jmol.shapebio.BioShape
 
bioPolymerCount - Variable in class org.jmol.modelset.Model
 
bioPolymers - Variable in class org.jmol.modelset.Model
 
BioShape - Class in org.jmol.shapebio
 
BioShape(BioShapeCollection, int, BioPolymer) - Constructor for class org.jmol.shapebio.BioShape
 
BioShapeCollection - Class in org.jmol.shapebio
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.
BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
 
BioShapeRenderer - Class in org.jmol.shapebio
 
BioShapeRenderer() - Constructor for class org.jmol.shapebio.BioShapeRenderer
 
bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
 
biosymmetryCount - Variable in class org.jmol.modelset.Model
 
bitmap - Variable in class org.jmol.g3d.Text3D
 
BITS - Static variable in class org.jmol.export.image.GifEncoder
 
bitsACchrominance - Static variable in class org.jmol.util.Huffman
 
bitsACluminance - Static variable in class org.jmol.util.Huffman
 
bitsDCchrominance - Static variable in class org.jmol.util.Huffman
 
bitsDCluminance - Static variable in class org.jmol.util.Huffman
 
bitset - Static variable in class org.jmol.viewer.Token
 
bitSetForModelFileNumber(int) - Method in class org.jmol.viewer.Eval
 
bitsets - Variable in class org.jmol.shape.Mesh
 
bitsetTokenVector(Object) - Method in class org.jmol.viewer.Eval
 
BitSetUtil - Class in org.jmol.util
 
BitSetUtil() - Constructor for class org.jmol.util.BitSetUtil
 
BLACK - Static variable in class org.jmol.g3d.Graphics3D
 
blockCubeData - Variable in class org.jmol.jvxl.readers.Parameters
 
BlockHeight - Variable in class org.jmol.util.JpegInfo
 
BlockWidth - Variable in class org.jmol.util.JpegInfo
 
blue - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
BLUE - Static variable in class org.jmol.g3d.Graphics3D
 
bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
 
BOND - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
Bond - Class in org.jmol.adapter.smarter
 
Bond() - Constructor for class org.jmol.adapter.smarter.Bond
 
Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
 
bond - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
Bond - Class in org.jmol.modelset
 
Bond(Atom, Atom, short, short, short) - Constructor for class org.jmol.modelset.Bond
 
bond - Variable in class org.jmol.shape.SticksRenderer
 
bond - Variable in class org.jmol.shapespecial.Dipole
 
bond - Variable in class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
Bond.BondSet - Class in org.jmol.modelset
 
Bond.BondSet(BitSet) - Constructor for class org.jmol.modelset.Bond.BondSet
 
Bond.BondSet(BitSet, int[]) - Constructor for class org.jmol.modelset.Bond.BondSet
 
BOND_AROMATIC - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_AROMATIC_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_AROMATIC_SINGLE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_COVALENT_DOUBLE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_COVALENT_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_COVALENT_SINGLE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_COVALENT_TRIPLE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_CALC - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_CALC_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_MINUS_3 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_MINUS_4 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_NUCLEOTIDE - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_PLUS_2 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_PLUS_3 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_PLUS_4 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_PLUS_5 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_H_REGULAR - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_HBOND_SHIFT - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_HYDROGEN_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_NEW - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_ORDER_ANY - Static variable in class org.jmol.viewer.JmolConstants
Extended Bond Definition Types
BOND_ORDER_NULL - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_PARTIAL01 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_PARTIAL12 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_PARTIAL23 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_PARTIAL32 - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_PARTIAL_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_STEREO_FAR - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_STEREO_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_STEREO_NEAR - Static variable in class org.jmol.viewer.JmolConstants
 
BOND_SULFUR_MASK - Static variable in class org.jmol.viewer.JmolConstants
 
bondAminoHydrogen(AminoMonomer, int, Point3f, BitSet, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
 
bondArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bondAtoms(Atom, Atom, short, short, BitSet) - Method in class org.jmol.modelset.BondCollection
 
bondAtoms(Object, Object, short) - Method in class org.jmol.modelset.ModelLoader
 
bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
BondCollection - Class in org.jmol.modelset
 
BondCollection() - Constructor for class org.jmol.modelset.BondCollection
 
bondCount - Variable in class org.jmol.adapter.readers.more.OdysseyReader
 
bondCount - Variable in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
bondCount - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
bondCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bondCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
bondCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
bondCount - Variable in class org.jmol.minimize.forcefield.ForceField
 
bondCount - Variable in class org.jmol.minimize.Minimizer
 
bondCount - Variable in class org.jmol.modelset.BondCollection
 
bondCount - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondCount - Variable in class org.jmol.modelset.Model
 
bondCount - Variable in class org.jmol.viewer.StateManager.Connections
 
bondcount - Static variable in class org.jmol.viewer.Token
 
bondCount0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bondData - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
bondedAtoms - Variable in class org.jmol.minimize.MinAtom
 
bondedOnly - Variable in class org.jmol.shapespecial.Polyhedra
 
bondFieldMap - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
bondFields - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
bondGrowthIncrement - Static variable in class org.jmol.modelset.BondCollection
 
bondIndex0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
BondIterator - Interface in org.jmol.modelset
 
BondIteratorSelected - Class in org.jmol.modelset
 
BondIteratorSelected(Bond[], int, short, BitSet, boolean) - Constructor for class org.jmol.modelset.BondIteratorSelected
 
BondIteratorSelected(Bond[], int, BitSet) - Constructor for class org.jmol.modelset.BondIteratorSelected
 
bondmode - Static variable in class org.jmol.viewer.Token
 
bondModeOr - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bondMutually(Atom, Atom, short, short) - Method in class org.jmol.modelset.BondCollection
 
bondOrder - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
bondOrder - Variable in class org.jmol.shape.SticksRenderer
 
bondorder() - Method in class org.jmol.viewer.Eval
 
bondorder - Static variable in class org.jmol.viewer.Token
 
bondOrderNames - Static variable in class org.jmol.viewer.JmolConstants
 
bondOrderNumbers - Static variable in class org.jmol.viewer.JmolConstants
 
bondOrderValues - Static variable in class org.jmol.viewer.JmolConstants
 
bondPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bondRadiusMilliAngstroms - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bonds - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
bonds - Variable in class org.jmol.minimize.forcefield.Calculations
 
bonds - Variable in class org.jmol.minimize.forcefield.ForceField
 
bonds - Variable in class org.jmol.minimize.MinAtom
 
bonds - Variable in class org.jmol.modelset.Atom
 
bonds - Variable in class org.jmol.modelset.BondCollection
 
bonds - Variable in class org.jmol.modelset.BondIteratorSelected
 
bonds - Variable in class org.jmol.smiles.SmilesAtom
 
bonds - Variable in class org.jmol.smiles.SmilesMolecule
 
bonds - Static variable in class org.jmol.viewer.Token
 
bondsBackbone - Variable in class org.jmol.shape.SticksRenderer
 
bondsCount - Variable in class org.jmol.smiles.SmilesAtom
 
bondsCount - Variable in class org.jmol.smiles.SmilesMolecule
 
bondSelectionModeOr - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondset - Static variable in class org.jmol.viewer.Token
 
bondTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
bondTolerance - Variable in class org.openscience.jmol.app.PreferencesDialog
 
bondType - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
bondType - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondType - Variable in class org.jmol.smiles.SmilesBond
 
booleanParameter(int) - Method in class org.jmol.viewer.Eval
 
border - Static variable in class org.openscience.jmol.app.Jmol
 
BORDERCOLOR - Static variable in class org.openscience.jmol.app.Splash
 
BORDERSIZE - Static variable in class org.openscience.jmol.app.Splash
 
bottom - Static variable in class org.jmol.viewer.Token
 
bottomAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
boundbox(int) - Method in class org.jmol.viewer.Eval
 
boundbox - Static variable in class org.jmol.viewer.Token
 
boundboxAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
Box(String) - Static method in class org.jmol.popup.PopupResourceBundle
 
boxFaces - Static variable in class org.jmol.shapebio.RocketsRenderer
 
boxHeight - Variable in class org.jmol.shape.Object2d
 
BoxInfo - Class in org.jmol.modelset
 
BoxInfo() - Constructor for class org.jmol.modelset.BoxInfo
 
boxInfo - Variable in class org.jmol.modelset.ModelCollection
 
boxWidth - Variable in class org.jmol.shape.Object2d
 
boxX - Variable in class org.jmol.shape.Object2d
 
boxXY - Variable in class org.jmol.shape.LabelsRenderer
 
boxXY - Variable in class org.jmol.shape.Object2d
 
boxY - Variable in class org.jmol.shape.Object2d
 
br - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
br - Variable in class org.jmol.shapesurface.Pmesh
 
braceCount - Variable in class org.jmol.viewer.Eval.Rpn
 
branch - Static variable in class org.jmol.viewer.Token
 
breakcmd - Static variable in class org.jmol.viewer.Token
 
breakOutAtomTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
breakOutBondTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
breakOutTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bsAll - Variable in class org.jmol.modelset.ModelCollection
 
bsAllModels - Variable in class org.jmol.shapespecial.Draw
 
bsAnions - Static variable in class org.jmol.viewer.JmolConstants
 
bsAromatic - Variable in class org.jmol.modelset.BondCollection
 
bsAromaticDouble - Variable in class org.jmol.modelset.BondCollection
 
bsAromaticSingle - Variable in class org.jmol.modelset.BondCollection
 
bsAtoms - Variable in class org.jmol.minimize.Minimizer
 
bsAtoms - Variable in class org.jmol.modelset.Model
 
bsAtoms - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
bsAtoms1 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
bsAtoms2 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
bsBgColixSet - Variable in class org.jmol.shape.Labels
 
bsBonds - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
bScaled - Variable in class org.jmol.g3d.Rgb16
 
bsCations - Static variable in class org.jmol.viewer.JmolConstants
 
bsColixSet - Variable in class org.jmol.shape.AtomShape
 
bsColixSet - Variable in class org.jmol.shape.Measures
 
bsColixSet - Variable in class org.jmol.shape.Sticks
 
bsColixSet - Variable in class org.jmol.shapebio.BioShape
 
bsConsidered - Variable in class org.jmol.g3d.Normix3D
 
bsDeleted - Variable in class org.jmol.viewer.SelectionManager
 
bsEmpty - Variable in class org.jmol.modelset.AtomCollection
 
bsFaces - Variable in class org.jmol.shape.MeshRenderer
 
bsFixed - Variable in class org.jmol.minimize.forcefield.ForceField
 
bsFixed - Variable in class org.jmol.minimize.Minimizer
 
bsFontSet - Variable in class org.jmol.shape.Labels
 
bsFoundRectangle - Variable in class org.jmol.modelset.AtomCollection
 
bsHidden - Variable in class org.jmol.modelset.AtomCollection
 
bsHidden - Variable in class org.jmol.viewer.SelectionManager
 
bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
 
bsIgnore - Variable in class org.jmol.shape.Dots
 
bsIgnored - Variable in class org.jmol.atomdata.AtomData
 
bsItem2(Object) - Static method in class org.jmol.viewer.Token.Token2
 
bsMinFixed - Variable in class org.jmol.minimize.Minimizer
 
bsMyIgnored - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsMySelected - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsMySelected - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsNull - Static variable in class org.jmol.util.BitSetUtil
 
bsOn - Variable in class org.jmol.shape.Dots
 
bsOrderSet - Variable in class org.jmol.shape.Sticks
 
Bspf - Class in org.jmol.bspt
A Binary Space Partitioning Forest
Bspf(int) - Constructor for class org.jmol.bspt.Bspf
 
bspf - Variable in class org.jmol.modelset.AtomCollection
 
bsPseudoHBonds - Variable in class org.jmol.modelset.BondCollection
 
Bspt - Class in org.jmol.bspt
a Binary Space Partitioning Tree
Bspt(int) - Constructor for class org.jmol.bspt.Bspt
Create a bspt with the specified number of dimensions.
bspt - Variable in class org.jmol.bspt.CubeIterator
 
bspt - Variable in class org.jmol.bspt.Element
 
bsptIter - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
bsptIter - Variable in class org.jmol.modelset.AtomIteratorWithinSet
 
bspts - Variable in class org.jmol.bspt.Bspf
 
bsSelect(Token) - Static method in class org.jmol.viewer.Token
 
bsSelect(Token, int) - Static method in class org.jmol.viewer.Token
 
bsSelected - Variable in class org.jmol.atomdata.AtomData
 
bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
 
bsSelected - Variable in class org.jmol.minimize.Minimizer
 
bsSelected - Variable in class org.jmol.modelset.AtomIteratorWithinSet
 
bsSelected - Variable in class org.jmol.modelset.BondIteratorSelected
 
bsSelected - Variable in class org.jmol.shape.Dots
 
bsSelected - Variable in class org.jmol.shape.Measures
 
bsSelected - Variable in class org.jmol.shapebio.Backbone
 
bsSelectedGroups - Variable in class org.jmol.modelset.Chain
 
bsSelectedMonomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
bsSelection - Variable in class org.jmol.viewer.SelectionManager
 
bsSizeDefault - Variable in class org.jmol.shapebio.BioShape
 
bsSizeSet - Variable in class org.jmol.shape.AtomShape
 
bsSizeSet - Variable in class org.jmol.shape.Sticks
 
bsSizeSet - Variable in class org.jmol.shapebio.BioShape
 
bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
 
bsSubset - Variable in class org.jmol.viewer.SelectionManager
 
bsSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsSurface - Variable in class org.jmol.modelset.AtomCollection
 
bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
 
bsSymmetry - Variable in class org.jmol.modelset.ModelCollection
 
bsTaint - Variable in class org.jmol.minimize.Minimizer
 
bsTemp - Variable in class org.jmol.modelset.ModelCollection
 
bsUserVdws - Variable in class org.jmol.viewer.DataManager
 
bsVertexCount - Variable in class org.jmol.shapespecial.Polyhedra
 
bsVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
bsVisible - Variable in class org.jmol.shapebio.BioShapeRenderer
 
bsVisibleFrames - Variable in class org.jmol.viewer.RepaintManager
 
btSlider - Variable in class org.openscience.jmol.app.PreferencesDialog
 
buf - Variable in class org.jmol.adapter.smarter.LimitedLineReader
 
buf - Variable in class org.jmol.jvxl.readers.LimitedLineReader
 
bufferHasBeenCleared - Variable in class org.jmol.g3d.Platform3D.ClearingThread
 
bufferHeight - Variable in class org.jmol.g3d.Platform3D
 
bufferIt(BufferedOutputStream, int, int) - Method in class org.jmol.util.Huffman
 
bufferPutBits - Variable in class org.jmol.util.Huffman
 
bufferPutBuffer - Variable in class org.jmol.util.Huffman
 
bufferSize - Variable in class org.jmol.g3d.Graphics3D
 
bufferSize - Variable in class org.jmol.g3d.Platform3D
 
bufferSizeT - Variable in class org.jmol.g3d.Platform3D
 
bufferWidth - Variable in class org.jmol.g3d.Platform3D
 
BufGra - Variable in class org.jmol.jcamp.ZoneVisu
 
BufImg - Variable in class org.jmol.jcamp.ZoneVisu
 
build(Object) - Method in class org.jmol.popup.JmolPopup
 
buildArrowHeadBox(Point3f, Vector3f, Vector3f, Point3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
buildAtomsPanel() - Method in class org.openscience.jmol.app.PreferencesDialog
 
buildBioPolymer(Group, Group[], int, boolean) - Method in interface org.jmol.api.JmolBioResolver
 
buildBioPolymer(Group, Group[], int, boolean) - Method in class org.jmol.modelsetbio.Resolver
 
buildBondPanel() - Method in class org.openscience.jmol.app.PreferencesDialog
 
buildBox(Point3f, Vector3f, Vector3f, Vector3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
buildDispPanel() - Method in class org.openscience.jmol.app.PreferencesDialog
 
buildPolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
 
buildSpaceGroup(String) - Method in class org.jmol.symmetry.SpaceGroup
 
buildStructure(String) - Method in class org.jmol.popup.PopupResourceBundle
 
BumpPixel() - Method in class org.jmol.export.image.GifEncoder
 
button - Variable in class org.openscience.jmol.app.Jmol.ActionChangedListener
 
BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.MouseManager
 
buttonRotate - Static variable in class org.openscience.jmol.app.Jmol
Button group for toggle buttons in the toolbar.
bValue(Token) - Static method in class org.jmol.viewer.Token
 
bw - Variable in class org.jmol.export._Exporter
 
BWR - Static variable in class org.jmol.util.ColorEncoder
 
bwSlider - Variable in class org.openscience.jmol.app.PreferencesDialog
 
BYELEMENT_JMOL - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_AMINO - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
byteArrayOS - Variable in class org.openscience.jmol.app.LoopedStreams
 
bytePos - Variable in class org.jmol.export.image.PngEncoder
 
bytesPerPixel - Variable in class org.jmol.export.image.PngEncoder
 

C

c - Variable in class org.jmol.minimize.forcefield.Calculation
 
C - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
c - Variable in class org.jmol.symmetry.UnitCell
 
c1 - Variable in class org.jmol.g3d.Hermite3D
 
c2 - Variable in class org.jmol.g3d.Hermite3D
 
C2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c2 - Static variable in class org.jmol.symmetry.PointGroup
 
c3 - Static variable in class org.jmol.symmetry.PointGroup
 
C3Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
C4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c4 - Static variable in class org.jmol.symmetry.PointGroup
 
C5 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c5 - Static variable in class org.jmol.symmetry.PointGroup
 
C6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c6 - Static variable in class org.jmol.symmetry.PointGroup
 
C8 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c8 - Static variable in class org.jmol.symmetry.PointGroup
 
c_ - Variable in class org.jmol.symmetry.UnitCell.Data
 
CA - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
cA_ - Variable in class org.jmol.symmetry.UnitCell.Data
 
calc(int, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
calc - Variable in class org.jmol.minimize.forcefield.ForceField
 
calc1Screen(Point3f, Vector3f, short, float, Point3i) - Method in class org.jmol.shapebio.BioShapeRenderer
 
CALC_ANGLE - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_DISTANCE - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_ES - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_MAX - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_OOP - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_TORSION - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_VDW - Static variable in class org.jmol.minimize.forcefield.Calculations
 
calcArgbEndcap(boolean, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
calcArgbsGreyscale() - Static method in class org.jmol.g3d.Colix3D
 
calcAtomsMinMax(BitSet, BoxInfo) - Method in class org.jmol.modelset.ModelCollection
 
calcAveragePoint(Point3f, Point3f, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
calcAveragePointN(Point3f[], int, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
calcAxis() - Method in class org.jmol.modelsetbio.Helix
 
calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcAxis() - Method in class org.jmol.modelsetbio.Sheet
 
calcBestAxisThroughPoints(Point3f[], Point3f, Vector3f, Vector3f, int) - Static method in class org.jmol.g3d.Graphics3D
 
calcBfactorRange(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
calcBfactorRange() - Method in class org.jmol.shapebio.BioShape
 
calcBoundBoxDimensions(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcBoundBoxDimensions(BitSet) - Method in class org.jmol.viewer.Viewer
 
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
sets all camera and scale factors needed by the specific perspective model instantiated
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager10
 
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager11
 
calcContourPoint(float, float, float, Point3f) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
calcConvexBits() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calcConvexMap(boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calcDitheredNoisyIntensity(float, float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
calcFaceNormixes(int) - Method in class org.jmol.g3d.Normix3D
 
calcFactors(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
calcFloatIntensityNormalized(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
calcFp8Intensity(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
calcGreyscaleRgbFromRgb(int) - Static method in class org.jmol.g3d.Graphics3D
Return a greyscale rgb value 0-FF using NTSC color luminance algorithm
calcHbondEnergy(Atom, Point3f, Point3f, AminoMonomer) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcHydrogenBonds(BitSet, BitSet) - Method in class org.jmol.modelset.Model
 
calcHydrogenBonds(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcHydrogenBonds(Polymer, BitSet, BitSet) - Method in class org.jmol.modelset.Polymer
 
calcHydrogenBonds() - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calcHydrogenBonds(Polymer, BitSet, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcHydrogenBonds(Polymer, BitSet, BitSet) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcIntensity(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
calcIntensityNormalized(float, float, float) - Static method in class org.jmol.g3d.Shade3D
 
calcIntensityScreen(Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
calcLeadMidpointsAndWingVectors(boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcMeanPositionalDisplacement(int) - Method in class org.jmol.shapebio.BioShape
Calculates the mean positional displacement in milliAngstroms.
calcMetrics(String, Font3D, boolean) - Method in class org.jmol.g3d.Text3D
 
calcMetrics() - Method in class org.jmol.shape.Frank
 
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
all navigation effects go through this method
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager11
All the magic happens here.
calcNavigationSlabAndDepth() - Method in class org.jmol.viewer.TransformManager11
 
calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.g3d.Graphics3D
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPhiPsiAngles(AminoMonomer, AminoMonomer) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPixelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
calcProteinMainchainHydrogenBonds(AminoPolymer, BitSet, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcRectRubberBand() - Method in class org.jmol.viewer.MouseManager
 
calcRopeMidPoints(boolean) - Method in class org.jmol.shapebio.RocketsRenderer
 
calcRotatedPoint(float, int, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
calcRotationRadius(int, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
calcRotationRadius(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcRotationRadius(Point3f) - Method in class org.jmol.viewer.Viewer
 
calcRotationRadius(BitSet) - Method in class org.jmol.viewer.Viewer
 
calcScreenControlPoints() - Method in class org.jmol.shapebio.BioShapeRenderer
 
calcScreenControlPoints(Point3f[]) - Method in class org.jmol.shapebio.BioShapeRenderer
 
calcScreenPoints(int[], float, int, int, int) - Method in class org.jmol.shape.DotsRenderer
calculates the screen xy coordinates for the dots or faces
calcScreens(float) - Method in class org.jmol.shapebio.BioShapeRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcSelectedGroupsCount(BitSet) - Method in class org.jmol.modelset.Chain
prior to coloring by group, we need the chain count per chain that is selected
calcSelectedGroupsCount(BitSet) - Method in class org.jmol.modelset.Model
 
calcSelectedGroupsCount(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcSelectedGroupsCount() - Method in class org.jmol.viewer.Viewer
 
calcSelectedMoleculesCount(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcSelectedMoleculesCount() - Method in class org.jmol.viewer.Viewer
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelset.Model
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelset.Polymer
 
calcSelectedMonomersCount(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcSelectedMonomersCount() - Method in class org.jmol.viewer.Viewer
 
calcSheetUnitVectors() - Method in class org.jmol.modelsetbio.Sheet
 
calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
calcSP(float, float, float, float, float) - Method in class org.jmol.quantum.MOCalculation
 
calcSphereShading() - Static method in class org.jmol.g3d.Shade3D
 
calcSurfaceDistances() - Method in class org.jmol.modelset.AtomCollection
 
calcSurfaceShade(Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
calcSurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
calcSurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
 
calculate(VolumeDataInterface, BitSet, Point3f[], float[]) - Method in interface org.jmol.api.MepCalculationInterface
 
calculate(VolumeDataInterface, BitSet, String, Point3f[], int, Vector, float[][], Hashtable, int[][], float[][], float[]) - Method in interface org.jmol.api.MOCalculationInterface
 
calculate(float, float, float, float, BitSet, BitSet, boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calculate(VolumeDataInterface, BitSet, Point3f[], float[]) - Method in class org.jmol.quantum.MepCalculation
 
calculate(VolumeDataInterface, BitSet, String, Point3f[], int, Vector, float[][], Hashtable, int[][], float[][], float[]) - Method in class org.jmol.quantum.MOCalculation
 
calculate() - Method in class org.jmol.viewer.Eval
 
calculate - Static variable in class org.jmol.viewer.Token
 
calculateAnglesInDegrees() - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateCodes(float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculatedDipole - Variable in class org.jmol.shapespecial.Dipoles
 
calculateGeodesicSurface(BitSet, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
calculateGeodesicSurface(BitSet, float) - Method in class org.jmol.shapesurface.Isosurface
 
calculateInverseNormixes() - Method in class org.jmol.g3d.Normix3D
 
calculateMolecularDipole(int) - Method in class org.jmol.modelset.ModelCollection
 
calculateMolecularDipole() - Method in class org.jmol.viewer.Viewer
 
calculatePointGroup(BitSet) - Method in class org.jmol.modelset.ModelSet
 
calculatePointGroup() - Method in class org.jmol.viewer.Viewer
 
calculatePointGroupForFirstModel(BitSet, boolean, boolean, boolean, String, int, float) - Method in class org.jmol.modelset.ModelSet
 
calculatePolymers(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
calculateR0(double, double, double, double, double) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
 
calculateRunsFourOrMore(byte[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateStraightness() - Method in class org.jmol.modelset.ModelCollection
 
calculateStraightness() - Method in class org.jmol.viewer.Viewer
 
calculateStructures() - Method in class org.jmol.modelset.Model
 
calculateStructures(BitSet) - Method in class org.jmol.modelset.ModelSet
 
calculateStructures() - Method in class org.jmol.modelset.Polymer
 
calculateStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
Uses Levitt & Greer algorithm to calculate protien secondary structures using only alpha-carbon atoms.
calculateStructures() - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateStructures(BitSet) - Method in class org.jmol.viewer.Viewer
 
calculateStructuresAllExcept(BitSet, boolean) - Method in class org.jmol.modelset.ModelCollection
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
calculateSurface(BitSet, float) - Method in class org.jmol.modelset.AtomCollection
 
calculateSurface(BitSet, float) - Method in class org.jmol.viewer.Viewer
 
Calculation - Class in org.jmol.minimize.forcefield
 
Calculation() - Constructor for class org.jmol.minimize.forcefield.Calculation
 
calculationNumber - Variable in class org.jmol.adapter.readers.more.GaussianReader
The number of the calculation being interpreted.
Calculations - Class in org.jmol.minimize.forcefield
 
Calculations(ForceField, MinAtom[], MinBond[], int[][], int[][], double[], Vector) - Constructor for class org.jmol.minimize.forcefield.Calculations
 
calculations - Variable in class org.jmol.minimize.forcefield.Calculations
 
CalculationsUFF - Class in org.jmol.minimize.forcefield
 
CalculationsUFF(ForceField, MinAtom[], MinBond[], int[][], int[][], double[], Vector) - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF
 
CalculationsUFF.AngleCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.AngleCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
 
CalculationsUFF.DistanceCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.DistanceCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
CalculationsUFF.ESCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.ESCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
 
CalculationsUFF.OOPCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.OOPCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
 
CalculationsUFF.PairCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.PairCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.PairCalc
 
CalculationsUFF.TorsionCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.TorsionCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
 
CalculationsUFF.VDWCalc - Class in org.jmol.minimize.forcefield
 
CalculationsUFF.VDWCalc() - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
 
calculationType - Variable in class org.jmol.adapter.readers.more.GamessReader
 
calculationType - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
calculationType - Variable in class org.jmol.jvxl.readers.Parameters
 
calculationType - Variable in class org.jmol.quantum.MOCalculation
 
calcUnitCellMinMax() - Method in class org.jmol.modelset.ModelCollection
 
calcUnitcellVertices() - Method in class org.jmol.symmetry.UnitCell
 
calcVertexPoint(int, int, int, int, Point3f) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
calcVertexPoints2d(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
calcVertexPoints3d(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
calcVoxelPlaneDistance(int, int, int) - Method in interface org.jmol.api.VolumeDataInterface
 
calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
calcXYNormalToLine(Point3f, Point3f, Vector3f) - Method in class org.jmol.g3d.Graphics3D
 
CALLBACK_ANIMFRAME - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_COUNT - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_ECHO - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_EVAL - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_HOVER - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_LOADSTRUCT - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_MEASURE - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_MESSAGE - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_MINIMIZATION - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_PICK - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_RESIZE - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_SCRIPT - Static variable in class org.jmol.viewer.JmolConstants
 
CALLBACK_SYNC - Static variable in class org.jmol.viewer.JmolConstants
 
callbackNames - Static variable in class org.jmol.viewer.JmolConstants
 
callbacks - Variable in class org.jmol.applet.Jmol
 
cameraDepth - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
cameraDepth - Variable in class org.jmol.viewer.TransformManager
 
cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
 
cameraDistance - Variable in class org.jmol.viewer.TransformManager
 
cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
 
CAN_CONTOUR - Static variable in class org.jmol.jvxl.readers.Parameters
 
canBeNormalized(Vector3d) - Static method in class org.jmol.minimize.Util
 
canBeSquared(double) - Static method in class org.jmol.minimize.Util
 
cancel() - Method in class org.openscience.jmol.app.PreferencesDialog
 
cancel() - Method in class org.openscience.jmol.app.RecentFilesDialog
 
cancelButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cancelButton - Variable in class org.openscience.jmol.app.RecentFilesDialog
 
cancelPressed() - Method in class org.openscience.jmol.app.PovrayDialog
Responds to cancel being press- or equivalent eg window closed.
canDownsample - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
canImport(JComponent, DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
canNavigate() - Method in class org.jmol.viewer.TransformManager
 
canNavigate() - Method in class org.jmol.viewer.TransformManager11
 
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.api.JmolAdapter
 
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.viewer.JmolConstants
 
canonicalSeitzList - Static variable in class org.jmol.symmetry.SpaceGroup
 
canonizeAlphaDigit(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeChainID(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
 
capData(Point4f, float) - Method in interface org.jmol.api.VolumeDataInterface
 
capData(Point4f, float) - Method in class org.jmol.jvxl.data.VolumeData
 
cappingPlane - Variable in class org.jmol.jvxl.readers.Parameters
 
carbohydrate - Static variable in class org.jmol.viewer.Token
 
CarbohydrateMonomer - Class in org.jmol.modelsetbio
 
CarbohydrateMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.CarbohydrateMonomer
 
CarbohydratePolymer - Class in org.jmol.modelsetbio
 
CarbohydratePolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.CarbohydratePolymer
 
cardinalityOf(BitSet) - Static method in class org.jmol.util.BitSetUtil
cardinality = "total number of set bits"
cartesianOffset - Variable in class org.jmol.symmetry.UnitCell
 
cartesians - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
CARTN_X - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CARTN_Y - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CARTN_Z - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
Cartoon - Class in org.jmol.shapebio
 
Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
 
cartoon - Static variable in class org.jmol.viewer.Token
 
CARTOON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JmolConstants
 
CartoonGenerator - Class in org.jmol.export
 
CartoonGenerator() - Constructor for class org.jmol.export.CartoonGenerator
 
CartoonRenderer - Class in org.jmol.shapebio
 
CartoonRenderer() - Constructor for class org.jmol.shapebio.CartoonRenderer
 
cartoonRockets - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
cationLookupTable - Static variable in class org.jmol.viewer.JmolConstants
 
cavityRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
cavityRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
cb - Variable in class org.jmol.export.dialog.Dialog
 
cB_ - Variable in class org.jmol.symmetry.UnitCell.Data
 
cbAxesOrientationRasmol - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cbClearConsoleButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cbOpenFilePreview - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cbPerspectiveDepth - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cbShowAxes - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cbShowBoundingBox - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cc1 - Variable in class org.jmol.g3d.Line3D
 
cc2 - Variable in class org.jmol.g3d.Line3D
 
cch - Variable in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
cchBuf - Variable in class org.jmol.adapter.smarter.LimitedLineReader
 
cchBuf - Variable in class org.jmol.jvxl.readers.LimitedLineReader
 
cchScript - Variable in class org.jmol.viewer.Compiler
 
cchToken - Variable in class org.jmol.viewer.Compiler
 
cell() - Method in class org.jmol.adapter.readers.more.ShelxReader
 
cell - Static variable in class org.jmol.viewer.Token
 
cellParameterType - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
cellParamNames - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
cellRange - Variable in class org.jmol.symmetry.SymmetryInfo
 
center - Variable in class org.jmol.export._Exporter
 
center - Variable in class org.jmol.jvxl.readers.Parameters
 
center - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
center - Variable in class org.jmol.shapespecial.Dipole
 
center - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
center - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
center - Variable in class org.jmol.shapesurface.Isosurface
 
center - Variable in class org.jmol.symmetry.PointGroup
 
center(int) - Method in class org.jmol.viewer.Eval
 
center - Variable in class org.jmol.viewer.StateManager.Orientation
 
center - Static variable in class org.jmol.viewer.Token
 
centerAt() - Method in class org.jmol.viewer.Eval
 
centerAt - Static variable in class org.jmol.viewer.Token
 
centerAtomIndex - Variable in class org.jmol.symmetry.PointGroup
 
centerDialog() - Method in class org.openscience.jmol.app.AboutDialog
 
centerDialog() - Method in class org.openscience.jmol.app.HelpDialog
 
centerDialog() - Method in class org.openscience.jmol.app.MeasurementTable
 
centerDialog() - Method in class org.openscience.jmol.app.PovrayDialog
Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.PreferencesDialog
 
centerDialog() - Method in class org.openscience.jmol.app.WhatsNewDialog
 
centerDipole() - Method in class org.jmol.shapespecial.Dipole
 
centerI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
centerParameter(int) - Method in class org.jmol.viewer.Eval
 
centers - Variable in class org.jmol.shapespecial.Polyhedra
 
centerT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
centerValues - Variable in class org.jmol.bspt.CubeIterator
 
centralAtom - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
cH - Variable in class org.openscience.jmol.app.PreferencesDialog
 
Chain - Class in org.jmol.modelset
 
Chain(ModelSet, Model, char) - Constructor for class org.jmol.modelset.Chain
 
chain - Variable in class org.jmol.modelset.Group
 
chain - Static variable in class org.jmol.viewer.Token
 
chainAtomCounts - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
chainCaseSensitive - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
chainCount - Variable in class org.jmol.modelset.Model
 
chainID - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
chainID - Variable in class org.jmol.adapter.smarter.Atom
 
chainID - Variable in class org.jmol.modelset.Chain
 
chainOf - Variable in class org.jmol.modelset.ModelLoader
 
chains - Variable in class org.jmol.modelset.Model
 
CHANGEABLE_MASK - Static variable in class org.jmol.g3d.Graphics3D
 
changeableColixMap - Variable in class org.jmol.g3d.Graphics3D
changeable colixes give me a short ID and a color, and I will give you a colix later, you can reassign the color if you want Used only for colorManager coloring of elements
changeColixArgb(short, int) - Method in class org.jmol.g3d.Graphics3D
 
changeElementColor(String, int) - Method in class org.jmol.viewer.Eval
 
char_init() - Method in class org.jmol.export.image.GifEncoder
 
char_out(byte, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
charge - Variable in class org.jmol.smiles.SmilesAtom
 
charges - Variable in class org.jmol.quantum.MepCalculation
 
chargesFound - Variable in class org.jmol.adapter.readers.more.MopacReader
 
ChargesOnly - Variable in class org.jmol.popup.JmolPopup
 
chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
charToken() - Method in class org.jmol.viewer.Compiler
 
check5D() - Method in class org.jmol.quantum.MOCalculation
Idea here is that we skip all the atoms, just increment moCoeff, and compare the number of coefficients run through to the size of the moCoefficients array.
checkAtomArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkAxisOrder(int, Vector3f, Point3f) - Method in class org.jmol.symmetry.PointGroup
 
checkBetaSheetAlphaHelixOverlap(byte[], float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
checkBondArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkBoolean(Hashtable, String) - Method in class org.jmol.popup.JmolPopup
 
checkBoundsMinMax(Point3f, Point3f) - Method in class org.jmol.shape.Shape
 
checkBoxListener - Variable in class org.openscience.jmol.app.PreferencesDialog
 
checkCalculationType() - Method in class org.jmol.quantum.MOCalculation
 
checkCarbohydrate(String) - Static method in class org.jmol.viewer.JmolConstants
 
checkColorIndex() - Static method in class org.jmol.util.ColorEncoder
 
checkCommand() - Method in class org.openscience.jmol.app.ConsoleTextPane
 
checkContinue() - Method in class org.jmol.viewer.Eval
 
checkCube(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
 
checkDiameter(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
checkFoldingXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkForCoordinate(boolean) - Method in class org.jmol.viewer.Compiler
 
checkForItemSelector() - Method in class org.jmol.viewer.Compiler
 
checkformat(int) - Method in class org.openscience.jmol.app.webexport.Molecules
 
checkformat(int) - Method in class org.openscience.jmol.app.webexport.Orbitals
 
checkHalt(String) - Method in class org.jmol.api.JmolViewer
 
checkHalt(String) - Method in class org.jmol.viewer.Viewer
 
checkIn(String, Applet) - Static method in class org.jmol.applet.JmolAppletRegistry
 
checking - Variable in class org.jmol.viewer.Viewer
 
checking - Variable in class org.openscience.jmol.app.ConsoleTextPane
 
checkInternalSlab(Point3f) - Method in class org.jmol.viewer.TransformManager
 
checkLength(int) - Method in class org.jmol.viewer.Eval
 
checkLength(int, int) - Method in class org.jmol.viewer.Eval
 
checkLength23() - Method in class org.jmol.viewer.Eval
 
checkLength34() - Method in class org.jmol.viewer.Eval
 
checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkMol(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkMopacGraphf(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkMotion() - Method in class org.jmol.viewer.MouseManager
 
checkNewGroup(int, int, char, String, int, char) - Method in class org.jmol.modelset.ModelLoader
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
checkObjectClicked(int, int, BitSet) - Method in class org.jmol.shape.Object2d
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shape.Object2dShape
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shape.Shape
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shape.Sticks
 
checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
 
checkObjectClicked(int, int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.shape.Shape
 
checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
 
checkObjectDragged(int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Object2dShape
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Shape
 
checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
 
checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
 
checkOdyssey(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkOffscreenSize(int, int) - Method in class org.jmol.g3d.Platform3D
 
checkOperation(Quaternion, Point3f, int) - Method in class org.jmol.symmetry.PointGroup
 
checkOption(JmolViewer, String) - Static method in class org.jmol.api.JmolViewer
 
checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
 
checkOut(String) - Static method in class org.jmol.applet.JmolAppletRegistry
 
checkPoint(Point3f) - Method in class org.jmol.modelset.MeasurementPending
 
checkPointOrAtomClicked(int, int, int, int) - Method in class org.jmol.viewer.MouseManager
 
checkResume(String) - Method in class org.jmol.viewer.Viewer
 
checkScriptOnly - Variable in class org.jmol.viewer.Viewer
 
checkScriptSilent(String) - Method in class org.jmol.viewer.Eval
 
checkSpecial - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
checkSpecial(int, String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkSpecialVoxel(Point3f, float, Point3f, float, float, Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
checkTimer(String) - Static method in class org.jmol.util.Logger
 
checkToken(int) - Method in class org.jmol.viewer.Eval
 
checkTrailingText(String, int, int) - Static method in class org.jmol.util.Parser
 
checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
 
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
checkType(String[][], String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkUnitCell(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkV3000(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkValencesAndBond(Atom, Atom, short, short, BitSet) - Method in class org.jmol.modelset.BondCollection
 
checkWingAtoms() - Method in class org.jmol.modelsetbio.AminoPolymer
 
checkXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
chem3dImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
CHEM_COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
CHEM_COMP_NAME - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chemCompFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chemFileProperty - Static variable in class org.openscience.jmol.app.Jmol
 
chemicalName - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
chiralClass - Variable in class org.jmol.smiles.SmilesAtom
 
CHIRALITY_ALLENE - Static variable in class org.jmol.smiles.SmilesAtom
Constant used for Allene chirality.
CHIRALITY_OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
Constant used for Octahedral chirality.
CHIRALITY_SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesAtom
Constant used for Square Planar chirality.
CHIRALITY_TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
Constant used for Tetrahedral chirality.
CHIRALITY_TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesAtom
Constant used for Trigonal Bipyramidal chirality.
chiralOrder - Variable in class org.jmol.smiles.SmilesAtom
 
choice - Variable in class org.jmol.export.dialog.Dialog
 
choices - Variable in class org.openscience.jmol.app.FileTyper
 
chooser - Variable in class org.jmol.export.dialog.FilePreview
 
chop(String) - Static method in class org.jmol.util.Escape
 
chpt0 - Variable in class org.jmol.viewer.Function
 
chrg - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
CifReader - Class in org.jmol.adapter.readers.cifpdb
A true line-free CIF file reader for CIF and mmCIF files.
CifReader() - Constructor for class org.jmol.adapter.readers.cifpdb.CifReader
 
CifReader.RidiculousFileFormatTokenizer - Class in org.jmol.adapter.readers.cifpdb
A special tokenizer class for dealing with quoted strings in CIF files.
CifReader.RidiculousFileFormatTokenizer() - Constructor for class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
cifRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
Circle3D - Class in org.jmol.g3d
Implements flat circle drawing/filling routines.
Circle3D(Graphics3D) - Constructor for class org.jmol.g3d.Circle3D
 
circle3d - Variable in class org.jmol.g3d.Graphics3D
 
cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.VoxelReader
 
cl_block(OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
cl_hash(int) - Method in class org.jmol.export.image.GifEncoder
 
classBase - Static variable in class org.jmol.adapter.smarter.Resolver
 
CLASSBASE_OPTIONS - Static variable in class org.jmol.viewer.JmolConstants
 
classifyName(String) - Method in class org.jmol.viewer.FileManager
 
ClassPreloader - Class in org.jmol.appletwrapper
 
ClassPreloader(AppletWrapper) - Constructor for class org.jmol.appletwrapper.ClassPreloader
 
clauseAlternateSpec() - Method in class org.jmol.viewer.Compiler
 
clauseAnd() - Method in class org.jmol.viewer.Compiler
 
clauseAtomSpec() - Method in class org.jmol.viewer.Compiler
 
clauseCell() - Method in class org.jmol.viewer.Compiler
 
clauseChainSpec(int) - Method in class org.jmol.viewer.Compiler
 
clauseComparator() - Method in class org.jmol.viewer.Compiler
 
clauseConnected() - Method in class org.jmol.viewer.Compiler
 
clauseDefine() - Method in class org.jmol.viewer.Compiler
 
clauseItemSelector() - Method in class org.jmol.viewer.Compiler
 
clauseModelSpec() - Method in class org.jmol.viewer.Compiler
 
clauseNot() - Method in class org.jmol.viewer.Compiler
 
clauseOr(boolean) - Method in class org.jmol.viewer.Compiler
 
clausePrimitive() - Method in class org.jmol.viewer.Compiler
 
clauseResidueSpec() - Method in class org.jmol.viewer.Compiler
 
clauseResNameSpec() - Method in class org.jmol.viewer.Compiler
 
clauseSequenceSpec() - Method in class org.jmol.viewer.Compiler
 
clauseSubstructure() - Method in class org.jmol.viewer.Compiler
 
clauseWithin() - Method in class org.jmol.viewer.Compiler
 
cleanRegistry() - Static method in class org.jmol.applet.JmolAppletRegistry
 
cleanScriptComments(String) - Static method in class org.jmol.viewer.Compiler
allows for three kinds of comments.
cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
clear(String) - Method in class org.jmol.jvxl.data.MeshData
 
clear() - Method in class org.jmol.minimize.Minimizer
 
clear() - Method in class org.jmol.shape.Measures
 
clear(String) - Method in class org.jmol.shape.Mesh
 
clear(boolean) - Method in class org.jmol.shapespecial.Dipoles
 
clear(String, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
clear(BitSet) - Static method in class org.jmol.util.BitSetUtil
 
clear() - Method in class org.jmol.util.CommandHistory
clears the history.
clear() - Method in class org.jmol.util.TempArray
 
clear() - Method in class org.jmol.viewer.ColorManager
 
clear() - Method in class org.jmol.viewer.DataManager
 
clear() - Method in class org.jmol.viewer.FileManager
 
clear() - Method in class org.jmol.viewer.FrameRenderer
 
clear() - Method in class org.jmol.viewer.ModelManager
 
clear() - Method in class org.jmol.viewer.MouseManager
 
clear() - Method in class org.jmol.viewer.PickingManager
 
clear() - Method in class org.jmol.viewer.RepaintManager
 
clear() - Method in class org.jmol.viewer.ScriptManager
 
clear() - Method in class org.jmol.viewer.SelectionManager
 
clear() - Method in class org.jmol.viewer.StateManager
 
clear() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
clear() - Method in class org.jmol.viewer.StatusManager
 
clear - Static variable in class org.jmol.viewer.Token
 
clear() - Method in class org.jmol.viewer.TransformManager
 
clear() - Method in class org.jmol.viewer.Viewer
 
clear_flg - Variable in class org.jmol.export.image.GifEncoder
 
clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearAnimation() - Method in class org.jmol.viewer.RepaintManager
 
clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
 
clearBfactorRange() - Method in class org.jmol.viewer.Viewer
 
clearBioPolymers(Group[], int, BitSet) - Method in interface org.jmol.api.JmolBioResolver
 
clearBioPolymers(Group[], int, BitSet) - Method in class org.jmol.modelsetbio.Resolver
 
clearBit(int[], int) - Static method in class org.jmol.geodesic.EnvelopeCalculation
 
clearBitmap(int[]) - Static method in class org.jmol.geodesic.EnvelopeCalculation
 
clearBonds() - Method in class org.jmol.modelset.Atom
 
clearBspt(int) - Method in class org.jmol.bspt.Bspf
 
clearButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
clearCalculatedHydrogenBonds(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
clearClickCount() - Method in class org.jmol.viewer.MouseManager
 
clearClickCount() - Method in class org.jmol.viewer.Viewer
 
ClearCode - Variable in class org.jmol.export.image.GifEncoder
 
clearConsole() - Method in class org.jmol.viewer.StatusManager
 
clearConsole() - Method in class org.jmol.viewer.Viewer
 
clearConsoleButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
clearContent() - Method in class org.openscience.jmol.app.ConsoleDocument
Removes all content of the script window, and add a new prompt.
clearContent() - Method in class org.openscience.jmol.app.ConsoleTextPane
 
clearContent(String) - Method in class org.openscience.jmol.app.ConsoleTextPane
 
clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelCollection
 
clearDefaultConsoleMessage() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
clearDefinitionsAndLoadPredefined() - Method in class org.jmol.viewer.Eval
 
clearForces() - Method in class org.jmol.minimize.forcefield.ForceField
 
clearInButton - Variable in class org.jmol.applet.Console
 
clearingThread - Variable in class org.jmol.g3d.Platform3D
 
clearLatticeParameters() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
clearMeasurements() - Method in class org.jmol.api.JmolViewer
 
clearMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearMinimization() - Method in class org.jmol.viewer.Viewer
 
clearOutButton - Variable in class org.jmol.applet.Console
 
clearPredefined(String[]) - Method in class org.jmol.viewer.Eval
 
clearQueue() - Method in class org.jmol.viewer.ScriptManager
 
clearScreenBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearScreenBufferThreaded() - Method in class org.jmol.g3d.Platform3D
 
clearScriptQueue() - Method in class org.jmol.viewer.Viewer
 
clearSelection() - Method in class org.jmol.api.JmolViewer
 
clearSelection(boolean) - Method in class org.jmol.viewer.SelectionManager
 
clearSelection() - Method in class org.jmol.viewer.Viewer
 
clearSg() - Method in class org.jmol.shapesurface.Isosurface
 
clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
 
clearSpin() - Method in class org.jmol.viewer.TransformManager
 
clearState(boolean) - Method in class org.jmol.viewer.Eval
 
clearStructures() - Method in class org.jmol.modelset.Polymer
 
clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
 
clearSymbolicMap() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
clearTBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearTempPoints() - Method in class org.jmol.util.TempArray
 
clearTempScreens() - Method in class org.jmol.util.TempArray
 
clearVibration() - Method in class org.jmol.viewer.TransformManager
 
clickabilityFlags - Variable in class org.jmol.modelset.Atom
 
clickable - Static variable in class org.jmol.viewer.Token
 
clickable_peaks_frame_name - Variable in class org.jmol.jcamp.Visua
 
clientAtomReferences - Variable in class org.jmol.modelset.AtomCollection
 
clientFile - Variable in class org.jmol.viewer.FileManager.DOMOpenThread
 
clientFile - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
clientFile - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
clientHasBuffer - Variable in class org.jmol.g3d.Platform3D.ClearingThread
 
clipboard - Static variable in class org.jmol.viewer.Token
 
clipCode(int, int, int) - Method in class org.jmol.g3d.Line3D
 
clipImage(String) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
clipImage() - Method in class org.jmol.applet.Jvm12
 
clipImage(String) - Method in class org.jmol.export.image.ImageCreator
 
clockBaseline - Variable in class org.jmol.appletwrapper.AppletWrapper
 
clockWidth - Variable in class org.jmol.appletwrapper.AppletWrapper
 
clockX - Variable in class org.jmol.appletwrapper.AppletWrapper
 
cloneAtom() - Method in class org.jmol.adapter.smarter.Atom
 
cloneAtomSetProperties(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Clones the properties of an atom set and associated it with the current atom set.
cloneFirstAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneFirstAtomSetWithBonds(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSetProperties() - Method in class org.jmol.adapter.smarter.AtomSetCollection
Clones the properties of the last atom set and associates it with the current atom set.
cloneMenu(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
cloneMenu(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
close() - Method in class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
close() - Method in class org.openscience.jmol.app.MeasurementTable
 
close() - Method in class org.openscience.jmol.app.RecentFilesDialog
 
closeAction - Static variable in class org.openscience.jmol.app.Jmol
 
closeButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
closePreview() - Method in class org.jmol.export.dialog.Dialog
 
closeReaders() - Method in class org.jmol.shapesurface.Pmesh
 
closest - Variable in class org.jmol.modelset.ModelSet
 
cM - Variable in class org.openscience.jmol.app.PreferencesDialog
 
cmdpt0 - Variable in class org.jmol.viewer.Function
 
cmil - Variable in class org.jmol.popup.JmolPopup
 
CML - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CML_NAMESPACE_URI - Static variable in class org.jmol.adapter.smarter.Resolver
 
cmlImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
code - Variable in class org.jmol.i18n.GT.Language
 
CODE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
 
CODE_BETA_SHEET - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
CODE_DIRECTIONAL_1 - Static variable in class org.jmol.smiles.SmilesBond
 
CODE_DIRECTIONAL_2 - Static variable in class org.jmol.smiles.SmilesBond
 
CODE_DOUBLE - Static variable in class org.jmol.smiles.SmilesBond
 
CODE_LEFT_HELIX - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
CODE_LEFT_TURN - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
CODE_NADA - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
CODE_NONE - Static variable in class org.jmol.smiles.SmilesBond
 
CODE_RIGHT_HELIX - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
CODE_RIGHT_TURN - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
CODE_SINGLE - Static variable in class org.jmol.smiles.SmilesBond
 
CODE_TRIPLE - Static variable in class org.jmol.smiles.SmilesBond
 
codetab - Variable in class org.jmol.export.image.GifEncoder
 
coef - Variable in class org.jmol.g3d.Sphere3D
 
coef - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
coef - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
coef_indices - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
coefCount - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
colix - Variable in class org.jmol.export.Export3D
 
colix - Variable in class org.jmol.modelset.Bond
 
colix - Variable in class org.jmol.modelset.Measurement
 
colix - Variable in class org.jmol.shape.Measures
 
colix - Variable in class org.jmol.shape.Mesh
 
colix - Variable in class org.jmol.shape.MeshCollection
 
colix - Variable in class org.jmol.shape.Object2d
 
colix - Variable in class org.jmol.shape.ShapeRenderer
 
colix - Variable in class org.jmol.shapespecial.Dipole
 
colix - Variable in class org.jmol.shapespecial.Dipoles
 
colix - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
colix - Variable in class org.jmol.viewer.StateManager.Connection
 
Colix3D - Class in org.jmol.g3d
Implements a color index model using a colix as a COLor IndeX.
Colix3D() - Constructor for class org.jmol.g3d.Colix3D
 
colixA - Variable in class org.jmol.g3d.Cylinder3D
 
colixA - Variable in class org.jmol.shape.SticksRenderer
 
colixAtom - Variable in class org.jmol.modelset.Atom
 
colixB - Variable in class org.jmol.g3d.Cylinder3D
 
colixB - Variable in class org.jmol.shape.SticksRenderer
 
colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
 
colixCurrent - Variable in class org.jmol.g3d.Graphics3D
 
colixEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
colixes - Variable in class org.jmol.shape.AtomShape
 
colixes - Variable in class org.jmol.shape.AxesRenderer
 
colixes - Variable in class org.jmol.shapebio.BioShape
 
colixes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
colixHash - Static variable in class org.jmol.g3d.Colix3D
 
colixMax - Static variable in class org.jmol.g3d.Colix3D
 
colixRubberband - Variable in class org.jmol.viewer.ColorManager
 
colixSelection - Variable in class org.jmol.shape.Halos
 
collapsed - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
COLLECTION - Static variable in class org.openscience.jmol.app.AtomSetChooser
String for prefix/resource identifier for the collection area.
collectionName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
colon - Static variable in class org.jmol.viewer.Token
 
COLOR - Static variable in class org.jmol.shape.Echo
 
color() - Method in class org.jmol.viewer.Eval
 
color - Static variable in class org.jmol.viewer.Token
 
color4(short) - Method in class org.jmol.export._PovrayExporter
 
colorArgbs - Static variable in class org.jmol.g3d.Graphics3D
 
colorByPhase - Variable in class org.jmol.jvxl.readers.Parameters
 
colorBySets - Variable in class org.jmol.jvxl.readers.Parameters
 
colorBySign - Variable in class org.jmol.jvxl.readers.Parameters
 
colorCommand - Variable in class org.jmol.shape.Mesh
 
colorCommand(SimpleAttributeSet) - Method in class org.openscience.jmol.app.ConsoleDocument
 
colorData() - Method in class org.jmol.jvxl.readers.VoxelReader
 
colorData - Variable in class org.jmol.viewer.ColorManager
 
colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlReader
 
colorEncoder - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
colorEncoder - Variable in class org.jmol.jvxl.readers.VoxelReader
 
colorEncoder - Variable in class org.jmol.shapesurface.Isosurface
 
ColorEncoder - Class in org.jmol.util
 
ColorEncoder() - Constructor for class org.jmol.util.ColorEncoder
 
colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionBase - Variable in class org.jmol.jvxl.readers.VoxelReader
 
colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionRange - Variable in class org.jmol.jvxl.readers.VoxelReader
 
colorHash - Variable in class org.jmol.export.image.GifEncoder
 
colorHi - Variable in class org.jmol.viewer.ColorManager
 
colorIndex(int, int) - Static method in class org.jmol.util.ColorEncoder
 
colorIsosurface() - Method in class org.jmol.jvxl.readers.VoxelReader
 
colorLo - Variable in class org.jmol.viewer.ColorManager
 
ColorManager - Class in org.jmol.viewer
 
ColorManager(Viewer, Graphics3D) - Constructor for class org.jmol.viewer.ColorManager
 
colorManager - Variable in class org.jmol.viewer.Viewer
 
colorModelRGB - Variable in class org.jmol.g3d.Awt3D
 
colorNames - Static variable in class org.jmol.appletwrapper.AppletWrapper
 
colorNames - Static variable in class org.jmol.g3d.Graphics3D
 
colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
 
colorNegLCAO - Variable in class org.jmol.jvxl.readers.Parameters
 
colorObject(int, int) - Method in class org.jmol.viewer.Eval
 
colorPhase - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPhases - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
colorPointFromInt(int, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
colorPointFromString(String, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
colorPos - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPosLCAO - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPtr - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
colorPtToInt(Point3f) - Static method in class org.jmol.viewer.Eval
 
colors - Static variable in class org.jmol.appletwrapper.AppletWrapper
 
colorSchemes - Static variable in class org.jmol.util.ColorEncoder
 
colorShape(int, int, boolean) - Method in class org.jmol.viewer.Eval
 
colorVector - Variable in class org.jmol.export.image.GifEncoder
 
comma - Static variable in class org.jmol.viewer.Token
 
command - Static variable in class org.jmol.viewer.Token
 
commandExpected() - Method in class org.jmol.viewer.Compiler
 
CommandHistory - Class in org.jmol.util
Implements a queue for a bash-like command history.
CommandHistory() - Constructor for class org.jmol.util.CommandHistory
Creates a new instance using the default size (100)
CommandHistory(int) - Constructor for class org.jmol.util.CommandHistory
Creates a new instance.
commandHistory - Variable in class org.jmol.viewer.Viewer
 
commandHistoryLevelMax - Variable in class org.jmol.viewer.Eval
 
commandLineOptions - Variable in class org.jmol.export._Exporter
 
commandList - Variable in class org.jmol.util.CommandHistory
Array of commands.
commands - Variable in class org.openscience.jmol.app.Jmol
 
commands - Variable in class org.openscience.jmol.app.PreferencesDialog
 
commandWatcherThread - Variable in class org.jmol.viewer.ScriptManager
 
Comment - Variable in class org.jmol.util.JpegInfo
 
COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
comparator - Static variable in class org.jmol.viewer.Token
 
comparatorInstruction(int, float[], int, int, float) - Method in class org.jmol.viewer.Eval
 
compare(Object, Object) - Method in class org.jmol.export.image.GifEncoder.ColorVector.CountComparator
 
compareBits(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
comparefloatx100 - Static variable in class org.jmol.viewer.Token
 
compareStrings(String, String) - Static method in class org.jmol.jcamp.utils.StringDataUtils
Compares two strings provided and returns an expected integer value based on the comparison
compHeight - Variable in class org.jmol.util.JpegInfo
 
CompID - Variable in class org.jmol.util.JpegInfo
 
compile(String, String, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Compiler
 
compile0() - Method in class org.jmol.viewer.Compiler
 
compileCommand() - Method in class org.jmol.viewer.Compiler
 
compileExpression() - Method in class org.jmol.viewer.Compiler
 
Compiler - Class in org.jmol.viewer
 
Compiler(Viewer) - Constructor for class org.jmol.viewer.Compiler
 
compiler - Variable in class org.jmol.viewer.Eval
 
compiler - Variable in class org.jmol.viewer.Viewer
 
Compiler.FlowContext - Class in org.jmol.viewer
 
Compiler.FlowContext(Token, int, Compiler.FlowContext) - Constructor for class org.jmol.viewer.Compiler.FlowContext
 
completeInitialization(Graphics, Dimension) - Method in class org.jmol.appletwrapper.AppletWrapper
 
compnd - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
compnd() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
component - Variable in class org.jmol.g3d.Awt3D
 
componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.DisplayPanel
 
componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.DisplayPanel
 
componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.DisplayPanel
 
Components - Variable in class org.jmol.util.JpegInfo
 
componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.DisplayPanel
 
CompoundDocument - Class in org.jmol.util
 
CompoundDocument(BufferedInputStream) - Constructor for class org.jmol.util.CompoundDocument
 
CompoundDocument.CmpDocDirectoryEntry - Class in org.jmol.util
 
CompoundDocument.CmpDocDirectoryEntry() - Constructor for class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
CompoundDocument.CmpDocHeader - Class in org.jmol.util
 
CompoundDocument.CmpDocHeader() - Constructor for class org.jmol.util.CompoundDocument.CmpDocHeader
 
compress(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
Compress() - Method in class org.jmol.util.JpegEncoder
 
compressionLevel - Variable in class org.jmol.export.image.PngEncoder
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.Calculations
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
 
computeAngle(Point3f, Point3f, Point3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
 
computeAngle(Point3f, Point3f, Point3f, boolean) - Static method in class org.jmol.util.Measure
 
computeTorsion(Point3f, Point3f, Point3f, Point3f, boolean) - Static method in class org.jmol.util.Measure
 
compWidth - Variable in class org.jmol.util.JpegInfo
 
concatList(Token, Token) - Static method in class org.jmol.viewer.Token
 
concatTokens(String[], int, int) - Static method in class org.jmol.util.Parser
 
conect() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
CONF_TYPE_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
configuration() - Method in class org.jmol.viewer.Eval
 
configuration - Static variable in class org.jmol.viewer.Token
 
configurationSelected - Variable in class org.jmol.popup.JmolPopup
 
connect() - Method in class org.jmol.viewer.Eval
 
connect - Static variable in class org.jmol.viewer.Token
 
CONNECT_AUTO_BOND - Static variable in class org.jmol.viewer.JmolConstants
 
CONNECT_CREATE_ONLY - Static variable in class org.jmol.viewer.JmolConstants
 
CONNECT_DELETE_BONDS - Static variable in class org.jmol.viewer.JmolConstants
 
CONNECT_IDENTIFY_ONLY - Static variable in class org.jmol.viewer.JmolConstants
 
CONNECT_MODIFY_ONLY - Static variable in class org.jmol.viewer.JmolConstants
 
CONNECT_MODIFY_OR_CREATE - Static variable in class org.jmol.viewer.JmolConstants
 
connectAll(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
connected - Static variable in class org.jmol.viewer.Token
 
connections - Variable in class org.jmol.viewer.StateManager.Connections
 
connectLast - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
connectNextAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
connectNextAtomSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
connectOperationFromString(String) - Static method in class org.jmol.viewer.JmolConstants
 
connectOperationName(int) - Static method in class org.jmol.viewer.JmolConstants
 
connectOperationStrings - Static variable in class org.jmol.viewer.JmolConstants
 
connectorFieldMap - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
connectorFields - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
connectors - Variable in class org.jmol.adapter.readers.more.CsfReader
 
Console - Class in org.jmol.applet
 
Console(Component, JmolViewer, Jvm12) - Constructor for class org.jmol.applet.Console
 
console - Variable in class org.jmol.applet.Jvm12
 
console() - Method in class org.jmol.viewer.Eval
 
console - Static variable in class org.jmol.viewer.Token
 
console - Variable in class org.openscience.jmol.app.ScriptWindow
 
Console.ControlEnterTextArea - Class in org.jmol.applet
 
Console.ControlEnterTextArea() - Constructor for class org.jmol.applet.Console.ControlEnterTextArea
 
CONSOLE_WINDOW_NAME - Static variable in class org.openscience.jmol.app.Jmol
 
consoleDoc - Variable in class org.openscience.jmol.app.ConsoleTextPane
 
ConsoleDocument - Class in org.openscience.jmol.app
 
ConsoleDocument() - Constructor for class org.openscience.jmol.app.ConsoleDocument
 
consoleframe - Static variable in class org.openscience.jmol.app.Jmol
 
consoleMessage(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
consoleMessage(String) - Method in class org.jmol.applet.Jvm12
 
ConsoleTextArea - Class in org.openscience.jmol.app
 
ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.ConsoleTextArea
 
ConsoleTextArea() - Constructor for class org.openscience.jmol.app.ConsoleTextArea
 
consoleTextPane - Variable in class org.openscience.jmol.app.ConsoleDocument
 
ConsoleTextPane - Class in org.openscience.jmol.app
 
ConsoleTextPane(ScriptWindow) - Constructor for class org.openscience.jmol.app.ConsoleTextPane
 
constrainQuadratic(double, double, double, int) - Method in class org.jmol.minimize.forcefield.Calculations
 
constraint - Static variable in class org.jmol.viewer.Token
 
constraintEnergy(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
constraintMap - Variable in class org.jmol.minimize.Minimizer
 
constraints - Variable in class org.jmol.minimize.forcefield.Calculations
 
constraints - Variable in class org.jmol.minimize.Minimizer
 
constructBitSetPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
constructBondsPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
constructDismissButtonPanel() - Method in class org.openscience.jmol.app.MeasurementTable
 
constructFractionalMatrices() - Method in class org.jmol.symmetry.UnitCell
 
constructMeasurementButtonPanel() - Method in class org.openscience.jmol.app.MeasurementTable
 
constructMeasurementTable() - Method in class org.openscience.jmol.app.MeasurementTable
 
constructRadiusPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
containsClickablePeaks - Variable in class org.jmol.jcamp.data.GraphControlData
 
containsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
contexte - Variable in class org.jmol.jcamp.Visua
 
contextTrace() - Method in class org.jmol.viewer.Eval
 
contextVariables - Variable in class org.jmol.viewer.Compiler
 
contextVariables - Variable in class org.jmol.viewer.Eval.Context
 
contextVariables - Variable in class org.jmol.viewer.Eval
 
continuecmd - Static variable in class org.jmol.viewer.Token
 
CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourBits - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
contourFromZero - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourFromZero - Variable in class org.jmol.jvxl.readers.Parameters
 
contourIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourLocateXYZ(int, int, Point3f) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
contourPlaneMaximumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourPlaneMinimumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourPoints - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourVertexCount - Variable in class org.jmol.jvxl.readers.VoxelReader
 
contourVertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contractions - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
controlHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
 
controlHermites - Variable in class org.jmol.shapespecial.DrawRenderer
 
controlPoints - Variable in class org.jmol.shapebio.BioShapeRenderer
 
controlPointScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
converged - Variable in class org.jmol.adapter.readers.more.NWChemReader
 
convertEncodedMad(Viewer, int) - Method in class org.jmol.modelset.Atom
 
convertToMegabytes(long) - Method in class org.jmol.popup.JmolPopup
 
convToIntelDouble(long) - Static method in class org.jmol.jcamp.utils.NumericDataUtils
 
convToIntelFloat(int) - Static method in class org.jmol.jcamp.utils.NumericDataUtils
 
convToIntelInt(int) - Static method in class org.jmol.jcamp.utils.NumericDataUtils
 
coord - Variable in class org.jmol.minimize.MinAtom
 
coord - Static variable in class org.jmol.viewer.Token
 
coordinateInRange(int, int, Point3f, int) - Method in class org.jmol.shape.Sticks
 
coordinateInRange(int, int, Point3f, int) - Method in class org.jmol.shapespecial.Draw
 
coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
Get the boolean whether coordinates are fractional.
coordinatesAreFractional - Variable in class org.jmol.symmetry.SymmetryInfo
 
coordinatesAreFractional - Variable in class org.jmol.viewer.Eval
 
coords - Variable in class org.jmol.shapespecial.Dipole
 
coords - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
coordSaved - Variable in class org.jmol.minimize.forcefield.ForceField
 
coordSaved - Variable in class org.jmol.minimize.Minimizer
 
Coorfile - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
CooropenButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
copy(BitSet) - Static method in class org.jmol.util.BitSetUtil
 
copy(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
copyBinaryFile(String, String) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
copyImageAction - Variable in class org.openscience.jmol.app.Jmol
 
copyImageActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
copyInvert(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
 
copyright - Static variable in class org.jmol.viewer.JmolConstants
 
copyScriptAction - Variable in class org.openscience.jmol.app.Jmol
 
copyScriptActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
cordMidPoints - Variable in class org.jmol.shapebio.RocketsRenderer
 
corner - Variable in class org.jmol.shape.Axes
 
corners - Variable in class org.jmol.shapebio.RocketsRenderer
 
cos - Static variable in class org.jmol.viewer.Token
 
cosAlpha - Variable in class org.jmol.symmetry.UnitCell.Data
 
cosBeta - Variable in class org.jmol.symmetry.UnitCell.Data
 
cosGamma - Variable in class org.jmol.symmetry.UnitCell.Data
 
cosPhi - Variable in class org.jmol.g3d.Cylinder3D
 
cossin - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
cosTheta - Variable in class org.jmol.g3d.Cylinder3D
 
cosTolerance - Variable in class org.jmol.symmetry.PointGroup
 
count - Variable in class org.jmol.bspt.Element
 
count - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
count - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
count - Variable in class org.jmol.modelset.Measurement
 
countData(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
countData(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
CountDown - Variable in class org.jmol.export.image.GifEncoder
 
countGroup(int, String, String) - Method in class org.jmol.modelset.ModelLoader
 
countPlusIndices - Variable in class org.jmol.modelset.Measurement
 
countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
 
countTokens(String, int) - Static method in class org.jmol.util.Parser
 
covalentMars - Static variable in class org.jmol.viewer.JmolConstants
Default table of covalent Radii stored as a short mar ...
crc - Variable in class org.jmol.export.image.PngEncoder
 
crcValue - Variable in class org.jmol.export.image.PngEncoder
 
createAndShowGUI(JmolViewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
createAtom() - Method in class org.jmol.smiles.SmilesMolecule
 
createAtomSerialMap() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
createBond(SmilesAtom, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesMolecule
 
createContours(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
createDialog(Component) - Method in class org.jmol.export.dialog.FileChooser
 
createEllipsoidShades() - Static method in class org.jmol.g3d.Sphere3D
 
createExportPanel(String[], String[], String) - Method in class org.jmol.export.dialog.Dialog
 
createFrankPopup() - Method in class org.jmol.popup.JmolPopup
 
createFrankPopup() - Method in class org.jmol.popup.JmolPopupAwt
 
createFrankPopup() - Method in class org.jmol.popup.JmolPopupSwing
 
createGaussianCube() - Method in class org.jmol.quantum.MOCalculation
 
createGeodesic() - Static method in class org.jmol.geodesic.Geodesic
 
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
 
createImage(String, String, Object, int, int, int) - Method in class org.jmol.api.JmolViewer
 
createImage(String, String, Object, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
createImage(String, String, Object, int) - Method in class org.jmol.applet.Jvm12
 
createImage(String, String, Object, int) - Method in class org.jmol.export.image.ImageCreator
 
createImage(String, String, Object, int) - Method in class org.jmol.viewer.StatusManager
 
createImage(String) - Method in class org.jmol.viewer.Viewer
 
createImage(String, String, Object, int, int, int) - Method in class org.jmol.viewer.Viewer
 
createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
createImageStatus(String, String, Object, int) - Method in class org.openscience.jmol.app.Jmol
 
createInstance(Component) - Static method in class org.jmol.g3d.Platform3D
 
createIsosurface(boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
createLanguageList() - Method in class org.jmol.i18n.GT
This is the place to put the list of supported languages.
createLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
 
createLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
createLcaoLobe(Vector3f, float) - Method in class org.jmol.shapesurface.Isosurface
 
createMenu(String) - Method in class org.openscience.jmol.app.Jmol
Create a menu for the app.
createMenubar() - Method in class org.jmol.applet.Console
 
createMenubar() - Method in class org.openscience.jmol.app.Jmol
Create the menubar for the app.
createMenuItem(String) - Method in class org.jmol.applet.Console
 
createMenuItem(String) - Method in class org.openscience.jmol.app.Jmol
This is the hook through which all menu items are created.
createMeshCylinder(int, int, int, int, int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
createMissingHydrogen(SmilesMolecule) - Method in class org.jmol.smiles.SmilesAtom
Creates missing hydrogen atoms in a SmilesMolecule.
createNewAtomSet(HashMap) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
createPdfDocument(File) - Method in class org.openscience.jmol.app.Jmol.ExportAction
 
createPlanarSquares() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
createResidueHydrogenBond(AminoMonomer, int, int, BitSet, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
 
createSet(int, int, int) - Method in class org.jmol.jvxl.data.MeshData
 
createSlaterByType(int, int, String, float, float) - Method in class org.jmol.adapter.readers.more.CsfReader
 
createSlaterCube() - Method in class org.jmol.quantum.MOCalculation
 
createSpaceGroup(int, String, float[], boolean) - Method in interface org.jmol.api.SymmetryInterface
 
createSpaceGroup(int, String, float[], boolean) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSpaceGroup(String, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSpaceGroup(int, String, float[], boolean) - Method in class org.jmol.symmetry.Symmetry
 
createSphereShape(int) - Static method in class org.jmol.g3d.Sphere3D
 
createStatusBar() - Method in class org.openscience.jmol.app.Jmol
 
createTool(String) - Method in class org.openscience.jmol.app.Jmol
Hook through which every toolbar item is created.
createToolbar() - Method in class org.openscience.jmol.app.Jmol
Create the toolbar.
createToolbarButton(String) - Method in class org.openscience.jmol.app.Jmol
Create a button to go inside of the toolbar.
createTransferable(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
createTreeModel() - Method in class org.openscience.jmol.app.AtomSetChooser
Creates the treeModel of the AtomSets available in the JmolViewer
createTriangleSet(int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
createVCRController(String) - Method in class org.openscience.jmol.app.AtomSetChooser
Creates a VCR type set of controller inside a JPanel.
creatingImage - Variable in class org.jmol.viewer.Viewer
 
crit - Variable in class org.jmol.minimize.Minimizer
 
criterion - Variable in class org.jmol.minimize.forcefield.ForceField
 
cross - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
cross - Static variable in class org.jmol.viewer.Token
 
cross0 - Variable in class org.jmol.shapespecial.DipolesRenderer
 
cross1 - Variable in class org.jmol.shapespecial.DipolesRenderer
 
crossEnd - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
crossOffset - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
crossWidth - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
crossWidthPixels - Variable in class org.jmol.shapespecial.DipolesRenderer
 
crtval - Static variable in class org.jmol.shapespecial.Ellipsoids
 
cryst1() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
CRYSTAL - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SCALAR - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY_TRANSFORM3 - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CsfReader - Class in org.jmol.adapter.readers.more
CSF file reader based on CIF idea -- fluid property fields.
CsfReader() - Constructor for class org.jmol.adapter.readers.more.CsfReader
 
csfRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CTRL - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_ALT_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_ALT_SHIFT_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_ALT_SHIFT_RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_MIDDLE - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_SHIFT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_SHIFT_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_SHIFT_MIDDLE - Static variable in class org.jmol.viewer.MouseManager
 
CTRL_SHIFT_RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
CubeIterator - Class in org.jmol.bspt
Iterator used for finding all points within a box or a hemi-box
CubeIterator(Bspt) - Constructor for class org.jmol.bspt.CubeIterator
 
cubeIterators - Variable in class org.jmol.bspt.Bspf
 
CubeReader - Class in org.jmol.adapter.readers.more
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
CubeReader() - Constructor for class org.jmol.adapter.readers.more.CubeReader
 
CubeReader - Class in org.jmol.jvxl.readers
 
CubeReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.CubeReader
 
cubeRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
cubeVertexOffsets - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
cur_accum - Variable in class org.jmol.export.image.GifEncoder
 
cur_bits - Variable in class org.jmol.export.image.GifEncoder
 
Current_Error - Variable in class org.jmol.jcamp.Visua
 
currentAtomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
currentBgColor - Variable in class org.jmol.shape.Object2dShape
 
currentBgTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
 
currentChain - Variable in class org.jmol.modelset.ModelLoader
 
currentChainID - Variable in class org.jmol.modelset.ModelLoader
 
currentColor - Variable in class org.jmol.shape.Object2dShape
 
currentCursor - Variable in class org.jmol.viewer.Viewer
 
currentDipole - Variable in class org.jmol.shapespecial.Dipoles
 
currentDirection - Variable in class org.jmol.viewer.RepaintManager
 
currentFont - Variable in class org.jmol.shape.Object2dShape
 
currentFrankId - Variable in class org.jmol.popup.JmolPopup
 
currentGroup3 - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
currentGroup3 - Variable in class org.jmol.modelset.ModelLoader
 
currentGroupInsertionCode - Variable in class org.jmol.modelset.ModelLoader
 
currentGroupSequenceNumber - Variable in class org.jmol.modelset.ModelLoader
 
currentIndex - Variable in class org.openscience.jmol.app.AtomSetChooser
 
currentIntensity - Variable in class org.jmol.g3d.Graphics3D
 
currentlyRendering - Variable in class org.jmol.g3d.Graphics3D
 
currentlyRendering() - Method in class org.jmol.g3d.Graphics3D
 
currentMenuItemId - Variable in class org.jmol.popup.JmolPopup
 
currentMesh - Variable in class org.jmol.shape.MeshCollection
 
currentMetricsFont3d - Variable in class org.jmol.shape.Frank
 
currentModel - Variable in class org.jmol.modelset.ModelLoader
 
currentModelIndex - Variable in class org.jmol.modelset.ModelLoader
 
currentModelIndex - Variable in class org.jmol.viewer.RepaintManager
 
currentObject - Variable in class org.jmol.shape.Object2dShape
 
currentPoints - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
currentProperties - Variable in class org.openscience.jmol.app.PreferencesDialog
 
currentSize - Variable in class org.jmol.export.dialog.FilePreview.JmolPanel
 
currentStep - Variable in class org.jmol.minimize.forcefield.ForceField
 
currentThread - Variable in class org.jmol.viewer.Eval
 
currentTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
 
cursor - Variable in class org.openscience.jmol.app.AboutDialog.PageLoader
 
cursor - Variable in class org.openscience.jmol.app.HelpDialog.PageLoader
 
cursor - Variable in class org.openscience.jmol.app.WhatsNewDialog.PageLoader
 
CURSOR_CROSSHAIR - Static variable in class org.jmol.viewer.Viewer
 
CURSOR_DEFAULT - Static variable in class org.jmol.viewer.Viewer
 
CURSOR_HAND - Static variable in class org.jmol.viewer.Viewer
 
CURSOR_MOVE - Static variable in class org.jmol.viewer.Viewer
 
CURSOR_WAIT - Static variable in class org.jmol.viewer.Viewer
 
cursorPos - Variable in class org.jmol.util.CommandHistory
Current position of the cursor;
curx - Variable in class org.jmol.export.image.GifEncoder
 
cury - Variable in class org.jmol.export.image.GifEncoder
 
cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cutoff - Variable in class org.jmol.jvxl.data.JvxlData
 
cutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
cvsDate - Static variable in class org.jmol.viewer.JmolConstants
 
cx - Variable in class org.jmol.bspt.CubeIterator
 
CX - Variable in class org.jmol.quantum.MOCalculation
 
cy - Variable in class org.jmol.bspt.CubeIterator
 
CY - Variable in class org.jmol.quantum.MOCalculation
 
CYAN - Static variable in class org.jmol.g3d.Graphics3D
 
Cylinder3D - Class in org.jmol.g3d
Draws shaded cylinders in 3D.
Cylinder3D(Graphics3D) - Constructor for class org.jmol.g3d.Cylinder3D
 
cylinder3d - Variable in class org.jmol.g3d.Graphics3D
 
cylinderBase - Static variable in class org.jmol.shapespecial.DipolesRenderer
 
cz - Variable in class org.jmol.bspt.CubeIterator
 
CZ - Variable in class org.jmol.quantum.MOCalculation
 

D

d - Variable in class org.jmol.minimize.forcefield.Calculation
 
d - Variable in class org.jmol.util.Eigen
 
d1 - Variable in class org.jmol.g3d.Hermite3D
 
d2 - Variable in class org.jmol.g3d.Hermite3D
 
da - Variable in class org.jmol.minimize.forcefield.Calculations
 
data - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
data - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
data - Variable in class org.jmol.symmetry.UnitCell
 
data - Variable in class org.jmol.util.CompoundDocument
 
data - Variable in class org.jmol.viewer.Eval
 
data() - Method in class org.jmol.viewer.Eval
 
data - Static variable in class org.jmol.viewer.Token
 
data - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
data1 - Variable in class org.jmol.shape.Mesh
 
data2 - Variable in class org.jmol.shape.Mesh
 
dataFrame(int) - Method in class org.jmol.viewer.Eval
 
dataFrames - Variable in class org.jmol.modelset.Model
 
DataManager - Class in org.jmol.viewer
 
DataManager() - Constructor for class org.jmol.viewer.DataManager
 
dataManager - Variable in class org.jmol.viewer.Viewer
 
dataPos - Variable in class org.jmol.export.image.PngEncoder
 
dataSeparator - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dataSourceFrame - Variable in class org.jmol.modelset.Model
 
Datatype - Variable in class org.jmol.jcamp.Visua
 
dataType - Variable in class org.jmol.jvxl.readers.Parameters
 
dataType - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
dataValues - Variable in class org.jmol.viewer.DataManager
 
date - Static variable in class org.jmol.viewer.JmolConstants
 
db - Variable in class org.jmol.minimize.forcefield.Calculations
 
dc - Variable in class org.jmol.minimize.forcefield.Calculations
 
DC_matrix - Variable in class org.jmol.util.Huffman
 
DC_matrix0 - Variable in class org.jmol.util.Huffman
 
DC_matrix1 - Variable in class org.jmol.util.Huffman
 
DCT - Class in org.jmol.util
 
DCT(int) - Constructor for class org.jmol.util.DCT
Constructs a new DCT object.
dct - Variable in class org.jmol.util.JpegEncoder
 
DCtableNumber - Variable in class org.jmol.util.JpegInfo
 
dd - Variable in class org.jmol.minimize.forcefield.Calculations
 
dData - Variable in class org.jmol.minimize.forcefield.Calculation
 
dE - Variable in class org.jmol.minimize.forcefield.Calculation
 
dE - Variable in class org.jmol.minimize.forcefield.ForceField
 
debug(String) - Method in class org.jmol.util.DefaultLogger
 
debug(String) - Static method in class org.jmol.util.Logger
Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at DEBUG level.
DEBUG_FACE_VECTORS - Static variable in class org.jmol.g3d.Normix3D
 
DEBUG_WITH_SEQUENTIAL_SEARCH - Static variable in class org.jmol.g3d.Normix3D
 
debugging - Static variable in class org.jmol.util.Logger
 
debugScript - Variable in class org.jmol.viewer.Eval
 
debugScript - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
decalx_gfx - Variable in class org.jmol.jcamp.ZoneVisu
 
decaly_gfx - Variable in class org.jmol.jcamp.ZoneVisu
 
decimal - Static variable in class org.jmol.viewer.Token
 
decimalScale - Static variable in class org.jmol.util.Parser
 
decode64 - Static variable in class org.jmol.util.Base64
 
decodeBase64(String) - Static method in class org.jmol.util.Base64
 
deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
deduceElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.Mol2Reader
 
DEFAULT - Static variable in class org.jmol.g3d.Triangle3D
 
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_CHIRALITY - Static variable in class org.jmol.smiles.SmilesAtom
Constant used for default chirality.
DEFAULT_DISTANCE_FACTOR - Static variable in class org.jmol.shapespecial.Polyhedra
 
DEFAULT_FACECENTEROFFSET - Static variable in class org.jmol.shapespecial.Polyhedra
 
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MAD - Static variable in class org.jmol.shapespecial.Dipoles
 
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MAX_SIZE - Static variable in class org.jmol.util.CommandHistory
 
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_OFFSETSIDE - Static variable in class org.jmol.shapespecial.Dipoles
 
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JmolConstants
 
DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
 
defaultActions - Variable in class org.openscience.jmol.app.Jmol
Actions defined by the Jmol class
defaultAlignment - Variable in class org.jmol.shape.Labels
 
defaultAngleLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultBgcolix - Variable in class org.jmol.shape.Labels
 
defaultChoice - Static variable in class org.jmol.export.dialog.Dialog
 
defaultColix - Variable in class org.jmol.shape.Labels
 
defaultColix - Variable in class org.jmol.shapesurface.Isosurface
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultColorNegative - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorNegativeLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorPositive - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorPositiveLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColors - Static variable in class org.jmol.viewer.Token
 
defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
defaultContourCount - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
 
defaultCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultCutoff - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultDirectory - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultDistanceLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultDrawArrowScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultFontId - Variable in class org.jmol.shape.Labels
 
defaultFontName - Static variable in class org.jmol.shape.Frank
 
defaultFontSize - Static variable in class org.jmol.shape.Frank
 
defaultFontStyle - Static variable in class org.jmol.shape.Frank
 
defaultGroupCount - Static variable in class org.jmol.modelset.ModelLoader
 
defaultLoadScript - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
DefaultLogger - Class in org.jmol.util
Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
 
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.VoxelReader
 
defaultMepCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMepMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMepMin - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMessage - Variable in class org.jmol.applet.Jmol.MyStatusListener
 
defaultOffset - Variable in class org.jmol.shape.Labels
 
defaultON - Static variable in class org.jmol.viewer.Token
 
defaultOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultPaletteID - Variable in class org.jmol.shape.Labels
 
defaultPointer - Variable in class org.jmol.shape.Labels
 
defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultRotationRadius - Variable in class org.jmol.modelset.Model
 
defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
 
defaultSolventRadius - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultsOnlyForNone - Variable in class org.jmol.shape.Labels
 
defaultTorsionLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultTranslucent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
defaultTypeIndex - Variable in class org.openscience.jmol.app.FileTyper
 
defaultVdw - Variable in class org.jmol.viewer.DataManager
 
defaultZPos - Variable in class org.jmol.shape.Labels
 
define(Vector, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
 
define(Measurement, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
 
define(Measurement, boolean, boolean) - Method in class org.jmol.shape.Measures
 
define() - Method in class org.jmol.viewer.Eval
 
define - Static variable in class org.jmol.viewer.Token
 
defineCenterAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
defineMeasurement(Vector, float[], boolean, boolean, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
 
defineStructure(int, String, char, int, char, char, int, char) - Method in class org.jmol.modelset.ModelCollection
 
defineStructure(int, String, char, int, char, char, int, char) - Method in class org.jmol.modelset.ModelLoader
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.forcefield.Calculations
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
 
degreesPerRadian - Static variable in class org.jmol.export._Exporter
 
degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
 
delay() - Method in class org.jmol.viewer.Eval
 
delay(long) - Method in class org.jmol.viewer.Eval
 
delay - Static variable in class org.jmol.viewer.Token
 
delayMaximumMs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
delete(Object) - Method in class org.jmol.shape.Measures
 
delete() - Method in class org.jmol.viewer.Eval
 
delete - Static variable in class org.jmol.viewer.Token
 
delete() - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
deleteAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
deleteAllBonds() - Method in class org.jmol.modelset.BondCollection
 
deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
 
deleteAllButton - Variable in class org.openscience.jmol.app.MeasurementTable
 
deleteAtomReferences() - Method in class org.jmol.modelset.Bond
 
deleteAtoms(int, int, BitSet) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
deleteAtoms(int, int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
deleteAtoms(int, int, int, BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
deleteAtoms(int, BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection.StateScript
 
deleteAtoms(BitSet, boolean) - Method in class org.jmol.modelset.ModelSet
 
deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
 
deleteAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
deleteAtoms(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
deleteAtomsInVariables(BitSet) - Method in class org.jmol.viewer.Eval
 
deleteBits(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
 
deleteBond(Bond) - Method in class org.jmol.modelset.Atom
 
deleteBond(int) - Method in class org.jmol.modelset.Atom
 
deleteBonds(BitSet) - Method in class org.jmol.modelset.BondCollection
 
deleteButton - Variable in class org.openscience.jmol.app.MeasurementTable
 
deleteConnections(float, float, short, BitSet, BitSet, boolean, boolean, float, float) - Method in class org.jmol.modelset.BondCollection
 
deleteDipole(Dipole) - Method in class org.jmol.shapespecial.Dipoles
 
deleteElements(Object, int, int) - Static method in class org.jmol.util.ArrayUtil
 
deleteInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
deleteLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
 
deleteLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
 
deleteMeasurement(int) - Method in class org.jmol.shape.Measures
 
deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
 
deleteMeasurement(int[]) - Method in class org.jmol.viewer.Viewer
 
deleteMesh() - Method in class org.jmol.shape.MeshCollection
 
deleteMesh(int) - Method in class org.jmol.shape.MeshCollection
 
deletePolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
 
delta - Variable in class org.jmol.minimize.forcefield.Calculation
 
depth - Variable in class org.jmol.g3d.Graphics3D
 
depth - Variable in class org.jmol.g3d.Sphere3D
 
depth - Static variable in class org.jmol.viewer.Token
 
depth1 - Variable in class org.jmol.g3d.Hermite3D
 
depthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
depthByPixels(int) - Method in class org.jmol.viewer.Viewer
 
depthPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
depthPlane - Variable in class org.jmol.viewer.TransformManager
 
depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
depthToPercent(int) - Method in class org.jmol.viewer.Viewer
 
depthValue - Variable in class org.jmol.viewer.TransformManager
 
depthZ - Variable in class org.jmol.export._Exporter
 
descent - Variable in class org.jmol.shape.LabelsRenderer
 
descent - Variable in class org.jmol.shape.Text
 
desireClearingThread - Static variable in class org.jmol.g3d.Platform3D
 
desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
destroy() - Method in class org.jmol.applet.Jmol
 
destroy() - Method in class org.jmol.appletwrapper.AppletWrapper
 
destroy() - Method in interface org.jmol.appletwrapper.WrappedApplet
 
destroy() - Method in class org.jmol.g3d.Graphics3D
 
detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
 
Determine_Extrem_y() - Method in class org.jmol.jcamp.ZoneVisu
 
determineAtomSetCollectionReader(BufferedReader, boolean) - Static method in class org.jmol.adapter.smarter.Resolver
 
determineFileType(BufferedReader) - Static method in class org.jmol.jvxl.readers.VolumeFileReader
 
determineSpaceGroup(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroup(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroup(String, SpaceGroup) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroup(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupIndex(String) - Method in interface org.jmol.api.SymmetryInterface
 
determineSpaceGroupIndex(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupIndex(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupIndex(String) - Method in class org.jmol.symmetry.Symmetry
 
determineUniqueAxis(float, float, float, float, float, float) - Static method in class org.jmol.symmetry.SpaceGroup
 
diagonalReferenceAxis - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
Dialog - Class in org.jmol.export.dialog
 
Dialog() - Constructor for class org.jmol.export.dialog.Dialog
 
dialog - Variable in class org.jmol.export.dialog.FileChooser
 
Dialog.ExportChoiceListener - Class in org.jmol.export.dialog
 
Dialog.ExportChoiceListener() - Constructor for class org.jmol.export.dialog.Dialog.ExportChoiceListener
 
Dialog.QualityListener - Class in org.jmol.export.dialog
 
Dialog.QualityListener(boolean, JSlider) - Constructor for class org.jmol.export.dialog.Dialog.QualityListener
 
Dialog.TypeFilter - Class in org.jmol.export.dialog
 
Dialog.TypeFilter(String) - Constructor for class org.jmol.export.dialog.Dialog.TypeFilter
 
dialogAsk(String, String) - Method in interface org.jmol.api.JmolStatusListener
 
dialogAsk(String, String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
dialogAsk(String, String) - Method in class org.jmol.applet.Jvm12
 
dialogAsk(String, String) - Method in class org.jmol.viewer.StatusManager
 
dialogAsk(String, String) - Method in class org.jmol.viewer.Viewer
 
dialogAsk(String, String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
dialogLocation - Variable in class org.jmol.export.dialog.FileChooser
 
dialogSize - Variable in class org.jmol.export.dialog.FileChooser
 
dialogType - Variable in class org.jmol.applet.Jvm12
 
Dialogue_Load_File - Variable in class org.jmol.jcamp.Visua
 
diameter - Variable in class org.jmol.g3d.Cylinder3D
 
diameter - Variable in class org.jmol.g3d.Sphere3D
 
diameter - Variable in class org.jmol.shape.Mesh
 
diameter - Variable in class org.jmol.shape.MeshRenderer
 
diameter - Variable in class org.jmol.shapespecial.DipolesRenderer
 
diameter - Variable in class org.jmol.shapespecial.Draw
 
diameter - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
diameter - Variable in class org.jmol.shapespecial.VectorsRenderer
 
diameter0 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
diameterBeg - Variable in class org.jmol.shapebio.BioShapeRenderer
 
diameterEnd - Variable in class org.jmol.shapebio.BioShapeRenderer
 
diameterMid - Variable in class org.jmol.shapebio.BioShapeRenderer
 
diameterP - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.g3d.Rgb16
 
diffuse - Static variable in class org.jmol.viewer.Token
 
DIFFUSE_PERCENT - Static variable in class org.jmol.g3d.Shade3D
 
diffusePercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dim - Variable in class org.jmol.bspt.Node
 
dimMax - Variable in class org.jmol.bspt.Bspf
 
dimMax - Variable in class org.jmol.bspt.Bspt
 
dimScreen - Variable in class org.jmol.viewer.Viewer
 
dimSize - Variable in class org.jmol.applet.Jvm12
 
dimSize - Variable in class org.openscience.jmol.app.DisplayPanel
 
Dipole - Class in org.jmol.shapespecial
 
Dipole() - Constructor for class org.jmol.shapespecial.Dipole
 
Dipole(int, String, String, short, short, boolean) - Constructor for class org.jmol.shapespecial.Dipole
 
dipole() - Method in class org.jmol.viewer.Eval
 
dipole - Static variable in class org.jmol.viewer.Token
 
DIPOLE_TYPE_ATOMS - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_BOND - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_MOLECULAR - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_POINTS - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_POINTVECTOR - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_UNKNOWN - Static variable in class org.jmol.shapespecial.Dipole
 
dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleInfo - Variable in class org.jmol.shapespecial.Dipole
 
Dipoles - Class in org.jmol.shapespecial
 
Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
 
dipoles - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
DipolesGenerator - Class in org.jmol.export
 
DipolesGenerator() - Constructor for class org.jmol.export.DipolesGenerator
 
DipolesRenderer - Class in org.jmol.shapespecial
 
DipolesRenderer() - Constructor for class org.jmol.shapespecial.DipolesRenderer
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipole
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleVectorScale - Variable in class org.jmol.shapespecial.DipolesRenderer
 
direction - Static variable in class org.jmol.viewer.Token
 
directory - Variable in class org.jmol.util.CompoundDocument
 
disableField(int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
used for turning off fractional or nonfractional coord.
disablePopupMenu - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
discardLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
 
DISORDER_GROUP - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
displacement - Static variable in class org.jmol.viewer.Token
 
display - Variable in class org.jmol.export.dialog.FilePreview
 
display - Variable in class org.jmol.i18n.GT.Language
 
display(boolean) - Method in class org.jmol.viewer.Eval
 
display(BitSet, BitSet, boolean) - Method in class org.jmol.viewer.SelectionManager
 
display - Static variable in class org.jmol.viewer.Token
 
display - Variable in class org.jmol.viewer.Viewer
 
display(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
display - Variable in class org.openscience.jmol.app.Jmol
 
displayCellParameters - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
displayed - Static variable in class org.jmol.viewer.Token
 
displayMaxX - Variable in class org.jmol.g3d.Graphics3D
 
displayMaxY - Variable in class org.jmol.g3d.Graphics3D
 
displayMinX - Variable in class org.jmol.g3d.Graphics3D
 
displayMinY - Variable in class org.jmol.g3d.Graphics3D
 
DisplayPanel - Class in org.openscience.jmol.app
 
DisplayPanel(StatusBar, GuiMap, boolean, int, int) - Constructor for class org.openscience.jmol.app.DisplayPanel
 
DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app
Action calling evalStringQuiet(<action> + CheckBoxState)
DisplayPanel.CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.DisplayPanel.CheckBoxMenuItemAction
 
DisplayPanel.DefineCenterAction - Class in org.openscience.jmol.app
 
DisplayPanel.DefineCenterAction() - Constructor for class org.openscience.jmol.app.DisplayPanel.DefineCenterAction
 
DisplayPanel.HomeAction - Class in org.openscience.jmol.app
 
DisplayPanel.HomeAction() - Constructor for class org.openscience.jmol.app.DisplayPanel.HomeAction
 
DisplayPanel.MoveToAction - Class in org.openscience.jmol.app
Action calling moveTo()
DisplayPanel.MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.DisplayPanel.MoveToAction
 
DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app
Action calling setStatus()
DisplayPanel.SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.DisplayPanel.SetStatusAction
 
displaySpeed - Variable in class org.openscience.jmol.app.DisplayPanel
 
displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
dispose() - Method in class org.jmol.applet.Console
 
dispose(JFrame) - Method in class org.openscience.jmol.app.Jmol
 
dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
disregardNeighbors - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
dist2(Vector3f, Vector3f) - Static method in class org.jmol.g3d.Normix3D
 
dist2(Vector3f, double, double, double) - Static method in class org.jmol.g3d.Normix3D
 
distance - Variable in class org.jmol.jvxl.readers.Parameters
 
distance - Static variable in class org.jmol.viewer.Token
 
distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
 
distance2(Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
distanceFactor - Variable in class org.jmol.shapespecial.Polyhedra
 
distancePointToPlane(Point3f) - Method in interface org.jmol.api.VolumeDataInterface
 
distancePointToPlane(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
distanceTolerance - Variable in class org.jmol.symmetry.PointGroup
 
distanceToPlane(Point4f, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
distanceToPlane(Point4f, float, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
distanceToPlane(Vector3f, float, Point3f) - Static method in class org.jmol.g3d.Graphics3D
 
distanceVerticalToPlane(float, float, Point3f, Point3f, Point3f) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int, int[], byte[], Atom[]) - Method in interface org.jmol.api.JmolBioResolver
 
distinguishAndPropagateGroup(int, Chain, String, int, int, int) - Method in class org.jmol.modelset.ModelLoader
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int, int[], byte[], Atom[]) - Method in class org.jmol.modelsetbio.Resolver
 
div(Quaternion) - Method in class org.jmol.util.Quaternion
 
div - Static variable in class org.jmol.viewer.Token
 
divide - Static variable in class org.jmol.viewer.Token
 
divisors - Variable in class org.jmol.util.DCT
 
DivisorsChrominance - Variable in class org.jmol.util.DCT
 
DivisorsLuminance - Variable in class org.jmol.util.DCT
 
divLeft(Quaternion) - Method in class org.jmol.util.Quaternion
 
dmesh - Variable in class org.jmol.shapespecial.DrawRenderer
 
dmeshes - Variable in class org.jmol.shapespecial.Draw
 
dna - Static variable in class org.jmol.viewer.Token
 
Do_Clickable_Peaks(double) - Method in class org.jmol.jcamp.ZoneVisu
 
Do_Find_Peak() - Method in class org.jmol.jcamp.Visua
 
Do_Grid() - Method in class org.jmol.jcamp.Visua
 
Do_Integrate() - Method in class org.jmol.jcamp.Visua
 
Do_Load_File() - Method in class org.jmol.jcamp.Visua
 
Do_Reverse() - Method in class org.jmol.jcamp.Visua
 
Do_Write_JCamp() - Method in class org.jmol.jcamp.Visua
 
Do_Zoomback() - Method in class org.jmol.jcamp.Visua
 
Do_Zoomin() - Method in class org.jmol.jcamp.Visua
 
Do_Zoomout() - Method in class org.jmol.jcamp.Visua
 
doAddHydrogens - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doBitsetSelect() - Method in class org.jmol.viewer.Eval.Rpn
 
doc - Variable in class org.jmol.shapesurface.Pmesh
 
doCalculateTroughs - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
doCap0 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
doCap1 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
doCapIsosurface - Variable in class org.jmol.jvxl.readers.Parameters
 
doClose() - Method in class org.openscience.jmol.app.Jmol
 
doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doDebug - Variable in class org.jmol.quantum.QuantumCalculation
 
doFormatText - Variable in class org.jmol.shape.Text
 
doJustify - Variable in class org.jmol.shape.MeasuresRenderer
 
dollarsign - Static variable in class org.jmol.viewer.Token
 
doLocalize - Variable in class org.jmol.shape.UccageRenderer
 
DOMResolve(Object) - Static method in class org.jmol.adapter.smarter.Resolver
 
doNormalize - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
doNormalize - Variable in class org.jmol.symmetry.SpaceGroup
 
doNormalize - Variable in class org.jmol.symmetry.SymmetryOperation
 
doOverWrite(JFileChooser, File) - Static method in class org.jmol.export.dialog.Dialog
 
doReportProperty(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
doShaft - Variable in class org.jmol.shapespecial.VectorsRenderer
 
doSmoothProperty - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
doSync() - Method in class org.jmol.viewer.StatusManager
 
dot(Quaternion) - Method in class org.jmol.util.Quaternion
 
dot - Static variable in class org.jmol.viewer.Token
 
dotCount - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
dotDensity - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
doTranslate - Variable in class org.jmol.applet.Jmol
 
doTranslate - Variable in class org.jmol.i18n.GT
 
dots - Variable in class org.jmol.jvxl.data.MeshData
 
Dots - Class in org.jmol.shape
 
Dots() - Constructor for class org.jmol.shape.Dots
 
dots(int) - Method in class org.jmol.viewer.Eval
 
dots - Static variable in class org.jmol.viewer.Token
 
dotsConvexMaps - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
dotsConvexMax - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
DotsGenerator - Class in org.jmol.export
 
DotsGenerator() - Constructor for class org.jmol.export.DotsGenerator
 
DotsRenderer - Class in org.jmol.shape
 
DotsRenderer() - Constructor for class org.jmol.shape.DotsRenderer
 
dotsSelectedOnly - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dotSurface - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dotted - Static variable in class org.jmol.viewer.Token
 
doubleLength(Object) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(String[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(float[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(int[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(short[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(byte[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleLength(boolean[]) - Static method in class org.jmol.util.ArrayUtil
 
doubleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.PovrayDialog
 
doUseIterator - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
doUsePlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.Parameters
 
downsampleFullSceneAntialiasing(boolean) - Method in class org.jmol.g3d.Graphics3D
 
downsampleRemainders - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
dragEnter(DropTargetDragEvent) - Method in class org.openscience.jmol.app.FileDropper
 
dragExit(DropTargetEvent) - Method in class org.openscience.jmol.app.FileDropper
 
dragOver(DropTargetDragEvent) - Method in class org.openscience.jmol.app.FileDropper
 
Draw - Class in org.jmol.shapespecial
 
Draw() - Constructor for class org.jmol.shapespecial.Draw
 
draw() - Method in class org.jmol.viewer.Eval
 
draw - Static variable in class org.jmol.viewer.Token
 
DRAW_ARC - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_ARROW - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_CIRCLE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_CIRCULARPLANE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_CURVE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_CYLINDER - Static variable in class org.jmol.viewer.JmolConstants
 
Draw_Graphics(double, double) - Method in class org.jmol.jcamp.ZoneVisu
 
DRAW_LINE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_MULTIPLE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_NONE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_PLANE - Static variable in class org.jmol.viewer.JmolConstants
 
DRAW_POINT - Static variable in class org.jmol.viewer.JmolConstants
 
Draw_Texte(String) - Method in class org.jmol.jcamp.ZoneVisu
 
DRAW_TRIANGLE - Static variable in class org.jmol.viewer.JmolConstants
 
drawArcs - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawArrowHeadBox(Point3f, Point3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
 
drawAxes - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawAxis() - Method in class org.jmol.jcamp.ZoneVisu
 
drawBackside - Variable in class org.jmol.g3d.Cylinder3D
 
drawBall - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawBox(Point3f, Point3f) - Method in class org.jmol.shapebio.RocketsRenderer
 
drawCircleCentered(short, int, int, int, int, boolean) - Method in interface org.jmol.api.JmolExportInterface
 
drawCircleCentered(short, int, int, int, int, boolean) - Method in interface org.jmol.api.JmolRendererInterface
draws a screened circle ...
drawCircleCentered(short, int, int, int, int, boolean) - Method in class org.jmol.export._MayaExporter
 
drawCircleCentered(short, int, int, int, int, boolean) - Method in class org.jmol.export._PovrayExporter
 
drawCircleCentered(short, int, int, int, int, boolean) - Method in class org.jmol.export._VrmlExporter
 
drawCircleCentered(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
draws a simple circle (draw circle)
drawCircleCentered(short, int, int, int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
draws a screened circle ...
drawCylinderTriangle(int, int, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawCylinderTriangle(int, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawCylinderTriangle(int, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawDashed(int, int, int, int, int, int) - Method in class org.jmol.shape.SticksRenderer
 
drawDashedLine(int, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDashedLine(int, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawDashedLine(int, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawDots - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawDottedLine(Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDottedLine(Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawDottedLine(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
 
drawEdges - Variable in class org.jmol.shapespecial.PolyhedraRenderer
 
drawFace(short, Atom, Atom, Atom, boolean, boolean) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
drawFill - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
drawfillTriangle(int, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawfillTriangle(int, int, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawfillTriangle(int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawfillTriangle(int, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Triangle3D
 
DrawGenerator - Class in org.jmol.export
 
DrawGenerator() - Constructor for class org.jmol.export.DrawGenerator
 
drawHermite(short, boolean, boolean, int, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, int) - Method in interface org.jmol.api.JmolExportInterface
 
drawHermite(short, int, Point3f, Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolExportInterface
 
drawHermite(int, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite(short, int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export._MayaExporter
 
drawHermite(short, boolean, boolean, int, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, int) - Method in class org.jmol.export._MayaExporter
 
drawHermite(short, int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export._PovrayExporter
 
drawHermite(short, boolean, boolean, int, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, int) - Method in class org.jmol.export._PovrayExporter
 
drawHermite(short, int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export._VrmlExporter
 
drawHermite(short, boolean, boolean, int, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, Point3f, int) - Method in class org.jmol.export._VrmlExporter
 
drawHermite(int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawHermite(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.export.Export3D
 
drawHermite(int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawHermite(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
 
drawHLine(int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawHLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawHover - Variable in class org.jmol.viewer.PickingManager
 
drawImage(Image, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawImage(Image, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
 
drawImage(Image, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawIndex - Variable in class org.jmol.symmetry.PointGroup
 
drawInfo - Variable in class org.jmol.symmetry.PointGroup
 
drawLcaoCartoon(Vector3f, Vector3f, Vector3f) - Method in class org.jmol.shapesurface.Isosurface
 
drawLine(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLine(Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawLine(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
DrawMesh - Class in org.jmol.shapespecial
 
DrawMesh(String, Graphics3D, short) - Constructor for class org.jmol.shapespecial.DrawMesh
 
drawMode - Variable in class org.jmol.viewer.MouseManager
 
drawPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
drawPixel(short, int, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPixel(short, int, int, int) - Method in class org.jmol.export._MayaExporter
 
drawPixel(short, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
drawPixel(short, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
 
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawPointer(JmolRendererInterface) - Method in class org.jmol.shape.Object2d
 
drawPoints(int, int[]) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPoints(int, int[]) - Method in class org.jmol.export.Export3D
 
drawPoints(int, int[]) - Method in class org.jmol.g3d.Graphics3D
 
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws a rectangle
DrawRenderer - Class in org.jmol.shapespecial
 
DrawRenderer() - Constructor for class org.jmol.shapespecial.DrawRenderer
 
drawSegment(int, int, int, int, int, int) - Method in class org.jmol.shape.MeasuresRenderer
 
drawSpectra() - Method in class org.jmol.jcamp.ZoneVisu
 
drawString(short, String, Font3D, int, int, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
drawString(String, Font3D, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawString(short, String, Font3D, int, int, int, int) - Method in class org.jmol.export._MayaExporter
 
drawString(short, String, Font3D, int, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
drawString(short, String, Font3D, int, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
drawString(String, Font3D, int, int, int, int) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawString(String, Font3D, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawStringNoSlab(String, Font3D, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawStringNoSlab(String, Font3D, int, int, int) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawStringNoSlab(String, Font3D, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawText() - Method in class org.jmol.jcamp.ZoneVisu
 
drawTextPixel(int, int, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export._MayaExporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
drawTriangle(Point3i, short, Point3i, short, Point3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawTriangle(Point3i, Point3i, Point3i, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawTriangle(Point3i, short, Point3i, short, Point3i, short, int) - Method in class org.jmol.export.Export3D
 
drawTriangle(Point3i, Point3i, Point3i, int) - Method in class org.jmol.export.Export3D
 
drawTriangle(Point3i, short, Point3i, short, Point3i, short, int) - Method in class org.jmol.g3d.Graphics3D
 
drawTriangle(Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
 
drawTriangles - Variable in class org.jmol.shape.Mesh
 
drawType - Variable in class org.jmol.shapespecial.DrawMesh
 
drawType - Variable in class org.jmol.shapespecial.DrawRenderer
 
drawType - Variable in class org.jmol.symmetry.PointGroup
 
drawTypes - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVertexCount - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVertexCounts - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVLine(int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawVLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawXAxis() - Method in class org.jmol.jcamp.ZoneVisu
 
drivingSync - Variable in class org.jmol.viewer.StatusManager
 
drop(DropTargetDropEvent) - Method in class org.openscience.jmol.app.FileDropper
 
dropActionChanged(DropTargetDragEvent) - Method in class org.openscience.jmol.app.FileDropper
 
DUMMY_ATOM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
dump() - Method in class org.jmol.util.Eigen
 
dump(int) - Method in class org.jmol.util.Eigen
 
dumpAll() - Static method in class org.jmol.symmetry.SpaceGroup
 
dumpAllSeitz() - Static method in class org.jmol.symmetry.SpaceGroup
 
dumpArray(String, float[][], int, int, int, int) - Static method in class org.jmol.util.ArrayUtil
 
dumpCanonicalSeitz(Matrix4f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
dumpCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
 
dumpDipoles(String) - Method in class org.jmol.shapespecial.Dipoles
 
dumpInfo(int, String) - Method in class org.jmol.quantum.MOCalculation
 
dumpInfo(int, int) - Method in class org.jmol.quantum.MOCalculation
 
dumpInfo() - Method in class org.jmol.symmetry.HallInfo
 
dumpInfo() - Method in class org.jmol.symmetry.HallInfo.RotationTerm
 
dumpInfo() - Method in class org.jmol.symmetry.SpaceGroup
 
dumpInfo() - Method in class org.jmol.symmetry.SymmetryOperation
 
dumpInfo(boolean) - Method in class org.jmol.symmetry.UnitCell
 
dumpIntArray(int[], int) - Static method in class org.jmol.util.ArrayUtil
 
dumpList - Static variable in class org.jmol.popup.JmolPopup
 
dumpSeitz(Matrix4f) - Static method in class org.jmol.symmetry.SymmetryOperation
 
dumpStacks() - Method in class org.jmol.viewer.Eval.Rpn
 
dumpStructure(String[][]) - Method in class org.jmol.popup.PopupResourceBundle
 
dumpWords() - Method in class org.jmol.popup.PopupResourceBundle
 
dVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
dValues - Static variable in class org.jmol.adapter.readers.more.MopacDataReader
 
dx - Variable in class org.jmol.bspt.CubeIterator
 
dx - Variable in class org.jmol.shape.SticksRenderer
 
dx - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
dxB - Variable in class org.jmol.g3d.Cylinder3D
 
dxBf - Variable in class org.jmol.g3d.Cylinder3D
 
dxStep - Variable in class org.jmol.shape.SticksRenderer
 
DXY - Variable in class org.jmol.quantum.MOCalculation
 
dxyz - Variable in class org.jmol.g3d.Sphere3D
 
DXZ - Variable in class org.jmol.quantum.MOCalculation
 
dy - Variable in class org.jmol.bspt.CubeIterator
 
dy - Variable in class org.jmol.shape.SticksRenderer
 
dyB - Variable in class org.jmol.g3d.Cylinder3D
 
dyBf - Variable in class org.jmol.g3d.Cylinder3D
 
dynamicMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
dyStep - Variable in class org.jmol.shape.SticksRenderer
 
DYZ - Variable in class org.jmol.quantum.MOCalculation
 
dz - Variable in class org.jmol.bspt.CubeIterator
 
dzB - Variable in class org.jmol.g3d.Cylinder3D
 
dzBf - Variable in class org.jmol.g3d.Cylinder3D
 

E

e - Variable in class org.jmol.util.Eigen
 
e0 - Variable in class org.jmol.minimize.forcefield.ForceField
 
E_ANG_PER_DEBYE - Static variable in class org.jmol.shapespecial.Dipoles
 
EANGLE - Static variable in class org.jmol.minimize.forcefield.ForceField
 
EBOND - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
ec - Variable in class org.jmol.shape.Dots
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
Echo - Class in org.jmol.shape
 
Echo() - Constructor for class org.jmol.shape.Echo
 
echo(int, boolean) - Method in class org.jmol.viewer.Eval
 
echo - Static variable in class org.jmol.viewer.Token
 
EchoGenerator - Class in org.jmol.export
 
EchoGenerator() - Constructor for class org.jmol.export.EchoGenerator
 
echoMessage(String) - Method in class org.jmol.viewer.Viewer
 
EchoRenderer - Class in org.jmol.shape
 
EchoRenderer() - Constructor for class org.jmol.shape.EchoRenderer
 
echoShapeActive - Variable in class org.jmol.modelset.ModelSet
 
eCounts - Variable in class org.jmol.symmetry.PointGroup
 
EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeCount - Variable in class org.jmol.jvxl.readers.VoxelReader
 
edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlReader
 
edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionBase - Variable in class org.jmol.jvxl.readers.VoxelReader
 
edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionRange - Variable in class org.jmol.jvxl.readers.VoxelReader
 
edgeMask12 - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
edgeMask12All - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
edges - Static variable in class org.jmol.shape.Bbcage
 
EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_NONE - Static variable in class org.jmol.shapespecial.Polyhedra
 
edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVector - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexes - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexes2d - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
editorScrollPane - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
EELECTROSTATIC - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eig_val - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
eig_vec - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
eig_vec_compressed - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
Eigen - Class in org.jmol.util
Eigenvalues and eigenvectors of a real 3x3 symmetric matrix.
Eigen(double[][]) - Constructor for class org.jmol.util.Eigen
 
eightPiSquared100 - Static variable in class org.jmol.shapebio.BioShape
 
eleLeft - Variable in class org.jmol.bspt.Node
 
Element - Class in org.jmol.bspt
the internal tree is made up of elements ...
Element() - Constructor for class org.jmol.bspt.Element
 
element - Static variable in class org.jmol.viewer.Token
 
elementCharMasks - Static variable in class org.jmol.adapter.smarter.Atom
Bits which indicate whether or not an element symbol is valid.
elementComputedMenu - Variable in class org.jmol.popup.JmolPopupAwt
 
elementComputedMenu - Variable in class org.jmol.popup.JmolPopupSwing
 
elementContext - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
elementCounts - Variable in class org.jmol.modelset.Molecule
 
elementNameFromNumber(int) - Static method in class org.jmol.viewer.JmolConstants
 
elementNames - Static variable in class org.jmol.viewer.JmolConstants
 
elementNumber - Variable in class org.jmol.adapter.smarter.Atom
 
elementNumberFromSymbol(String) - Static method in class org.jmol.viewer.JmolConstants
 
elementNumberMax - Variable in class org.jmol.modelset.Molecule
 
elementNumberMax - Static variable in class org.jmol.viewer.JmolConstants
one larger than the last elementNumber, same as elementSymbols.length
elements - Variable in class org.jmol.symmetry.PointGroup
 
elementsPresent - Variable in class org.jmol.modelset.ModelCollection
 
elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
 
elementSymbolFromNumber(int) - Static method in class org.jmol.viewer.JmolConstants
 
elementSymbols - Static variable in class org.jmol.viewer.JmolConstants
The default elementSymbols.
elemno - Static variable in class org.jmol.viewer.Token
 
eleRight - Variable in class org.jmol.bspt.Node
 
eleRoot - Variable in class org.jmol.bspt.Bspt
 
ellipsoid - Variable in class org.jmol.adapter.smarter.Atom
 
ellipsoid - Variable in class org.jmol.shapespecial.Ellipsoids
 
ellipsoid() - Method in class org.jmol.viewer.Eval
 
ellipsoid - Static variable in class org.jmol.viewer.Token
 
ellipsoidArcs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidAxes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidAxisDiameter - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidBall - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidDotCount - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidDots - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoidFill - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ellipsoids - Variable in class org.jmol.modelset.AtomCollection
 
Ellipsoids - Class in org.jmol.shapespecial
 
Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
 
ellipsoids - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
Ellipsoids.Ellipsoid - Class in org.jmol.shapespecial
 
Ellipsoids.Ellipsoid(String, int) - Constructor for class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
EllipsoidsGenerator - Class in org.jmol.export
 
EllipsoidsGenerator() - Constructor for class org.jmol.export.EllipsoidsGenerator
 
ellipsoidShades - Static variable in class org.jmol.g3d.Sphere3D
 
EllipsoidsRenderer - Class in org.jmol.shapespecial
 
EllipsoidsRenderer() - Constructor for class org.jmol.shapespecial.EllipsoidsRenderer
 
elsecmd - Static variable in class org.jmol.viewer.Token
 
elseif - Static variable in class org.jmol.viewer.Token
 
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JmolConstants
 
embeddedCrystal - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
empty - Variable in class org.jmol.viewer.SelectionManager
 
enableButtons(JList) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
enableMenu(Object, boolean) - Method in class org.jmol.popup.JmolPopup
 
enableMenu(Object, boolean) - Method in class org.jmol.popup.JmolPopupAwt
 
enableMenu(Object, boolean) - Method in class org.jmol.popup.JmolPopupSwing
 
enableMenuItem(Object, boolean) - Method in class org.jmol.popup.JmolPopup
 
enableMenuItem(Object, boolean) - Method in class org.jmol.popup.JmolPopupAwt
 
enableMenuItem(Object, boolean) - Method in class org.jmol.popup.JmolPopupSwing
 
encapsulateData(String, Object) - Static method in class org.jmol.util.Escape
 
encode() - Method in class org.jmol.export.image.ImageEncoder
 
ENCODE_ALPHA - Static variable in class org.jmol.export.image.PngEncoder
Constant specifying that alpha channel should be encoded.
encodeAlpha - Variable in class org.jmol.export.image.PngEncoder
 
encodeColor(short) - Method in class org.jmol.shape.Shape
 
encodeDone() - Method in class org.jmol.export.image.GifEncoder
 
encodeDone() - Method in class org.jmol.export.image.ImageEncoder
 
encodeDone() - Method in class org.jmol.export.image.PpmEncoder
 
encodeFinish() - Method in class org.jmol.export.image.ImageEncoder
 
encodePixels(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.GifEncoder
 
encodePixels(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
encodePixels(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.PpmEncoder
 
encodePixelsWrapper(int, int, int, int, int[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
encodeStart(int, int) - Method in class org.jmol.export.image.GifEncoder
 
encodeStart(int, int) - Method in class org.jmol.export.image.ImageEncoder
 
encodeStart(int, int) - Method in class org.jmol.export.image.PpmEncoder
 
encodeTransColor(byte, short, boolean) - Method in class org.jmol.shape.Shape
 
encoding - Variable in class org.jmol.export.image.ImageEncoder
 
end - Static variable in class org.jmol.viewer.Token
 
END_ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
END_INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
END_SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
endcaps - Variable in class org.jmol.g3d.Cylinder3D
 
endcaps - Variable in class org.jmol.shape.SticksRenderer
 
ENDCAPS_FLAT - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_NONE - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_OPEN - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_OPENEND - Static variable in class org.jmol.g3d.Graphics3D
 
ENDCAPS_SPHERICAL - Static variable in class org.jmol.g3d.Graphics3D
 
endChainID - Variable in class org.jmol.adapter.smarter.Structure
 
endChainID - Variable in class org.jmol.modelset.ModelCollection.Structure
 
endCheck - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
endCheck - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
endCoord - Variable in class org.jmol.shapespecial.Dipoles
 
endDegrees - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
endifcmd - Static variable in class org.jmol.viewer.Token
 
endIndexPending - Variable in class org.jmol.shapebio.RocketsRenderer
 
endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
endMinimization() - Method in class org.jmol.minimize.Minimizer
 
endOfData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
endPos - Variable in class org.jmol.export.image.PngEncoder
 
endRendering() - Method in class org.jmol.g3d.Graphics3D
 
endSeqcode - Variable in class org.jmol.modelset.ModelCollection.Structure
 
endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
energy - Variable in class org.jmol.adapter.readers.more.AdfReader
 
energy - Variable in class org.jmol.minimize.forcefield.Calculation
 
ENERGY - Static variable in class org.jmol.minimize.forcefield.ForceField
 
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyES(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyES(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyKey - Variable in class org.jmol.adapter.readers.more.GaussianReader
Type of energy calculated, e.g., E(RB+HF-PW91).
energyKey - Variable in class org.jmol.adapter.readers.more.NWChemReader
The type of energy last calculated.
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyString - Variable in class org.jmol.adapter.readers.more.GaussianReader
Calculated energy with units (if possible).
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyValue - Variable in class org.jmol.adapter.readers.more.NWChemReader
The last calculated energy value.
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
ensureLength(Object, int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(String[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(float[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(int[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(short[], int) - Static method in class org.jmol.util.ArrayUtil
 
ensureLength(byte[], int) - Static method in class org.jmol.util.ArrayUtil
 
enterListener - Variable in class org.openscience.jmol.app.ConsoleTextPane
 
EnterListener - Interface in org.openscience.jmol.app
 
enterMeasurementMode() - Method in class org.jmol.viewer.MouseManager
 
enterPressed() - Method in class org.openscience.jmol.app.ConsoleTextPane
 
enterPressed() - Method in interface org.openscience.jmol.app.EnterListener
 
enterPressed() - Method in class org.openscience.jmol.app.ScriptWindow
 
entries - Variable in class org.jmol.util.Int2IntHash
 
entryCount - Variable in class org.jmol.util.Int2IntHash
 
entryName - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
entryType - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
EnvelopeCalculation - Class in org.jmol.geodesic
 
EnvelopeCalculation(AtomDataServer, int, short[]) - Constructor for class org.jmol.geodesic.EnvelopeCalculation
 
envelopeRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
envelopeRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
EOF - Static variable in class org.jmol.export.image.GifEncoder
 
EOFCode - Variable in class org.jmol.export.image.GifEncoder
 
eol(char) - Method in class org.jmol.viewer.Compiler
 
EOOP - Static variable in class org.jmol.minimize.forcefield.ForceField
 
equals(Object) - Method in class org.jmol.modelset.Atom
 
equals(Object) - Method in class org.jmol.util.Point3fi
 
equivalentAtomSets - Variable in class org.jmol.adapter.readers.more.GaussianReader
The number of equivalent atom sets.
equivalentAtomSets - Variable in class org.jmol.adapter.readers.more.NWChemReader
The number of equivalent atom sets.
error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
error(String) - Method in class org.jmol.util.DefaultLogger
 
error(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
error(String) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level.
error(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level with detail on exception.
error(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level.
error(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
error(int) - Method in class org.jmol.viewer.Compiler
 
error(int, String) - Method in class org.jmol.viewer.Compiler
 
error(int, String, String) - Method in class org.jmol.viewer.Compiler
 
error(String) - Method in class org.jmol.viewer.Compiler
 
error - Variable in class org.jmol.viewer.Eval
 
error(int) - Method in class org.jmol.viewer.Eval
 
error(int, String) - Method in class org.jmol.viewer.Eval
 
error(int, String, String) - Method in class org.jmol.viewer.Eval
 
error(int, String, String, boolean) - Method in class org.jmol.viewer.Eval
 
ERROR_axisExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_badArgumentCount - Static variable in class org.jmol.viewer.Compiler
 
ERROR_badArgumentCount - Static variable in class org.jmol.viewer.Eval
 
ERROR_badContext - Static variable in class org.jmol.viewer.Compiler
 
ERROR_badMillerIndices - Static variable in class org.jmol.viewer.Eval
 
ERROR_badRGBColor - Static variable in class org.jmol.viewer.Eval
 
ERROR_booleanExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_booleanOrNumberExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_booleanOrWhateverExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_colorExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_colorOrPaletteRequired - Static variable in class org.jmol.viewer.Eval
 
ERROR_commandExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_coordinateExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_coordinateOrNameOrExpressionRequired - Static variable in class org.jmol.viewer.Eval
 
ERROR_drawObjectNotDefined - Static variable in class org.jmol.viewer.Eval
 
ERROR_endOfCommandUnexpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_endOfExpressionExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_endOfStatementUnexpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_expressionExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_filenameExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_fileNotFoundException - Static variable in class org.jmol.viewer.Eval
 
ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
 
ERROR_identifierOrResidueSpecificationExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_incompatibleArguments - Static variable in class org.jmol.viewer.Eval
 
ERROR_insufficientArguments - Static variable in class org.jmol.viewer.Eval
 
ERROR_integerExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_integerOutOfRange - Static variable in class org.jmol.viewer.Eval
 
ERROR_invalidArgument - Static variable in class org.jmol.viewer.Eval
 
ERROR_invalidAtomSpecification - Static variable in class org.jmol.viewer.Compiler
 
ERROR_invalidChainSpecification - Static variable in class org.jmol.viewer.Compiler
 
ERROR_invalidExpressionToken - Static variable in class org.jmol.viewer.Compiler
 
ERROR_invalidModelSpecification - Static variable in class org.jmol.viewer.Compiler
 
ERROR_invalidParameterOrder - Static variable in class org.jmol.viewer.Eval
 
ERROR_keywordExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_missingEnd - Static variable in class org.jmol.viewer.Compiler
 
ERROR_multipleModelsNotOK - Static variable in class org.jmol.viewer.Eval
 
ERROR_noUnitCell - Static variable in class org.jmol.viewer.Eval
 
ERROR_numberExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_numberExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_numberMustBe - Static variable in class org.jmol.viewer.Eval
 
ERROR_numberOrVariableNameExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_numberOutOfRange - Static variable in class org.jmol.viewer.Eval
 
ERROR_objectNameExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_propertyNameExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_residueSpecificationExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_spaceGroupNotFound - Static variable in class org.jmol.viewer.Eval
 
ERROR_stringExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_stringOrIdentifierExpected - Static variable in class org.jmol.viewer.Eval
 
ERROR_tokenExpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_tokenUnexpected - Static variable in class org.jmol.viewer.Compiler
 
ERROR_tooManyScriptLevels - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedAtomProperty - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedBondProperty - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedCommand - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedExpression - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedExpressionToken - Static variable in class org.jmol.viewer.Compiler
 
ERROR_unrecognizedObject - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.viewer.Compiler
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedParameterWarning - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedShowParameter - Static variable in class org.jmol.viewer.Eval
 
ERROR_unrecognizedToken - Static variable in class org.jmol.viewer.Compiler
 
ERROR_what - Static variable in class org.jmol.viewer.Eval
 
errorLine - Variable in class org.jmol.viewer.Compiler
 
errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
errorMessage - Variable in class org.jmol.viewer.Compiler
 
errorMessage - Variable in class org.jmol.viewer.Eval
 
errorMessage - Variable in class org.jmol.viewer.FileManager.DOMOpenThread
 
errorMessage - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
errorMessage - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
errors - Static variable in class org.jmol.viewer.Compiler
 
errors - Static variable in class org.jmol.viewer.Eval
 
esCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
escapable - Static variable in class org.jmol.util.Escape
 
Escape - Class in org.jmol.util
For defining the state, mostly
Escape() - Constructor for class org.jmol.util.Escape
 
escape(Object) - Static method in class org.jmol.util.Escape
 
escape(Point4f) - Static method in class org.jmol.util.Escape
 
escape(Tuple3f) - Static method in class org.jmol.util.Escape
 
escape(float[]) - Static method in class org.jmol.util.Escape
 
escape(float[][], boolean) - Static method in class org.jmol.util.Escape
 
escape(int[]) - Static method in class org.jmol.util.Escape
 
escape(String) - Static method in class org.jmol.util.Escape
 
escape(String[]) - Static method in class org.jmol.util.Escape
Serialize a simple string-based array as a single string followed by a .split(x) where x is some character not in the string.
escape(BitSet, boolean) - Static method in class org.jmol.util.Escape
 
escape(BitSet) - Static method in class org.jmol.util.Escape
 
ESCAPE_SET - Static variable in class org.jmol.util.Escape
 
escapeColor(int) - Static method in class org.jmol.util.Escape
 
escapeHTML(String) - Static method in class org.jmol.i18n.GT
 
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
 
escapeUserVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
escapeVariable(String, Object) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
ESTRBND - Static variable in class org.jmol.minimize.forcefield.ForceField
 
ETORSION - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eval(String) - Method in interface org.jmol.api.JmolStatusListener
 
eval(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
Eval - Class in org.jmol.viewer
 
Eval(Viewer) - Constructor for class org.jmol.viewer.Eval
 
eval(String) - Method in class org.jmol.viewer.StatusManager
 
eval - Variable in class org.jmol.viewer.Viewer
 
eval(String) - Method in class org.jmol.viewer.Viewer
 
eval(String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
Eval.Context - Class in org.jmol.viewer
 
Eval.Context() - Constructor for class org.jmol.viewer.Eval.Context
 
Eval.Rpn - Class in org.jmol.viewer
 
Eval.Rpn(int, boolean, boolean) - Constructor for class org.jmol.viewer.Eval.Rpn
 
Eval.ScriptException - Exception in org.jmol.viewer
 
Eval.ScriptException(String) - Constructor for exception org.jmol.viewer.Eval.ScriptException
 
evalError(String) - Method in class org.jmol.viewer.Eval
 
evalFile(String) - Method in class org.jmol.api.JmolSimpleViewer
 
evalFile(String) - Method in class org.jmol.viewer.Viewer
 
evalString(String) - Method in class org.jmol.api.JmolSimpleViewer
 
evalString(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
 
evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuiet(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evalStringWaitStatus(String, String, String) - Method in class org.jmol.viewer.Viewer
 
evalStringWaitStatus(String, String, String, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evaluateArray(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateBoundBox(Token) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateConnected(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateCross(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateData(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateDistance(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateExpression(Viewer, Object) - Static method in class org.jmol.viewer.Eval
a general-use method to evaluate a "SET" type expression.
evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
 
evaluateFind(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateFunction() - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateGetProperty(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateLabel(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateList(int, Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateLoad(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateMath(Token[], int) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateMeasure(Token[], boolean) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluatePlane(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluatePoint(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluatePointOrBitsetOperation(Token, Token) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateRandom(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateReplace(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateScript(Token[], int) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateString(int, Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateSubstructure(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateUserFunction(String, Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateWithin(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evaluateWrite(Token[]) - Method in class org.jmol.viewer.Eval.Rpn
 
evalVariables - Variable in class org.jmol.viewer.Viewer
 
EVDW - Static variable in class org.jmol.minimize.forcefield.ForceField
 
EX - Variable in class org.jmol.quantum.MOCalculation
 
excludeMaximumSet() - Method in class org.jmol.jvxl.readers.VoxelReader
 
excludeMinimumSet() - Method in class org.jmol.jvxl.readers.VoxelReader
 
excludeSelectionSet(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
execThread - Variable in class org.openscience.jmol.app.ScriptWindow
 
execute(String) - Method in class org.jmol.applet.Console
 
executeCommand(String) - Method in class org.openscience.jmol.app.ScriptWindow
 
executeCommandAsThread() - Method in class org.openscience.jmol.app.ScriptWindow
 
executeScriptAction - Variable in class org.openscience.jmol.app.Jmol
 
executionPaused - Variable in class org.jmol.viewer.Eval
 
exit - Static variable in class org.jmol.viewer.Token
 
exitAction - Static variable in class org.openscience.jmol.app.Jmol
 
exitMeasurementMode() - Method in class org.jmol.viewer.MouseManager
 
expdta() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
explicitID - Variable in class org.jmol.shape.MeshCollection
 
Export3D - Class in org.jmol.export
Provides high-level graphics primitives for 3D graphics export.
Export3D() - Constructor for class org.jmol.export.Export3D
 
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JmolConstants
 
exportAction - Variable in class org.openscience.jmol.app.Jmol
 
exportActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
exportDone(JComponent, Transferable, int) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
exporter - Variable in class org.jmol.export.Export3D
 
expression(int) - Method in class org.jmol.viewer.Eval
 
expression(Token[], int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Eval
 
expression - Static variable in class org.jmol.viewer.Token
 
EXPRESSION_KEY - Static variable in class org.jmol.viewer.Eval
 
expressionBegin - Static variable in class org.jmol.viewer.Token
 
expressionEnd - Static variable in class org.jmol.viewer.Token
 
expressionResult - Variable in class org.jmol.viewer.Eval
 
extendRuns(byte[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
extension - Variable in class org.jmol.export.dialog.Dialog
 
extensions - Variable in class org.jmol.export.dialog.Dialog
 
extents - Variable in class org.jmol.jvxl.readers.JaguarReader
 
extractCommandOption(String) - Method in class org.jmol.viewer.Eval
 
extractData(String, int, int, int) - Static method in class org.jmol.util.Parser
 
extractLatticeInfo(String) - Method in class org.jmol.symmetry.HallInfo
 
extractLine() - Method in class org.jmol.symmetry.SpaceGroup
 
extractProperty(Object, Token[], int) - Static method in class org.jmol.viewer.PropertyManager
 
extractRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo
 
extractTerm(char) - Method in class org.jmol.symmetry.SpaceGroup
 
extractVectorInfo(String) - Method in class org.jmol.symmetry.HallInfo
 
EY - Variable in class org.jmol.quantum.MOCalculation
 
EZ - Variable in class org.jmol.quantum.MOCalculation
 

F

f(double) - Method in class org.jmol.jcamp.ZoneVisu
 
FACE_COUNT_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
 
faceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra
 
faceId(int, int, int) - Method in class org.jmol.shapespecial.Polyhedra
 
faceMap - Variable in class org.jmol.shape.DotsRenderer
 
faceNormixesArrays - Static variable in class org.jmol.g3d.Normix3D
 
facePt1 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
 
facePt2 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
 
facePt3 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
 
faceVertexesArrays - Static variable in class org.jmol.g3d.Normix3D
 
faceVertexesArrays - Static variable in class org.jmol.geodesic.Geodesic
 
faceVertexesIcosahedron - Static variable in class org.jmol.geodesic.Geodesic
 
fact - Static variable in class org.jmol.adapter.readers.more.MopacData
 
fact - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
factorDs - Static variable in class org.jmol.adapter.readers.more.MopacData
 
factoredLengths - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
FALSE - Static variable in class org.jmol.viewer.SelectionManager
 
falsifyMesh(int, boolean) - Method in class org.jmol.shapebio.BioShape
 
fatal(String) - Method in class org.jmol.util.DefaultLogger
 
fatal(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
fatal(String) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level.
fatal(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level with detail on exception.
fatal(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at FATAL level.
fatal(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
fc - Variable in class org.openscience.jmol.app.webexport.Molecules
 
fc - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
fc - Variable in class org.openscience.jmol.app.webexport.Test
 
fc - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
fd_oldFileName - Variable in class org.openscience.jmol.app.FileDropper
 
FD_PROPERTY_FILENAME - Static variable in class org.openscience.jmol.app.FileDropper
 
FD_PROPERTY_INLINE - Static variable in class org.openscience.jmol.app.FileDropper
 
fd_propSupport - Variable in class org.openscience.jmol.app.FileDropper
 
Fenetre_Load_File - Variable in class org.jmol.jcamp.Visua
 
ff - Variable in class org.jmol.minimize.forcefield.Calculations
 
ff - Variable in class org.jmol.minimize.Minimizer
 
FF - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
FFParam - Class in org.jmol.minimize.forcefield
 
FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
 
ffParams - Variable in class org.jmol.minimize.forcefield.Calculations
 
fid - Variable in class org.jmol.g3d.Font3D
 
fid - Variable in class org.jmol.shape.Text
 
fid - Variable in class org.jmol.shape.UccageRenderer
 
fidPrevious - Variable in class org.jmol.shape.LabelsRenderer
 
fids - Variable in class org.jmol.shape.Labels
 
field - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldCount - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldCount - Variable in class org.jmol.adapter.readers.more.CsfReader
 
fieldOf - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldProperty(int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
fieldTypes - Variable in class org.jmol.adapter.readers.more.CsfReader
 
file - Variable in class org.jmol.export.dialog.HistoryFile
The location of the history file.
file() - Method in class org.jmol.viewer.Eval
 
file - Static variable in class org.jmol.viewer.Token
 
FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.Jmol
 
FileButton - Variable in class org.openscience.jmol.app.webexport.Test
 
FileChooser - Class in org.jmol.export.dialog
JFileChooser with possibility to fix size and location
FileChooser() - Constructor for class org.jmol.export.dialog.FileChooser
 
fileCoordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileDotModel - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
FileDropper - Class in org.openscience.jmol.app
A simple Dropping class to allow files to be dragged onto a target.
FileDropper() - Constructor for class org.openscience.jmol.app.FileDropper
 
fileHeader - Variable in class org.jmol.modelset.ModelLoader
 
fileIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
fileIndex - Variable in class org.jmol.modelset.Model
 
fileList - Variable in class org.openscience.jmol.app.RecentFilesDialog
 
FileManager - Class in org.jmol.viewer
 
FileManager(Viewer, JmolAdapter) - Constructor for class org.jmol.viewer.FileManager
 
fileManager - Variable in class org.jmol.viewer.Viewer
 
FileManager.DOMOpenThread - Class in org.jmol.viewer
 
FileManager.DOMOpenThread(Object) - Constructor for class org.jmol.viewer.FileManager.DOMOpenThread
 
FileManager.FileOpenThread - Class in org.jmol.viewer
 
FileManager.FileOpenThread(String, String, String, BufferedReader, Hashtable) - Constructor for class org.jmol.viewer.FileManager.FileOpenThread
 
FileManager.FilesOpenThread - Class in org.jmol.viewer
 
FileManager.FilesOpenThread(String[], String[], String[], Reader[]) - Constructor for class org.jmol.viewer.FileManager.FilesOpenThread
 
fileName - Variable in class org.jmol.atomdata.AtomData
 
fileName - Variable in class org.jmol.export._Exporter
 
fileName - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
fileName - Variable in class org.jmol.jvxl.readers.Parameters
 
filename - Variable in class org.jmol.viewer.Compiler
 
filename - Variable in class org.jmol.viewer.Eval.Context
 
filename - Variable in class org.jmol.viewer.Eval
 
fileName - Variable in class org.jmol.viewer.FileManager
 
fileName - Variable in class org.jmol.viewer.ModelManager
 
fileOpenCheck - Variable in class org.jmol.viewer.Eval
 
fileOpenCheck - Variable in class org.jmol.viewer.Viewer
 
fileOpenThread - Variable in class org.jmol.viewer.FileManager
 
FilePreview - Class in org.jmol.export.dialog
File previsualisation before opening
FilePreview(JFileChooser, JmolAdapter, boolean, String) - Constructor for class org.jmol.export.dialog.FilePreview
Constructor
FilePreview.JmolPanel - Class in org.jmol.export.dialog
 
FilePreview.JmolPanel(JmolAdapter, String) - Constructor for class org.jmol.export.dialog.FilePreview.JmolPanel
 
FileReader - Class in org.openscience.jvxl
 
FileReader() - Constructor for class org.openscience.jvxl.FileReader
 
files - Variable in class org.openscience.jmol.app.RecentFilesDialog
 
filesOpenThread - Variable in class org.jmol.viewer.FileManager
 
fileStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
fileType - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
fileType - Variable in class org.jmol.adapter.readers.more.PqrReader
 
fileType - Variable in class org.jmol.viewer.FileManager
 
fileType - Variable in class org.openscience.jmol.app.FileTyper
 
fileTypeComboBox - Variable in class org.openscience.jmol.app.FileTyper
 
fileTypeInThread - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
fileTypeLabel - Variable in class org.openscience.jmol.app.FileTyper
 
fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
FileTyper - Class in org.openscience.jmol.app
 
FileTyper() - Constructor for class org.openscience.jmol.app.FileTyper
A simple panel with a combo box for allowing the user to choose the input file type.
fileTypesInThread - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
fileWriter(File, JList) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
fill - Static variable in class org.jmol.viewer.Token
 
fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
 
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
 
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
 
fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
 
fillCone(short, byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolExportInterface
 
fillCone(byte, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCone(byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCone(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export._MayaExporter
 
fillCone(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export._PovrayExporter
 
fillCone(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export._VrmlExporter
 
fillCone(byte, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillCone(byte, int, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillCone(byte, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillCone(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillCsfArray(String, String[], int, Object) - Method in class org.jmol.adapter.readers.more.CsfReader
 
fillCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
fillCylinder(short, byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolExportInterface
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(byte, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in class org.jmol.export._MayaExporter
 
fillCylinder(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export._MayaExporter
 
fillCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in class org.jmol.export._PovrayExporter
 
fillCylinder(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export._PovrayExporter
 
fillCylinder(Point3f, Point3f, short, short, byte, int, int) - Method in class org.jmol.export._VrmlExporter
 
fillCylinder(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export._VrmlExporter
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinder(byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinder(byte, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.SticksGenerator
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(byte, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.shape.SticksRenderer
 
fillCylinderBits(byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderBits(byte, int, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillCylinderBits(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillDataBlock(String[][]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fillFace(short, Atom, Atom, Atom) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
fillHermite(short, int, int, int, int, Point3f, Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolExportInterface
 
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillHermite(short, int, int, int, int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export._MayaExporter
 
fillHermite(short, int, int, int, int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export._PovrayExporter
 
fillHermite(short, int, int, int, int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export._VrmlExporter
 
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillMeshData(MeshData, int) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
fillMeshData(MeshData, int) - Method in class org.jmol.shapesurface.Isosurface
 
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillQuadrilateral(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
 
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillQuadrilateral(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.export.Export3D
 
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillQuadrilateral(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.g3d.Graphics3D
 
fillRaster(int, int, boolean, boolean, int) - Method in class org.jmol.g3d.Triangle3D
 
fillRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills background rectangle for label
fillRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
fills background rectangle for label
fillRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills background rectangle for label
fillScreenedCircleCentered(short, int, int, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
fillScreenedCircleCentered(short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a screened circle ...
fillScreenedCircleCentered(short, int, int, int, int) - Method in class org.jmol.export._MayaExporter
 
fillScreenedCircleCentered(short, int, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
fillScreenedCircleCentered(short, int, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
fillScreenedCircleCentered(short, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a screened circle ...
fillScreenedCircleCentered(short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillSphereCentered(short, int, Point3f) - Method in interface org.jmol.api.JmolExportInterface
 
fillSphereCentered(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereCentered(int, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereCentered(int, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereCentered(short, int, Point3f) - Method in class org.jmol.export._MayaExporter
 
fillSphereCentered(short, int, Point3f) - Method in class org.jmol.export._PovrayExporter
 
fillSphereCentered(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
fillSphereCentered(short, int, Point3f) - Method in class org.jmol.export._VrmlExporter
 
fillSphereCentered(int, int, int, int) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereCentered(int, Point3i) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereCentered(int, Point3f) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereCentered(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphereCentered(int, Point3i) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphereCentered(int, Point3f) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSquare(MarchingSquares.PlanarSquare, int, int, boolean, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
fillTriangle(short, Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolExportInterface
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(short, int, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3f, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3i, int, Point3i, int, Point3i, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle(short, Point3f, Point3f, Point3f) - Method in class org.jmol.export._MayaExporter
 
fillTriangle(short, Point3f, Point3f, Point3f) - Method in class org.jmol.export._PovrayExporter
 
fillTriangle(short, Point3f, Point3f, Point3f) - Method in class org.jmol.export._VrmlExporter
 
fillTriangle(Point3i, int, Point3i, int, Point3i, int) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.export.Export3D
 
fillTriangle(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3f, Point3f, Point3f) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in class org.jmol.export.Export3D
 
fillTriangle(Point3i, int, Point3i, int, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle(int, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(Point3i, Point3i, Point3i, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(Point3i, Point3i, Point3i, float, boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangle(boolean) - Method in class org.jmol.g3d.Triangle3D
 
fillTriangles - Variable in class org.jmol.shape.Mesh
 
filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filter - Variable in class org.jmol.export.image.PngEncoder
 
FILTER_LAST - Static variable in class org.jmol.export.image.PngEncoder
 
FILTER_NONE - Static variable in class org.jmol.export.image.PngEncoder
Constants for filters
FILTER_SUB - Static variable in class org.jmol.export.image.PngEncoder
 
FILTER_UP - Static variable in class org.jmol.export.image.PngEncoder
 
filterAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterData(boolean, float) - Method in interface org.jmol.api.VolumeDataInterface
 
filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
 
filterSub(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
Perform "sub" filtering on the given row.
filterUp(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
Perform "up" filtering on the given row.
fin - Variable in class org.jmol.jcamp.SaisieDlg
 
finalize(AtomSetCollection, String) - Static method in class org.jmol.adapter.smarter.Resolver
 
finalize() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
finalize() - Method in class org.jmol.viewer.Viewer
 
finalizeGroupBuild() - Method in class org.jmol.modelset.ModelLoader
 
finalizeModels(int) - Method in class org.jmol.modelset.ModelLoader
Model numbers are considerably more complicated in Jmol 11.
finalizeOutput() - Method in interface org.jmol.api.JmolExportInterface
 
finalizeOutput() - Method in class org.jmol.export._Exporter
 
finalizeOutput() - Method in class org.jmol.export._PovrayExporter
 
finalizeShapes() - Method in class org.jmol.modelset.ModelLoader
 
finalizeTrajectories() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
 
finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
 
finalOperations - Variable in class org.jmol.symmetry.SpaceGroup
 
find - Static variable in class org.jmol.viewer.Token
 
Find_Peak - Variable in class org.jmol.jcamp.Visua
 
Find_Peak() - Method in class org.jmol.jcamp.ZoneVisu
 
findAdditionalAxes(int) - Method in class org.jmol.symmetry.PointGroup
 
findApplets(String, String, String, Vector) - Static method in class org.jmol.applet.JmolAppletRegistry
 
findAromaticNeighbor(BitSet) - Method in class org.jmol.modelset.Atom
 
findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
 
findAtomsInRectangle(Rectangle, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
findAxis(Point3f[], int, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.g3d.Graphics3D
 
findBestFit(int, int[]) - Static method in class org.jmol.util.TempArray
 
findBondDipole(Bond) - Method in class org.jmol.shapespecial.Dipoles
 
findCAxes() - Method in class org.jmol.symmetry.PointGroup
 
findClosest(String) - Method in class org.jmol.i18n.GT
 
findContourVertex(int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
findDipole(String) - Method in class org.jmol.shapespecial.Dipoles
 
findDipole(Atom, Atom, boolean) - Method in class org.jmol.shapespecial.Dipoles
 
findDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
findElementsPresent() - Method in class org.jmol.modelset.ModelLoader
 
findFrequency(int, int) - Method in class org.openscience.jmol.app.AtomSetChooser
Have the viewer show a particular frame with frequencies if it can be found.
findInversionCenter() - Method in class org.jmol.symmetry.PointGroup
 
findLeftLeaf() - Method in class org.jmol.bspt.CubeIterator
does the work
findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
 
findMeasurement(int[], Point3fi[]) - Method in class org.jmol.shape.Measures
 
findMeasurement(Measurement) - Method in class org.jmol.shape.Measures
 
findMinMaxX(int) - Method in class org.jmol.g3d.Cylinder3D
 
findMinMaxY() - Method in class org.jmol.g3d.Cylinder3D
 
findNearestAtomIndex(int, int, Atom[]) - Method in class org.jmol.modelset.AtomCollection
 
findNearestAtomIndex(int, int) - Method in class org.jmol.modelset.ModelSet
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.AminoMonomer
 
findNearestAtomIndex(int, int, Atom[], short[], int) - Method in class org.jmol.modelsetbio.BioPolymer
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
findNearestAtomIndex(int, int, Atom[]) - Method in class org.jmol.shape.Shape
 
findNearestAtomIndex(int, int, Atom[]) - Method in class org.jmol.shapebio.BioShape
 
findNearestAtomIndex(int, int, Atom[]) - Method in class org.jmol.shapebio.BioShapeCollection
 
findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
 
findNearestThreePoints(float, float, float[][], int[]) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
 
findPickedBond(int, int, BitSet, Point3f) - Method in class org.jmol.shape.Sticks
 
findPickedObject(int, int, boolean, BitSet) - Method in class org.jmol.shapespecial.Draw
 
findPlanes() - Method in class org.jmol.symmetry.PointGroup
 
findSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
findShorter(int, int[]) - Static method in class org.jmol.util.TempArray
 
fini(boolean) - Method in class org.jmol.jcamp.SaisieDlg
 
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
finish(Object) - Method in class org.jmol.api.JmolAdapter
 
firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
 
firstAtomIndex - Variable in class org.jmol.modelset.Group
 
firstAtomIndex - Variable in class org.jmol.modelset.Model
 
firstAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
firstAtomOffset - Variable in class org.jmol.quantum.MOCalculation
 
firstChar - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
firstFrameDelay - Variable in class org.jmol.viewer.RepaintManager
 
firstFrameDelayMs - Variable in class org.jmol.viewer.RepaintManager
 
firstIsotope - Static variable in class org.jmol.viewer.JmolConstants
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstModelIndex - Variable in class org.jmol.atomdata.AtomData
 
firstModelIndex - Variable in class org.jmol.viewer.RepaintManager
Animation support
firstMolecule - Variable in class org.jmol.modelset.Model
 
firstNearbyAtom - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
firstProper - Static variable in class org.jmol.symmetry.PointGroup
 
firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
firstSetBit(BitSet) - Static method in class org.jmol.util.BitSetUtil
 
Firstx - Variable in class org.jmol.jcamp.Visua
 
Firstx - Variable in class org.jmol.jcamp.ZoneVisu
 
fixBasisLine(String) - Static method in class org.jmol.adapter.readers.more.GamessReader
 
fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
 
fixedtemp - Static variable in class org.jmol.viewer.Token
 
fixedTranslation - Variable in class org.jmol.viewer.TransformManager
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
fixIndices(int) - Method in class org.jmol.modelset.Chain
 
fixIndices(int, int, BitSet) - Method in class org.jmol.modelset.Model
 
fixLabel(Atom, String) - Method in class org.jmol.shape.HoverRenderer
 
fixName(String) - Static method in class org.jmol.util.ColorEncoder
 
fixQ(Quaternion) - Method in class org.jmol.util.Quaternion
 
fixScript(String, String) - Method in class org.jmol.popup.JmolPopup
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.more.GamessReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.more.GamessUKReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.more.GamessUSReader
 
fixString(String) - Static method in class org.jmol.util.Escape
 
fixTag(String) - Method in class org.jmol.adapter.readers.more.NWChemReader
Returns a modified identifier for a tag, so that the element can be determined from it in the Atom.
fixText(String) - Method in class org.jmol.shape.Text
 
fixTitleLine(int) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
fixTitleLine(int, Hashtable) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
Flag_Clickable_Peaks - Variable in class org.jmol.jcamp.ZoneVisu
 
Flag_Dialogue_File_Enabled - Variable in class org.jmol.jcamp.Visua
 
Flag_Find_Peak - Variable in class org.jmol.jcamp.Visua
 
Flag_Grid - Variable in class org.jmol.jcamp.ZoneVisu
 
Flag_Integrate - Variable in class org.jmol.jcamp.Visua
 
Flag_Integrate - Variable in class org.jmol.jcamp.ZoneVisu
 
Flag_Load_Now_Html - Variable in class org.jmol.jcamp.ZoneVisu
 
FLAG_MASK - Static variable in class org.jmol.modelset.Atom
 
FLAG_OFFSET - Static variable in class org.jmol.shape.Labels
 
Flag_Redraw - Variable in class org.jmol.jcamp.Visua
 
Flag_Reverse - Variable in class org.jmol.jcamp.Visua
 
Flag_Reverse - Variable in class org.jmol.jcamp.ZoneVisu
 
Flag_Write_JCamp - Variable in class org.jmol.jcamp.Visua
 
Flag_Zoomback - Variable in class org.jmol.jcamp.Visua
 
Flag_Zoomin - Variable in class org.jmol.jcamp.Visua
 
Flag_Zoomout - Variable in class org.jmol.jcamp.Visua
 
FLAGS - Static variable in class org.jmol.shape.Labels
 
flipLighting(int) - Method in class org.jmol.shape.Mesh
 
floatinfo - Variable in class org.jmol.adapter.readers.more.MopacDataReader
 
floatParameter(int, float, float) - Method in class org.jmol.viewer.Eval
 
floatParameter(int) - Method in class org.jmol.viewer.Eval
 
floatParameterSet(int, float[]) - Method in class org.jmol.viewer.Eval
 
floatRange - Variable in class org.jmol.shapebio.BioShape
 
floatSetting(int, float, float) - Method in class org.jmol.viewer.Eval
 
floatSetting(int) - Method in class org.jmol.viewer.Eval
 
floatValue() - Method in class org.jmol.viewer.Compiler
 
flowCommand - Static variable in class org.jmol.viewer.Token
 
flowContext - Variable in class org.jmol.viewer.Compiler
 
flowControl(int) - Method in class org.jmol.viewer.Eval
 
flush_char(OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
flushBuffer(BufferedOutputStream) - Method in class org.jmol.util.Huffman
 
flushCaches() - Static method in class org.jmol.viewer.ColorManager
 
flushLines() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
flushLines() - Method in class org.jmol.adapter.readers.more.V3000Reader
 
flushQueue(String) - Method in class org.jmol.viewer.ScriptManager
 
flushShades() - Static method in class org.jmol.g3d.Colix3D
 
flushShadesAndSphereCaches() - Static method in class org.jmol.g3d.Graphics3D
 
flushSphereCache() - Static method in class org.jmol.g3d.Sphere3D
 
fm - Variable in class org.jmol.shape.Text
 
fmt(int) - Method in class org.jmol.applet.Jmol
 
fmt(int) - Method in class org.openscience.jmol.app.DisplayPanel
 
FoldingXyzReader - Class in org.jmol.adapter.readers.more
This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.more.FoldingXyzReader
 
font - Variable in class org.jmol.appletwrapper.AppletWrapper
 
font - Variable in class org.jmol.g3d.Font3D
 
font - Variable in class org.jmol.shape.Text
 
font(int, float) - Method in class org.jmol.viewer.Eval
 
font - Static variable in class org.jmol.viewer.Token
 
Font3D - Class in org.jmol.g3d
Provides font support using a byte fid (Font ID) as an index into font table.
Font3D(byte, int, int, float, float, Font, FontMetrics) - Constructor for class org.jmol.g3d.Font3D
 
font3d - Variable in class org.jmol.shape.FontLineShape
 
font3d - Variable in class org.jmol.shape.LabelsRenderer
 
font3d - Variable in class org.jmol.shape.Measures
 
font3d - Variable in class org.jmol.shape.MeasuresRenderer
 
font3dCurrent - Variable in class org.jmol.g3d.Graphics3D
 
font3ds - Static variable in class org.jmol.g3d.Font3D
 
FONT_ALLOCATION_UNIT - Static variable in class org.jmol.g3d.Font3D
 
FONT_FACE_MONO - Static variable in class org.jmol.g3d.Font3D
 
FONT_FACE_SANS - Static variable in class org.jmol.g3d.Font3D
 
FONT_FACE_SERIF - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_BOLD - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_ITALIC - Static variable in class org.jmol.g3d.Font3D
 
FONT_STYLE_PLAIN - Static variable in class org.jmol.g3d.Font3D
 
fontAscent - Variable in class org.jmol.appletwrapper.AppletWrapper
 
fontFace - Static variable in class org.jmol.appletwrapper.AppletWrapper
 
fontFace - Variable in class org.jmol.g3d.Font3D
 
FONTFACE - Static variable in class org.jmol.shape.Echo
 
FONTFACE - Static variable in class org.jmol.shape.Hover
 
fontFaces - Static variable in class org.jmol.g3d.Font3D
 
fontHeight - Variable in class org.jmol.appletwrapper.AppletWrapper
 
fontkeyCount - Static variable in class org.jmol.g3d.Font3D
 
fontkeys - Static variable in class org.jmol.g3d.Font3D
 
FontLineShape - Class in org.jmol.shape
 
FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
 
FontLineShapeRenderer - Class in org.jmol.shape
 
FontLineShapeRenderer() - Constructor for class org.jmol.shape.FontLineShapeRenderer
 
fontMetrics - Variable in class org.jmol.appletwrapper.AppletWrapper
 
fontMetrics - Variable in class org.jmol.g3d.Font3D
 
fontScale - Variable in class org.jmol.shape.Text
 
fontScaling - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
fontSize - Variable in class org.jmol.appletwrapper.AppletWrapper
 
fontSize - Variable in class org.jmol.g3d.Font3D
 
FONTSIZE - Static variable in class org.jmol.shape.Echo
 
FONTSIZE - Static variable in class org.jmol.shape.Hover
 
fontsize - Static variable in class org.jmol.viewer.Token
 
fontSizeDivisor - Static variable in class org.jmol.appletwrapper.AppletWrapper
 
fontSizeNominal - Variable in class org.jmol.g3d.Font3D
 
fontStyle - Variable in class org.jmol.g3d.Font3D
 
FONTSTYLE - Static variable in class org.jmol.shape.Hover
 
fontStyles - Static variable in class org.jmol.g3d.Font3D
 
force - Variable in class org.jmol.minimize.MinAtom
 
forceAutoBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
forceAwt - Static variable in class org.jmol.popup.JmolPopup
 
ForceField - Class in org.jmol.minimize.forcefield
 
ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
 
ForceFieldUFF - Class in org.jmol.minimize.forcefield
 
ForceFieldUFF() - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
 
forcePlatformAWT - Static variable in class org.jmol.g3d.Platform3D
 
forcmd - Static variable in class org.jmol.viewer.Token
 
FORMAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_INDEX_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_INDEX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
FORMAL_CHARGE_MIN - Static variable in class org.jmol.viewer.JmolConstants
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
FORMAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
 
formalCharge - Variable in class org.jmol.adapter.smarter.Atom
 
formalCharge - Static variable in class org.jmol.viewer.Token
 
formalChargeAndFlags - Variable in class org.jmol.modelset.Atom
 
format(float, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
format(String, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
formatAngle(float) - Method in class org.jmol.modelset.Measurement
 
FormatBox - Variable in class org.openscience.jmol.app.webexport.Molecules
 
FormatBox - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
formatDecimal(float, int) - Static method in class org.jmol.util.TextFormat
 
formatDistance(float) - Method in class org.jmol.modelset.Measurement
 
formatLabel(String) - Method in class org.jmol.modelset.Atom
 
formatLabel(String, char, int[]) - Method in class org.jmol.modelset.Atom
 
formatLabel(String, int[]) - Method in class org.jmol.modelset.Bond
 
formatMeasurement(String, boolean) - Method in class org.jmol.modelset.Measurement
 
formatMeasurement() - Method in class org.jmol.modelset.Measurement
 
formats - Variable in class org.jmol.shape.Labels
 
formatString(float, String) - Method in class org.jmol.modelset.Measurement
 
formatString(String, String, String) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, float) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, int) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, String, float) - Static method in class org.jmol.util.TextFormat
 
formatString(String, String, String, float, boolean) - Static method in class org.jmol.util.TextFormat
generic string formatter based on formatLabel in Atom
formatters - Static variable in class org.jmol.util.TextFormat
 
formatText() - Method in class org.jmol.shape.Text
 
formatText(String) - Method in class org.jmol.viewer.Viewer
 
formattingStrings - Static variable in class org.jmol.util.TextFormat
 
formul() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
formula - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
forwardDCT(float[][]) - Static method in class org.jmol.util.DCT
 
foundDistance2() - Method in class org.jmol.bspt.CubeIterator
After calling nextElement(), allows one to find out the value of the distance squared.
foundDistance2() - Method in interface org.jmol.modelset.AtomIndexIterator
 
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinSet
 
fourPi - Static variable in class org.jmol.adapter.readers.more.MopacData
 
fp8IntensityUp - Variable in class org.jmol.g3d.Cylinder3D
 
FPS_MAX - Static variable in class org.openscience.jmol.app.AtomSetChooser
Maximum value for the fps slider.
fpsSlider - Variable in class org.openscience.jmol.app.AtomSetChooser
 
FRACT_X - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
FRACT_Y - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
FRACT_Z - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
fractionalOffset - Variable in class org.jmol.symmetry.UnitCell
 
fractionData - Variable in class org.jmol.jvxl.readers.VoxelReader
 
fractionPtr - Variable in class org.jmol.jvxl.readers.JvxlReader
 
fractions - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
fracX - Static variable in class org.jmol.viewer.Token
 
fracXyz - Static variable in class org.jmol.viewer.Token
 
fracY - Static variable in class org.jmol.viewer.Token
 
fracZ - Static variable in class org.jmol.viewer.Token
 
frame(int) - Method in class org.jmol.viewer.Eval
 
frame - Static variable in class org.jmol.viewer.Token
 
frame - Variable in class org.openscience.jmol.app.Jmol
 
frameControl(int, boolean) - Method in class org.jmol.viewer.Eval
 
FrameExportJmolAdapter - Class in org.jmol.viewer
 
FrameExportJmolAdapter(Viewer, ModelSet) - Constructor for class org.jmol.viewer.FrameExportJmolAdapter
 
FrameExportJmolAdapter.AtomIterator - Class in org.jmol.viewer
 
FrameExportJmolAdapter.AtomIterator() - Constructor for class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
FrameExportJmolAdapter.BondIterator - Class in org.jmol.viewer
 
FrameExportJmolAdapter.BondIterator() - Constructor for class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
framePointer - Variable in class org.jmol.viewer.RepaintManager.AnimationThread
 
framePointer2 - Variable in class org.jmol.viewer.RepaintManager.AnimationThread
 
FrameRenderer - Class in org.jmol.viewer
 
FrameRenderer(Viewer) - Constructor for class org.jmol.viewer.FrameRenderer
 
frameRenderer - Variable in class org.jmol.viewer.RepaintManager
 
FramesOnly - Variable in class org.jmol.popup.JmolPopup
 
frameStep - Variable in class org.jmol.viewer.RepaintManager
 
frameTitles - Variable in class org.jmol.modelset.ModelCollection
 
Frank - Class in org.jmol.shape
 
Frank() - Constructor for class org.jmol.shape.Frank
 
frank(int) - Method in class org.jmol.viewer.Eval
 
frank - Static variable in class org.jmol.viewer.Token
 
frankAscent - Variable in class org.jmol.shape.Frank
 
frankClicked(int, int) - Method in class org.jmol.modelset.ModelSet
 
frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
 
frankDescent - Variable in class org.jmol.shape.Frank
 
FrankGenerator - Class in org.jmol.export
 
FrankGenerator() - Constructor for class org.jmol.export.FrankGenerator
 
frankList - Variable in class org.jmol.popup.JmolPopup
 
frankMargin - Static variable in class org.jmol.shape.Frank
 
frankOn - Variable in class org.jmol.viewer.Viewer
 
frankPopup - Variable in class org.jmol.popup.JmolPopup
 
FrankRenderer - Class in org.jmol.shape
 
FrankRenderer() - Constructor for class org.jmol.shape.FrankRenderer
 
frankString - Variable in class org.jmol.shape.Frank
 
frankWidth - Variable in class org.jmol.shape.Frank
 
free_ent - Variable in class org.jmol.export.image.GifEncoder
 
freeBonds - Variable in class org.jmol.modelset.BondCollection
 
freeBytes - Variable in class org.jmol.util.TempArray
 
freeBytesSize - Static variable in class org.jmol.util.TempArray
 
freePoints - Variable in class org.jmol.util.TempArray
 
freePointsSize - Static variable in class org.jmol.util.TempArray
 
freeScreens - Variable in class org.jmol.util.TempArray
 
freeScreensSize - Static variable in class org.jmol.util.TempArray
 
freeTempArrays() - Method in class org.jmol.shapebio.BioShapeRenderer
 
freeTempBytes(byte[]) - Method in class org.jmol.util.TempArray
 
freeTempBytes(byte[]) - Method in class org.jmol.viewer.Viewer
 
freeTempPoints(Point3f[]) - Method in class org.jmol.util.TempArray
 
freeTempPoints(Point3f[]) - Method in class org.jmol.viewer.Viewer
 
freeTempScreens(Point3i[]) - Method in class org.jmol.util.TempArray
 
freeTempScreens(Point3i[]) - Method in class org.jmol.viewer.Viewer
 
freeze() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
freeze() - Method in class org.jmol.modelset.ModelLoader
 
freeze() - Method in class org.jmol.modelset.Polymer
 
freeze() - Method in class org.jmol.modelsetbio.AminoPolymer
 
freezeModels() - Method in class org.jmol.modelset.ModelCollection
 
FREQ_FIRST_VECTOR_OFFSET - Static variable in class org.jmol.adapter.readers.more.GaussianReader
Word index of the first X vector of the first frequency in the frequency output.
freqAtomSet - Variable in class org.jmol.adapter.readers.more.MoldenReader
 
frequencies - Variable in class org.jmol.adapter.readers.more.MoldenReader
 
frequencyCount - Variable in class org.jmol.adapter.readers.xml.XmlMolproReader
 
fReturn - Variable in class org.jmol.jvxl.readers.VoxelReader
 
FromLinks - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
FromMenu - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
front - Static variable in class org.jmol.viewer.Token
 
FRONT_FLAG - Static variable in class org.jmol.shape.Labels
 
frontAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
FRONTLIT - Static variable in class org.jmol.viewer.JmolConstants
 
frontlit - Static variable in class org.jmol.viewer.Token
 
frontOnly - Variable in class org.jmol.shape.Mesh
 
frontOnly - Variable in class org.jmol.shape.MeshRenderer
 
frontonly - Static variable in class org.jmol.viewer.Token
 
fullCommand - Variable in class org.jmol.viewer.Eval
 
fullName - Variable in class org.jmol.applet.Jmol
 
fullName - Variable in class org.jmol.viewer.Viewer
 
fullPathName - Variable in class org.jmol.viewer.FileManager
 
fullPathName - Variable in class org.jmol.viewer.ModelManager
 
fullPathNameInThread - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
fullPathNamesInThread - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
fullTrim(String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
specially for names that might be multiline
FULLYLIT - Static variable in class org.jmol.viewer.JmolConstants
 
fullylit - Static variable in class org.jmol.viewer.Token
 
function - Variable in class org.jmol.viewer.Compiler.FlowContext
 
function() - Method in class org.jmol.viewer.Eval
 
Function - Class in org.jmol.viewer
 
Function(String) - Constructor for class org.jmol.viewer.Function
 
function - Static variable in class org.jmol.viewer.Token
 
functionName - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
functionName - Variable in class org.jmol.viewer.Eval.Context
 
functionName - Variable in class org.jmol.viewer.Eval
 
functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
 
functionXY(String, int, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
functionXY(String, int, int) - Method in class org.jmol.viewer.StatusManager
 
functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
functionXY(String, int, int) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
functionXYinfo - Variable in class org.jmol.jvxl.readers.Parameters
 
fValue(Token) - Static method in class org.jmol.viewer.Token
 

G

g3d - Variable in class org.jmol.export._Exporter
 
g3d - Variable in class org.jmol.export.Export3D
 
g3d - Variable in class org.jmol.g3d.Circle3D
 
g3d - Variable in class org.jmol.g3d.Cylinder3D
 
g3d - Variable in class org.jmol.g3d.Hermite3D
 
g3d - Variable in class org.jmol.g3d.Line3D
 
g3d - Variable in class org.jmol.g3d.Sphere3D
 
g3d - Variable in class org.jmol.g3d.Triangle3D
 
g3d - Variable in class org.jmol.modelset.AtomCollection
 
g3d - Variable in class org.jmol.shape.Mesh
 
g3d - Variable in class org.jmol.shape.Object2d
 
g3d - Variable in class org.jmol.shape.Shape
 
g3d - Variable in class org.jmol.shape.ShapeRenderer
 
g3d - Variable in class org.jmol.viewer.ColorManager
 
g3d - Variable in class org.jmol.viewer.Viewer
 
g_init_bits - Variable in class org.jmol.export.image.GifEncoder
 
GamessReader - Class in org.jmol.adapter.readers.more
 
GamessReader() - Constructor for class org.jmol.adapter.readers.more.GamessReader
 
GamessUKReader - Class in org.jmol.adapter.readers.more
 
GamessUKReader() - Constructor for class org.jmol.adapter.readers.more.GamessUKReader
 
gamessUKRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GamessUSReader - Class in org.jmol.adapter.readers.more
 
GamessUSReader() - Constructor for class org.jmol.adapter.readers.more.GamessUSReader
 
gamessUSRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
gamma - Variable in class org.jmol.symmetry.UnitCell
 
gaussianCount - Variable in class org.jmol.adapter.readers.more.GamessReader
 
gaussianCount - Variable in class org.jmol.adapter.readers.more.GaussianReader
 
gaussianCount - Variable in class org.jmol.adapter.readers.more.JaguarReader
 
gaussianCount - Variable in class org.jmol.adapter.readers.more.PsiReader
 
gaussianCount - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
 
GaussianReader - Class in org.jmol.adapter.readers.more
Reader for Gaussian 94/98/03 output files.
GaussianReader() - Constructor for class org.jmol.adapter.readers.more.GaussianReader
 
gaussianRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
gaussians - Variable in class org.jmol.quantum.MOCalculation
 
generalResourceBundle - Variable in class org.openscience.jmol.app.JmolResourceHandler
 
generateAllOperators(HallInfo) - Method in class org.jmol.symmetry.SpaceGroup
 
generateBaseEllipse() - Method in class org.jmol.g3d.Cylinder3D
 
generateBaseEllipsePrecisely() - Method in class org.jmol.g3d.Cylinder3D
 
generateContourData(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
generateContourData(float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoMepReader
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateCube() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
generateOperatorsFromXyzInfo(String) - Method in class org.jmol.symmetry.SpaceGroup
 
generateOutput(String, String, int, int) - Method in class org.jmol.api.JmolViewer
 
generateOutput(String, Graphics3D, ModelSet, String) - Method in class org.jmol.viewer.FrameRenderer
 
generateOutput(String, Graphics3D, ModelSet, String) - Method in class org.jmol.viewer.RepaintManager
 
generateOutput(String, String, int, int) - Method in class org.jmol.viewer.Viewer
 
generateRaster(int, int, int, int[], int[], int, Rgb16[]) - Method in class org.jmol.g3d.Triangle3D
 
generateResidueSpecCode(Token) - Method in class org.jmol.viewer.Compiler
 
generateSolventCavity() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateSolventCube(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
generateSurfaceData(boolean) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
generateSurfaceData() - Method in class org.jmol.jvxl.readers.VoxelReader
 
Geodesic - Class in org.jmol.geodesic
Consolidated Geodesic from dotsRenderer 3/19/07 Bob Hanson Constructs a canonical geodesic sphere of unit radius.
Geodesic() - Constructor for class org.jmol.geodesic.Geodesic
 
geodesicCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
geodesicMap - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
GEOM_BOND_ATOM_SITE_LABEL_1 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
GEOM_BOND_ATOM_SITE_LABEL_2 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
GEOM_BOND_SITE_SYMMETRY_2 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
geomBondFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
GeoSurface - Class in org.jmol.shapespecial
 
GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
 
geosurface - Static variable in class org.jmol.viewer.Token
 
GeoSurfaceGenerator - Class in org.jmol.export
 
GeoSurfaceGenerator() - Constructor for class org.jmol.export.GeoSurfaceGenerator
 
GeoSurfaceRenderer - Class in org.jmol.shapespecial
 
GeoSurfaceRenderer() - Constructor for class org.jmol.shapespecial.GeoSurfaceRenderer
 
get(String) - Method in class org.jmol.applet.GuiMap
 
get(int) - Method in class org.jmol.util.Int2IntHash
 
get(String) - Method in class org.openscience.jmol.app.GuiMap
 
get2SidedNormix(Vector3f) - Method in class org.jmol.g3d.Graphics3D
 
getAatokenCompiled() - Method in class org.jmol.viewer.Compiler
 
getAction(String) - Method in class org.openscience.jmol.app.Jmol
Fetch the action that was created for the given command.
getAction(String) - Method in class org.openscience.jmol.app.PreferencesDialog
 
getActions() - Method in class org.openscience.jmol.app.DisplayPanel
 
getActions() - Method in class org.openscience.jmol.app.Jmol
 
getActions() - Method in class org.openscience.jmol.app.PreferencesDialog
 
getAdapterName() - Method in class org.jmol.api.JmolAdapter
 
getAdditionalHydrogens(BitSet, int[]) - Method in class org.jmol.modelset.AtomCollection
 
getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
 
getAlignment(int) - Static method in class org.jmol.shape.Labels
 
getAlignment(int) - Static method in class org.jmol.shape.Object2d
 
getAllAtomInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllAtomInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllAxes(Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
getAllBondInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllBondInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllChainInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllChainInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllData() - Method in class org.jmol.util.CompoundDocument
 
getAllInfo() - Method in class org.jmol.shape.Measures
 
getAllInfoAsString() - Method in class org.jmol.shape.Measures
 
getAllowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
 
getAllPolymerInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAllPolymerInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAllSettings(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getAllSettings(String) - Method in class org.jmol.viewer.Viewer
 
getAlternateLocationID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAlternateLocationID() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAlternateLocationID() - Method in class org.jmol.modelset.Atom
 
getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelCollection
 
getAltLocListInModel(int) - Method in class org.jmol.api.JmolViewer
 
getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getAltLocListInModel(int) - Method in class org.jmol.viewer.Viewer
 
getAltLocLists() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAmbientPercent() - Static method in class org.jmol.g3d.Graphics3D
 
getAmbientPercent() - Static method in class org.jmol.viewer.ColorManager
 
getAmbientPercent() - Static method in class org.jmol.viewer.Viewer
 
getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
 
getAngles() - Method in class org.jmol.minimize.Minimizer
 
getAnimationDirection() - Method in class org.jmol.viewer.Viewer
 
getAnimationFps() - Method in class org.jmol.api.JmolViewer
 
getAnimationFps() - Method in class org.jmol.viewer.Viewer
 
getAnimationInfo() - Method in class org.jmol.viewer.RepaintManager
 
getAnimationInfo() - Method in class org.jmol.viewer.Viewer
 
getAnimationModeName() - Method in class org.jmol.viewer.RepaintManager
 
getAnimationReplayMode() - Method in class org.jmol.viewer.Viewer
 
getAppendNew() - Method in class org.jmol.viewer.Viewer
 
getAppletDefs(int, String, StringBuffer, JmolInstance) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
getAppletDefs(int, String, StringBuffer, JmolInstance) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
getAppletDefs(int, String, StringBuffer, JmolInstance) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getAppletDocumentBase() - Method in class org.jmol.viewer.FileManager
 
getAppletInfo() - Method in class org.jmol.applet.Jmol
 
getAppletInfo() - Method in class org.jmol.appletwrapper.AppletWrapper
 
getAppletInfo() - Method in interface org.jmol.appletwrapper.WrappedApplet
 
getAppletInfo() - Method in class org.jmol.viewer.Viewer
 
getAppletPath(boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getApplySymmetryToBonds() - Method in class org.jmol.viewer.Viewer
 
getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getArgb(short) - Static method in class org.jmol.g3d.Colix3D
 
getArgb() - Method in class org.jmol.g3d.Rgb16
 
getArgb1() - Method in class org.jmol.modelset.Bond
 
getArgb2() - Method in class org.jmol.modelset.Bond
 
getArgbFromPalette(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
 
getArgbFromString(String) - Static method in class org.jmol.g3d.Graphics3D
accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or a valid JavaScript color
getArgbGreyscale(short) - Static method in class org.jmol.g3d.Colix3D
 
getArgbHbondType(short) - Static method in class org.jmol.viewer.JmolConstants
 
getArgbParam(int) - Method in class org.jmol.viewer.Eval
 
getArgbParam(int, boolean) - Method in class org.jmol.viewer.Eval
 
getArgbParamLast(int, boolean) - Method in class org.jmol.viewer.Eval
 
getAromaticDottedBondMask() - Method in class org.jmol.shape.SticksRenderer
 
getAssociatedAtoms() - Method in class org.jmol.modelset.Bond.BondSet
 
getAtom(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtom(int) - Method in class org.jmol.modelset.Chain
 
getAtom(int) - Method in class org.jmol.modelset.Measurement
 
getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtom(int) - Method in class org.jmol.shape.MeasuresRenderer
 
getAtom(int) - Method in class org.jmol.smiles.SmilesMolecule
 
getAtom1() - Method in class org.jmol.modelset.Bond
 
getAtom1() - Method in class org.jmol.smiles.SmilesBond
 
getAtom2() - Method in class org.jmol.modelset.Bond
 
getAtom2() - Method in class org.jmol.smiles.SmilesBond
 
getAtomArgb(int) - Method in class org.jmol.api.JmolViewer
 
getAtomArgb(int) - Method in class org.jmol.viewer.Viewer
 
getAtomAt(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomBits(int, Object) - Method in class org.jmol.modelset.AtomCollection
general unqualified lookup of atom set type
getAtomBits(int, Object) - Method in class org.jmol.modelset.BondCollection
 
getAtomBits(int, Object) - Method in class org.jmol.modelset.ModelCollection
general unqualified lookup of atom set type
getAtomBits(int, Object) - Method in class org.jmol.modelset.ModelSet
general lookup for integer type -- from Eval
getAtomBits(int, Object) - Method in class org.jmol.viewer.Eval
 
getAtomBits(int, Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSet(Eval, Viewer, Object) - Static method in class org.jmol.viewer.Eval
 
getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSetVector(Eval, Viewer, Object) - Static method in class org.jmol.viewer.Eval
 
getAtomBitSetVector(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomChain(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomChain(int) - Method in class org.jmol.viewer.Viewer
 
getAtomColix(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomCount() - Method in class org.jmol.api.JmolViewer
 
getAtomCount() - Method in class org.jmol.modelset.AtomCollection
 
getAtomCount() - Method in class org.jmol.modelset.Chain
 
getAtomCount() - Method in class org.jmol.viewer.Viewer
 
getAtomCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getAtomCountInModel(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getAtomCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getAtomDataServer() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic mass of the atom.
getAtomicPropertyState(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomicPropertyState(StringBuffer, Atom[], int, byte, BitSet, String, float[]) - Static method in class org.jmol.modelset.AtomCollection
 
getAtomIdentityInfo(int, Hashtable) - Method in class org.jmol.modelset.ModelCollection
 
getAtomIdentityInfo(int, Hashtable) - Method in class org.jmol.viewer.Viewer
 
getAtomIndex() - Method in class org.jmol.modelset.Atom
 
getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
 
getAtomIndex1() - Method in class org.jmol.modelset.Bond
 
getAtomIndex2() - Method in class org.jmol.modelset.Bond
 
getAtomIndexFromAtomNumber(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndexFromAtomNumber(int) - Method in class org.jmol.viewer.Viewer
 
getAtomIndices(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndices(BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomInfo(int) - Method in class org.jmol.api.JmolViewer
 
getAtomInfo(int, String) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
 
getAtomInfoLong(int) - Method in class org.jmol.modelset.ModelCollection
 
getAtomInfoXYZ(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfoXYZ(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get an AtomIterator for retrieval of all atoms in the file.
getAtomIterator(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.Calculations
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
getAtomModelIndex(int) - Method in class org.jmol.api.JmolViewer
 
getAtomModelIndex(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
getAtomName() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomName() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomName(int) - Method in class org.jmol.api.JmolViewer
 
getAtomName() - Method in class org.jmol.modelset.Atom
 
getAtomName(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomName(int) - Method in class org.jmol.viewer.Viewer
 
getAtomNameIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomNames() - Method in class org.jmol.modelset.AtomCollection
 
getAtomNumber(int) - Method in class org.jmol.api.JmolViewer
 
getAtomNumber() - Method in class org.jmol.modelset.Atom
 
getAtomNumber(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomNumber(int) - Method in class org.jmol.viewer.Viewer
 
getAtomPicking() - Method in class org.jmol.viewer.Viewer
 
getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtomPoint3f(int) - Method in class org.jmol.api.JmolViewer
 
getAtomPoint3f(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomPoint3f(int) - Method in class org.jmol.viewer.Viewer
 
getAtomRadius(int) - Method in class org.jmol.api.JmolViewer
 
getAtomRadius(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomRadius(int) - Method in class org.jmol.viewer.Viewer
 
getAtomRecordMOL(StringBuffer, int) - Method in class org.jmol.modelset.ModelCollection
 
getAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtoms(float, boolean, boolean) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getAtoms() - Method in class org.jmol.modelset.AtomCollection
 
getAtomsAndElements(Atom[], BitSet) - Method in class org.jmol.symmetry.PointGroup
 
getAtomsConnected(float, float, int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAtomsConnected(float, float, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomsCount() - Method in class org.jmol.smiles.SmilesMolecule
 
getAtomSequenceCode(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomSequenceCode(int) - Method in class org.jmol.viewer.Viewer
 
getAtomSerial() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSerial() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSerialNumberIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for a particular atomSet.
getAtomSetCenter(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAtomSetCenter(BitSet) - Method in class org.jmol.viewer.Viewer
 
getAtomSetCollectionAuxiliaryInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for this atomSetCollection.
getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
Get the name of the atom set collection, if known.
getAtomSetCollectionName(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter
 
getAtomSetCollectionProperties(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionProperties(Object) - Method in class org.jmol.api.JmolAdapter
Get the properties for this atomSetCollection.
getAtomSetCollectionProperty(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
Get number of atomSets in the file.
getAtomSetIndex() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSetIndex() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSetIndex() - Method in class org.openscience.jmol.app.AtomSetChooser.AtomSet
 
getAtomSetName(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the name of an atomSet.
getAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the number identifying each atomSet.
getAtomSetProperties(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetProperties(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetProperties(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the properties for an atomSet.
getAtomSite() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSite() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSite() - Method in class org.jmol.modelset.Atom
 
getAtomsWithin(float, Point4f) - Method in class org.jmol.modelset.AtomCollection
 
getAtomsWithin(float, BitSet, boolean) - Method in class org.jmol.modelset.ModelCollection
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
getAtomsWithin(float, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
getAtomsWithin(float, Point3f) - Method in class org.jmol.viewer.Viewer
 
getAtomsWithin(float, Point4f) - Method in class org.jmol.viewer.Viewer
 
getAtomsWithin(float, BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
getAtomSymmetry() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getAtomSymmetry() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getAtomSymmetry() - Method in class org.jmol.modelset.Atom
 
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceField
 
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getAtomTypes() - Method in class org.jmol.minimize.Minimizer
 
getAtomUniqueID1() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
getAtomUniqueID1() - Method in class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
getAtomUniqueID2() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
getAtomUniqueID2() - Method in class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
getAtomVdwRadius(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomVdwRadius(int) - Method in class org.jmol.viewer.Viewer
 
getAtomX(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomX(int) - Method in class org.jmol.viewer.Viewer
 
getAtomY(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomY(int) - Method in class org.jmol.viewer.Viewer
 
getAtomZ(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomZ(int) - Method in class org.jmol.viewer.Viewer
 
getAttributes(Attributes) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
getAttributes(JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
getAutoBond() - Method in class org.jmol.api.JmolViewer
 
getAutoBond() - Method in class org.jmol.viewer.Viewer
 
getAutoFps() - Method in class org.jmol.viewer.Viewer
 
getAuxiliaryFileData() - Method in class org.jmol.export._PovrayExporter
 
getAuxiliaryInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getAuxiliaryInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getAverageAtomPoint() - Method in class org.jmol.modelset.ModelCollection
 
getAverageAtomPoint() - Method in class org.jmol.viewer.Viewer
 
getAwtComponent() - Method in class org.jmol.api.JmolViewer
 
getAwtComponent() - Method in class org.jmol.viewer.Viewer
 
getAxesForEllipsoid(double[], Vector3f[], float[]) - Static method in class org.jmol.util.Quadric
 
getAxesMode() - Method in class org.jmol.viewer.Viewer
 
getAxesOrientationRasmol() - Method in class org.jmol.api.JmolViewer
 
getAxesOrientationRasmol() - Method in class org.jmol.viewer.Viewer
 
getAxesScale() - Method in class org.jmol.viewer.Viewer
 
getAxisAngle(Vector3f) - Method in class org.jmol.export._Exporter
 
getAxisAngle() - Method in class org.jmol.modelset.Measurement
 
getAxisAngle(AxisAngle4f) - Method in class org.jmol.viewer.TransformManager
 
getAxisAngle(AxisAngle4f) - Method in class org.jmol.viewer.Viewer
 
getAxisColor() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getAxisPoint(int, boolean) - Method in class org.jmol.shape.Axes
 
getAxisPoints() - Method in class org.jmol.viewer.Viewer
 
getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getAxisTextColor() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
 
getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
 
getBackgroundModelIndex() - Method in class org.jmol.viewer.Viewer
 
getBase64(StringBuffer) - Static method in class org.jmol.util.Base64
 
getBase64(byte[]) - Static method in class org.jmol.util.Base64
 
getBaseRing6Points(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getBboxVertices() - Method in class org.jmol.modelset.BoxInfo
 
getBboxVertices() - Method in class org.jmol.modelset.ModelCollection
 
getBfactor() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getBfactor() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getBfactor100() - Method in class org.jmol.modelset.Atom
 
getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
 
getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
 
getBFactors() - Method in class org.jmol.modelset.AtomCollection
 
getBioPolymer(int) - Method in class org.jmol.modelset.Model
 
getBioPolymer() - Method in class org.jmol.modelsetbio.Monomer
 
getBioPolymerCount() - Method in class org.jmol.modelset.Model
 
getBioPolymerCount() - Method in class org.jmol.modelset.ModelCollection
 
getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getBioPolymerIndex() - Method in class org.jmol.modelset.Group
 
getBioPolymerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getBioPolymerLength() - Method in class org.jmol.modelset.Group
 
getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
 
getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
 
getBit(int[], int) - Static method in class org.jmol.geodesic.EnvelopeCalculation
 
getBitsetIdent(BitSet, String, Object, boolean) - Method in class org.jmol.viewer.Eval
 
getBitsetProperty(BitSet, int, Point3f, Point4f, Object, Object, boolean, int) - Method in class org.jmol.viewer.Eval
 
getBitsetPropertySelector(int, boolean) - Method in class org.jmol.viewer.Eval
 
getBitSetSelection() - Method in class org.jmol.viewer.Viewer
 
getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
 
getBitSetTrajectories() - Method in class org.jmol.viewer.Viewer
 
getBond(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBond(Atom) - Method in class org.jmol.modelset.Atom
 
getBond(int) - Method in class org.jmol.smiles.SmilesAtom
Returns the bond at index number.
getBond(int) - Method in class org.jmol.smiles.SmilesMolecule
 
getBondArgb1(int) - Method in class org.jmol.api.JmolViewer
 
getBondArgb1(int) - Method in class org.jmol.viewer.Viewer
 
getBondArgb2(int) - Method in class org.jmol.api.JmolViewer
 
getBondArgb2(int) - Method in class org.jmol.viewer.Viewer
 
getBondAt(int) - Method in class org.jmol.modelset.BondCollection
 
getBondAtom1(int) - Method in class org.jmol.modelset.BondCollection
 
getBondAtom2(int) - Method in class org.jmol.modelset.BondCollection
 
getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
 
getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
 
getBondCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBondCount() - Method in class org.jmol.api.JmolViewer
 
getBondCount() - Method in class org.jmol.modelset.BondCollection
 
getBondCount() - Method in class org.jmol.viewer.Viewer
For use in setting a for() construct max value
getBondCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
for general use
getBondCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getBondCountInModel(int) - Method in class org.jmol.viewer.Viewer
from JmolPopup.udateModelSetComputedMenu
getBondDipoles() - Method in class org.jmol.shapespecial.Dipoles
 
getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
 
getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
 
getBondInfo(int) - Method in class org.jmol.modelset.ModelCollection
 
getBondingMar() - Method in class org.jmol.modelset.Atom
 
getBondingMar(int, int) - Static method in class org.jmol.viewer.JmolConstants
 
getBondingMar(int, int, short[]) - Static method in class org.jmol.viewer.JmolConstants
 
getBondingRadiusFloat() - Method in class org.jmol.modelset.Atom
 
getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a BondIterator for retrieval of all bonds in the file.
getBondIterator(short, BitSet) - Method in class org.jmol.modelset.BondCollection
 
getBondIterator(BitSet) - Method in class org.jmol.modelset.BondCollection
 
getBondIterator(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter
 
getBondModelIndex(int) - Method in class org.jmol.api.JmolViewer
 
getBondModelIndex(int) - Method in class org.jmol.modelset.BondCollection
 
getBondModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
getBondOrder(int) - Method in class org.jmol.api.JmolViewer
 
getBondOrder(int) - Method in class org.jmol.modelset.BondCollection
 
getBondOrder(Atom, float, Atom, float, float, float, float) - Method in class org.jmol.modelset.BondCollection
 
getBondOrder(int) - Method in class org.jmol.viewer.Viewer
 
getBondOrderFromFloat(float) - Static method in class org.jmol.viewer.JmolConstants
 
getBondOrderFromString(String) - Static method in class org.jmol.viewer.JmolConstants
 
getBondOrderNameFromOrder(short) - Static method in class org.jmol.viewer.JmolConstants
 
getBondOrderNumberFromOrder(short) - Static method in class org.jmol.viewer.JmolConstants
used for formatting labels and in the connect PARTIAL command
getBondPicking() - Method in class org.jmol.viewer.Viewer
 
getBondPoint3f1(int) - Method in class org.jmol.api.JmolViewer
 
getBondPoint3f1(int) - Method in class org.jmol.viewer.Viewer
 
getBondPoint3f2(int) - Method in class org.jmol.api.JmolViewer
 
getBondPoint3f2(int) - Method in class org.jmol.viewer.Viewer
 
getBondRadius(int) - Method in class org.jmol.api.JmolViewer
 
getBondRadius(int) - Method in class org.jmol.modelset.BondCollection
 
getBondRadius(int) - Method in class org.jmol.viewer.Viewer
 
getBondRecordMOL(StringBuffer, int, int[]) - Method in class org.jmol.modelset.ModelCollection
 
getBonds() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBonds() - Method in class org.jmol.modelset.Atom
 
getBonds() - Method in class org.jmol.modelset.BondCollection
 
getBondsCount() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of bonds of this atom.
getBondsCount() - Method in class org.jmol.smiles.SmilesMolecule
 
getBondSelectionModeOr() - Method in class org.jmol.viewer.Viewer
 
getBondsForSelectedAtoms(BitSet) - Method in class org.jmol.modelset.BondCollection
 
getBondsForSelectedAtoms(BitSet, boolean) - Method in class org.jmol.modelset.BondCollection
 
getBondsForSelectedAtoms(BitSet) - Method in class org.jmol.viewer.Viewer
 
getBondTo(int) - Method in class org.jmol.minimize.MinAtom
 
getBondTolerance() - Method in class org.jmol.api.JmolViewer
 
getBondTolerance() - Method in class org.jmol.viewer.Viewer
 
getBondType() - Method in class org.jmol.smiles.SmilesBond
 
getBondTypeFromCode(char) - Static method in class org.jmol.smiles.SmilesBond
 
getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
 
getBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
 
getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
 
getBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
 
getBooleanValue(String, boolean) - Method in class org.jmol.applet.Jmol
 
getBoundBoxCenter() - Method in class org.jmol.modelset.BoxInfo
 
getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxCommand(boolean) - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCornerVector() - Method in class org.jmol.modelset.BoxInfo
 
getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxInfo() - Method in class org.jmol.modelset.BoxInfo
 
getBoundBoxInfo() - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxInfo() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxModels() - Method in class org.jmol.modelset.ModelCollection
 
getBoundBoxModels() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxPoints() - Method in class org.jmol.modelset.BoxInfo
 
getBoxInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getBoxInfo(BitSet) - Method in class org.jmol.viewer.Viewer
 
getBranchBitSet(int, int) - Method in class org.jmol.modelset.ModelCollection
 
getBranchBitSet(int, int) - Method in class org.jmol.viewer.Viewer
 
getBreakableContext(int) - Method in class org.jmol.viewer.Compiler
 
getBsIgnore() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getBsptCount() - Method in class org.jmol.bspt.Bspf
 
getBsSelected() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getBufferedReader(int) - Method in interface org.jmol.api.JmolFileReaderInterface
 
getBufferedReader(int) - Method in class org.jmol.viewer.FileManager.FilesOpenThread
called by SmartJmolAdapter to request another buffered reader, rather than opening all the readers at once.
getBufferedReaderForString(String) - Method in class org.jmol.viewer.FileManager
 
getBufferedReaderForString(String) - Method in class org.jmol.viewer.Viewer
 
getBufferedReaderOrErrorMessageFromName(String, String[], boolean) - Method in class org.jmol.viewer.FileManager
 
getBufferedReaderOrErrorMessageFromName(String, String[], boolean) - Method in class org.jmol.viewer.Viewer
 
getBufferedReaderOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
 
getCachedLine() - Method in class org.jmol.g3d.Line3D
 
getCalcPoint(Point3f) - Method in class org.jmol.jvxl.readers.VoxelReader
 
getCallbackName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getCallbackScript(String) - Method in class org.jmol.viewer.StatusManager
 
getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCarbonylCarbonAtomPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCarbonylOxygenAtomPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
 
getCartesianOffset() - Method in class org.jmol.symmetry.UnitCell
 
getCartoonRocketFlag() - Method in class org.jmol.viewer.Viewer
 
getCellInfos() - Method in class org.jmol.modelset.ModelCollection
 
getCellRange() - Method in interface org.jmol.api.SymmetryInterface
 
getCellRange() - Method in class org.jmol.symmetry.Symmetry
 
getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
getCenterText() - Method in class org.jmol.viewer.TransformManager
 
getChain() - Method in class org.jmol.modelset.Atom
 
getChain(char) - Method in class org.jmol.modelset.Model
 
getChain(int) - Method in class org.jmol.modelset.Model
 
getChainBits(char) - Method in class org.jmol.modelset.AtomCollection
 
getChainCaseSensitive() - Method in class org.jmol.viewer.Viewer
 
getChainCount() - Method in class org.jmol.api.JmolViewer
 
getChainCount(boolean) - Method in class org.jmol.modelset.Model
 
getChainCount(boolean) - Method in class org.jmol.modelset.ModelCollection
 
getChainCount() - Method in class org.jmol.viewer.Viewer
 
getChainCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getChainCountInModel(int, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getChainCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getChainCountInModel(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getChainID() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getChainID() - Method in class org.jmol.modelset.Atom
 
getChainID() - Method in class org.jmol.modelset.Chain
 
getChainID() - Method in class org.jmol.modelset.Group
 
getChainInfo(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getChains() - Method in class org.jmol.modelset.Model
 
getChangeableColix(short, int) - Method in class org.jmol.g3d.Graphics3D
 
getChangeableColixIndex(short) - Static method in class org.jmol.g3d.Graphics3D
 
getCharge() - Method in class org.jmol.smiles.SmilesAtom
Returns the charge of the atom.
getChimeInfo(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getChimeInfo(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
 
getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
Returns the chiral class of the atom.
getChiralOrder() - Method in class org.jmol.smiles.SmilesAtom
Returns the chiral order of the atom.
getClickabilityFlags() - Method in class org.jmol.modelset.Atom
 
getClickableSet() - Method in class org.jmol.modelset.AtomCollection
 
getClickableSet() - Method in class org.jmol.viewer.Viewer
 
getClientAtomReference() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getClientAtomStringProperty(Object, String) - Method in class org.jmol.api.JmolAdapter
Get a property from a clientAtom.
getClientAtomStringProperty(String) - Method in class org.jmol.modelset.Atom
 
getClientAtomStringProperty(Object, String) - Method in class org.jmol.viewer.Viewer
 
getClientFile() - Method in class org.jmol.viewer.Viewer
 
getClipboardText() - Method in interface org.jmol.api.JmolImageCreatorInterface
 
getClipboardText() - Method in class org.jmol.applet.Jvm12
 
getClipboardText() - Method in class org.jmol.export.image.ImageCreator
 
getClipboardText() - Static method in class org.jmol.export.image.ImageSelection
Get the String residing on the clipboard.
getClipboardTextStatic() - Static method in class org.jmol.export.image.ImageCreator
 
getClipBounds(Graphics) - Method in class org.jmol.applet.Jvm12
 
getColix(int) - Static method in class org.jmol.g3d.Colix3D
 
getColix(int) - Static method in class org.jmol.g3d.Graphics3D
 
getColix(String) - Static method in class org.jmol.g3d.Graphics3D
 
getColix(Object) - Static method in class org.jmol.g3d.Graphics3D
 
getColix() - Method in class org.jmol.modelset.Atom
 
getColix() - Method in class org.jmol.modelset.Bond
 
getColix() - Method in class org.jmol.modelset.Measurement
 
getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
 
getColix(Object) - Method in class org.jmol.viewer.Viewer
 
getColix1() - Method in class org.jmol.modelset.Bond
 
getColix2() - Method in class org.jmol.modelset.Bond
 
getColixArgb(short) - Method in interface org.jmol.api.JmolRendererInterface
 
getColixArgb(short) - Method in class org.jmol.export.Export3D
 
getColixArgb(short) - Method in class org.jmol.g3d.Graphics3D
 
getColixArgb(short) - Method in class org.jmol.viewer.Viewer
 
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
 
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.Viewer
 
getColixBackgroundContrast() - Method in class org.jmol.viewer.Viewer
 
getColixForPropertyValue(float) - Method in class org.jmol.viewer.ColorManager
 
getColixForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
 
getColixInherited(short, short) - Static method in class org.jmol.g3d.Graphics3D
 
getColixRubberband() - Method in class org.jmol.viewer.Viewer
 
getColixTranslucencyLevel(short) - Static method in class org.jmol.g3d.Graphics3D
 
getColixTranslucent(short, boolean, float) - Static method in class org.jmol.g3d.Graphics3D
 
getColor(int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getColorArgb(int) - Static method in class org.jmol.g3d.Graphics3D
 
getColorCommand(String, short) - Method in class org.jmol.shape.Shape
 
getColorCommand(String, byte, short) - Method in class org.jmol.shape.Shape
 
getColorEncoder() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getColorFromName(String) - Method in class org.jmol.appletwrapper.AppletWrapper
 
getColorIndex(int) - Static method in class org.jmol.util.ColorEncoder
 
getColorIndexFromPalette(float) - Method in class org.jmol.jvxl.readers.VoxelReader
 
getColorIndexFromPalette(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
 
getColorIndexFromPalette(float, float, float) - Method in class org.jmol.util.ColorEncoder
 
getColorPhaseIndex(String) - Static method in class org.jmol.jvxl.readers.VoxelReader
 
getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
 
getColorScheme(String, boolean) - Static method in class org.jmol.util.ColorEncoder
 
getColorScheme(String, boolean, boolean) - Static method in class org.jmol.util.ColorEncoder
 
getColorSchemeArray(int) - Static method in class org.jmol.util.ColorEncoder
 
getColorSchemeArray(String) - Method in class org.jmol.viewer.ColorManager
 
getColorSchemeArray(String) - Method in class org.jmol.viewer.Viewer
 
getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(String, boolean) - Method in class org.jmol.viewer.ColorManager
 
getColorSchemeList(String, boolean) - Method in class org.jmol.viewer.Viewer
 
getColorSchemeName() - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeName(int) - Static method in class org.jmol.util.ColorEncoder
 
getColorTriad(int) - Method in class org.jmol.viewer.Eval
 
getColumnClass(int) - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
getColumnCount() - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
getColumnName(int) - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
getCommand() - Method in class org.jmol.util.CommandHistory
Calculates the command to return.
getCommand(int) - Method in class org.jmol.viewer.Eval
 
getCommandDown() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the top of the list, updates list position.
getCommandLine() - Method in class org.openscience.jmol.app.PovrayDialog
Generates a commandline from the options set for povray path etc and sets in the textField.
getCommands(Hashtable) - Static method in class org.jmol.viewer.StateManager
 
getCommands(Hashtable, Hashtable, int) - Static method in class org.jmol.viewer.StateManager
 
getCommands(Hashtable, Hashtable, int, String) - Static method in class org.jmol.viewer.StateManager
 
getCommands(Hashtable, StringBuffer, String, int, String) - Static method in class org.jmol.viewer.StateManager
 
getCommandSet(String) - Static method in class org.jmol.viewer.Token
retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCommandString() - Method in class org.openscience.jmol.app.ConsoleDocument
 
getCommandString() - Method in class org.openscience.jmol.app.ConsoleTextPane
 
getCommandUp() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the bottom of the list, updates list position.
getComment() - Method in class org.jmol.util.JpegInfo
 
getCompiler() - Method in class org.jmol.viewer.Viewer
 
getCompressionLevel() - Method in class org.jmol.export.image.PngEncoder
Retrieve compression level
getConsole() - Method in class org.jmol.applet.Jvm12
 
getConsoleMessage() - Method in class org.jmol.applet.Jvm12
 
getContextVariableAsToken(String) - Method in class org.jmol.viewer.Eval
 
getContextVariables() - Method in class org.jmol.viewer.Compiler
 
getContourType() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getContourType(Point4f, Vector3f[]) - Static method in class org.jmol.jvxl.calc.MarchingSquares
 
getContourVertexCount() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getContrastingBlackOrWhite(Color) - Method in class org.jmol.appletwrapper.AppletWrapper
 
getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
 
getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
 
getCoordinateState(BitSet) - Method in class org.jmol.viewer.Viewer
 
getCount() - Method in class org.jmol.modelset.Measurement
 
getCountPlusIndices() - Method in class org.jmol.modelset.Measurement
 
getCovalentBondCount() - Method in class org.jmol.modelset.Atom
 
getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getCovalentlyConnectedBitSet(Atom, BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getCurrentAtomSetIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getCurrentBondCount() - Method in class org.jmol.modelset.Atom
 
getCurrentColorRange() - Method in class org.jmol.viewer.ColorManager
 
getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
 
getCurrentFileAsBytes() - Method in class org.jmol.viewer.Viewer
 
getCurrentFileAsString() - Method in class org.jmol.viewer.Viewer
 
getCurrentModelIndex() - Method in class org.jmol.viewer.Viewer
 
getCurrentSolventProbeRadius() - Method in class org.jmol.viewer.Viewer
 
getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
 
getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
 
getCurrentUnitCellOffset() - Method in class org.jmol.viewer.Viewer
 
getCursorX() - Method in class org.jmol.viewer.Viewer
 
getCursorY() - Method in class org.jmol.viewer.Viewer
 
getCutoff() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getData() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
getData() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
general reader for loop data fills loopData with fieldCount fields
getData(String, String) - Method in class org.jmol.api.JmolViewer
 
getData(String) - Method in class org.jmol.viewer.Compiler
 
getData(String) - Method in class org.jmol.viewer.DataManager
 
getData(String) - Method in class org.jmol.viewer.Viewer
 
getData(String, String) - Method in class org.jmol.viewer.Viewer
 
getDataFloat(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat(String, int) - Method in class org.jmol.viewer.DataManager
 
getDataFloat(String) - Method in class org.jmol.viewer.Viewer
 
getDataFloat(String, int) - Method in class org.jmol.viewer.Viewer
 
getDataFloat2D(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat2D(String) - Method in class org.jmol.viewer.Viewer
 
getDataSeparator() - Method in class org.jmol.viewer.Viewer
 
getDataState(StringBuffer, StringBuffer, Atom[], int, String) - Method in class org.jmol.viewer.DataManager
 
getDE(MinAtom, int, int, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugScript() - Method in class org.jmol.viewer.Viewer
 
getDefaultColix() - Method in class org.jmol.shapesurface.Isosurface
 
getDefaultColorRasmol() - Method in class org.jmol.viewer.ColorManager
 
getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
 
getDefaultDrawArrowScale() - Method in class org.jmol.viewer.Viewer
 
getDefaultLattice() - Method in class org.jmol.viewer.Viewer
 
getDefaultLatticeArray() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getDefaultLatticePoint() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getDefaultLoadScript() - Method in class org.jmol.viewer.Viewer
 
getDefaultMadAtom() - Method in class org.jmol.viewer.Viewer
 
getDefaultMadFromOrder(short) - Method in class org.jmol.modelset.BondCollection
When creating a new bond, determine bond diameter from order
getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
 
getDefaultParam(int) - Static method in class org.jmol.viewer.PropertyManager
 
getDefaultState() - Method in class org.jmol.shape.Labels
 
getDefaultTranslucent() - Method in class org.jmol.viewer.Viewer
 
getDefaultVdw(int, BitSet) - Method in class org.jmol.viewer.DataManager
 
getDefaultVdw(int) - Method in class org.jmol.viewer.Viewer
 
getDefinedState(StringBuffer, boolean) - Method in class org.jmol.modelset.ModelSet
 
getDelayMaximum() - Method in class org.jmol.viewer.Viewer
 
getDeletedAtoms() - Method in class org.jmol.viewer.SelectionManager
 
getDeletedAtoms() - Method in class org.jmol.viewer.Viewer
 
getDepth() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d depth
getDepth() - Method in class org.jmol.export.Export3D
gets g3d depth
getDepth() - Method in class org.jmol.g3d.Graphics3D
gets g3d depth
getDescription() - Method in class org.jmol.export.dialog.Dialog.TypeFilter
 
getDialog() - Method in class org.jmol.export.dialog.FileChooser
 
getDictRefValue(HashMap) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
getDiffusePercent() - Static method in class org.jmol.g3d.Graphics3D
 
getDiffusePercent() - Static method in class org.jmol.viewer.ColorManager
 
getDiffusePercent() - Static method in class org.jmol.viewer.Viewer
 
getDimensionValue(Point3f, int) - Static method in class org.jmol.bspt.Node
 
getDimensionValue(int) - Method in class org.jmol.modelset.Atom
 
getDipoleIndex(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
getDipoleIndex(int, int) - Method in class org.jmol.shapespecial.Dipoles
 
getDipoleScale() - Method in class org.jmol.viewer.Viewer
 
getDirectedNormalThroughPoints(Point3f, Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.g3d.Graphics3D
 
getDirectory() - Method in class org.jmol.util.CompoundDocument
 
getDirectoryListing(String) - Method in class org.jmol.util.CompoundDocument
 
getDirectoryTable() - Method in class org.jmol.util.CompoundDocument
 
getDisablePopupMenu() - Method in class org.jmol.viewer.Viewer
 
getDisplayCellParameters() - Method in class org.jmol.viewer.Viewer
 
getDisplayModelIndex() - Method in class org.jmol.api.JmolViewer
 
getDisplayModelIndex() - Method in class org.jmol.viewer.Viewer
 
getDotDensity() - Method in class org.jmol.viewer.Viewer
 
getDoTranslate() - Static method in class org.jmol.i18n.GT
 
getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDotsSelectedOnlyFlag() - Method in class org.jmol.viewer.Viewer
 
getDotSurfaceFlag() - Method in class org.jmol.viewer.Viewer
 
getDrawCommand(DrawMesh) - Method in class org.jmol.shapespecial.Draw
 
getDrawCommand(DrawMesh, int) - Method in class org.jmol.shapespecial.Draw
 
getDrawHover() - Method in class org.jmol.viewer.PickingManager
 
getDrawHover() - Method in class org.jmol.viewer.Viewer
 
getDrawObjectAxis(String) - Method in class org.jmol.viewer.Eval
 
getDrawObjectCenter(String) - Method in class org.jmol.viewer.Eval
 
getDrawPicking() - Method in class org.jmol.viewer.Viewer
 
getDrawTypeName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getDynamicMeasurements() - Method in class org.jmol.viewer.Viewer
 
getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
 
getEchoStateActive() - Method in class org.jmol.viewer.Viewer
 
getEigenvalues() - Method in class org.jmol.util.Eigen
 
getEigenvectors() - Method in class org.jmol.util.Eigen
 
getElementAndAtomCount(BitSet) - Method in class org.jmol.modelset.Molecule
 
getElementCounts() - Method in class org.jmol.symmetry.PointGroup
 
getElementName(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getElementNumber() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
 
getElementNumber() - Method in class org.jmol.modelset.Atom
 
getElementNumber(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementNumber() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getElementNumber(int) - Method in class org.jmol.viewer.Viewer
 
getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
 
getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelCollection
 
getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
 
getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getElementSymbol() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getElementSymbol() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
 
getElementSymbol() - Method in class org.jmol.modelset.Atom
 
getElementSymbol(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementSymbol() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getElementSymbol(int) - Method in class org.jmol.viewer.Viewer
 
getEllipsoid() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getEllipsoid() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getEllipsoid(float[]) - Method in interface org.jmol.api.SymmetryInterface
 
getEllipsoid() - Method in class org.jmol.modelset.Atom
 
getEllipsoid(int) - Method in class org.jmol.modelset.AtomCollection
 
getEllipsoid(float[]) - Method in class org.jmol.symmetry.Symmetry
 
getEllipsoid(float[]) - Method in class org.jmol.symmetry.UnitCell.Data
 
getEllipsoid(float[]) - Method in class org.jmol.symmetry.UnitCell
 
getEllipsoidShade(float, float, float, int, Matrix4f) - Static method in class org.jmol.g3d.Sphere3D
 
getEncodeAlpha() - Method in class org.jmol.export.image.PngEncoder
Retrieve alpha encoding status.
getEncodedOrder() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
getEncodedOrder() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
getEncodedOrder() - Method in class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
getEndChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getEndChainID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getEndInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getEndInsertionCode() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getEnergy() - Method in class org.jmol.minimize.forcefield.Calculation
 
getEnergy(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergyOnly() - Method in class org.jmol.minimize.Minimizer
 
getEquationForQuadricWithCenter(float, float, float, Matrix3f, Vector3f, Matrix3f, double[], Matrix4f) - Static method in class org.jmol.util.Quadric
 
getErrorMessage() - Method in class org.jmol.viewer.Compiler
 
getErrorMessage() - Method in class org.jmol.viewer.Eval
 
getEstimatedAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getEstimatedAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
Get the estimated number of atoms contained in the file.
getEstimatedAtomCount(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter
 
getEvalVariables() - Method in class org.jmol.viewer.Viewer
 
getExecutionWalltime() - Method in class org.jmol.viewer.Eval
 
getExportDate() - Method in class org.jmol.export._Exporter
 
getExportDriverList() - Method in class org.jmol.viewer.Viewer
 
getExporter() - Method in interface org.jmol.api.JmolRendererInterface
 
getExporter() - Method in class org.jmol.export.Export3D
 
getExporter() - Method in class org.jmol.g3d.Graphics3D
 
getExportJmolAdapter() - Method in class org.jmol.viewer.Viewer
This is the method that should be used to extract the model data from Jmol.
getFaceNormixes(int) - Method in class org.jmol.g3d.Normix3D
 
getFaceVertexes(int) - Static method in class org.jmol.geodesic.Geodesic
 
getFaceVertexesArrays() - Static method in class org.jmol.geodesic.Geodesic
 
getFactorD(int) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceField
 
getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getFile() - Method in class org.jmol.export.dialog.HistoryFile
 
getFile() - Method in class org.openscience.jmol.app.RecentFilesDialog
 
getFileAsBytes(String) - Method in class org.jmol.viewer.FileManager
 
getFileAsBytes(String) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
getFileAsImage(String, Hashtable) - Method in class org.jmol.viewer.FileManager
 
getFileAsImage(String, Hashtable) - Method in class org.jmol.viewer.Viewer
 
getFileAsString(String) - Method in class org.jmol.api.JmolViewer
 
getFileAsString(String) - Method in class org.jmol.util.CompoundDocument
 
getFileAsString(CompoundDocument.CmpDocDirectoryEntry) - Method in class org.jmol.util.CompoundDocument
 
getFileAsString(String) - Method in class org.jmol.viewer.Viewer
 
getFileAsString(String[]) - Method in class org.jmol.viewer.Viewer
 
getFileDataOrErrorAsString(String[]) - Method in class org.jmol.viewer.FileManager
 
getFileHeader(int) - Method in class org.jmol.modelset.ModelCollection
 
getFileHeader() - Method in class org.jmol.viewer.Viewer
 
getFileInfo() - Method in class org.jmol.viewer.FileManager
 
getFileInfo() - Method in class org.jmol.viewer.Viewer
 
getFileName() - Method in class org.jmol.viewer.FileManager
 
getFileName() - Method in class org.jmol.viewer.Viewer
 
getFiles() - Method in class org.openscience.jmol.app.RecentFilesDialog
 
getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
 
getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
Get the type of this file or molecular model, if known.
getFileTypeName(String) - Method in class org.jmol.viewer.FileManager
 
getFilter() - Method in class org.jmol.export.image.PngEncoder
Retrieve filtering scheme
getFirstAtomIndex() - Method in class org.jmol.modelset.Group
 
getFirstAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getFloat(int, int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
getFont(float) - Method in class org.jmol.shape.Frank
 
getFont3D(int, int, float, float, Platform3D) - Static method in class org.jmol.g3d.Font3D
 
getFont3D(byte) - Static method in class org.jmol.g3d.Font3D
 
getFont3D(float) - Method in class org.jmol.g3d.Graphics3D
 
getFont3D(String, float) - Method in class org.jmol.g3d.Graphics3D
 
getFont3D(String, String, float) - Method in class org.jmol.g3d.Graphics3D
 
getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
 
getFont3DCurrent() - Method in interface org.jmol.api.JmolRendererInterface
 
getFont3DCurrent() - Method in class org.jmol.export.Export3D
 
getFont3DCurrent() - Method in class org.jmol.g3d.Graphics3D
 
getFont3DScaled(Font3D, float) - Method in interface org.jmol.api.JmolRendererInterface
 
getFont3DScaled(Font3D, float) - Method in class org.jmol.export.Export3D
 
getFont3DScaled(Font3D, float) - Method in class org.jmol.g3d.Graphics3D
 
getFontCommand(String, Font3D) - Static method in class org.jmol.shape.Shape
 
getFontFaceID(String) - Static method in class org.jmol.g3d.Font3D
 
getFontFid(String, float) - Method in interface org.jmol.api.JmolRendererInterface
 
getFontFid(float) - Method in interface org.jmol.api.JmolRendererInterface
 
getFontFid(String, float) - Method in class org.jmol.export.Export3D
 
getFontFid(float) - Method in class org.jmol.export.Export3D
 
getFontFid(float) - Method in class org.jmol.g3d.Graphics3D
 
getFontFid(String, float) - Method in class org.jmol.g3d.Graphics3D
 
getFontMap(String, int, float) - Static method in class org.jmol.g3d.Font3D
 
getFontMetrics() - Method in class org.jmol.shape.Text
 
getFontScaling() - Method in class org.jmol.viewer.Viewer
 
getFontStyleID(String) - Static method in class org.jmol.g3d.Font3D
 
getFooter() - Method in interface org.jmol.api.JmolExportInterface
 
getFooter() - Method in class org.jmol.export._MayaExporter
 
getFooter() - Method in class org.jmol.export._PovrayExporter
 
getFooter() - Method in class org.jmol.export._VrmlExporter
 
getForceAutoBond() - Method in class org.jmol.viewer.Viewer
 
getForceField() - Method in class org.jmol.minimize.Minimizer
 
getFormalCharge() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getFormalCharge() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getFormalCharge() - Method in class org.jmol.modelset.Atom
 
getFormalCharge() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
 
getFractionalCoord(char) - Method in class org.jmol.modelset.Atom
 
getFractionalCoord() - Method in class org.jmol.modelset.Atom
 
getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
 
getFractionalOffset() - Method in class org.jmol.symmetry.UnitCell
 
getFrame() - Method in class org.openscience.jmol.app.Jmol
 
getFrame() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getFrameRenderer() - Method in class org.jmol.viewer.Viewer
 
getFrameTitle(int) - Method in class org.jmol.modelset.ModelCollection
 
getFrameTitle(int) - Method in class org.jmol.viewer.Viewer
 
getFrameTitle() - Method in class org.jmol.viewer.Viewer
 
getFullFilePathAsString(String) - Method in class org.jmol.viewer.FileManager
 
getFullPathName() - Method in class org.jmol.viewer.Eval
 
getFullPathName() - Method in class org.jmol.viewer.FileManager
 
getFullPathName() - Method in class org.jmol.viewer.Viewer
 
getFullPDBHeader(int) - Method in class org.jmol.modelset.ModelCollection
 
getFunction(String) - Method in class org.jmol.viewer.Eval
 
getFunctionCalls(String) - Method in class org.jmol.viewer.Eval
 
getFunctionReturn(String, Vector) - Method in class org.jmol.viewer.Eval
 
getFunctionZfromXY() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getGenerator(int, Graphics3D) - Method in class org.jmol.viewer.FrameRenderer
 
getGlobalSettings(StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager
 
getGlobalSettings() - Method in class org.jmol.viewer.Viewer
 
getGraphCurveColor() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getGraphics(Image) - Method in class org.jmol.g3d.Awt3D
 
getGraphics(Image) - Method in class org.jmol.g3d.Platform3D
 
getGraphics(Image) - Method in class org.jmol.g3d.Swing3D
 
getGraphics3D() - Method in class org.jmol.viewer.Viewer
 
getGreyscaleRendering() - Method in class org.jmol.viewer.Viewer
 
getGrid() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getGroup() - Method in class org.jmol.modelset.Atom
 
getGroup(int) - Method in class org.jmol.modelset.Chain
 
getGroup1() - Method in class org.jmol.modelset.Atom
 
getGroup1() - Method in class org.jmol.modelset.Group
 
getGroup3() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getGroup3() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getGroup3() - Method in class org.jmol.modelset.Atom
 
getGroup3() - Method in class org.jmol.modelset.Group
 
getGroup3(short) - Static method in class org.jmol.modelset.Group
 
getGroup3List() - Static method in class org.jmol.viewer.JmolConstants
 
getGroupCount() - Method in class org.jmol.api.JmolViewer
 
getGroupCount() - Method in class org.jmol.modelset.Chain
 
getGroupCount(boolean) - Method in class org.jmol.modelset.Model
 
getGroupCount() - Method in class org.jmol.modelset.Model
 
getGroupCount() - Method in class org.jmol.modelset.ModelCollection
 
getGroupCount() - Method in class org.jmol.viewer.Viewer
 
getGroupCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getGroupCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getGroupID() - Method in class org.jmol.modelset.Atom
 
getGroupID() - Method in class org.jmol.modelset.Group
 
getGroupID(String) - Static method in class org.jmol.modelset.Group
 
getGroupPhi() - Method in class org.jmol.modelset.Atom
 
getGroupPsi() - Method in class org.jmol.modelset.Atom
 
getHallLatticeEquivalent(int) - Static method in class org.jmol.symmetry.Translation
 
getHbondsBackbone() - Method in class org.jmol.viewer.Viewer
 
getHbondsSolid() - Method in class org.jmol.viewer.Viewer
 
getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getHeader(int) - Method in class org.jmol.adapter.smarter.LimitedLineReader
 
getHeader() - Method in interface org.jmol.api.JmolExportInterface
 
getHeader() - Method in class org.jmol.export._MayaExporter
 
getHeader() - Method in class org.jmol.export._PovrayExporter
 
getHeader() - Method in class org.jmol.export._VrmlExporter
 
getHeightUnitVector() - Method in class org.jmol.modelsetbio.Sheet
 
getHelp(String) - Method in class org.jmol.viewer.Viewer
 
getHermiteLevel() - Method in class org.jmol.viewer.Viewer
 
getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int) - Static method in class org.jmol.g3d.Graphics3D
 
getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int) - Static method in class org.jmol.g3d.Hermite3D
 
getHeteroList(int) - Method in class org.jmol.api.JmolViewer
 
getHeteroList(int) - Method in class org.jmol.modelset.ModelCollection
 
getHeteroList(int) - Method in class org.jmol.viewer.Viewer
 
getHexColorFromIndex(short) - Method in interface org.jmol.api.JmolRendererInterface
 
getHexColorFromIndex(short) - Method in class org.jmol.export.Export3D
 
getHexColorFromIndex(short) - Method in class org.jmol.g3d.Graphics3D
 
getHexColorFromIndex(short) - Method in class org.jmol.viewer.Viewer
 
getHexColorFromRGB(int) - Static method in class org.jmol.g3d.Graphics3D
 
getHexitValue(char) - Static method in class org.jmol.viewer.Compiler
 
getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
 
getHiddenSet() - Method in class org.jmol.viewer.Viewer
 
getHideNameInPopup() - Method in class org.jmol.viewer.Viewer
 
getHideNotSelected() - Method in class org.jmol.viewer.SelectionManager
 
getHighestOrder() - Method in class org.jmol.symmetry.PointGroup
 
getHighResolution() - Method in class org.jmol.viewer.Viewer
 
getHistoryFile() - Static method in class org.openscience.jmol.app.Jmol
 
getHistoryFile() - Static method in class org.openscience.jmol.app.webexport.WebMaker
 
getHoverDelay() - Method in class org.jmol.viewer.Viewer
 
getHtmlName() - Method in class org.jmol.viewer.Viewer
 
getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getHybridizationAndAxes(int, Vector3f, Vector3f, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getHybridizationAndAxes(int, Vector3f, Vector3f, String, boolean) - Method in class org.jmol.viewer.Viewer
 
getHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of hydrogen atoms bonded with this atom.
getIAddGridPoints() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getIcon(String) - Method in class org.openscience.jmol.app.JmolResourceHandler
 
getIconX(String) - Static method in class org.openscience.jmol.app.JmolResourceHandler
 
getId(Object) - Method in class org.jmol.popup.JmolPopup
 
getId(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
getId(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
getID(String, int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
getId(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getIdentifierOrNull(String) - Method in class org.jmol.modelset.AtomCollection
overhauled by RMH Nov 1, 2006.
getIdentity() - Method in class org.jmol.minimize.MinAtom
 
getIdentity(boolean) - Method in class org.jmol.modelset.Atom
 
getIdentity() - Method in class org.jmol.modelset.Bond
 
getIdentityXYZ() - Method in class org.jmol.modelset.Atom
 
getImage(boolean) - Method in class org.jmol.viewer.Viewer
 
getImageFileNameFromDialog(JmolViewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
 
getImageFileNameFromDialog(JmolViewer, String, String, String[], String[], int, int) - Method in class org.jmol.export.dialog.Dialog
 
getImageFontScaling() - Method in class org.jmol.viewer.Viewer
 
getIndex() - Method in class org.jmol.modelset.Measurement
 
getIndex(char, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
 
getIndexFromName(String) - Method in class org.jmol.shape.Shape
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
 
getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
 
getInfo() - Method in class org.jmol.modelset.Atom
 
getInfo() - Method in class org.jmol.modelset.Molecule
 
getInfo(Hashtable) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getInfo(int) - Method in class org.jmol.shape.Measures
 
getInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.PointGroup
 
getInfo(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
 
getInfo(int) - Method in class org.jmol.symmetry.UnitCell
 
getInfo() - Method in class org.jmol.util.Quaternion
 
getInfoAsString(int) - Method in class org.jmol.shape.Measures
 
getInfoHeight() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInfoWidth() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInfoXYZ(boolean) - Method in class org.jmol.modelset.Atom
 
getINI() - Method in class org.openscience.jmol.app.PovrayDialog
Save INI file
getInitiatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getInitiatorAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getInitiatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
 
getInlineChar() - Method in class org.jmol.viewer.Viewer
 
getInlineData(int) - Method in class org.jmol.viewer.FileManager
 
getInMotion() - Method in class org.jmol.viewer.Viewer
 
getInputStream(String, boolean, URL, String) - Static method in class org.jmol.viewer.FileManager
 
getInputStream() - Method in class org.openscience.jmol.app.LoopedStreams
 
getInputStreamOrErrorMessageFromName(String, boolean) - Method in class org.jmol.viewer.FileManager
 
getInputStreamOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
 
getInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getInsertionCode() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getInsertionCode() - Method in class org.jmol.modelset.Atom
 
getInsertionCode() - Method in class org.jmol.modelset.Group
 
getInsertionCode(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelCollection
 
getInsertionCodeValue(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getInsertionListInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getInsertionLists() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getInstance() - Static method in class org.openscience.jmol.app.JmolResourceHandler
 
getInstanceName(int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInt() - Method in class org.jmol.shapesurface.Pmesh
 
getIntegrate() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getIntegrateCurveColor() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getIntegrateTextColor() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getIntegrationCurveAreaValue(Double) - Method in class org.jmol.jcamp.GraphCharacteristics
 
getIntensity(short) - Method in class org.jmol.g3d.Normix3D
 
getInterpolatedPixelValue(Point3f) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getInterpolatedVoxelValue(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
getInterruptScript() - Method in class org.jmol.viewer.Viewer
 
getInverseNormix(short) - Method in interface org.jmol.api.JmolRendererInterface
 
getInverseNormix(short) - Method in class org.jmol.export.Export3D
 
getInverseNormix(short) - Method in class org.jmol.g3d.Graphics3D
 
getIsHetero() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getIsHetero() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getIsosurfaceJvxl() - Method in class org.jmol.viewer.Eval
 
getIsosurfacePropertySmoothing() - Method in class org.jmol.viewer.Viewer
 
getIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getIsPositiveOnly() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelCollection
only some models can be iterated through.
getIUseBitSets() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getJavaVendor() - Method in class org.jmol.api.JmolViewer
 
getJavaVendor() - Method in class org.jmol.viewer.Viewer
 
getJavaVersion() - Method in class org.jmol.api.JmolViewer
 
getJavaVersion() - Method in class org.jmol.viewer.Viewer
 
getJmol(JFrame, int, int, String) - Static method in class org.openscience.jmol.app.Jmol
 
getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getJmolDataFrameIndex(int, String) - Method in class org.jmol.viewer.Viewer
 
getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelCollection
 
getJmolDataSourceFrame(int) - Method in class org.jmol.viewer.Viewer
 
getJmolFrameType(int) - Method in class org.jmol.modelset.ModelCollection
 
getJmolFrameType(int) - Method in class org.jmol.viewer.Viewer
 
getJmolOrRasmolArgb(int, int) - Static method in class org.jmol.viewer.ColorManager
 
getJmolVersion() - Static method in class org.jmol.api.JmolViewer
 
getJmolVersion() - Static method in class org.jmol.viewer.Viewer
 
getJmolVersionInt() - Static method in class org.jmol.viewer.Viewer
 
getJpeg(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getJustifyMeasurements() - Method in class org.jmol.viewer.Viewer
 
getJvxlData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getKey(Object) - Static method in class org.jmol.applet.GuiMap
 
getKey() - Method in interface org.jmol.applet.GuiMap.GetKey
 
getKey() - Method in class org.jmol.applet.GuiMap.KeyJMenu
 
getKey() - Method in class org.jmol.applet.GuiMap.KeyJMenuItem
 
getKey(int) - Static method in class org.jmol.export.image.GifEncoder
 
getKey(Object) - Static method in class org.openscience.jmol.app.GuiMap
 
getKey() - Method in interface org.openscience.jmol.app.GuiMap.GetKey
 
getKey() - Method in class org.openscience.jmol.app.GuiMap.KeyJCheckBox
 
getKey() - Method in class org.openscience.jmol.app.GuiMap.KeyJCheckBoxMenuItem
 
getKey() - Method in class org.openscience.jmol.app.GuiMap.KeyJMenu
 
getKey() - Method in class org.openscience.jmol.app.GuiMap.KeyJMenuItem
 
getKey() - Method in class org.openscience.jmol.app.GuiMap.KeyJRadioButtonMenuItem
 
getLabel(String) - Method in class org.jmol.applet.GuiMap
 
getLabel(int, boolean) - Method in class org.jmol.modelset.Measurement
 
getLabel(int) - Method in class org.jmol.shape.Labels
 
getLabel() - Method in class org.jmol.symmetry.PointGroup.Operation
 
getLabel(String) - Method in class org.openscience.jmol.app.GuiMap
 
getLabelWithoutMnemonic(String) - Static method in class org.jmol.applet.GuiMap
 
getLabelWithoutMnemonic(String) - Static method in class org.openscience.jmol.app.GuiMap
 
getLanguage() - Static method in class org.jmol.i18n.GT
 
getLanguageList() - Static method in class org.jmol.i18n.GT
 
getLastAtomIndex() - Method in class org.jmol.modelset.Group
 
getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastIndex() - Method in class org.jmol.modelset.Measurement
 
getLatticeCode(int) - Static method in class org.jmol.symmetry.Translation
 
getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeDesignation() - Method in class org.jmol.symmetry.HallInfo
 
getLatticeDesignation() - Method in class org.jmol.symmetry.SpaceGroup
 
getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
 
getLatticeDesignation(int) - Static method in class org.jmol.symmetry.Translation
 
getLatticeDesignation(char, boolean) - Static method in class org.jmol.symmetry.Translation
 
getLatticeExtension(char, boolean) - Static method in class org.jmol.symmetry.Translation
 
getLatticeIndex(char) - Static method in class org.jmol.symmetry.Translation
 
getLeadAtom(Atom) - Method in class org.jmol.modelset.Group
 
getLeadAtom() - Method in class org.jmol.modelset.Group
 
getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getLeadAtomIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadAtomPoint() - Method in class org.jmol.modelsetbio.Monomer
 
getLeadColix(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
getLeadMidPoint(int, Point3f) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadMidpoints() - Method in class org.jmol.modelset.Polymer
 
getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoint(int, Point3f) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeftPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getLength() - Method in class org.jmol.viewer.MonitorInputStream
 
getLength() - Method in class org.openscience.jvxl.MonitorInputStream
 
getLevel(int) - Static method in class org.jmol.util.Logger
Returns the text corresponding to a level.
getLightSource() - Static method in class org.jmol.g3d.Graphics3D
 
getLine() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
getLine() - Method in class org.jmol.jvxl.readers.XplorReader
 
getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getLineIndices() - Method in class org.jmol.viewer.Compiler
 
getLinenumber() - Method in class org.jmol.viewer.Eval
 
getLineNumbers() - Method in class org.jmol.viewer.Compiler
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
 
getListVariable(String, Object) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getListVariable(String, Object) - Method in class org.jmol.viewer.Viewer
 
getLoadFormat() - Method in class org.jmol.viewer.Viewer
 
getLoadScript() - Method in class org.jmol.viewer.FileManager
 
getLoadState() - Method in class org.jmol.viewer.StateManager.GlobalSettings
these settings are determined when the file is loaded and are kept even though they might later change.
getLoadState() - Method in class org.jmol.viewer.Viewer
 
getLocalDirectory(JmolViewer) - Static method in class org.jmol.viewer.FileManager
 
getLocalUrl(File) - Static method in class org.jmol.export.dialog.Dialog
 
getLogData() - Method in class org.jmol.minimize.forcefield.Calculations
 
getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
 
getLogLevel() - Static method in class org.jmol.viewer.Viewer
 
getMad() - Method in class org.jmol.modelset.Bond
 
getMad(int) - Method in class org.jmol.shape.ShapeRenderer
 
getMadAtom() - Method in class org.jmol.modelset.Atom
 
getMadBond() - Method in class org.jmol.api.JmolViewer
 
getMadBond() - Method in class org.jmol.viewer.Viewer
 
getMadParameter() - Method in class org.jmol.viewer.Eval
 
getMapStorageCount(int[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getMarBond() - Method in class org.jmol.viewer.Viewer
 
getMarchingSquares() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of a matching atom in a molecule.
getMatrix() - Method in class org.jmol.util.Quaternion
 
getMatrixRotate() - Method in class org.jmol.viewer.TransformManager
 
getMatrixRotate() - Method in class org.jmol.viewer.Viewer
 
getMatrixtransform() - Method in class org.jmol.viewer.TransformManager
 
getMatrixtransform() - Method in class org.jmol.viewer.Viewer
 
getMaxMappedValue() - Method in class org.jmol.jvxl.readers.VoxelReader
 
getMaxMathParams(int) - Static method in class org.jmol.viewer.Token
 
getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
 
getMaxZoomPercent() - Method in class org.jmol.viewer.Viewer
 
getMeasureAllModelsFlag() - Method in class org.jmol.viewer.Viewer
 
getMeasureDistanceUnits() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getMeasureDistanceUnits() - Method in class org.jmol.viewer.Viewer
 
getMeasurement() - Method in class org.jmol.modelset.Measurement
 
getMeasurementCount() - Method in class org.jmol.api.JmolViewer
 
getMeasurementCount() - Method in class org.jmol.viewer.Viewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
 
getMeasurementInfo() - Method in class org.jmol.viewer.Viewer
 
getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getMeasurementScript(String) - Method in class org.jmol.modelset.Measurement
Used by MouseManager and Picking Manager to build the script
getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
 
getMenu(String) - Method in class org.jmol.popup.JmolPopup
 
getMenu(String) - Method in class org.jmol.popup.PopupResourceBundle
 
getMenu(String) - Method in class org.jmol.viewer.Viewer
 
getMenuCurrent() - Method in class org.jmol.popup.JmolPopup
 
getMenuCurrent() - Method in class org.jmol.popup.JmolPopupAwt
 
getMenuCurrent(StringBuffer, int, Menu, String) - Method in class org.jmol.popup.JmolPopupAwt
 
getMenuCurrent() - Method in class org.jmol.popup.JmolPopupSwing
 
getMenuCurrent(StringBuffer, int, Object, String) - Method in class org.jmol.popup.JmolPopupSwing
 
getMenuItem(String) - Method in class org.openscience.jmol.app.Jmol
Fetch the menu item that was created for the given command.
getMenuItemCount(Object) - Method in class org.jmol.popup.JmolPopup
 
getMenuItemCount(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
getMenuItemCount(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
getMenuItemHeight() - Method in class org.jmol.popup.JmolPopup
 
getMenuItemHeight() - Method in class org.jmol.popup.JmolPopupAwt
 
getMenuItemHeight() - Method in class org.jmol.popup.JmolPopupSwing
 
getMenuListener() - Method in class org.openscience.jmol.app.DisplayPanel
 
getMenuText(String) - Method in class org.jmol.popup.JmolPopup
 
getMeshCommand(StringBuffer, int) - Method in class org.jmol.shape.MeshCollection
 
getMeshData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getMeshDataServer() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getMessageQueue() - Method in class org.jmol.viewer.StatusManager
 
getMessageQueue() - Method in class org.jmol.viewer.Viewer
 
getMessageStyleChime() - Method in class org.jmol.viewer.Viewer
 
getMinBondDistance() - Method in class org.jmol.api.JmolViewer
 
getMinBondDistance() - Method in class org.jmol.viewer.Viewer
 
getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
 
getMinimizer() - Method in class org.jmol.viewer.Eval
 
getMinimizer() - Method in class org.jmol.viewer.Viewer
 
getMiniPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getMinMappedValue() - Method in class org.jmol.jvxl.readers.VoxelReader
 
getMinZ() - Method in class org.jmol.modelset.Group
 
getMnemonic(String) - Static method in class org.jmol.applet.GuiMap
 
getMnemonic(String) - Static method in class org.openscience.jmol.app.GuiMap
 
getMoData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getModel() - Method in class org.jmol.modelset.Group
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelAtomBitSet(int, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getModelAtomBitSet(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelAuxiliaryInfo(int) - Method in class org.jmol.api.JmolViewer
 
getModelAuxiliaryInfo(int, String) - Method in class org.jmol.api.JmolViewer
 
getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelAuxiliaryInfo(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelAuxiliaryInfo(int) - Method in class org.jmol.viewer.Viewer
 
getModelAuxiliaryInfo(int, String) - Method in class org.jmol.viewer.Viewer
 
getModelAuxiliaryInfoBoolean(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelAuxiliaryInfoInt(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelBitSet(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
getModelBitSet(BitSet) - Method in class org.jmol.viewer.Viewer
 
getModelCellRange(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelCount() - Method in class org.jmol.api.JmolViewer
 
getModelCount() - Method in class org.jmol.modelset.ModelCollection
 
getModelCount() - Method in class org.jmol.viewer.Viewer
 
getModelDipole(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelDipole() - Method in class org.jmol.viewer.Viewer
 
getModelExtract(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getModelExtract(Object) - Method in class org.jmol.viewer.Viewer
 
getModelFileIndex() - Method in class org.jmol.modelset.Atom
 
getModelFileInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getModelFileInfo() - Method in class org.jmol.viewer.Viewer
 
getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
 
getModelFileName(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelFileName(int) - Method in class org.jmol.viewer.Viewer
 
getModelFileNumber() - Method in class org.jmol.modelset.Atom
 
getModelFileNumber(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelFileType(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelIndex() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getModelIndex() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getModelIndex() - Method in interface org.jmol.api.SymmetryInterface
 
getModelIndex() - Method in class org.jmol.modelset.Atom
 
getModelIndex() - Method in class org.jmol.modelset.Group
 
getModelIndex() - Method in class org.jmol.modelset.Model
 
getModelIndex(String) - Method in class org.jmol.shape.MeshCollection
 
getModelIndex() - Method in class org.jmol.symmetry.Symmetry
 
getModelInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getModelInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getModelInfoAsString() - Method in class org.jmol.modelset.ModelCollection
 
getModelInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getModelLabel() - Method in class org.jmol.popup.JmolPopup
 
getModelName(int) - Method in class org.jmol.api.JmolViewer
 
getModelName(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelName(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumber() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
getModelNumber(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumber() - Method in class org.jmol.modelset.Atom
 
getModelNumber(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
 
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelOrientation(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelProperties(int) - Method in class org.jmol.api.JmolViewer
 
getModelProperties(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelProperties(int) - Method in class org.jmol.viewer.Viewer
 
getModelProperty(int, String) - Method in class org.jmol.api.JmolViewer
 
getModelProperty(int, String) - Method in class org.jmol.modelset.ModelCollection
 
getModelProperty(int, String) - Method in class org.jmol.viewer.Viewer
 
getModels() - Method in class org.jmol.modelset.ModelCollection
 
getModelSet() - Method in class org.jmol.modelset.Chain
 
getModelSet() - Method in class org.jmol.modelset.Model
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelSet() - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.modelset.ModelCollection
 
getModelSetAuxiliaryInfo(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetAuxiliaryInfo(String) - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfoBoolean(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetAuxiliaryInfoInt(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetFileName() - Method in class org.jmol.api.JmolViewer
 
getModelSetFileName() - Method in class org.jmol.viewer.ModelManager
 
getModelSetFileName() - Method in class org.jmol.viewer.Viewer
 
getModelSetName() - Method in class org.jmol.api.JmolViewer
 
getModelSetName() - Method in class org.jmol.modelset.ModelCollection
 
getModelSetName() - Method in class org.jmol.viewer.Viewer
 
getModelSetPathName() - Method in class org.jmol.api.JmolViewer
 
getModelSetPathName() - Method in class org.jmol.viewer.ModelManager
 
getModelSetPathName() - Method in class org.jmol.viewer.Viewer
 
getModelSetProperties() - Method in class org.jmol.api.JmolViewer
 
getModelSetProperties() - Method in class org.jmol.modelset.ModelCollection
 
getModelSetProperties() - Method in class org.jmol.viewer.Viewer
 
getModelSetProperty(String) - Method in class org.jmol.modelset.ModelCollection
 
getModelSetProperty(String) - Method in class org.jmol.viewer.Viewer
 
getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
 
getModelSetTypeName() - Method in class org.jmol.viewer.Viewer
 
getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelSymmetryList(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelTitle(int) - Method in class org.jmol.modelset.ModelCollection
 
getModelTitle(int) - Method in class org.jmol.viewer.Viewer
 
getModeMultipleBond() - Method in class org.jmol.viewer.Viewer
 
getMOHeader(String[], Hashtable[], int) - Method in class org.jmol.adapter.readers.more.GamessReader
 
getMOHeader(String[], Hashtable[], int) - Method in class org.jmol.adapter.readers.more.GamessUKReader
 
getMOHeader(String[], Hashtable[], int) - Method in class org.jmol.adapter.readers.more.GamessUSReader
 
getMoJvxl(int) - Method in class org.jmol.viewer.Eval
 
getMolecularFormula() - Method in class org.jmol.modelset.Molecule
 
getMoleculeBitSet(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeBitSet(int) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeIndex(int) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getMoleculeInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getMoleculeNumber() - Method in class org.jmol.modelset.Atom
 
getMolecules() - Method in class org.jmol.modelset.ModelCollection
 
getMolName() - Method in class org.jmol.adapter.readers.more.HinReader
 
getMonomerCount() - Method in class org.jmol.modelsetbio.BioPolymer
 
getMonomerCount() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getMonomerIndex() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getMonomers() - Method in class org.jmol.modelsetbio.BioPolymer
 
getMonomerSequenceAtoms(BitSet, BitSet) - Method in class org.jmol.modelsetbio.Monomer
 
getMopacConstD(int, float) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getMopacConstP(int, float) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getMopacConstS(int, float) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getMoState(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
 
getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
 
getMoveToText() - Method in class org.jmol.viewer.StateManager.Orientation
 
getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
getMoveToText(float) - Method in class org.jmol.viewer.Viewer
 
getMpsShapeCount() - Method in class org.jmol.shapebio.BioShapeCollection
 
getMyInfo() - Method in class org.jmol.modelset.Group
 
getMyInfo() - Method in class org.jmol.modelsetbio.Monomer
 
getMyMenuBar() - Method in class org.jmol.applet.Console
 
getN1() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN4() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN6() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getName() - Method in class org.jmol.symmetry.PointGroup
 
getName() - Method in class org.jmol.symmetry.SpaceGroup
 
getNavigating() - Method in class org.jmol.viewer.TransformManager
 
getNavigating() - Method in class org.jmol.viewer.Viewer
 
getNavigationCenter() - Method in class org.jmol.viewer.TransformManager
 
getNavigationCenter() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationCenter() - Method in class org.jmol.viewer.Viewer
 
getNavigationCentered() - Method in class org.jmol.viewer.Viewer
 
getNavigationDepthPercent() - Method in class org.jmol.viewer.TransformManager
 
getNavigationDepthPercent() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationDepthPercent() - Method in class org.jmol.viewer.Viewer
 
getNavigationManager(Viewer, int, int) - Method in class org.jmol.viewer.TransformManager
 
getNavigationMode() - Method in class org.jmol.viewer.Viewer
 
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationOffset() - Method in class org.jmol.viewer.Viewer
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager11
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.Viewer
 
getNavigationPeriodic() - Method in class org.jmol.viewer.Viewer
 
getNavigationSlabOffsetPercent() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationSpeed() - Method in class org.jmol.viewer.Viewer
 
getNavigationState() - Method in class org.jmol.viewer.TransformManager
 
getNavigationState() - Method in class org.jmol.viewer.TransformManager11
 
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager11
 
getNBackbonesDisplayed() - Method in class org.jmol.modelset.Atom
 
getNeighbors() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getNeighborVertexesArrays() - Static method in class org.jmol.geodesic.Geodesic
 
getNewFixedRotationCenter() - Method in class org.jmol.viewer.TransformManager
 
getNextComment() - Method in class org.jmol.viewer.Eval
 
getNextDataToken() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
first checks to see if the next token is an unquoted control code, and if so, returns null
getNextPreloadClassName() - Method in class org.jmol.appletwrapper.AppletWrapper
 
getNextQuotedString(String, int) - Static method in class org.jmol.util.Parser
 
getNextToken() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
getNextVoxelValue(StringBuffer) - Method in class org.jmol.jvxl.readers.JvxlReader
 
getNextVoxelValue(StringBuffer) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getNHPoint(Point3f, Vector3f) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenAtomPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNoneSelected() - Method in class org.jmol.viewer.Viewer
 
getNormal(Point3f, Vector3f) - Method in class org.jmol.export._PovrayExporter
 
getNormal() - Method in class org.jmol.util.Quaternion
 
getNormalFromCenter(Point3f, Point3f, Point3f, Point3f, boolean, Vector3f) - Static method in class org.jmol.g3d.Graphics3D
 
getNormalizedDE() - Method in class org.jmol.minimize.forcefield.ForceField
 
getNormalThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.g3d.Graphics3D
 
getNormix(Vector3f) - Method in interface org.jmol.api.JmolRendererInterface
 
getNormix(Vector3f) - Method in class org.jmol.export.Export3D
 
getNormix(Vector3f) - Method in class org.jmol.g3d.Graphics3D
 
getNormix(Vector3f) - Method in class org.jmol.g3d.Normix3D
 
getNormix(double, double, double, int) - Method in class org.jmol.g3d.Normix3D
 
getNormixVector(short) - Method in interface org.jmol.api.JmolRendererInterface
 
getNormixVector(short) - Method in class org.jmol.export.Export3D
 
getNormixVector(short) - Method in class org.jmol.g3d.Graphics3D
 
getNotionalUnitcell(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getNotionalUnitcell(Object) - Method in class org.jmol.api.JmolAdapter
Get the notional unit cell.
getNotionalUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
getNotionalUnitcell() - Method in class org.jmol.modelset.ModelCollection
deprecated due to multimodel issues, but required by an interface -- do NOT remove.
getNotionalUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
getNotionalUnitCell() - Method in class org.jmol.symmetry.UnitCell
 
getNotionalUnitcell(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter
 
getNPQ(int) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getNPQd(int) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getNPQp(int) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getNPQs(int) - Static method in class org.jmol.adapter.readers.more.MopacData
 
getNucleicPhosphorusAtom(int) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
getNumber() - Method in class org.jmol.smiles.SmilesAtom
Returns the atom number of the atom.
getNumericalToken() - Method in class org.jmol.viewer.Compiler
 
getNumericParameter(String) - Method in class org.jmol.viewer.Eval
 
getNumSet() - Method in class org.jmol.modelset.MeasurementPending
 
getO2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getO4() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getO6() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getObjectArgb(int) - Method in class org.jmol.viewer.Viewer
 
getObjectColix(int) - Method in class org.jmol.viewer.Viewer
 
getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
 
getObjectMad(int) - Method in class org.jmol.viewer.Viewer
 
getObjectNameFromId(int) - Static method in class org.jmol.viewer.StateManager
 
getObjectState(String) - Method in class org.jmol.viewer.Viewer
 
getOccupancy() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getOccupancy() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getOccupancy() - Method in class org.jmol.modelset.Atom
 
getOctant(Point3f) - Static method in class org.jmol.util.Quadric
 
getOffset(int) - Method in class org.jmol.util.CompoundDocument
 
getOmega() - Method in class org.jmol.modelset.Group
 
getOpenFileError() - Method in class org.jmol.api.JmolSimpleViewer
 
getOpenFileError() - Method in class org.jmol.viewer.Viewer
misnamed -- really this opens the file, gets the data, and returns error or null
getOpenFileError(boolean) - Method in class org.jmol.viewer.Viewer
the opener for Jmol
getOpenFileNameFromDialog(JmolAdapter, String, JmolViewer, String, Object, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
getOpenFileNameFromDialog(JmolAdapter, String, JmolViewer, String, Object, String, boolean) - Method in class org.jmol.export.dialog.Dialog
 
getOpenFileNameFromDialog(String) - Method in class org.openscience.jmol.app.Jmol
 
getOperatingSystemName() - Method in class org.jmol.api.JmolViewer
 
getOperatingSystemName() - Method in class org.jmol.viewer.Viewer
 
getOperation(int) - Method in class org.jmol.symmetry.SpaceGroup
 
getOperationCount() - Method in class org.jmol.symmetry.SpaceGroup
 
getOptionInterface(String) - Static method in class org.jmol.api.Interface
 
getOrAddBond(Atom, Atom, short, short, BitSet) - Method in class org.jmol.modelset.BondCollection
 
getOrAllocateChain(Model, char) - Method in class org.jmol.modelset.ModelLoader
 
getOrder() - Method in class org.jmol.modelset.Bond
 
getOrderName() - Method in class org.jmol.modelset.Bond
 
getOrderNumber() - Method in class org.jmol.modelset.Bond
 
getOrientation() - Method in class org.jmol.viewer.StateManager
 
getOrientationInfo() - Method in class org.jmol.viewer.TransformManager
 
getOrientationInfo() - Method in class org.jmol.viewer.Viewer
 
getOrientationText(int) - Method in class org.jmol.viewer.TransformManager
 
getOrientationText(int) - Method in class org.jmol.viewer.Viewer
 
getOriginFloat() - Method in interface org.jmol.api.VolumeDataInterface
 
getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
 
getOriginPoint(boolean) - Method in class org.jmol.shape.Axes
 
getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
 
getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
 
getOutputStream() - Method in class org.openscience.jmol.app.LoopedStreams
 
getPageAuthorName() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPaletteID() - Method in class org.jmol.modelset.Atom
 
getPaletteID(String) - Static method in class org.jmol.viewer.JmolConstants
 
getPaletteName(byte) - Static method in class org.jmol.viewer.JmolConstants
 
getPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getPanel() - Method in class org.openscience.jmol.app.webexport.Molecules
 
getPanel() - Method in class org.openscience.jmol.app.webexport.Orbitals
 
getPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getParameter(String) - Method in class org.jmol.api.JmolViewer
 
getParameter(String) - Method in class org.jmol.applet.Jmol
 
getParameter(String, Hashtable) - Static method in class org.jmol.minimize.forcefield.Calculations
 
getParameter(String, boolean) - Method in class org.jmol.viewer.Eval
 
getParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getParameter(String) - Method in class org.jmol.viewer.Viewer
 
getParameterEscaped(String) - Method in class org.jmol.viewer.Eval
 
getParameterEscaped(String, int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getParameterEscaped(String) - Method in class org.jmol.viewer.Viewer
 
getParams() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getParamType(int) - Static method in class org.jmol.viewer.PropertyManager
 
getParent(Object) - Method in class org.jmol.popup.JmolPopup
 
getParent(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
getParent(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
getPartialBondDotted(int) - Static method in class org.jmol.viewer.JmolConstants
 
getPartialBondOrder(int) - Static method in class org.jmol.viewer.JmolConstants
 
getPartialBondOrderFromInteger(int) - Static method in class org.jmol.viewer.JmolConstants
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
getPartialCharge() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getPartialCharge() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getPartialCharge() - Method in class org.jmol.modelset.Atom
 
getPartialCharge() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
 
getPartialCharges() - Method in class org.jmol.viewer.Viewer
 
getPath(Mesh) - Method in class org.jmol.shapespecial.Draw
 
getPathHistory() - Method in class org.openscience.jmol.app.PovrayDialog
Just recovers the path settings from last session.
getPdbAtomData(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getPdbData(int, String, BitSet, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getPdbData(char, char, int, boolean, BitSet, StringBuffer, StringBuffer, BitSet, boolean, BitSet) - Method in class org.jmol.modelset.Polymer
 
getPdbData(char, char, int, boolean, BitSet, StringBuffer, StringBuffer, BitSet, boolean, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
 
getPdbData(BioPolymer, char, char, int, boolean, BitSet, StringBuffer, StringBuffer, BitSet, boolean, BitSet) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getPdbData(char, char, int, boolean, BitSet, StringBuffer, StringBuffer, BitSet, boolean, BitSet) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
getPdbData(BitSet) - Method in class org.jmol.viewer.Viewer
 
getPdbData(int, String) - Method in class org.jmol.viewer.Viewer
 
getPDBHeader(int) - Method in class org.jmol.modelset.ModelCollection
 
getPDBHeader() - Method in class org.jmol.viewer.Viewer
 
getPdbLoadInfo(int) - Method in class org.jmol.viewer.Viewer
 
getPdbScaleMatrix(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getPdbScaleMatrix(Object) - Method in class org.jmol.api.JmolAdapter
Get the PDB scale matrix.
getPdbScaleTranslate(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getPdbScaleTranslate(Object) - Method in class org.jmol.api.JmolAdapter
Get the PDB scale translation vector.
getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
 
getPercentageRead() - Method in class org.jmol.viewer.MonitorInputStream
 
getPercentageRead() - Method in class org.openscience.jvxl.MonitorInputStream
 
getPercentVdwAtom() - Method in class org.jmol.api.JmolViewer
 
getPercentVdwAtom() - Method in class org.jmol.viewer.Viewer
 
getPerspectiveDepth() - Method in class org.jmol.api.JmolViewer
 
getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
 
getPerspectiveDepth() - Method in class org.jmol.viewer.Viewer
 
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
calculate the perspective factor based on z
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager10
 
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager11
 
getPhase(Point3f) - Method in class org.jmol.jvxl.readers.VoxelReader
 
getPhi() - Method in class org.jmol.modelset.Group
 
getPickingMode(String) - Static method in class org.jmol.viewer.JmolConstants
 
getPickingMode() - Method in class org.jmol.viewer.PickingManager
 
getPickingMode() - Method in class org.jmol.viewer.Viewer
 
getPickingModeName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getPickingSpinRate() - Method in class org.jmol.viewer.Viewer
 
getPickingStyle(String) - Static method in class org.jmol.viewer.JmolConstants
 
getPickingStyle() - Method in class org.jmol.viewer.PickingManager
 
getPickingStyle() - Method in class org.jmol.viewer.Viewer
 
getPickingStyleName(int) - Static method in class org.jmol.viewer.JmolConstants
 
GetPixel(int, int) - Method in class org.jmol.export.image.GifEncoder
 
getPixelCounts() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getPlanarOrigin() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getPlanarVectors() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getPlane() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getPlane(int, Vector3f, Point3f) - Method in class org.jmol.symmetry.PointGroup
 
getPlane(String) - Static method in class org.openscience.jvxl.Jvxl
 
getPlaneShade(int, int, double[]) - Method in class org.jmol.g3d.Sphere3D
 
getPoint3f(int, boolean) - Method in class org.jmol.viewer.Eval
 
getPoint4f(int) - Method in class org.jmol.viewer.Eval
 
getPointArc() - Method in class org.jmol.modelset.Measurement
 
getPointAtomPoint() - Method in class org.jmol.modelsetbio.Monomer
 
getPointCount(int[], int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getPointer(int) - Static method in class org.jmol.shape.Object2d
 
getPointers(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
 
getPointGroup(PointGroup, Atom[], BitSet, boolean, float, float) - Static method in class org.jmol.symmetry.PointGroup
 
getPointGroupAsString(BitSet, boolean, String, int, float) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupAsString(boolean, String, int, float) - Method in class org.jmol.viewer.Viewer
 
getPointGroupInfo(int, boolean, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupInfo(BitSet) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
 
getPointGroupInfo(Object) - Method in class org.jmol.viewer.Viewer
 
getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getPointGroupTolerance(int) - Method in class org.jmol.viewer.Viewer
 
getPointOrPlane(int, boolean, boolean, boolean, boolean, int, int) - Method in class org.jmol.viewer.Eval
 
getPointPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getPoints() - Method in class org.jmol.modelset.Measurement
 
getPolygonCount() - Method in class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
getPolymerCount() - Method in class org.jmol.api.JmolViewer
 
getPolymerCount() - Method in class org.jmol.viewer.Viewer
 
getPolymerCountInModel(int) - Method in class org.jmol.api.JmolViewer
 
getPolymerCountInModel(int) - Method in class org.jmol.viewer.Viewer
 
getPolymerIndex() - Method in class org.jmol.modelset.Atom
 
getPolymerInfo(BitSet) - Method in class org.jmol.modelset.Polymer
 
getPolymerInfo(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerLeadMidPoints(int, int) - Method in class org.jmol.api.JmolViewer
 
getPolymerLeadMidPoints(int, int) - Method in class org.jmol.modelset.ModelCollection
 
getPolymerLeadMidPoints(int, int) - Method in class org.jmol.viewer.Viewer
 
getPolymerLength() - Method in class org.jmol.modelset.Atom
 
getPolymerPointsAndVectors(BitSet, Vector) - Method in class org.jmol.modelset.ModelCollection
 
getPolymerPointsAndVectors(int, BitSet, Vector, boolean, float) - Method in class org.jmol.modelset.Polymer
 
getPolymerPointsAndVectors(int, BitSet, Vector, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerPointsAndVectors(BitSet, Vector) - Method in class org.jmol.viewer.Viewer
 
getPolymerSequenceAtoms(int, int, int, int, BitSet, BitSet) - Method in class org.jmol.modelset.Polymer
 
getPolymerSequenceAtoms(int, int, int, int, BitSet, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPopupMenu(boolean) - Method in class org.jmol.applet.Jmol
 
getPosition(Object) - Method in class org.jmol.popup.JmolPopup
 
getPosition(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
getPosition(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
getPosition() - Method in class org.jmol.viewer.MonitorInputStream
 
getPosition() - Method in class org.openscience.jvxl.MonitorInputStream
 
getPrecedence(int) - Static method in class org.jmol.viewer.Token
 
getProperties() - Method in class org.jmol.export.dialog.HistoryFile
 
getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getProperty(String, String, String) - Method in class org.jmol.api.JmolViewer
 
getProperty(String, int) - Method in interface org.jmol.api.MinimizerInterface
 
getProperty(String) - Method in class org.jmol.applet.Jmol
 
getProperty(String, String) - Method in class org.jmol.applet.Jmol
 
getProperty(String, String) - Method in class org.jmol.export.dialog.HistoryFile
Get the value of a property
getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
 
getProperty(String, int) - Method in class org.jmol.shape.Axes
 
getProperty(String, int) - Method in class org.jmol.shape.Echo
 
getProperty(String, int) - Method in class org.jmol.shape.Labels
 
getProperty(String, int) - Method in class org.jmol.shape.Measures
 
getProperty(String, int) - Method in class org.jmol.shape.MeshCollection
 
getProperty(String, int) - Method in class org.jmol.shape.Shape
 
getProperty(String, int) - Method in class org.jmol.shape.Sticks
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
 
getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Pmesh
 
getProperty(String, boolean) - Static method in class org.jmol.util.Logger
 
getProperty() - Method in class org.jmol.viewer.Eval
 
getProperty(Viewer, String, String, Object) - Static method in class org.jmol.viewer.PropertyManager
 
getproperty - Static variable in class org.jmol.viewer.Token
 
getProperty(String, String, String) - Method in class org.jmol.viewer.Viewer
 
getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
 
getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsJSON(String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsJSON(String, String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsObject(Viewer, String, Object, String) - Static method in class org.jmol.viewer.PropertyManager
 
getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsString(String) - Method in class org.jmol.applet.Jmol
 
getPropertyAsString(String, String) - Method in class org.jmol.applet.Jmol
 
getPropertyColix(int) - Method in class org.jmol.viewer.ColorManager
 
getPropertyColorScheme() - Method in class org.jmol.viewer.Viewer
 
getPropertyCount(String) - Method in class org.jmol.adapter.readers.more.CsfReader
 
getPropertyName(int) - Static method in class org.jmol.viewer.PropertyManager
 
getPropertyNumber(String) - Static method in class org.jmol.viewer.PropertyManager
 
getProteinStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getProteinStructure() - Method in class org.jmol.modelsetbio.Monomer
 
getProteinStructureID() - Method in class org.jmol.modelset.Atom
 
getProteinStructureID() - Method in class org.jmol.modelset.Group
 
getProteinStructureID() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getProteinStructureState(BitSet, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getProteinStructureState() - Method in class org.jmol.viewer.Viewer
 
getProteinStructureType() - Method in class org.jmol.modelset.Atom
 
getProteinStructureType() - Method in class org.jmol.modelset.Group
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getPsi() - Method in class org.jmol.modelset.Group
 
getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
 
getQuality(String) - Method in class org.jmol.export.dialog.Dialog
 
getQuantumShellTag(int) - Static method in class org.jmol.viewer.JmolConstants
 
getQuantumShellTagID(String) - Static method in class org.jmol.api.JmolAdapter
 
getQuantumShellTagID(String) - Static method in class org.jmol.viewer.JmolConstants
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.api.JmolAdapter
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.viewer.JmolConstants
 
getQuantumSubshellTag(int, int) - Static method in class org.jmol.api.JmolAdapter
 
getQuantumSubshellTag(int, int) - Static method in class org.jmol.viewer.JmolConstants
 
getQuantumSubshellTagID(int, String) - Static method in class org.jmol.api.JmolAdapter
 
getQuantumSubshellTagID(int, String) - Static method in class org.jmol.viewer.JmolConstants
 
getQuardricZ(double, double, double[], double[]) - Static method in class org.jmol.util.Quadric
 
getQuaternion(char) - Method in class org.jmol.modelset.Atom
 
getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getQuaternion(char) - Method in class org.jmol.modelset.Group
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternionFrame(Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Quaternion
 
getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.Monomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternionStraightness(String, Quaternion, Quaternion) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getQuotedString(String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
getRadius() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getRadius() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getRadius() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getRadius() - Method in class org.jmol.modelset.Atom
 
getRadius() - Method in class org.jmol.modelset.Bond
 
getRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoids
 
getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
 
getRasmolHeteroSetting() - Method in class org.jmol.viewer.Viewer
 
getRasmolHydrogenSetting() - Method in class org.jmol.viewer.Viewer
 
getRasMolRadius() - Method in class org.jmol.modelset.Atom
 
getRasmolScale(boolean) - Static method in class org.jmol.util.ColorEncoder
 
getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getReaderFromType(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getReadingTimeMillis() - Method in class org.openscience.jvxl.MonitorInputStream
 
getRefreshing() - Method in class org.jmol.viewer.Viewer
 
getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
 
getRegistryInfo() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
getRegistryInfo() - Method in class org.jmol.viewer.StatusManager
 
getRegistryInfo() - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
getRenderBondOrder(int) - Method in class org.jmol.shape.SticksRenderer
 
getRenderer(int, Graphics3D) - Method in class org.jmol.viewer.FrameRenderer
 
getRenderHeight() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d height
getRenderHeight() - Method in class org.jmol.export.Export3D
gets g3d height
getRenderHeight() - Method in class org.jmol.g3d.Graphics3D
gets g3d height
getRenderWidth() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d width
getRenderWidth() - Method in class org.jmol.export.Export3D
gets g3d width
getRenderWidth() - Method in class org.jmol.g3d.Graphics3D
gets g3d width
getResno() - Method in class org.jmol.modelset.Atom
 
getResno() - Method in class org.jmol.modelset.Group
 
getResource(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getResourceString(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getResult(boolean, String) - Method in class org.jmol.viewer.Eval.Rpn
 
getReverse() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getRibbonAspectRatio() - Method in class org.jmol.viewer.Viewer
 
getRibbonBorder() - Method in class org.jmol.viewer.Viewer
 
getRocketBarrelFlag() - Method in class org.jmol.viewer.Viewer
 
getRotateXyzText() - Method in class org.jmol.viewer.TransformManager
 
getRotateZyzText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getRotation(Vector3f) - Method in class org.jmol.export._Exporter
 
getRotation(Matrix3f) - Method in class org.jmol.viewer.TransformManager
 
getRotation(Matrix3f) - Method in class org.jmol.viewer.Viewer
 
getRotationCenter() - Method in class org.jmol.viewer.TransformManager
 
getRotationCenter() - Method in class org.jmol.viewer.Viewer
 
getRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo.RotationTerm
 
getRotationRadius() - Method in class org.jmol.api.JmolViewer
 
getRotationRadius() - Method in class org.jmol.viewer.TransformManager
 
getRotationRadius() - Method in class org.jmol.viewer.Viewer
 
getRotationText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getRowCount() - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
getRubberBand() - Method in class org.jmol.viewer.MouseManager
 
getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
 
getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
 
getSavedCoordinates(String) - Method in class org.jmol.viewer.Viewer
 
getSavedState(String) - Method in class org.jmol.viewer.StateManager
 
getSavedState(String) - Method in class org.jmol.viewer.Viewer
 
getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
 
getSavedStructure(String) - Method in class org.jmol.viewer.Viewer
 
getSaveFileNameFromDialog(JmolViewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getSaveFileNameFromDialog(JmolViewer, String, String) - Method in class org.jmol.export.dialog.Dialog
 
getScalePixelsPerAngstrom() - Method in class org.jmol.viewer.Viewer
 
getScalePixelsPerMicron() - Method in class org.jmol.shape.Object2d
 
getScreenDim() - Method in class org.jmol.viewer.Viewer
 
getScreenHeight() - Method in class org.jmol.api.JmolViewer
 
getScreenHeight() - Method in class org.jmol.viewer.Viewer
 
getScreenImage() - Method in class org.jmol.api.JmolViewer
 
getScreenImage() - Method in class org.jmol.g3d.Graphics3D
 
getScreenImage() - Method in class org.jmol.viewer.Viewer
 
getScreenRadius() - Method in class org.jmol.modelset.Atom
 
getScreenWidth() - Method in class org.jmol.api.JmolViewer
 
getScreenWidth() - Method in class org.jmol.viewer.Viewer
 
getScript() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getScript() - Method in class org.jmol.shape.Object2d
 
getScript() - Method in class org.jmol.viewer.Compiler
 
getScript() - Method in class org.jmol.viewer.Eval
 
getScriptBitSets(String, BitSet[]) - Method in class org.jmol.shapesurface.Isosurface
 
getScriptCount() - Method in class org.jmol.viewer.ScriptManager
 
getScriptDelay() - Method in class org.jmol.viewer.Viewer
 
getScriptItem(boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
 
getSearch(String, int, BitSet) - Method in class org.jmol.minimize.Minimizer
 
getSectorAllocationTable() - Method in class org.jmol.util.CompoundDocument
 
getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getSelectAllModels() - Method in class org.jmol.viewer.Viewer
 
getSelectedGroupCount() - Method in class org.jmol.modelset.Chain
 
getSelectedGroupCountWithinChain() - Method in class org.jmol.modelset.Atom
 
getSelectedGroupIndex() - Method in class org.jmol.modelset.Group
 
getSelectedGroupIndexWithinChain() - Method in class org.jmol.modelset.Atom
 
getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerCountWithinPolymer() - Method in class org.jmol.modelset.Atom
 
getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerIndexWithinPolymer() - Method in class org.jmol.modelset.Atom
 
getSelectionCount() - Method in class org.jmol.api.JmolViewer
 
getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
 
getSelectionCount() - Method in class org.jmol.viewer.Viewer
 
getSelectionHaloEnabled() - Method in class org.jmol.modelset.ModelSet
 
getSelectionHaloEnabled() - Method in class org.jmol.viewer.Viewer
 
getSelectionSet() - Method in class org.jmol.viewer.Viewer
 
getSelectionSubset() - Method in class org.jmol.viewer.Viewer
 
getSeqcode() - Method in class org.jmol.modelset.Atom
 
getSeqcode() - Method in class org.jmol.modelset.Group
 
getSeqcode(int, char) - Static method in class org.jmol.modelset.Group
 
getSeqCode(Token) - Static method in class org.jmol.viewer.Eval
 
getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSeqcodeString() - Method in class org.jmol.modelset.Atom
 
getSeqcodeString() - Method in class org.jmol.modelset.Group
 
getSeqcodeString(int) - Static method in class org.jmol.modelset.Group
 
getSeqNumber() - Method in class org.jmol.modelset.Atom
 
getSeqNumber() - Method in class org.jmol.modelset.Group
 
getSequence() - Method in class org.jmol.modelset.Polymer
 
getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSequenceBits(String, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
getSequenceBits(String, BitSet) - Method in class org.jmol.viewer.Viewer
 
getSequenceCode(boolean) - Method in class org.jmol.viewer.Compiler
 
getSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getSequenceNumber() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getSequenceNumber(int) - Static method in class org.jmol.modelset.Group
 
getSetAxesTypeMad(int) - Method in class org.jmol.viewer.Eval
 
getSetHistory(int) - Method in class org.jmol.api.JmolViewer
 
getSetHistory(int) - Method in class org.jmol.util.CommandHistory
Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n <= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
getSetHistory(int) - Method in class org.jmol.viewer.Viewer
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
getSettableTokFromString(String) - Static method in class org.jmol.viewer.Token
 
getSettings(String) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getShades(short) - Static method in class org.jmol.g3d.Colix3D
 
getShades(short) - Method in class org.jmol.g3d.Graphics3D
 
getShades(int, boolean) - Static method in class org.jmol.g3d.Shade3D
 
getShadesGreyscale(short) - Static method in class org.jmol.g3d.Colix3D
 
getShape(int) - Method in class org.jmol.modelset.ModelSet
 
getShapeClassName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getShapeCommands(Hashtable, Hashtable, int) - Static method in class org.jmol.shape.Shape
 
getShapeCommands(Hashtable, Hashtable, int, String) - Static method in class org.jmol.shape.Shape
 
getShapeDetail() - Method in class org.jmol.shape.Shape
 
getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeDetail() - Method in class org.jmol.shapespecial.Draw
 
getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeIdFromObjectName(String) - Method in class org.jmol.modelset.ModelSet
 
getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.Viewer
 
getShapeInfo() - Method in class org.jmol.modelset.ModelSet
 
getShapeInfo() - Method in class org.jmol.viewer.Viewer
 
getShapeNameParameter(int) - Method in class org.jmol.viewer.Eval
 
getShapeProperty(int, String, int) - Method in class org.jmol.modelset.ModelSet
 
getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapeProperty(int, String, int) - Method in class org.jmol.viewer.Viewer
 
getShapePropertyAsInt(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapeState() - Method in class org.jmol.shape.AtomShape
 
getShapeState() - Method in class org.jmol.shape.Axes
 
getShapeState() - Method in class org.jmol.shape.Balls
 
getShapeState() - Method in class org.jmol.shape.Dots
 
getShapeState() - Method in class org.jmol.shape.Echo
 
getShapeState() - Method in class org.jmol.shape.FontLineShape
 
getShapeState() - Method in class org.jmol.shape.Halos
 
getShapeState() - Method in class org.jmol.shape.Hover
 
getShapeState() - Method in class org.jmol.shape.Labels
 
getShapeState() - Method in class org.jmol.shape.Measures
 
getShapeState() - Method in class org.jmol.shape.MeshCollection
 
getShapeState() - Method in class org.jmol.shape.Shape
 
getShapeState() - Method in class org.jmol.shape.Sticks
 
getShapeState() - Method in class org.jmol.shape.Uccage
 
getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
 
getShapeState() - Method in class org.jmol.shapespecial.Dipole
 
getShapeState() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeState() - Method in class org.jmol.shapespecial.Draw
 
getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
 
getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
 
getShapeState() - Method in class org.jmol.shapespecial.Vectors
 
getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
 
getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
 
getShapeType(int) - Method in class org.jmol.viewer.Eval
 
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JmolConstants
 
getShapeVisibilityFlags() - Method in class org.jmol.modelset.Atom
 
getShapeVisibilityFlags() - Method in class org.jmol.modelset.Bond
 
getSheetPoints(float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getSheetSmoothing() - Method in class org.jmol.viewer.Viewer
 
getShellOrder(int) - Static method in class org.jmol.viewer.JmolConstants
 
getShortSectorAllocationTable() - Method in class org.jmol.util.CompoundDocument
 
getShortStringData(int, int) - Method in class org.jmol.util.CompoundDocument
 
getShowAxes() - Method in class org.jmol.api.JmolViewer
 
getShowAxes() - Method in class org.jmol.viewer.Viewer
 
getShowBbcage() - Method in class org.jmol.api.JmolViewer
 
getShowBbcage() - Method in class org.jmol.viewer.Viewer
 
getShowFrank() - Method in class org.jmol.viewer.Viewer
 
getShowHiddenSelectionHalos() - Method in class org.jmol.viewer.Viewer
 
getShowHydrogens() - Method in class org.jmol.api.JmolViewer
 
getShowHydrogens() - Method in class org.jmol.viewer.Viewer
 
getShowMeasurementLabels() - Method in class org.jmol.viewer.Viewer
 
getShowMeasurements() - Method in class org.jmol.api.JmolViewer
 
getShowMeasurements() - Method in class org.jmol.viewer.Viewer
 
getShowMultipleBonds() - Method in class org.jmol.viewer.Viewer
 
getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
 
getShowUnitCell() - Method in class org.jmol.viewer.Viewer
 
getSize() - Method in class org.jmol.applet.Jvm12
 
getSlab() - Method in interface org.jmol.api.JmolRendererInterface
gets g3d slab
getSlab() - Method in class org.jmol.export.Export3D
gets g3d slab
getSlab() - Method in class org.jmol.g3d.Graphics3D
gets g3d slab
getSlabDepthPlane(boolean) - Method in class org.jmol.viewer.TransformManager
 
getSlabEnabled() - Method in class org.jmol.viewer.Viewer
 
getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
 
getSmartAromatic() - Method in class org.jmol.viewer.Viewer
 
getSolventOn() - Method in class org.jmol.viewer.Viewer
 
getSolventProbeRadius() - Method in class org.jmol.viewer.Viewer
 
getSourceActions(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfo(String, float[]) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupInfo(String, float[]) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfoText(String) - Method in class org.jmol.modelset.ModelCollection
 
getSpaceGroupInfoText(String) - Method in class org.jmol.viewer.Viewer
 
getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecialAtomID() - Method in class org.jmol.modelset.Atom
 
getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecModel(int) - Method in class org.jmol.modelset.ModelSet
 
getSpecName(String) - Method in class org.jmol.modelset.AtomCollection
 
getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSpecular() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecular() - Static method in class org.jmol.viewer.ColorManager
 
getSpecular() - Method in class org.jmol.viewer.Viewer
 
getSpecularExponent() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularPercent() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularPercent() - Static method in class org.jmol.viewer.ColorManager
 
getSpecularPercent() - Static method in class org.jmol.viewer.Viewer
 
getSpecularPower() - Static method in class org.jmol.g3d.Graphics3D
 
getSpecularState() - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getSpecularState() - Method in class org.jmol.viewer.Viewer
 
getSphereShape(int) - Static method in class org.jmol.g3d.Sphere3D
 
getSpinAxis(String, int) - Method in class org.jmol.shapespecial.Draw
 
getSpinCenter(String, int) - Method in class org.jmol.shapespecial.Draw
 
getSpinFps() - Method in class org.jmol.viewer.Viewer
 
getSpinOn() - Method in class org.jmol.viewer.TransformManager
 
getSpinOn() - Method in class org.jmol.viewer.Viewer
 
getSpinState(boolean) - Method in class org.jmol.viewer.TransformManager
 
getSpinState() - Method in class org.jmol.viewer.Viewer
 
getSpinX() - Method in class org.jmol.viewer.Viewer
 
getSpinY() - Method in class org.jmol.viewer.Viewer
 
getSpinZ() - Method in class org.jmol.viewer.Viewer
 
getSsbondsBackbone() - Method in class org.jmol.viewer.Viewer
 
getStandardLabelFormat() - Method in class org.jmol.viewer.StateManager
 
getStandardLabelFormat() - Method in class org.jmol.viewer.Viewer
 
getStandardStringData(int, int) - Method in class org.jmol.util.CompoundDocument
 
getStartChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStartChainID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStartInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStartInsertionCode() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getState(StringBuffer, boolean) - Method in class org.jmol.modelset.ModelSet
 
getState(int) - Method in class org.jmol.shape.Measures
 
getState(String) - Method in class org.jmol.shape.Mesh
 
getState() - Method in class org.jmol.shape.Text
 
getState(Hashtable) - Method in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
getState(StringBuffer) - Static method in class org.jmol.util.ColorEncoder
 
getState(StringBuffer) - Static method in class org.jmol.viewer.ColorManager
 
getState() - Method in class org.jmol.viewer.Eval
 
getState(StringBuffer) - Method in class org.jmol.viewer.FileManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.RepaintManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.SelectionManager
 
getState(StringBuffer) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getState(StringBuffer) - Method in class org.jmol.viewer.TransformManager
 
getStateInfo() - Method in class org.jmol.api.JmolViewer
 
getStateInfo() - Method in class org.jmol.viewer.Viewer
 
getStateInfo(String) - Method in class org.jmol.viewer.Viewer
 
getStaticGraphics(Image) - Static method in class org.jmol.g3d.Swing3D
 
getStatusChanged(String) - Method in class org.jmol.viewer.StatusManager
 
getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
 
getStatusList() - Method in class org.jmol.viewer.StatusManager
 
getStereoDegrees() - Method in class org.jmol.viewer.Viewer
 
getStereoImage(int) - Method in class org.jmol.viewer.Viewer
 
getStereoMode(String) - Static method in class org.jmol.viewer.JmolConstants
 
getStereoMode() - Method in class org.jmol.viewer.Viewer
 
getStereoModeName(int) - Static method in class org.jmol.viewer.JmolConstants
 
getStereoRotationMatrix(boolean) - Method in class org.jmol.viewer.TransformManager
 
getStraightness() - Method in class org.jmol.modelset.Atom
 
getStraightness() - Method in class org.jmol.modelset.Group
 
getStrandCount(int) - Method in class org.jmol.viewer.Viewer
 
getStreamAsBytes(BufferedInputStream) - Static method in class org.jmol.util.ZipUtil
 
getStrFormat() - Method in class org.jmol.modelset.Measurement
 
getString(String) - Method in class org.jmol.i18n.GT
 
getString(String, Object[]) - Method in class org.jmol.i18n.GT
 
getString() - Method in class org.jmol.modelset.Measurement
 
getString(String) - Method in class org.openscience.jmol.app.JmolResourceHandler
 
getStringDetail() - Method in class org.jmol.modelset.Measurement
 
getStringObjectAsToken(String, String) - Method in class org.jmol.viewer.Eval
 
getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getStringX(String) - Static method in class org.openscience.jmol.app.JmolResourceHandler
 
getStructure() - Method in class org.jmol.modelset.Group
 
getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getStructure(String) - Method in class org.jmol.popup.PopupResourceBundle
 
getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a StructureIterator.
getStructureMidPoint(int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getStructureState() - Method in class org.jmol.viewer.Viewer
 
getStructureType() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
getStructureType() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
getStructureTypeName(byte) - Static method in class org.jmol.modelsetbio.Monomer
 
getSubstructureSet(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSet(String) - Method in class org.jmol.smiles.PatternMatcher
Returns a vector of bits indicating which atoms match the pattern.
getSubstructureSet(SmilesMolecule) - Method in class org.jmol.smiles.PatternMatcher
Returns a vector of bits indicating which atoms match the pattern.
getSupported(String, boolean) - Method in class org.jmol.i18n.GT
 
getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
 
getSurfaceDistance100(int) - Method in class org.jmol.modelset.AtomCollection
 
getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
 
getSurfaceDistanceMax() - Method in class org.jmol.viewer.Viewer
 
getSurfacePointIndex(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean) - Method in interface org.jmol.jvxl.api.MeshDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndex(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndex(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
getSurfacePointIndex(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean) - Method in class org.jmol.shapesurface.Isosurface
 
getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
 
getSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
getSymbol(String) - Method in class org.jmol.adapter.readers.more.ShelxReader
 
getSymbol() - Method in class org.jmol.smiles.SmilesAtom
Returns the symbol of the atom.
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getSymmetry() - Method in class org.jmol.viewer.Eval
 
getSymmetryInfoAsString(int) - Method in class org.jmol.modelset.ModelCollection
 
getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelCollection
 
getSymmetryInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getSymmetryInfoString() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoString() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryOperatorList() - Method in class org.jmol.modelset.Atom
 
getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
getSymTemp() - Method in class org.jmol.modelset.ModelCollection
 
getSyncMode() - Method in class org.jmol.viewer.StatusManager
 
getTaintedAtoms(byte) - Method in class org.jmol.modelset.AtomCollection
 
getTaintedAtoms(byte) - Method in class org.jmol.viewer.Viewer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getTerminatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
 
getTestFlag1() - Method in class org.jmol.viewer.Viewer
 
getTestFlag2() - Method in class org.jmol.viewer.Viewer
 
getTestFlag3() - Method in class org.jmol.viewer.Viewer
 
getTestFlag4() - Method in class org.jmol.viewer.Viewer
 
getText() - Method in class org.jmol.applet.Console
 
getText() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getText3D(String, Font3D, Platform3D, boolean) - Static method in class org.jmol.g3d.Text3D
 
getTextColor() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getTextWrapper - Static variable in class org.jmol.i18n.GT
 
getTextWrapper() - Static method in class org.jmol.i18n.GT
 
getTheta() - Method in class org.jmol.util.Quaternion
 
getThetaDirected(Point4f) - Method in class org.jmol.util.Quaternion
 
getTitle() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getToken() - Method in class org.jmol.viewer.Compiler
gets the next token and sets global theToken and theValue
getToken(int) - Method in class org.jmol.viewer.Eval
 
getTokenFromName(String) - Static method in class org.jmol.viewer.Token
 
getTokenPeeked() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
getTokens() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
getTokens(String) - Static method in class org.jmol.adapter.readers.more.SpartanArchive
 
getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens(String, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getTokens() - Method in class org.jmol.shapesurface.MeshFileCollection
 
getTokens(String) - Static method in class org.jmol.util.Parser
 
getTokens(String, int) - Static method in class org.jmol.util.Parser
 
getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokensLike(String) - Static method in class org.jmol.viewer.Token
 
getTorsionAngleRadians(double[], double[], double[], double[], Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
getTorsions() - Method in class org.jmol.minimize.Minimizer
 
getTraceAlpha() - Method in class org.jmol.viewer.Viewer
 
getTrajectoryCount() - Method in class org.jmol.modelset.ModelCollection
 
getTrajectoryIndex(int) - Method in class org.jmol.modelset.ModelCollection
 
getTrajectoryInfo() - Method in class org.jmol.modelset.ModelSet
 
getTrajectoryInfo() - Method in class org.jmol.viewer.Viewer
 
getTransferData(DataFlavor) - Method in class org.jmol.export.image.ImageSelection
 
getTransferData(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
getTransferDataFlavors() - Method in class org.jmol.export.image.ImageSelection
 
getTransferDataFlavors() - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
getTransformedVectors() - Method in class org.jmol.g3d.Normix3D
 
getTransformedVertexVectors() - Method in interface org.jmol.api.JmolRendererInterface
 
getTransformedVertexVectors() - Method in class org.jmol.export.Export3D
 
getTransformedVertexVectors() - Method in class org.jmol.g3d.Graphics3D
 
getTransformText() - Method in class org.jmol.viewer.TransformManager
 
getTransformText() - Method in class org.jmol.viewer.Viewer
 
getTranslation(String) - Method in class org.jmol.i18n.GT
 
getTranslationScript() - Method in class org.jmol.viewer.TransformManager
 
getTranslationScript() - Method in class org.jmol.viewer.Viewer
 
getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationXPercent() - Method in class org.jmol.viewer.Viewer
 
getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationYPercent() - Method in class org.jmol.viewer.Viewer
 
getTranslationZPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationZPercent() - Method in class org.jmol.viewer.Viewer
 
getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
 
getTranslucentLevel(int) - Method in class org.jmol.viewer.Eval
 
getTrimmedLine() - Method in class org.jmol.g3d.Line3D
Cohen-Sutherland line clipping used to check visibility.
getType() - Method in interface org.jmol.api.JmolDialogInterface
 
getType() - Method in class org.jmol.export.dialog.Dialog
 
getType() - Method in class org.jmol.modelset.Polymer
 
getType() - Method in class org.openscience.jmol.app.FileTyper
 
getUnescapedStringLiteral() - Method in class org.jmol.viewer.Compiler
 
getUniqueID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getUniqueID() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getUniqueID() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getUnit() - Method in class org.jmol.minimize.forcefield.Calculations
 
getUnit() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getUnitCell(int) - Method in class org.jmol.modelset.ModelCollection
 
getUnitCellInfo(int) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfo() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfo(int) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfo() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfoText() - Method in class org.jmol.modelset.ModelCollection
 
getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
 
getUnitCellOffset(int) - Method in class org.jmol.modelset.ModelCollection
 
getUnitCellVertices() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellVertices() - Method in class org.jmol.symmetry.Symmetry
 
getUnits() - Method in class org.jmol.minimize.forcefield.ForceField
 
getUnitsymmetryInfo() - Method in class org.jmol.symmetry.Symmetry
 
getUnitsymmetryInfo(int) - Method in class org.jmol.symmetry.Symmetry
 
getUnscaledTransformMatrix() - Method in class org.jmol.api.JmolViewer
 
getUnscaledTransformMatrix() - Method in class org.jmol.viewer.TransformManager
 
getUnscaledTransformMatrix() - Method in class org.jmol.viewer.Viewer
 
getUnzippedBufferedReaderOrErrorMessageFromName(String, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getUseNumberLocalization() - Method in class org.jmol.viewer.Viewer
 
getUserColorScheme(String) - Method in class org.jmol.shapesurface.Isosurface
 
getUserDirectory() - Static method in class org.openscience.jmol.app.Jmol
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserParameterValue(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
 
getValence() - Method in class org.jmol.modelset.Atom
 
getValence() - Method in class org.jmol.modelset.Bond
 
getValue(String, String) - Method in class org.jmol.applet.Jmol
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
getValue() - Method in class org.jmol.modelset.Measurement
 
getValueAt(int, int) - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
getValueLowerCase(String, String) - Method in class org.jmol.applet.Jmol
 
getVanderwaalsMad(Viewer) - Method in class org.jmol.modelset.Atom
 
getVanderwaalsMar(int) - Method in class org.jmol.modelset.ModelSet
 
getVanderwaalsMar(int, int) - Static method in class org.jmol.viewer.JmolConstants
 
getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsMar(int, int) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsRadiusFloat() - Method in class org.jmol.modelset.Atom
 
getVdwType(String) - Static method in class org.jmol.viewer.JmolConstants
 
getVector(short) - Method in class org.jmol.g3d.Normix3D
 
getVector(int) - Method in class org.jmol.util.Quaternion
 
getVectorScale() - Method in class org.jmol.viewer.Viewer
 
getVectorX() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getVectorX() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getVectorY() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getVectorY() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getVectorZ() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getVectorZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getVertex(short, short) - Static method in class org.jmol.geodesic.Geodesic
 
getVertexCount(int) - Static method in class org.jmol.geodesic.Geodesic
 
getVertexCount() - Method in class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
getVertexList(DrawMesh, int, int) - Static method in class org.jmol.shapespecial.Draw
 
getVertexNormals() - Method in class org.jmol.shape.Mesh
 
getVertexVector(int) - Static method in class org.jmol.geodesic.Geodesic
 
getVertexVectors() - Static method in class org.jmol.geodesic.Geodesic
 
getVertexVectorsCount() - Static method in class org.jmol.geodesic.Geodesic
 
getVertices() - Method in class org.jmol.symmetry.UnitCell
 
getVibrationCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getVibrationCoord(int, char) - Method in class org.jmol.viewer.Viewer
 
getVibrationPeriod() - Method in class org.jmol.viewer.Viewer
 
getVibrationScale() - Method in class org.jmol.viewer.Viewer
 
getVibrationVector() - Method in class org.jmol.modelset.Atom
 
getVibrationVector(int) - Method in class org.jmol.modelset.AtomCollection
 
getVibrationVector(int) - Method in class org.jmol.viewer.Viewer
 
getViewer() - Method in class org.jmol.applet.Console
 
getViewer() - Method in class org.jmol.export.dialog.FilePreview.JmolPanel
 
getViewer() - Method in class org.jmol.shape.Shape
 
getViewerData() - Method in class org.jmol.popup.JmolPopup
 
getVisibleFramesBitSet() - Method in class org.jmol.viewer.RepaintManager
 
getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
 
getVisibleSet() - Method in class org.jmol.modelset.AtomCollection
 
getVisibleSet() - Method in class org.jmol.viewer.Viewer
 
getVolumeData() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getVolumeData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getVolumetricVectorLengths() - Method in interface org.jmol.api.VolumeDataInterface
 
getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelCounts() - Method in interface org.jmol.api.VolumeDataInterface
 
getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelData() - Method in interface org.jmol.api.VolumeDataInterface
 
getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
 
getWidth() - Method in class org.jmol.g3d.Text3D
 
getWidthUnitVector() - Method in class org.jmol.modelsetbio.Sheet
 
getWindowBorder(String) - Method in class org.jmol.export.dialog.HistoryFile
 
getWindowPosition(String) - Method in class org.jmol.export.dialog.HistoryFile
 
getWindowSize(String) - Method in class org.jmol.export.dialog.HistoryFile
 
getWindowState(StringBuffer) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
getWindowVisibility(String) - Method in class org.jmol.export.dialog.HistoryFile
 
getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getWingAtomPoint() - Method in class org.jmol.modelsetbio.Monomer
 
getWingPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
getWireframeRotation() - Method in class org.jmol.viewer.Viewer
 
getWithinAtomSetIterator(int, float, BitSet, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
 
getWithinAtomSetIterator(int, float, BitSet, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
 
getWithinAtomSetIterator(int, float, BitSet, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getWithinModelIterator(Atom, float) - Method in class org.jmol.modelset.ModelCollection
 
getWithinModelIterator(int, Point3f, float) - Method in class org.jmol.modelset.ModelCollection
 
getWithinModelIterator(Atom, float) - Method in class org.jmol.viewer.Viewer
 
getWord(String) - Method in class org.jmol.popup.PopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.PopupResourceBundle
 
getWorkingRadius(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getX() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getX() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getX() - Method in class org.jmol.viewer.Eval.Rpn
 
getX() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getXmlReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
getXmlType(JSObject) - Static method in class org.jmol.adapter.smarter.Resolver
 
getXmlType(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getXOffset(int) - Static method in class org.jmol.shape.Object2d
 
getXPlatformLook(JFileChooser) - Static method in class org.jmol.export.dialog.Dialog
 
getXYZ(boolean) - Method in class org.jmol.symmetry.HallInfo.RotationTerm
 
getXyz(int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
getXyz(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
 
getXYZFromMatrix(Matrix4f, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getY() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getY() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getY() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getYCCArray() - Method in class org.jmol.util.JpegInfo
 
getYOffset(int) - Static method in class org.jmol.shape.Object2d
 
getZ() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
getZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
getZ() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
getZeroBasedXyzRasmol() - Method in class org.jmol.viewer.Viewer
 
getZipDirectory(String, boolean) - Method in class org.jmol.viewer.FileManager
 
getZipDirectoryAndClose(InputStream, boolean) - Static method in class org.jmol.util.ZipUtil
 
getZipDirectoryAsString(String) - Method in class org.jmol.viewer.FileManager
 
getZipDirectoryAsStringAndClose(InputStream) - Static method in class org.jmol.util.ZipUtil
 
getZipDirectoryOrErrorAndClose(InputStream, boolean) - Static method in class org.jmol.util.ZipUtil
 
getZipEntryAsBytes(ZipInputStream) - Static method in class org.jmol.util.ZipUtil
 
getZipEntryAsString(ZipInputStream) - Static method in class org.jmol.util.ZipUtil
 
getZipFileContents(InputStream, String[], int, boolean) - Static method in class org.jmol.util.ZipUtil
iteratively drills into zip files of zip files to extract file content or zip file directory.
getZipFileContentsAsBytes(InputStream, String[], int) - Static method in class org.jmol.util.ZipUtil
 
getZoomEnabled() - Method in class org.jmol.viewer.Viewer
 
getZoomFactor(int, int, float, float) - Method in class org.jmol.viewer.Eval
 
getZoomIn() - Method in class org.jmol.jcamp.GraphCharacteristics
 
getZoomLarge() - Method in class org.jmol.viewer.Viewer
 
getZoomPercent() - Method in class org.jmol.api.JmolViewer
 
getZoomPercent() - Method in class org.jmol.viewer.Viewer
 
getZoomPercentFloat() - Method in class org.jmol.api.JmolViewer
 
getZoomPercentFloat() - Method in class org.jmol.viewer.TransformManager
 
getZoomPercentFloat() - Method in class org.jmol.viewer.Viewer
 
getZoomSetting() - Method in class org.jmol.viewer.TransformManager
 
getZoomSetting() - Method in class org.jmol.viewer.Viewer
 
getZShade() - Method in class org.jmol.viewer.Viewer
 
getZShift(int) - Method in class org.jmol.g3d.Graphics3D
 
GhemicalMMReader - Class in org.jmol.adapter.readers.more
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.more.GhemicalMMReader
 
ghemicalMMRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GIFEncode(OutputStream, int, int, boolean, byte, int, int, byte[], byte[], byte[]) - Method in class org.jmol.export.image.GifEncoder
 
GifEncoder - Class in org.jmol.export.image
 
GifEncoder(Image, OutputStream) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder(Image, OutputStream, boolean) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder(ImageProducer, OutputStream) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder(ImageProducer, OutputStream, boolean) - Constructor for class org.jmol.export.image.GifEncoder
 
GifEncoder.AdaptiveColorCollection - Class in org.jmol.export.image
 
GifEncoder.AdaptiveColorCollection(int) - Constructor for class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
GifEncoder.ColorItem - Class in org.jmol.export.image
 
GifEncoder.ColorItem(int, int, int, boolean) - Constructor for class org.jmol.export.image.GifEncoder.ColorItem
 
GifEncoder.ColorVector - Class in org.jmol.export.image
 
GifEncoder.ColorVector() - Constructor for class org.jmol.export.image.GifEncoder.ColorVector
 
GifEncoder.ColorVector.CountComparator - Class in org.jmol.export.image
 
GifEncoder.ColorVector.CountComparator() - Constructor for class org.jmol.export.image.GifEncoder.ColorVector.CountComparator
 
GIFNextPixel() - Method in class org.jmol.export.image.GifEncoder
 
global - Variable in class org.jmol.viewer.Viewer
 
GLOBAL_FRACTCOORD - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_latticeCells - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_SYMMETRY - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
globalBooleans - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
globalFunctions - Static variable in class org.jmol.viewer.Compiler
 
globalSerialID - Static variable in class org.jmol.modelsetbio.ProteinStructure
 
goButton - Variable in class org.openscience.jmol.app.PovrayDialog
 
gOffscreen - Variable in class org.jmol.g3d.Platform3D
 
GOLD - Static variable in class org.jmol.g3d.Graphics3D
 
goPressed() - Method in class org.openscience.jmol.app.PovrayDialog
Save or else launch povray- ie do our thang!
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
gotocmd() - Method in class org.jmol.viewer.Eval
 
gotocmd - Static variable in class org.jmol.viewer.Token
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.VoxelReader
 
gotoSector(int) - Method in class org.jmol.util.CompoundDocument
 
gradients - Variable in class org.jmol.minimize.forcefield.Calculations
 
GraphCharacteristics - Class in org.jmol.jcamp
 
GraphCharacteristics() - Constructor for class org.jmol.jcamp.GraphCharacteristics
 
GraphCharacteristics(boolean, boolean, boolean, boolean, String, String, String, String, String, String, String) - Constructor for class org.jmol.jcamp.GraphCharacteristics
 
GraphControlData - Class in org.jmol.jcamp.data
 
GraphControlData() - Constructor for class org.jmol.jcamp.data.GraphControlData
 
Graphics3D - Class in org.jmol.g3d
Provides high-level graphics primitives for 3D visualization.
Graphics3D(Component) - Constructor for class org.jmol.g3d.Graphics3D
Allocates a g3d object
graphicsOffscreen - Static variable in class org.jmol.g3d.Font3D
 
GRAY - Static variable in class org.jmol.g3d.Graphics3D
 
GRAY - Static variable in class org.jmol.util.ColorEncoder
 
green - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
GREEN - Static variable in class org.jmol.g3d.Graphics3D
 
greyscaleRendering - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Grid - Variable in class org.jmol.jcamp.Visua
 
group - Variable in class org.jmol.modelset.Atom
 
Group - Class in org.jmol.modelset
 
Group(Chain, String, int, int, int) - Constructor for class org.jmol.modelset.Group
 
group - Static variable in class org.jmol.viewer.Token
 
group3 - Variable in class org.jmol.adapter.smarter.Atom
 
group3Count - Static variable in class org.jmol.viewer.JmolConstants
 
group3Counts - Variable in class org.jmol.modelset.ModelLoader
 
group3Counts - Variable in class org.jmol.popup.JmolPopup
 
group3List - Variable in class org.jmol.popup.JmolPopup
 
group3List - Static variable in class org.jmol.viewer.JmolConstants
 
group3Lists - Variable in class org.jmol.modelset.ModelLoader
 
group3NameCount - Static variable in class org.jmol.modelset.Group
 
group3Names - Static variable in class org.jmol.modelset.Group
 
group3Of - Variable in class org.jmol.modelset.ModelLoader
 
GROUP_FLAG - Static variable in class org.jmol.shape.Labels
 
GROUP_PDB - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
groupCount - Variable in class org.jmol.modelset.Chain
 
groupCount - Variable in class org.jmol.modelset.Model
 
groupCount - Variable in class org.jmol.modelset.ModelCollection
 
groupID - Variable in class org.jmol.modelset.Group
 
groupID - Static variable in class org.jmol.viewer.Token
 
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_SULPHATE - Static variable in class org.jmol.viewer.JmolConstants
 
GROUPID_WATER - Static variable in class org.jmol.viewer.JmolConstants
 
groups - Variable in class org.jmol.modelset.Chain
 
groups - Variable in class org.jmol.modelset.ModelCollection
 
growAtomArrays(int) - Method in class org.jmol.modelset.ModelLoader
 
gScaled - Variable in class org.jmol.g3d.Rgb16
 
GT - Class in org.jmol.i18n
 
GT(String) - Constructor for class org.jmol.i18n.GT
 
GT() - Constructor for class org.jmol.i18n.GT
 
GT.Language - Class in org.jmol.i18n
 
GT.Language(String, String, boolean) - Constructor for class org.jmol.i18n.GT.Language
 
gto_exp - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
guimap - Variable in class org.jmol.applet.Console
 
GuiMap - Class in org.jmol.applet
 
GuiMap() - Constructor for class org.jmol.applet.GuiMap
 
guimap - Variable in class org.openscience.jmol.app.DisplayPanel
 
GuiMap - Class in org.openscience.jmol.app
 
GuiMap() - Constructor for class org.openscience.jmol.app.GuiMap
 
guimap - Variable in class org.openscience.jmol.app.Jmol
 
guimap - Variable in class org.openscience.jmol.app.PreferencesDialog
 
GuiMap.GetKey - Interface in org.jmol.applet
 
GuiMap.GetKey - Interface in org.openscience.jmol.app
 
GuiMap.KeyJCheckBox - Class in org.openscience.jmol.app
 
GuiMap.KeyJCheckBox(String, String, char, boolean) - Constructor for class org.openscience.jmol.app.GuiMap.KeyJCheckBox
 
GuiMap.KeyJCheckBoxMenuItem - Class in org.openscience.jmol.app
 
GuiMap.KeyJCheckBoxMenuItem(String, String, char, boolean) - Constructor for class org.openscience.jmol.app.GuiMap.KeyJCheckBoxMenuItem
 
GuiMap.KeyJMenu - Class in org.jmol.applet
 
GuiMap.KeyJMenu(String, String, char) - Constructor for class org.jmol.applet.GuiMap.KeyJMenu
 
GuiMap.KeyJMenu - Class in org.openscience.jmol.app
 
GuiMap.KeyJMenu(String, String, char) - Constructor for class org.openscience.jmol.app.GuiMap.KeyJMenu
 
GuiMap.KeyJMenuItem - Class in org.jmol.applet
 
GuiMap.KeyJMenuItem(String, String, char) - Constructor for class org.jmol.applet.GuiMap.KeyJMenuItem
 
GuiMap.KeyJMenuItem - Class in org.openscience.jmol.app
 
GuiMap.KeyJMenuItem(String, String, char) - Constructor for class org.openscience.jmol.app.GuiMap.KeyJMenuItem
 
GuiMap.KeyJRadioButtonMenuItem - Class in org.openscience.jmol.app
 
GuiMap.KeyJRadioButtonMenuItem(String, String, char) - Constructor for class org.openscience.jmol.app.GuiMap.KeyJRadioButtonMenuItem
 

H

H3T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
H5T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
halfRoot5 - Static variable in class org.jmol.geodesic.Geodesic
 
hAlignNames - Static variable in class org.jmol.shape.Object2d
 
HallInfo - Class in org.jmol.symmetry
 
HallInfo(String) - Constructor for class org.jmol.symmetry.HallInfo
 
hallInfo - Variable in class org.jmol.symmetry.SpaceGroup
 
HallInfo.RotationTerm - Class in org.jmol.symmetry
 
HallInfo.RotationTerm() - Constructor for class org.jmol.symmetry.HallInfo.RotationTerm
 
HallInfo.RotationTerm(String, int, char) - Constructor for class org.jmol.symmetry.HallInfo.RotationTerm
 
hallRotationTerms - Static variable in class org.jmol.symmetry.Rotation
 
hallSymbol - Variable in class org.jmol.symmetry.HallInfo
 
hallSymbol - Variable in class org.jmol.symmetry.SpaceGroup
 
hallTranslationTerms - Static variable in class org.jmol.symmetry.Translation
 
halo - Static variable in class org.jmol.viewer.Token
 
Halos - Class in org.jmol.shape
 
Halos() - Constructor for class org.jmol.shape.Halos
 
HalosGenerator - Class in org.jmol.export
 
HalosGenerator() - Constructor for class org.jmol.export.HalosGenerator
 
HalosRenderer - Class in org.jmol.shape
 
HalosRenderer() - Constructor for class org.jmol.shape.HalosRenderer
 
haltButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
haltExecution() - Method in class org.jmol.viewer.Eval
 
haltScriptExecution() - Method in class org.jmol.api.JmolViewer
 
haltScriptExecution() - Method in class org.jmol.viewer.Viewer
 
handleError() - Method in class org.jmol.viewer.Compiler
 
handleEvent(Event) - Method in class org.jmol.applet.Jmol
 
handleEvent(Event) - Method in class org.jmol.appletwrapper.AppletWrapper
 
handleEvent(Event) - Method in interface org.jmol.appletwrapper.WrappedApplet
 
handleEvent(Event) - Method in class org.jmol.jcamp.SaisieDlg
 
handleEvent(Event) - Method in class org.jmol.jcamp.Visua
 
handleOldJvm10Event(Event) - Method in class org.jmol.api.JmolViewer
 
handleOldJvm10Event(Event) - Method in class org.jmol.viewer.MouseManager
 
handleOldJvm10Event(Event) - Method in class org.jmol.viewer.MouseManager10
 
handleOldJvm10Event(Event) - Method in class org.jmol.viewer.MouseManager11
 
handleOldJvm10Event(Event) - Method in class org.jmol.viewer.Viewer
 
handlePopupMenu(int, int) - Method in interface org.jmol.api.JmolStatusListener
 
handlePopupMenu(int, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
handlePopupMenu(int, int) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
HAS_MAXGRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
hasAlternateLocations() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
hasBfactorRange - Variable in class org.jmol.modelset.AtomCollection
 
hasBfactorRange - Variable in class org.jmol.shapebio.BioShape
 
hasCalculatedHBonds - Variable in class org.jmol.modelset.Model
 
hasCalculatedHBonds(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
hasCalculatedHBonds(BitSet) - Method in class org.jmol.viewer.Viewer
 
hasContent() - Method in class org.jmol.g3d.Graphics3D
 
hasContent() - Method in class org.jmol.g3d.Platform3D
 
hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
hashCode() - Method in class org.jmol.modelset.Atom
 
hashCode() - Method in class org.jmol.util.Point3fi
 
hasInsertions() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
hasLocalArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
normal iterator predicate
hasMoreTokens() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
hasNext() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
hasNext() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
hasNext() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapter.AtomIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapter.BondIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapter.StructureIterator
 
hasNext() - Method in interface org.jmol.modelset.AtomIndexIterator
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinSet
 
hasNext() - Method in interface org.jmol.modelset.BondIterator
 
hasNext() - Method in class org.jmol.modelset.BondIteratorSelected
 
hasNext() - Method in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
hasNext() - Method in class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
hasOAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
hasOAtoms - Variable in class org.jmol.modelsetbio.AminoPolymer
 
hasPrivilege - Variable in class org.jmol.jcamp.Visua
 
hasProgressBar - Variable in class org.jmol.applet.Jmol
 
hasRnaO2Prime - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
hasSerialArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
hasWingPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
 
hasWingPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
hasWingPoints() - Method in class org.jmol.modelsetbio.NucleicPolymer
 
hAtomRadius - Variable in class org.jmol.atomdata.AtomData
 
hAtoms - Variable in class org.jmol.atomdata.AtomData
 
hauteur - Variable in class org.jmol.jcamp.ZoneVisu
 
hauteur_bandeau - Variable in class org.jmol.jcamp.ZoneVisu
 
hauteur_gfx - Variable in class org.jmol.jcamp.ZoneVisu
 
haveAt - Variable in class org.jmol.adapter.readers.more.NWChemReader
 
haveAtoms - Variable in class org.jmol.shapespecial.Dipole
 
haveAxis(int, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
haveBFactors - Variable in class org.jmol.popup.JmolPopup
 
haveBioClasses - Variable in class org.jmol.modelset.ModelCollection
 
haveBitSetVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
haveBorder - Static variable in class org.openscience.jmol.app.Jmol
 
haveCharges - Variable in class org.jmol.popup.JmolPopup
 
haveCheckByte - Variable in class org.jmol.shape.Mesh
 
haveConsole() - Method in class org.jmol.applet.Jvm12
 
haveConsole - Static variable in class org.openscience.jmol.app.Jmol
 
haveControlPointScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
haveDisplay - Variable in class org.jmol.viewer.Viewer
 
haveDisplay - Variable in class org.openscience.jmol.app.DisplayPanel
 
haveDisplay - Static variable in class org.openscience.jmol.app.Jmol
 
haveDocumentAccess - Variable in class org.jmol.applet.Jmol
 
haveEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
haveEnergy - Variable in class org.jmol.adapter.readers.more.NWChemReader
 
haveFileSet() - Method in class org.jmol.viewer.Viewer
 
haveFrame() - Method in class org.jmol.api.JmolViewer
 
haveFrame() - Method in class org.jmol.viewer.Viewer
 
haveInversionCenter - Variable in class org.jmol.symmetry.PointGroup
 
haveMappedSerials - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
haveMappedSerials - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveModelSet() - Method in class org.jmol.viewer.Viewer
 
haveMolecule - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
haveNotifiedError - Variable in class org.jmol.applet.Jmol.MyStatusListener
 
haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
 
haveParams() - Method in class org.jmol.minimize.forcefield.Calculations
 
havePartialCharges() - Method in class org.jmol.api.JmolViewer
 
havePartialCharges - Variable in class org.jmol.minimize.forcefield.Calculations
 
havePartialCharges() - Method in class org.jmol.viewer.Viewer
 
haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
 
haveSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
 
haveSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
 
haveString - Variable in class org.jmol.viewer.Compiler
 
haveTarget - Variable in class org.jmol.modelset.MeasurementPending
 
haveTarget() - Method in class org.jmol.modelset.MeasurementPending
 
haveTranslations - Static variable in class org.jmol.export.dialog.Dialog
 
haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
 
haveTranslucentObjects() - Method in class org.jmol.export.Export3D
 
haveTranslucentObjects - Variable in class org.jmol.g3d.Graphics3D
 
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
 
haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
haveWarned - Variable in class org.jmol.modelset.BondCollection
 
haveXyPoints - Variable in class org.jmol.shape.Mesh
 
hbond(boolean) - Method in class org.jmol.viewer.Eval
 
hbond - Static variable in class org.jmol.viewer.Token
 
HBOND_MASK - Static variable in class org.jmol.modelsetbio.NucleicPolymer
 
hbondMax - Variable in class org.jmol.modelset.BondCollection
 
hbondMin - Variable in class org.jmol.modelset.BondCollection
 
hbondMin2 - Variable in class org.jmol.modelset.BondCollection
 
hbondsBackbone - Variable in class org.jmol.shape.SticksRenderer
 
hbondsBackbone - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hbondsSolid - Variable in class org.jmol.shape.SticksRenderer
 
hbondsSolid - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hdrPos - Variable in class org.jmol.export.image.PngEncoder
 
header() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
header - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
header - Variable in class org.jmol.export.dialog.HistoryFile
The information written to the header of the history file.
header - Variable in class org.jmol.util.CompoundDocument
 
headerAtomCount - Variable in class org.jmol.adapter.readers.more.V3000Reader
 
headerBondCount - Variable in class org.jmol.adapter.readers.more.V3000Reader
 
headOffsetVector - Variable in class org.jmol.shapespecial.VectorsRenderer
 
headScale - Variable in class org.jmol.shapespecial.VectorsRenderer
 
headWidthPixels - Variable in class org.jmol.shapespecial.DipolesRenderer
 
headWidthPixels - Variable in class org.jmol.shapespecial.VectorsRenderer
 
height - Variable in class org.jmol.export.Export3D
 
height - Variable in class org.jmol.export.image.GifEncoder
 
Height - Variable in class org.jmol.export.image.GifEncoder
 
height - Variable in class org.jmol.export.image.ImageEncoder
 
height - Variable in class org.jmol.export.image.PngEncoder
 
height - Variable in class org.jmol.g3d.Graphics3D
 
height - Variable in class org.jmol.g3d.Sphere3D
 
height - Variable in class org.jmol.g3d.Text3D
 
height - Variable in class org.jmol.viewer.TransformManager
 
height - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
heightOffscreen - Variable in class org.jmol.g3d.Platform3D
 
heightUnitVector - Variable in class org.jmol.modelsetbio.Sheet
 
Helix - Class in org.jmol.modelsetbio
 
Helix(AlphaPolymer, int, int) - Constructor for class org.jmol.modelsetbio.Helix
 
help() - Method in class org.jmol.viewer.Eval
 
help - Static variable in class org.jmol.viewer.Token
 
helpButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
helpButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
HelpDialog - Class in org.openscience.jmol.app
 
HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.HelpDialog
 
HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.HelpDialog
If url is null, then the default help url is taken.
HelpDialog.PageLoader - Class in org.openscience.jmol.app
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
HelpDialog.PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.HelpDialog.PageLoader
 
helpPath - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hermite3d - Variable in class org.jmol.export.Export3D
 
hermite3d - Variable in class org.jmol.g3d.Graphics3D
 
Hermite3D - Class in org.jmol.g3d
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
Hermite3D(JmolRendererInterface) - Constructor for class org.jmol.g3d.Hermite3D
 
hermiteLevel - Variable in class org.jmol.shapebio.BioShapeRenderer
 
hermiteLevel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
het() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
hetatmData - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
optional nonloop format -- see 1jsa.cif
hetero - Static variable in class org.jmol.viewer.Token
 
hetnam() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
hidden - Variable in class org.jmol.shape.Object2d
 
hidden - Static variable in class org.jmol.viewer.Token
 
hide(BitSet, boolean) - Method in class org.jmol.viewer.SelectionManager
 
hide - Static variable in class org.jmol.viewer.Token
 
hide(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
hideBackground - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
hideMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
hideNameInPopup - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hideNavigationPoint - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hideNotSelected - Variable in class org.jmol.viewer.SelectionManager
 
HIGH - Static variable in class org.jmol.util.ColorEncoder
 
highResolutionFlag - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
HinReader - Class in org.jmol.adapter.readers.more
Support for .hin, HyperChem's native file format.
HinReader() - Constructor for class org.jmol.adapter.readers.more.HinReader
 
hinRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
hintflags - Variable in class org.jmol.export.image.ImageEncoder
 
history(int) - Method in class org.jmol.viewer.Eval
 
history - Static variable in class org.jmol.viewer.Token
 
historyButton - Variable in class org.jmol.applet.Console
 
historyButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
historyDisabled - Variable in class org.jmol.viewer.Eval
 
HistoryFile - Class in org.jmol.export.dialog
The history file contains data from previous uses of Jmol.
HistoryFile(File, String) - Constructor for class org.jmol.export.dialog.HistoryFile
Creates a history file.
historyFile - Static variable in class org.openscience.jmol.app.Jmol
 
historyFile - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
historyFile - Static variable in class org.openscience.jmol.app.webexport.WebMaker
 
hklParameter(int) - Method in class org.jmol.viewer.Eval
 
hmSymbol - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAbbr - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAbbrShort - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAlternative - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolExt - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolFull - Variable in class org.jmol.symmetry.SpaceGroup
 
holdRepaint - Variable in class org.jmol.viewer.RepaintManager
 
homeAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
homePosition() - Method in class org.jmol.api.JmolViewer
 
homePosition() - Method in class org.jmol.viewer.TransformManager
 
homePosition() - Method in class org.jmol.viewer.Viewer
 
HOTPINK - Static variable in class org.jmol.g3d.Graphics3D
 
Hover - Class in org.jmol.shape
 
Hover() - Constructor for class org.jmol.shape.Hover
 
hover() - Method in class org.jmol.viewer.Eval
 
hover - Static variable in class org.jmol.viewer.Token
 
hoverActive - Variable in class org.jmol.viewer.MouseManager
 
hoverAtomIndex - Variable in class org.jmol.viewer.Viewer
 
hoverDelayMs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
hoverOff() - Method in class org.jmol.viewer.MouseManager
 
hoverOff() - Method in class org.jmol.viewer.Viewer
 
hoverOn(int) - Method in class org.jmol.viewer.MouseManager
 
hoverOn(int) - Method in class org.jmol.viewer.Viewer
 
hoverOn(int, int, String) - Method in class org.jmol.viewer.Viewer
 
HoverRenderer - Class in org.jmol.shape
 
HoverRenderer() - Constructor for class org.jmol.shape.HoverRenderer
 
hoverText - Variable in class org.jmol.shape.Hover
 
hoverText - Variable in class org.jmol.viewer.Viewer
 
hoverWatcherThread - Variable in class org.jmol.viewer.MouseManager
 
HsampFactor - Variable in class org.jmol.util.JpegInfo
 
HSIZE - Static variable in class org.jmol.export.image.GifEncoder
 
hsize - Variable in class org.jmol.export.image.GifEncoder
 
htab - Variable in class org.jmol.export.image.GifEncoder
 
htAtom - Static variable in class org.jmol.modelset.ModelLoader
 
htAtomMap - Variable in class org.jmol.modelset.ModelLoader
 
htCallbacks - Variable in class org.jmol.viewer.StatusManager
 
htCheckbox - Variable in class org.jmol.popup.JmolPopup
 
htElementMap - Static variable in class org.jmol.viewer.JmolConstants
 
htElementsInCurrentGroup - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
htFont3d - Static variable in class org.jmol.g3d.Text3D
 
htFont3dAntialias - Static variable in class org.jmol.g3d.Text3D
 
htFormul - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htGroup - Static variable in class org.jmol.modelset.Group
 
htHetero - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
htHetero - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htMenus - Variable in class org.jmol.popup.JmolPopup
 
html - Variable in class org.openscience.jmol.app.AboutDialog
 
html - Variable in class org.openscience.jmol.app.HelpDialog
 
html - Variable in class org.openscience.jmol.app.WhatsNewDialog
 
htmlAppletTemplate - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
htmlName - Variable in class org.jmol.applet.Jmol
 
htmlName - Variable in class org.jmol.viewer.Viewer
 
htModels - Variable in class org.jmol.shapesurface.MolecularOrbital
 
htParameterValues - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htParams - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
htParamsSet - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
htPropertyFlags - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htPropertyFlagsRemoved - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htRegistry - Static variable in class org.jmol.applet.JmolAppletRegistry
 
htSites - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
htSites - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
htUserVariables - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
htVertex - Static variable in class org.jmol.geodesic.Geodesic
 
Huf - Variable in class org.jmol.util.JpegEncoder
 
Huffman - Class in org.jmol.util
 
Huffman(int, int) - Constructor for class org.jmol.util.Huffman
 
HuffmanBlockEncoder(BufferedOutputStream, int[], int, int, int) - Method in class org.jmol.util.Huffman
HuffmanBlockEncoder run length encodes and Huffman encodes the quantized data.
hydrogen - Static variable in class org.jmol.viewer.Token
 
hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
 
hydrogenAtomPsiAt(Point3f, int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
hydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
hydrogensAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.AboutDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.HelpDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.WhatsNewDialog
 
hypot(double, double) - Static method in class org.jmol.util.Eigen
 

I

ia - Variable in class org.jmol.minimize.forcefield.Calculation
 
ia - Variable in class org.jmol.minimize.forcefield.Calculations
 
iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
 
iatom - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
iatom - Variable in class org.jmol.viewer.FrameExportJmolAdapter.AtomIterator
 
ib - Variable in class org.jmol.minimize.forcefield.Calculation
 
ib - Variable in class org.jmol.minimize.forcefield.Calculations
 
ibond - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
iBond - Variable in class org.jmol.modelset.BondIteratorSelected
 
ibond - Variable in class org.jmol.viewer.FrameExportJmolAdapter.BondIterator
 
ic - Variable in class org.jmol.g3d.Awt3D
 
ic - Variable in class org.jmol.minimize.forcefield.Calculation
 
ic - Variable in class org.jmol.minimize.forcefield.Calculations
 
ich - Variable in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
ichCurrent - Variable in class org.jmol.adapter.smarter.LimitedLineReader
 
ichCurrent - Variable in class org.jmol.jvxl.readers.LimitedLineReader
 
ichCurrentCommand - Variable in class org.jmol.viewer.Compiler
 
ichPeeked - Variable in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
ichToken - Variable in class org.jmol.viewer.Compiler
 
iCommand - Variable in class org.jmol.viewer.Compiler
 
iCutout - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
ID - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
id - Variable in class org.jmol.export._MayaExporter
 
id - Variable in class org.jmol.minimize.forcefield.Calculation
 
id - Variable in class org.jmol.minimize.forcefield.Calculations
 
id - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
iData - Variable in class org.jmol.minimize.forcefield.Calculation
 
identifier - Static variable in class org.jmol.viewer.Token
 
identify - Static variable in class org.jmol.viewer.Token
 
idFontFace - Variable in class org.jmol.g3d.Font3D
 
idFontStyle - Variable in class org.jmol.g3d.Font3D
 
ifCmd() - Method in class org.jmol.viewer.Eval
 
ifcmd - Static variable in class org.jmol.viewer.Token
 
ignoreApplicationBundle - Static variable in class org.jmol.i18n.GT
 
ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
 
ignoreError - Variable in class org.jmol.viewer.Eval
 
ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ihalf - Static variable in class org.jmol.util.ColorEncoder
 
iHaveAtomSet - Variable in class org.jmol.adapter.readers.more.ShelxReader
 
iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
 
iHaveCenterBitSet - Variable in class org.jmol.shapespecial.Polyhedra
 
iHaveDesiredModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveModelIndex - Variable in class org.jmol.shape.MeshCollection
 
iHaveModelIndex - Variable in class org.jmol.shapesurface.Pmesh
 
iHaveQuotedString - Variable in class org.jmol.viewer.Compiler
 
iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveTwoEnds - Variable in class org.jmol.shapespecial.Dipoles
 
iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHideBackground - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
ijkToPoint3f(int) - Method in interface org.jmol.api.SymmetryInterface
 
ijkToPoint3f(int) - Method in class org.jmol.symmetry.Symmetry
 
ijkToPoint3f(int) - Static method in class org.jmol.symmetry.UnitCell
 
iLine - Variable in class org.jmol.jvxl.readers.LimitedLineReader
 
iLine() - Method in class org.jmol.jvxl.readers.LimitedLineReader
 
image - Variable in class org.jmol.export.image.ImageSelection
The image to transfer into the clipboard.
image - Variable in class org.jmol.export.image.PngEncoder
 
image - Variable in class org.jmol.shape.Text
 
image - Static variable in class org.jmol.viewer.Token
 
imageChoices - Static variable in class org.jmol.applet.Jvm12
 
imageChoices - Static variable in class org.openscience.jmol.app.Jmol
 
imageChooser - Static variable in class org.jmol.export.dialog.Dialog
 
imageComplete(int) - Method in class org.jmol.export.image.ImageEncoder
 
ImageCreator - Class in org.jmol.export.image
 
ImageCreator() - Constructor for class org.jmol.export.image.ImageCreator
 
ImageCreator(JmolViewer) - Constructor for class org.jmol.export.image.ImageCreator
 
ImageEncoder - Class in org.jmol.export.image
 
ImageEncoder(Image, OutputStream) - Constructor for class org.jmol.export.image.ImageEncoder
 
ImageEncoder(ImageProducer, OutputStream) - Constructor for class org.jmol.export.image.ImageEncoder
 
imageExtensions - Static variable in class org.jmol.applet.Jvm12
 
imageExtensions - Static variable in class org.openscience.jmol.app.Jmol
 
imageFontScaling - Variable in class org.jmol.shape.EchoRenderer
 
imageFontScaling - Variable in class org.jmol.shape.FontLineShapeRenderer
 
imageFontScaling - Variable in class org.jmol.shape.MeshRenderer
 
imageFontScaling - Variable in class org.jmol.viewer.Viewer
 
ImageHeight - Variable in class org.jmol.util.Huffman
 
imageHeight - Variable in class org.jmol.util.JpegInfo
 
imageobj - Variable in class org.jmol.util.JpegInfo
 
imageOffscreen - Variable in class org.jmol.g3d.Platform3D
 
imagePixelBuffer - Variable in class org.jmol.g3d.Platform3D
 
imageQuality - Variable in class org.jmol.applet.Jvm12
 
ImageSelection - Class in org.jmol.export.image
This class is used to transfer an Image into the clipboard.
ImageSelection(Image) - Constructor for class org.jmol.export.image.ImageSelection
Constructs a ImageSelection.
ImageSelection(String) - Constructor for class org.jmol.export.image.ImageSelection
Constructs a ImageSelection.
imageSizeChanged() - Method in class org.openscience.jmol.app.PovrayDialog
Called when the ImageSize check box is modified
imageSizeHeight - Variable in class org.openscience.jmol.app.PovrayDialog
 
imageSizeRatioBox - Variable in class org.openscience.jmol.app.PovrayDialog
 
imageSizeRatioCombo - Variable in class org.openscience.jmol.app.PovrayDialog
 
imageSizeTextHeight - Variable in class org.openscience.jmol.app.PovrayDialog
 
imageSizeTextWidth - Variable in class org.openscience.jmol.app.PovrayDialog
 
imageSizeWidth - Variable in class org.openscience.jmol.app.PovrayDialog
 
imageType - Variable in class org.jmol.applet.Jvm12
 
imageType - Variable in class org.openscience.jmol.app.Jmol
 
ImageWidth - Variable in class org.jmol.util.Huffman
 
imageWidth - Variable in class org.jmol.util.JpegInfo
 
imesh - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
imgHeight - Variable in class org.openscience.jmol.app.Splash
 
imgWidth - Variable in class org.openscience.jmol.app.Splash
 
implementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
implicitStringCommand - Static variable in class org.jmol.viewer.Token
 
importData(JComponent, Transferable) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
IN_JMOL - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
includeAllRelatedFrames(BitSet) - Method in class org.jmol.modelset.ModelSet
 
Incrx - Variable in class org.jmol.jcamp.ZoneVisu
 
index - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
index - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
index - Variable in class org.jmol.minimize.MinAtom
 
index - Variable in class org.jmol.modelset.Bond
 
index - Variable in class org.jmol.modelset.Measurement
 
index - Variable in class org.jmol.symmetry.PointGroup.Operation
 
index - Variable in class org.jmol.symmetry.SpaceGroup
 
indexColorNegative - Variable in class org.jmol.shapesurface.Isosurface
 
indexColorPositive - Variable in class org.jmol.shapesurface.Isosurface
 
indexDown(float, int) - Static method in class org.jmol.jvxl.data.VolumeData
 
indexes - Variable in class org.openscience.jmol.app.AtomSetChooser
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
indexI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
indexInModel - Variable in class org.jmol.modelset.Molecule
 
indicatedModelIndex - Variable in class org.jmol.shapespecial.Draw
 
indice - Variable in class org.jmol.jcamp.ZoneVisu
 
inExplorer - Variable in class org.jmol.jcamp.Visua
 
iNext - Variable in class org.jmol.modelset.AtomIteratorWithinSet
 
iNext - Variable in class org.jmol.shapebio.BioShapeRenderer
 
iNext2 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
iNext3 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
info() - Method in class org.jmol.jvxl.readers.LimitedLineReader
 
info - Variable in class org.jmol.symmetry.PointGroup
 
info(String) - Method in class org.jmol.util.DefaultLogger
 
info(String) - Static method in class org.jmol.util.Logger
Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at INFO level.
info - Static variable in class org.jmol.viewer.Token
 
INFO_A - Static variable in class org.jmol.viewer.JmolConstants
 
INFO_ALPHA - Static variable in class org.jmol.viewer.JmolConstants
 
INFO_B - Static variable in class org.jmol.viewer.JmolConstants
 
INFO_BETA - Static variable in class org.jmol.viewer.JmolConstants
 
INFO_C - Static variable in class org.jmol.viewer.JmolConstants
 
INFO_GAMMA - Static variable in class org.jmol.viewer.JmolConstants
 
infoLabel - Variable in class org.openscience.jmol.app.AtomSetChooser
 
inGreyscaleMode - Variable in class org.jmol.g3d.Graphics3D
 
INHERIT_ALL - Static variable in class org.jmol.g3d.Graphics3D
 
INHERIT_COLOR - Static variable in class org.jmol.g3d.Graphics3D
 
inInput - Variable in class org.jmol.adapter.readers.more.NWChemReader
 
init() - Method in class org.jmol.adapter.readers.more.NWChemReader
 
init() - Method in class org.jmol.applet.Jmol
 
init() - Method in class org.jmol.appletwrapper.AppletWrapper
 
init() - Method in interface org.jmol.appletwrapper.WrappedApplet
 
init() - Method in class org.jmol.jcamp.Visua
 
init() - Method in class org.jmol.jcamp.ZoneVisu
 
Init_File() - Method in class org.jmol.jcamp.ZoneVisu
 
initApplication() - Method in class org.jmol.applet.Jmol
 
initFile(String) - Method in class org.jmol.jcamp.Visua
 
initGraphParameters() - Method in class org.jmol.jcamp.Visua
Method to initialize the GraphCharacteristics object in this class
initHuf() - Method in class org.jmol.util.Huffman
 
INITIAL_ATOMS - Static variable in class org.jmol.smiles.SmilesMolecule
 
INITIAL_BONDS - Static variable in class org.jmol.smiles.SmilesAtom
 
INITIAL_BONDS - Static variable in class org.jmol.smiles.SmilesMolecule
 
initialFile - Variable in class org.jmol.export.dialog.Dialog
 
initialize(AtomSetCollectionReader, AtomSetCollection, Hashtable, String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
initialize() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initialize(Hashtable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initialize(int, Point3f[], BitSet) - Method in class org.jmol.bspt.Bspf
 
initialize(Point3f, float) - Method in class org.jmol.bspt.CubeIterator
initialize to return all points within the sphere defined by center and radius
initialize(Platform3D) - Static method in class org.jmol.g3d.Font3D
 
initialize(boolean) - Method in class org.jmol.g3d.Platform3D
 
initialize() - Method in class org.jmol.jvxl.readers.Parameters
 
initialize(Bspf, int, Point3f, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
just the basic iterator for finding atoms within a cube centered on some point in space Used for select within(distance, atom)
initialize(Bspf, int, int, Point3f, float, BitSet, boolean, int) - Method in class org.jmol.modelset.AtomIteratorWithinSet
a more powerful iterator than AtomIteratorWithinModel allowing excluding a specific atom, finding only those atoms with an atom index greater than that specified or atoms within a specific selected subset of atoms.
initialize(int) - Method in class org.jmol.quantum.QuantumCalculation
 
initialize() - Method in class org.jmol.shape.Dots
 
initialize(int) - Method in class org.jmol.shape.Mesh
 
initialize() - Method in class org.jmol.shapebio.BioShapeCollection
 
initialize - Static variable in class org.jmol.viewer.Token
 
initialize() - Method in class org.jmol.viewer.Viewer
 
initializeAtomBondModelCounts() - Method in class org.jmol.modelset.ModelLoader
 
initializeBonding() - Method in class org.jmol.modelset.ModelLoader
 
initializeBspf() - Method in class org.jmol.modelset.ModelCollection
 
initializeBspt(int) - Method in class org.jmol.modelset.ModelCollection
 
initializeBuild(int) - Method in class org.jmol.modelset.ModelLoader
 
initializeCartesianToFractional() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeGroupBuild() - Method in class org.jmol.modelset.ModelLoader
also from calculateStructures
initializeHemisphere(Point3f, float) - Method in class org.jmol.bspt.CubeIterator
initialize to return all points within the hemisphere defined by center and radius.
initializeInfo(String, int, Properties, Hashtable) - Method in class org.jmol.modelset.ModelLoader
 
initializeIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initializeIsosurface() - Method in class org.jmol.shapesurface.Isosurface
 
initializeMerge() - Method in class org.jmol.modelset.ModelLoader
 
initializeModel() - Method in class org.jmol.viewer.Viewer
 
initializeModelSet(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
initializeNormixes(int, Vector3f[]) - Method in class org.jmol.shape.Mesh
 
initializeOutput(Viewer, Graphics3D, Object) - Method in interface org.jmol.api.JmolExportInterface
 
initializeOutput(Viewer, Graphics3D, Object) - Method in class org.jmol.export._Exporter
 
initializePointers(int) - Method in class org.jmol.viewer.RepaintManager
 
initializePolymer(BioShape) - Method in class org.jmol.shapebio.BioShapeRenderer
 
initializeProperties() - Method in class org.openscience.jmol.app.PreferencesDialog
 
initializeShape(Viewer, Graphics3D, ModelSet, int) - Method in class org.jmol.shape.Shape
 
initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeUnitCellAndSymmetry() - Method in class org.jmol.modelset.ModelLoader
 
initializeVolumetricData() - Method in class org.jmol.jvxl.readers.VoxelReader
 
initializeVoxelData() - Method in class org.jmol.jvxl.readers.JvxlReader
 
initIsosurface(int) - Method in class org.jmol.viewer.Eval
 
initMatrix(int) - Method in class org.jmol.util.DCT
 
initModelSet() - Method in class org.jmol.shape.AtomShape
 
initModelSet() - Method in class org.jmol.shape.Measures
 
initModelSet() - Method in class org.jmol.shape.Object2dShape
 
initModelSet() - Method in class org.jmol.shape.Shape
 
initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
 
initModelSet() - Method in class org.jmol.shapespecial.Vectors
 
initRenderer() - Method in class org.jmol.shape.DotsRenderer
 
initRenderer() - Method in class org.jmol.shape.ShapeRenderer
 
initShape() - Method in class org.jmol.shape.Axes
 
initShape() - Method in class org.jmol.shape.Bbcage
 
initShape() - Method in class org.jmol.shape.Dots
 
initShape() - Method in class org.jmol.shape.Echo
 
initShape() - Method in class org.jmol.shape.FontLineShape
 
initShape() - Method in class org.jmol.shape.Frank
 
initShape() - Method in class org.jmol.shape.Hover
 
initShape() - Method in class org.jmol.shape.Labels
 
initShape() - Method in class org.jmol.shape.Measures
 
initShape() - Method in class org.jmol.shape.MeshCollection
 
initShape() - Method in class org.jmol.shape.Shape
 
initShape() - Method in class org.jmol.shape.Sticks
 
initShape() - Method in class org.jmol.shape.Uccage
 
initShape() - Method in class org.jmol.shapebio.Backbone
 
initShape() - Method in class org.jmol.shapebio.Cartoon
 
initShape() - Method in class org.jmol.shapebio.MeshRibbon
 
initShape() - Method in class org.jmol.shapebio.Rockets
 
initShape() - Method in class org.jmol.shapebio.Trace
 
initShape() - Method in class org.jmol.shapespecial.Draw
 
initShape() - Method in class org.jmol.shapespecial.GeoSurface
 
initShape() - Method in class org.jmol.shapesurface.Isosurface
 
initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
 
initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
 
initShape() - Method in class org.jmol.shapesurface.Pmesh
 
initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initState() - Method in class org.jmol.shape.Halos
 
initState() - Method in class org.jmol.shapesurface.Isosurface
 
initVariables() - Method in class org.openscience.jmol.app.PreferencesDialog
 
initWindows() - Method in class org.jmol.applet.Jmol
 
inlineData - Variable in class org.jmol.viewer.FileManager
 
inlineNewlineChar - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
inMotion - Variable in class org.jmol.viewer.RepaintManager
 
inNavigator - Variable in class org.jmol.jcamp.Visua
 
input - Variable in class org.jmol.applet.Console
 
inputCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
inputFileName - Variable in class org.jmol.applet.Jvm12
 
INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
insertArrayValue(String, Token) - Method in class org.jmol.viewer.Eval
 
insertion - Static variable in class org.jmol.viewer.Token
 
INSERTION_CODE_MASK - Static variable in class org.jmol.modelset.Group
 
insertionCode - Variable in class org.jmol.adapter.smarter.Atom
 
insertMenuSubMenu(Object, Object, int) - Method in class org.jmol.popup.JmolPopup
 
insertMenuSubMenu(Object, Object, int) - Method in class org.jmol.popup.JmolPopupAwt
 
insertMenuSubMenu(Object, Object, int) - Method in class org.jmol.popup.JmolPopupSwing
 
insertString(int, String, AttributeSet) - Method in class org.openscience.jmol.app.ConsoleDocument
 
insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
insideMaskTable2d - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
insideOut - Variable in class org.jmol.jvxl.data.JvxlData
 
insideOut - Variable in class org.jmol.jvxl.readers.Parameters
 
insideOut - Variable in class org.jmol.shape.Mesh
 
installMainMenu(Object) - Method in class org.jmol.popup.JmolPopup
 
installMainMenu(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
installMainMenu(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
instance - Static variable in class org.openscience.jmol.app.JmolResourceHandler
 
instanceList - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
instructionDispatchLoop(boolean) - Method in class org.jmol.viewer.Eval
 
Int2IntHash - Class in org.jmol.util
 
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
 
Int2IntHash() - Constructor for class org.jmol.util.Int2IntHash
 
Int2IntHash.Entry - Class in org.jmol.util
 
Int2IntHash.Entry(int, int, Int2IntHash.Entry) - Constructor for class org.jmol.util.Int2IntHash.Entry
 
intAnimThread - Variable in class org.jmol.viewer.RepaintManager
 
integer - Static variable in class org.jmol.viewer.Token
 
integerOutOfRange(int, int) - Method in class org.jmol.viewer.Eval
 
Integrate - Variable in class org.jmol.jcamp.Visua
 
Integrate() - Method in class org.jmol.jcamp.ZoneVisu
 
INTEGRATION_DELIM - Static variable in class org.jmol.jcamp.GraphCharacteristics
 
INTEGRATION_VALUES_DELIM - Static variable in class org.jmol.jcamp.GraphCharacteristics
 
INTENSE_FRACTION - Static variable in class org.jmol.g3d.Shade3D
 
intensities - Variable in class org.jmol.g3d.Normix3D
 
intensities2Sided - Variable in class org.jmol.g3d.Normix3D
 
INTENSITY_DIFFUSE - Static variable in class org.jmol.g3d.Shade3D
 
INTENSITY_SPECULAR - Static variable in class org.jmol.g3d.Shade3D
 
intensityEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
intensitySpecularSurfaceLimit - Static variable in class org.jmol.g3d.Graphics3D
 
intensitySpecularSurfaceLimit - Static variable in class org.jmol.g3d.Shade3D
 
interestingAminoAtomIDs - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
interestingNucleicAtomIDs - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
Interface - Class in org.jmol.api
 
Interface() - Constructor for class org.jmol.api.Interface
 
interlace - Variable in class org.jmol.export.image.GifEncoder
 
Interlace - Variable in class org.jmol.export.image.GifEncoder
 
internalRotationAngle - Variable in class org.jmol.viewer.TransformManager
 
internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
internalRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
internalSlab - Variable in class org.jmol.viewer.TransformManager
 
interpolate(int, int) - Method in class org.jmol.g3d.Cylinder3D
 
interpolatePrecisely(int, int) - Method in class org.jmol.g3d.Cylinder3D
 
interruptExecution - Variable in class org.jmol.viewer.Eval
 
interruptQueueThreads() - Method in class org.jmol.viewer.ScriptManager
 
interruptScript - Variable in class org.jmol.viewer.Viewer
 
intersectionPoints - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
intinfo - Variable in class org.jmol.adapter.readers.more.MopacDataReader
 
intlTableNumber - Variable in class org.jmol.symmetry.SpaceGroup
 
intlTableNumberExt - Variable in class org.jmol.symmetry.SpaceGroup
 
intlTableNumberFull - Variable in class org.jmol.symmetry.SpaceGroup
 
intParameter(int) - Method in class org.jmol.viewer.Eval
 
intParameter(int, int, int) - Method in class org.jmol.viewer.Eval
 
intPeek() - Method in class org.jmol.viewer.Compiler
 
intSetting(int, int, int, int) - Method in class org.jmol.viewer.Eval
 
intSetting(int) - Method in class org.jmol.viewer.Eval
 
intThread - Variable in class org.jmol.viewer.RepaintManager.AnimationThread
 
intToken(int) - Static method in class org.jmol.viewer.Token
 
intValue - Variable in class org.jmol.viewer.Token
 
intValue2 - Variable in class org.jmol.viewer.Token.Token2
 
inv() - Method in class org.jmol.util.Quaternion
 
invalidateMesh - Variable in class org.jmol.shapebio.BioShapeRenderer
 
invalidateSheets - Variable in class org.jmol.shapebio.BioShapeRenderer
 
invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
invalidateTriangles() - Method in class org.jmol.jvxl.data.MeshData
 
invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
 
invalidateTriangles() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
InvalidSmilesException - Exception in org.jmol.smiles
Exception thrown for invalid SMILES String
InvalidSmilesException() - Constructor for exception org.jmol.smiles.InvalidSmilesException
Constructs a InvalideSmilesException without any detail.
InvalidSmilesException(String) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Constructs a InvalidSmilesException with a detail message.
InvalidSmilesException(Throwable) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Contructs a InvalidSmilesException with the specified cause and a detail message of (cause == null ? null : cause.toString()) (which typically contains the class and detail message of cause).
InvalidSmilesException(String, Throwable) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Construcst a InvalidSmilesException with the specified detail message and cause.
inverseNormixes - Variable in class org.jmol.g3d.Normix3D
 
invertInPlace(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertNormixes() - Method in class org.jmol.shape.Mesh
 
invertSelected(Point3f, Point4f, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
invertSelected() - Method in class org.jmol.viewer.Eval
 
invertSelected - Static variable in class org.jmol.viewer.Token
 
invertSelected(Point3f, BitSet) - Method in class org.jmol.viewer.Viewer
 
invertSelected(Point3f, Point4f) - Method in class org.jmol.viewer.Viewer
 
invertSelection() - Method in class org.jmol.viewer.SelectionManager
 
invertSelection() - Method in class org.jmol.viewer.Viewer
 
invMatrix - Variable in class org.jmol.adapter.readers.more.MopacGraphfReader
 
ionic - Static variable in class org.jmol.viewer.Token
 
iox - Variable in class org.jmol.export.image.ImageEncoder
 
iPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
is(int) - Method in class org.jmol.modelset.Bond
 
is3DContour - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
IS_HETERO_FLAG - Static variable in class org.jmol.modelset.Atom
 
IS_SILENT - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
 
isActive - Variable in class org.jmol.jcamp.Visua
 
isActive - Variable in class org.jmol.shape.AtomShape
 
isActive - Variable in class org.jmol.shapebio.BioShape
 
isActive - Variable in class org.jmol.shapebio.BioShapeCollection
 
isActiveLevel(int) - Static method in class org.jmol.util.Logger
Tells if a logging level is active.
isAligned(Point3f, Point3f, Point3f) - Method in class org.jmol.shapespecial.Polyhedra
 
isAll - Variable in class org.jmol.shape.Object2dShape
 
isAllConnected - Variable in class org.jmol.shape.Measures
 
isAlphaMonomer() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isAlternateLocationMatch(String) - Method in class org.jmol.modelset.Atom
 
isAmide - Variable in class org.jmol.minimize.MinBond
 
isAmino - Variable in class org.jmol.modelset.Group
 
isAminoMonomer() - Method in class org.jmol.modelsetbio.AminoMonomer
 
isAngstroms - Variable in class org.jmol.adapter.readers.more.CubeReader
 
isAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
isAngstroms - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
isAnimationOn() - Method in class org.jmol.viewer.Viewer
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.Parameters
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
isAntialiased() - Method in interface org.jmol.api.JmolRendererInterface
 
isAntialiased() - Method in class org.jmol.export.Export3D
is full scene / oversampling antialiasing in effect
isAntialiased() - Method in class org.jmol.g3d.Graphics3D
is full scene / oversampling antialiasing in effect
isAntialiased - Variable in class org.jmol.shape.HalosRenderer
 
isAntialiased - Variable in class org.jmol.shape.SticksRenderer
 
isApbsDx - Variable in class org.jmol.jvxl.readers.VoxelReader
 
isAppendSelected() - Method in class org.jmol.export.dialog.FilePreview
 
isApplet() - Method in class org.jmol.api.JmolViewer
 
isApplet - Variable in class org.jmol.popup.JmolPopup
 
isApplet - Variable in class org.jmol.viewer.Viewer
 
isApplet() - Method in class org.jmol.viewer.Viewer
 
isApprox(Vector3d, Vector3d, double) - Static method in class org.jmol.minimize.Util
 
isArc - Variable in class org.jmol.shapespecial.Draw
 
isAromatic - Variable in class org.jmol.minimize.MinBond
 
isAromatic() - Method in class org.jmol.modelset.Bond
 
isaromatic - Static variable in class org.jmol.viewer.Token
 
isArrow - Variable in class org.jmol.shapespecial.Draw
 
isAssignment - Variable in class org.jmol.viewer.Eval.Rpn
 
isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
 
isAtomHidden(int) - Method in class org.jmol.modelset.Group
 
isAtomHidden(int) - Method in class org.jmol.modelset.Model
 
isAtomNameMatch(Atom, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
isBbcageDefault - Variable in class org.jmol.modelset.ModelCollection
 
isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
 
isBicolorMap - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
isBigEndian - Variable in class org.jmol.util.BinaryDocument
 
isBinary - Variable in class org.jmol.shapesurface.Pmesh
 
isBioShape - Variable in class org.jmol.shape.Shape
 
isBond - Variable in class org.jmol.shapespecial.Dipoles
 
isBondBitSet - Variable in class org.jmol.modelset.BondIteratorSelected
 
isBondDipole(int) - Method in class org.jmol.shapespecial.Dipoles
 
isBonded(Atom) - Method in class org.jmol.modelset.Atom
 
isBondedCorrectly(int, int, int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
isBondedCorrectly(int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
isBondSet - Variable in class org.jmol.viewer.Eval
 
isBondType() - Method in class org.jmol.shapespecial.Dipole
 
isCarbohydrate() - Method in class org.jmol.modelset.Atom
 
isCarbohydrate() - Method in class org.jmol.modelset.Group
 
isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isCarbohydrate - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isCavity - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isCavity - Variable in class org.jmol.jvxl.readers.Parameters
 
isCellEditable(int, int) - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
isCenterParameter(int) - Method in class org.jmol.viewer.Eval
 
isCentrosymmetric - Variable in class org.jmol.symmetry.HallInfo
 
isCheckOnly - Variable in class org.jmol.viewer.Compiler
 
isCircle - Variable in class org.jmol.shapespecial.Draw
 
isClickable() - Method in class org.jmol.modelset.Atom
 
isClipped(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
isClipped(int, int) - Method in class org.jmol.g3d.Graphics3D
 
isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
 
isClippedXY(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
isClippedZ(int) - Method in interface org.jmol.api.JmolRendererInterface
 
isClippedZ(int) - Method in class org.jmol.export.Export3D
 
isClippedZ(int) - Method in class org.jmol.g3d.Graphics3D
 
isCmdf - Variable in class org.jmol.adapter.readers.more.ShelxReader
 
isColixColorInherited(short) - Static method in class org.jmol.g3d.Graphics3D
 
isColixTranslucent(short) - Static method in class org.jmol.g3d.Graphics3D
 
isCollapsed - Variable in class org.jmol.shapespecial.Polyhedra
 
isColorIndex - Static variable in class org.jmol.util.ColorEncoder
 
isColorParam(int) - Method in class org.jmol.viewer.Eval
 
isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
 
isColorReversed - Variable in class org.jmol.jvxl.readers.Parameters
 
isColorSolid - Variable in class org.jmol.shape.Mesh
 
isCommaAsOrAllowed - Variable in class org.jmol.viewer.Compiler
 
isCompoundDocument - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
isCompoundDocument(InputStream) - Static method in class org.jmol.util.CompoundDocument
 
isCompoundDocument(byte[]) - Static method in class org.jmol.util.CompoundDocument
 
isConnect() - Method in class org.jmol.modelset.ModelCollection.StateScript
 
isConnected(Measurement, int) - Method in class org.jmol.shape.Measures
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AminoMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.Monomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isConsumer(ImageConsumer) - Method in class org.jmol.g3d.Awt3D
 
isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isContoured - Variable in class org.jmol.jvxl.data.JvxlData
 
isContoured - Variable in class org.jmol.jvxl.readers.Parameters
 
isCovalent() - Method in class org.jmol.modelset.Bond
 
isCrossed - Variable in class org.jmol.shapespecial.Draw
 
isCubeData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isCursorOnTopOf(int, int, int, Atom) - Method in class org.jmol.modelset.Atom
 
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.AtomCollection
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
 
isCurve - Variable in class org.jmol.shapespecial.Draw
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
 
isCylinder - Variable in class org.jmol.shapespecial.Draw
 
isDataFlavorSupported(DataFlavor) - Method in class org.jmol.export.image.ImageSelection
 
isDataFlavorSupported(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
isDefaultColorRasmol - Variable in class org.jmol.viewer.ColorManager
 
isDirectedTowardsCamera(short) - Method in interface org.jmol.api.JmolRendererInterface
 
isDirectedTowardsCamera(short) - Method in class org.jmol.export.Export3D
 
isDirectedTowardsCamera(short) - Method in class org.jmol.g3d.Graphics3D
 
isDirectedTowardsCamera(short) - Method in class org.jmol.g3d.Normix3D
 
isDirectory - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
isDisplayAntialiased() - Method in class org.jmol.g3d.Graphics3D
is full scene / oversampling antialiasing GENERALLY in effect
isDna() - Method in class org.jmol.modelset.Atom
 
isDna - Variable in class org.jmol.modelset.Chain
 
isDna() - Method in class org.jmol.modelset.Chain
 
isDna() - Method in class org.jmol.modelset.Group
 
isDna() - Method in class org.jmol.modelsetbio.Monomer
 
isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isDrawType(String, int) - Method in class org.jmol.symmetry.PointGroup
 
isDynamic - Variable in class org.jmol.modelset.Measurement
 
isDynamic() - Method in class org.jmol.modelset.Measurement
 
isEccentric - Variable in class org.jmol.jvxl.readers.Parameters
 
isEccentric - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
isEmbeddedExpression - Variable in class org.jmol.viewer.Compiler
 
isEmpty - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
isEqual(PointGroup) - Method in class org.jmol.symmetry.PointGroup
 
isError - Variable in class org.openscience.jmol.app.ScriptWindow
 
isExecuting - Variable in class org.jmol.viewer.Eval
 
isExecutionPaused() - Method in class org.jmol.viewer.Eval
 
isExpressionNext() - Method in class org.jmol.viewer.Compiler
 
isFinite(double) - Static method in class org.jmol.minimize.Util
 
isFixed - Variable in class org.jmol.shape.MeshCollection
 
isFixed - Variable in class org.jmol.shapespecial.DrawMesh
 
isFloatParameter(int) - Method in class org.jmol.viewer.Eval
 
isForCheck - Variable in class org.jmol.viewer.Eval
 
isFullSceneAntialiasingEnabled - Variable in class org.jmol.g3d.Graphics3D
 
isFunction(String) - Method in class org.jmol.viewer.Compiler
 
isGenerator - Variable in class org.jmol.shape.ShapeRenderer
 
isGreaterOnly - Variable in class org.jmol.modelset.AtomIteratorWithinSet
 
isGroup3(String) - Method in class org.jmol.modelset.Atom
 
isGroup3(String) - Method in class org.jmol.modelset.Group
 
isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isGzip(InputStream) - Static method in class org.jmol.viewer.FileManager
 
isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isHelix(float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
isHelix() - Method in class org.jmol.modelsetbio.Monomer
 
isHelix(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
isHetero - Variable in class org.jmol.adapter.smarter.Atom
 
isHetero(String) - Static method in class org.jmol.api.JmolAdapter
 
isHetero() - Method in class org.jmol.modelset.Atom
 
isHetero() - Method in class org.jmol.modelset.Group
 
isHetero(String) - Static method in class org.jmol.viewer.JmolConstants
 
isHidden - Variable in class org.jmol.modelset.Measurement
 
isHidden() - Method in class org.jmol.modelset.Measurement
 
isHighRes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isHover - Variable in class org.jmol.shape.Object2dShape
 
iShowNormals - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
iShowSolid - Variable in class org.jmol.shape.DotsRenderer
 
isHydrogen() - Method in class org.jmol.modelset.Bond
 
isImplicitExpression - Variable in class org.jmol.viewer.Compiler
 
isImproper - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
 
isInDisplayRange(int, int) - Method in class org.jmol.g3d.Graphics3D
 
isInitialized(int) - Method in class org.jmol.bspt.Bspf
 
isInLatticeCell(int, Point3f) - Method in class org.jmol.modelset.AtomCollection
 
isInPosition(Point3f, float) - Method in class org.jmol.viewer.TransformManager
 
isInPosition(Point3f, float) - Method in class org.jmol.viewer.Viewer
 
isInSelectionSubset(int) - Method in class org.jmol.viewer.SelectionManager
 
isInSelectionSubset(int) - Method in class org.jmol.viewer.Viewer
 
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
 
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.readers.VoxelReader
 
isInside2d(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
isInsideOut() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isInSymmetryRange(Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
isIntegrationCurvePoint(Double) - Method in class org.jmol.jcamp.GraphCharacteristics
 
isInvertible(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
isJmolDataFrame(int) - Method in class org.jmol.modelset.ModelCollection
 
isJmolDataFrame(Atom) - Method in class org.jmol.modelset.ModelCollection
 
isJmolDataFrame(int) - Method in class org.jmol.viewer.Viewer
 
isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
 
isJmolParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
isJmolParameter(String) - Method in class org.jmol.viewer.Viewer
 
isJPEG - Variable in class org.jmol.export.dialog.Dialog.QualityListener
 
isJvm12orGreater() - Method in class org.jmol.api.JmolViewer
 
isJvm12orGreater() - Method in class org.jmol.viewer.Viewer
 
isJvxl - Variable in class org.jmol.jvxl.readers.VoxelReader
 
isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
 
isLabelOrHover - Variable in class org.jmol.shape.Object2d
 
isLatticeRange - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
isLinear(Point3f[]) - Method in class org.jmol.symmetry.PointGroup
 
isLineContinuation(int) - Method in class org.jmol.viewer.Compiler
 
isMac - Static variable in class org.jmol.export.dialog.Dialog
 
isMatch(String, String) - Static method in class org.jmol.adapter.readers.cifpdb.CifReader
 
isMatch(String, String, boolean, boolean) - Static method in class org.jmol.util.TextFormat
 
isMeasurementUnit(String) - Static method in class org.jmol.viewer.StateManager
 
isMesh - Variable in class org.jmol.shapebio.Strands
 
isModelVisible() - Method in class org.jmol.modelset.Atom
 
isMolecular - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isMonomerSelected(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
isMultiCell - Variable in class org.jmol.symmetry.SymmetryInfo
 
isMultiConfiguration - Variable in class org.jmol.popup.JmolPopup
 
isMultiFrame - Variable in class org.jmol.popup.JmolPopup
 
isNaturalIsotope(String) - Static method in class org.jmol.viewer.JmolConstants
 
isNavigationCentered() - Method in class org.jmol.viewer.TransformManager
 
isNavigationCentered - Variable in class org.jmol.viewer.TransformManager11
 
isNavigationCentered() - Method in class org.jmol.viewer.TransformManager11
 
isNavigationMode - Variable in class org.jmol.viewer.TransformManager
 
isNear(double, double) - Static method in class org.jmol.minimize.Util
 
isNear(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNearZero(double) - Static method in class org.jmol.minimize.Util
 
isNearZero(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNewSet - Variable in class org.jmol.viewer.Compiler
 
isNMRdata - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
isNoble(int) - Static method in class org.jmol.adapter.readers.more.MopacData
 
isNucleic() - Method in class org.jmol.modelset.Atom
 
isNucleic() - Method in class org.jmol.modelset.Group
 
isNucleic() - Method in class org.jmol.modelsetbio.Monomer
 
isNucleic - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
IsoFxyReader - Class in org.jmol.jvxl.readers
 
IsoFxyReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoFxyReader
 
IsoMepReader - Class in org.jmol.jvxl.readers
 
IsoMepReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoMepReader
 
isomeshes - Variable in class org.jmol.shapesurface.Isosurface
 
IsoMOReader - Class in org.jmol.jvxl.readers
 
IsoMOReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoMOReader
 
isOn - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
isOn - Variable in class org.jmol.util.CommandHistory
 
isOneOf(String, String) - Static method in class org.jmol.util.Parser
 
isOnePerLine - Variable in class org.jmol.shapesurface.Pmesh
 
isOpFunc(Token) - Method in class org.jmol.viewer.Eval.Rpn
 
IsoPlaneReader - Class in org.jmol.jvxl.readers
 
IsoPlaneReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoPlaneReader
 
IsoShapeReader - Class in org.jmol.jvxl.readers
 
IsoShapeReader(SurfaceGenerator, float) - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
 
IsoShapeReader(SurfaceGenerator, int, int, int, float) - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
 
IsoSolventReader - Class in org.jmol.jvxl.readers
 
IsoSolventReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader
 
Isosurface - Class in org.jmol.shapesurface
 
Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
 
isosurface(int) - Method in class org.jmol.viewer.Eval
 
isosurface - Static variable in class org.jmol.viewer.Token
 
IsosurfaceGenerator - Class in org.jmol.export
 
IsosurfaceGenerator() - Constructor for class org.jmol.export.IsosurfaceGenerator
 
IsosurfaceMesh - Class in org.jmol.shapesurface
 
IsosurfaceMesh(String, Graphics3D, short) - Constructor for class org.jmol.shapesurface.IsosurfaceMesh
 
isosurfacePropertySmoothing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
IsosurfaceRenderer - Class in org.jmol.shapesurface
 
IsosurfaceRenderer() - Constructor for class org.jmol.shapesurface.IsosurfaceRenderer
 
isotopeMap0 - Static variable in class org.jmol.adapter.readers.molxyz.MolReader
 
isotopeMap1 - Static variable in class org.jmol.adapter.readers.molxyz.MolReader
 
isPaletteVariable(byte) - Static method in class org.jmol.viewer.JmolConstants
 
isParallel(Vector3f, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
isPartial() - Method in class org.jmol.modelset.Bond
 
isPass2 - Variable in class org.jmol.g3d.Graphics3D
 
isPDB - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
isPDB - Variable in class org.jmol.modelset.Model
 
isPDB - Variable in class org.jmol.modelset.ModelCollection
 
isPDB - Variable in class org.jmol.popup.JmolPopup
 
isPeriodic() - Method in interface org.jmol.api.SymmetryInterface
 
isPeriodic() - Method in class org.jmol.symmetry.Symmetry
 
isPeriodic() - Method in class org.jmol.symmetry.SymmetryInfo
 
isPerpendicular - Variable in class org.jmol.shapespecial.Draw
 
isPerpendicular(Vector3f, Vector3f) - Method in class org.jmol.symmetry.PointGroup
 
isPhaseColored - Variable in class org.jmol.shapesurface.Isosurface
 
isPhosphorusMonomer() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPlanar(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.shapespecial.Polyhedra
 
isPlanarMapping - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
isPlane - Variable in class org.jmol.shapespecial.Draw
 
isPocket - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isPoint3f(int) - Method in class org.jmol.viewer.Eval
 
isPolygonDisplayable(int) - Method in class org.jmol.shape.MeshRenderer
 
isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
 
isPolygonDisplayable(int) - Method in class org.jmol.shapespecial.DrawRenderer
 
isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
 
isPreliminary - Variable in class org.jmol.minimize.forcefield.Calculations
 
isPreviewOnly - Variable in class org.jmol.viewer.Viewer
 
isPreviewOnly() - Method in class org.jmol.viewer.Viewer
 
isPrimitive - Variable in class org.jmol.symmetry.UnitCell
 
isProgressive - Variable in class org.jmol.jvxl.readers.VoxelReader
 
isProperty - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isProtein() - Method in class org.jmol.modelset.Atom
 
isProtein() - Method in class org.jmol.modelset.Group
 
isProtein() - Method in class org.jmol.modelsetbio.Monomer
 
isPurine() - Method in class org.jmol.modelset.Atom
 
isPurine() - Method in class org.jmol.modelset.Group
 
isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPurine - Variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.modelset.Atom
 
isPyrimidine() - Method in class org.jmol.modelset.Group
 
isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPyrimidine - Variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isRandom - Variable in class org.jmol.util.BinaryDocument
 
isRangeSelected() - Method in class org.jmol.viewer.Viewer
 
isReadableAsString(String) - Static method in class org.jmol.viewer.PropertyManager
 
isReversed - Variable in class org.jmol.shapespecial.Draw
 
isRna() - Method in class org.jmol.modelset.Atom
 
isRna - Variable in class org.jmol.modelset.Chain
 
isRna() - Method in class org.jmol.modelset.Chain
 
isRna() - Method in class org.jmol.modelset.Group
 
isRna() - Method in class org.jmol.modelsetbio.Monomer
 
isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isRotated45 - Variable in class org.jmol.shapespecial.Draw
 
isSameAtoms(Dipole, String) - Method in class org.jmol.shapespecial.Dipoles
 
isScreened - Variable in class org.jmol.g3d.Graphics3D
 
isScreenedA - Variable in class org.jmol.g3d.Cylinder3D
 
isScreenedB - Variable in class org.jmol.g3d.Cylinder3D
 
isScriptCheck - Variable in class org.jmol.viewer.Eval
 
isScriptExecuting() - Method in class org.jmol.api.JmolViewer
 
isScriptExecuting() - Method in class org.jmol.viewer.Eval
 
isScriptExecuting() - Method in class org.jmol.viewer.Viewer
 
isScriptQueued - Variable in class org.jmol.viewer.Viewer
 
isSelected(String) - Method in class org.jmol.applet.GuiMap
 
isSelected(BitSet) - Method in class org.jmol.modelset.Group
 
isSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isSelected(int) - Method in class org.jmol.viewer.Viewer
 
isSetBrace - Variable in class org.jmol.viewer.Compiler
 
isSetOrDefine - Variable in class org.jmol.viewer.Compiler
 
isShapeSecondary(int) - Static method in class org.jmol.viewer.JmolConstants
 
isShapeVisible(int) - Method in class org.jmol.modelset.Atom
 
isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isSheet(float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
isSheet() - Method in class org.jmol.modelsetbio.Monomer
 
isSheet(int) - Method in class org.jmol.shapebio.RocketsRenderer
 
isShowCommand - Variable in class org.jmol.viewer.Compiler
 
isShowScriptOutput - Variable in class org.jmol.viewer.Compiler
 
isSigned - Variable in class org.jmol.applet.Jmol
 
isSigned - Variable in class org.jmol.appletwrapper.AppletWrapper
 
isSigned() - Method in class org.jmol.appletwrapper.AppletWrapper
 
isSigned - Variable in class org.jmol.popup.JmolPopup
 
isSignedApplet - Variable in class org.jmol.viewer.Viewer
 
isSignedApplet() - Method in class org.jmol.viewer.Viewer
 
isSilent - Variable in class org.jmol.jvxl.readers.Parameters
 
isSilent - Variable in class org.jmol.viewer.Compiler
 
isSilent - Variable in class org.jmol.viewer.Viewer
 
isSilent - Static variable in class org.openscience.jmol.app.Jmol
 
isSimple - Variable in class org.jmol.modelset.Atom
 
isSimple() - Method in class org.jmol.modelset.Atom
 
isSlabEnabled - Variable in class org.jmol.export._PovrayExporter
 
isSpaceOrTab(char) - Static method in class org.jmol.viewer.Compiler
 
isSpartanArchive(String) - Method in class org.jmol.adapter.readers.more.SpartanReader
 
isSpecTerminator(int) - Method in class org.jmol.viewer.Compiler
 
isSpinFixed - Variable in class org.jmol.viewer.TransformManager
 
isSpinInternal - Variable in class org.jmol.viewer.TransformManager
 
isSpinSelected - Variable in class org.jmol.viewer.TransformManager
 
isSquared - Variable in class org.jmol.jvxl.readers.Parameters
 
isStandard - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
isStateDataRead() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isStateScript - Variable in class org.jmol.viewer.Eval.Context
 
isStateScript - Variable in class org.jmol.viewer.Eval
 
isStereo() - Method in class org.jmol.modelset.Bond
 
isStructureTainted() - Method in class org.jmol.modelset.Model
 
isSurface - Variable in class org.jmol.shape.Dots
 
isSymmetry - Variable in class org.jmol.popup.JmolPopup
 
isSynced - Variable in class org.jmol.viewer.StatusManager
 
isSyntaxCheck - Variable in class org.jmol.viewer.Eval
 
isTainted - Variable in class org.jmol.viewer.Viewer
 
isToFile - Variable in class org.jmol.export._Exporter
 
isToken(int) - Method in class org.jmol.viewer.Compiler
 
isTraceAlpha - Variable in class org.jmol.shapebio.BioShapeRenderer
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isTrajectory - Variable in class org.jmol.modelset.Measurement
 
isTrajectory() - Method in class org.jmol.modelset.Measurement
 
isTrajectory - Variable in class org.jmol.modelset.Model
 
isTrajectory(int) - Method in class org.jmol.modelset.ModelCollection
 
isTrajectory(int[]) - Method in class org.jmol.modelset.ModelCollection
 
isTrajectory - Variable in class org.jmol.modelset.ModelLoader
 
isTrajectory(int) - Method in class org.jmol.viewer.Viewer
 
isTranslucent - Variable in class org.jmol.g3d.Graphics3D
 
isTranslucent() - Method in class org.jmol.modelset.Atom
 
isTranslucent() - Method in class org.jmol.modelset.Bond
 
isTranslucent - Variable in class org.jmol.shape.MeshRenderer
 
isTranslucent - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isTransparent - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
istructure - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
 
isTurn(float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
isTwoSided - Variable in class org.jmol.shape.Mesh
 
isUnitCell - Variable in class org.jmol.popup.JmolPopup
 
isUpdating - Variable in class org.jmol.applet.Jmol
 
isUserValue - Variable in class org.jmol.shapespecial.Dipole
 
isUserValue - Variable in class org.jmol.shapespecial.Dipoles
 
isValid() - Method in class org.jmol.modelset.ModelCollection.StateScript
 
isValid - Variable in class org.jmol.shape.Mesh
 
isValid - Variable in class org.jmol.shapespecial.Dipole
 
isValid - Variable in class org.jmol.shapespecial.Draw
 
isValid - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
isValidElementSymbol(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidElementSymbol(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidElementSymbolNoCaseSecondChar(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidFirstSymbolChar(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isVector - Variable in class org.jmol.shapespecial.Draw
 
isVector - Variable in class org.jmol.shapespecial.DrawMesh
 
isVertices - Variable in class org.jmol.shapespecial.Draw
 
isVibration - Variable in class org.jmol.popup.JmolPopup
 
isVibrationOn() - Method in class org.jmol.viewer.TransformManager
 
isVibrationOn() - Method in class org.jmol.viewer.Viewer
 
isVisible() - Method in class org.jmol.modelset.Atom
determine if an atom or its PDB group is visible
isVisible - Variable in class org.jmol.modelset.Measurement
 
isVisible() - Method in class org.jmol.modelset.Measurement
 
isVisible - Variable in class org.jmol.shape.Bbcage
 
isWhiteSpace(String, int) - Static method in class org.jmol.util.Parser
 
isWild(String) - Static method in class org.jmol.util.TextFormat
 
isWindowCentered() - Method in class org.jmol.viewer.TransformManager
 
isWindowCentered() - Method in class org.jmol.viewer.Viewer
 
isWithin(Point3f) - Method in class org.jmol.modelset.BoxInfo
 
isWithinRadius(Point3f) - Method in class org.jmol.bspt.CubeIterator
checks one Point3f for distance
isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.VoxelReader
 
isXYZ - Variable in class org.jmol.modelset.ModelCollection
 
isZapped - Variable in class org.jmol.popup.JmolPopup
 
isZipFile - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
isZipFile(InputStream) - Static method in class org.jmol.util.ZipUtil
 
isZipFile(byte[]) - Static method in class org.jmol.util.ZipUtil
 
itemStateChanged(ItemEvent) - Method in class org.jmol.export.dialog.Dialog.ExportChoiceListener
 
itemStateChanged(ItemEvent) - Method in class org.jmol.popup.JmolPopup.CheckboxMenuItemListener
 
itemStateChanged(ItemEvent) - Method in class org.openscience.jmol.app.FileTyper
 
iterateOverAllNewAtoms(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewBonds(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewModels(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
Pull in all spans of helix, etc.
iToken - Variable in class org.jmol.viewer.Eval.Context
 
iToken - Variable in class org.jmol.viewer.Eval
 
itokenInfix - Variable in class org.jmol.viewer.Compiler
 
iUseBitSets - Variable in class org.jmol.jvxl.readers.Parameters
 
iVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
iValue(Token) - Static method in class org.jmol.viewer.Token
 

J

JaguarReader - Class in org.jmol.adapter.readers.more
Jaguar reader tested for the two samples files in CVS.
JaguarReader() - Constructor for class org.jmol.adapter.readers.more.JaguarReader
 
JaguarReader - Class in org.jmol.jvxl.readers
 
JaguarReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.JaguarReader
 
jaguarRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
javaname - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
javascript - Static variable in class org.jmol.viewer.Token
 
jbr - Variable in class org.jmol.modelset.ModelCollection
 
JCamp - Variable in class org.jmol.jcamp.Visua
 
jcampSubString(String, int, int) - Static method in class org.jmol.jcamp.utils.StringDataUtils
Returns the sub-string of the string provided
jf - Variable in class org.jmol.applet.Console
 
JmeReader - Class in org.jmol.adapter.readers.more
 
JmeReader() - Constructor for class org.jmol.adapter.readers.more.JmeReader
 
Jmol - Class in org.jmol.applet
 
Jmol() - Constructor for class org.jmol.applet.Jmol
 
JMOL - Static variable in class org.jmol.util.ColorEncoder
 
jmol - Static variable in class org.jmol.viewer.Token
 
Jmol - Class in org.openscience.jmol.app
 
Jmol(Splash, JFrame, Jmol, int, int, String) - Constructor for class org.openscience.jmol.app.Jmol
 
Jmol(Splash, JFrame, Jmol, int, int, String, Point) - Constructor for class org.openscience.jmol.app.Jmol
 
Jmol.AboutAction - Class in org.openscience.jmol.app
 
Jmol.AboutAction() - Constructor for class org.openscience.jmol.app.Jmol.AboutAction
 
Jmol.ActionChangedListener - Class in org.openscience.jmol.app
 
Jmol.ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.Jmol.ActionChangedListener
 
Jmol.AppCloser - Class in org.openscience.jmol.app
To shutdown when run as an application.
Jmol.AppCloser() - Constructor for class org.openscience.jmol.app.Jmol.AppCloser
 
Jmol.AtomSetChooserAction - Class in org.openscience.jmol.app
 
Jmol.AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.Jmol.AtomSetChooserAction
 
Jmol.CloseAction - Class in org.openscience.jmol.app
 
Jmol.CloseAction() - Constructor for class org.openscience.jmol.app.Jmol.CloseAction
 
Jmol.ConsoleAction - Class in org.openscience.jmol.app
 
Jmol.ConsoleAction() - Constructor for class org.openscience.jmol.app.Jmol.ConsoleAction
 
Jmol.CopyImageAction - Class in org.openscience.jmol.app
An Action to copy the current image into the clipboard.
Jmol.CopyImageAction() - Constructor for class org.openscience.jmol.app.Jmol.CopyImageAction
 
Jmol.CopyScriptAction - Class in org.openscience.jmol.app
 
Jmol.CopyScriptAction() - Constructor for class org.openscience.jmol.app.Jmol.CopyScriptAction
 
Jmol.ExecuteScriptAction - Class in org.openscience.jmol.app
 
Jmol.ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.Jmol.ExecuteScriptAction
 
Jmol.ExitAction - Class in org.openscience.jmol.app
Really lame implementation of an exit command
Jmol.ExitAction() - Constructor for class org.openscience.jmol.app.Jmol.ExitAction
 
Jmol.ExportAction - Class in org.openscience.jmol.app
 
Jmol.ExportAction() - Constructor for class org.openscience.jmol.app.Jmol.ExportAction
 
Jmol.MyStatusListener - Class in org.jmol.applet
 
Jmol.MyStatusListener() - Constructor for class org.jmol.applet.Jmol.MyStatusListener
 
Jmol.MyStatusListener - Class in org.openscience.jmol.app
 
Jmol.MyStatusListener() - Constructor for class org.openscience.jmol.app.Jmol.MyStatusListener
 
Jmol.NewAction - Class in org.openscience.jmol.app
 
Jmol.NewAction() - Constructor for class org.openscience.jmol.app.Jmol.NewAction
 
Jmol.NewAction(String) - Constructor for class org.openscience.jmol.app.Jmol.NewAction
 
Jmol.NewwinAction - Class in org.openscience.jmol.app
 
Jmol.NewwinAction() - Constructor for class org.openscience.jmol.app.Jmol.NewwinAction
 
Jmol.OpenAction - Class in org.openscience.jmol.app
 
Jmol.OpenAction() - Constructor for class org.openscience.jmol.app.Jmol.OpenAction
 
Jmol.OpenUrlAction - Class in org.openscience.jmol.app
 
Jmol.OpenUrlAction() - Constructor for class org.openscience.jmol.app.Jmol.OpenUrlAction
 
Jmol.PasteClipboardAction - Class in org.openscience.jmol.app
 
Jmol.PasteClipboardAction() - Constructor for class org.openscience.jmol.app.Jmol.PasteClipboardAction
 
Jmol.PovrayAction - Class in org.openscience.jmol.app
 
Jmol.PovrayAction() - Constructor for class org.openscience.jmol.app.Jmol.PovrayAction
 
Jmol.PrintAction - Class in org.openscience.jmol.app
 
Jmol.PrintAction() - Constructor for class org.openscience.jmol.app.Jmol.PrintAction
 
Jmol.RecentFilesAction - Class in org.openscience.jmol.app
 
Jmol.RecentFilesAction() - Constructor for class org.openscience.jmol.app.Jmol.RecentFilesAction
 
Jmol.ScriptWindowAction - Class in org.openscience.jmol.app
 
Jmol.ScriptWindowAction() - Constructor for class org.openscience.jmol.app.Jmol.ScriptWindowAction
 
Jmol.ToWebAction - Class in org.openscience.jmol.app
 
Jmol.ToWebAction() - Constructor for class org.openscience.jmol.app.Jmol.ToWebAction
 
Jmol.UguideAction - Class in org.openscience.jmol.app
 
Jmol.UguideAction() - Constructor for class org.openscience.jmol.app.Jmol.UguideAction
 
Jmol.ViewMeasurementTableAction - Class in org.openscience.jmol.app
 
Jmol.ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.Jmol.ViewMeasurementTableAction
 
Jmol.WhatsNewAction - Class in org.openscience.jmol.app
 
Jmol.WhatsNewAction() - Constructor for class org.openscience.jmol.app.Jmol.WhatsNewAction
 
Jmol.WriteAction - Class in org.openscience.jmol.app
 
Jmol.WriteAction() - Constructor for class org.openscience.jmol.app.Jmol.WriteAction
 
JMOL_DATA_OTHER - Static variable in class org.jmol.viewer.JmolConstants
 
JMOL_DATA_QUATERNION - Static variable in class org.jmol.viewer.JmolConstants
 
JMOL_DATA_RAMACHANDRAN - Static variable in class org.jmol.viewer.JmolConstants
 
JMOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.Jmol
 
JmolAdapter - Class in org.jmol.api
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapter(String) - Constructor for class org.jmol.api.JmolAdapter
 
JmolAdapter.AtomIterator - Class in org.jmol.api
AtomIterator is used to enumerate all the clientAtom objects in a specified frame.
JmolAdapter.AtomIterator() - Constructor for class org.jmol.api.JmolAdapter.AtomIterator
 
JmolAdapter.BondIterator - Class in org.jmol.api
BondIterator is used to enumerate all the bonds
JmolAdapter.BondIterator() - Constructor for class org.jmol.api.JmolAdapter.BondIterator
 
JmolAdapter.StructureIterator - Class in org.jmol.api
StructureIterator is used to enumerate Structures Helix, Sheet, Turn
JmolAdapter.StructureIterator() - Constructor for class org.jmol.api.JmolAdapter.StructureIterator
 
JmolAppletInterface - Interface in org.jmol.api
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAppletRegistry - Class in org.jmol.applet
 
JmolAppletRegistry() - Constructor for class org.jmol.applet.JmolAppletRegistry
 
JmolBioResolver - Interface in org.jmol.api
 
jmolComponent - Variable in class org.jmol.popup.JmolPopup
 
JmolConstants - Class in org.jmol.viewer
 
JmolConstants() - Constructor for class org.jmol.viewer.JmolConstants
 
jmolData - Variable in class org.jmol.modelset.Model
 
jmolData - Variable in class org.jmol.modelset.ModelLoader
 
jmolDefaultProperties - Variable in class org.openscience.jmol.app.PreferencesDialog
 
jmolDefaults - Static variable in class org.openscience.jmol.app.PreferencesDialog
 
jmolDefaultsButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
JmolDialogInterface - Interface in org.jmol.api
 
JmolExportInterface - Interface in org.jmol.api
 
JmolFileReaderInterface - Interface in org.jmol.api
 
jmolFrameType - Variable in class org.jmol.modelset.Model
 
JmolImageCreatorInterface - Interface in org.jmol.api
 
JmolInstance - Class in org.openscience.jmol.app.webexport
 
JmolInstance(JmolViewer, String, String, int, int) - Constructor for class org.openscience.jmol.app.webexport.JmolInstance
 
jmolpopup - Variable in class org.jmol.applet.Jmol
 
JmolPopup - Class in org.jmol.popup
 
JmolPopup(JmolViewer, boolean) - Constructor for class org.jmol.popup.JmolPopup
 
jmolpopup - Variable in class org.openscience.jmol.app.Jmol
 
JmolPopup.CheckboxMenuItemListener - Class in org.jmol.popup
 
JmolPopup.CheckboxMenuItemListener() - Constructor for class org.jmol.popup.JmolPopup.CheckboxMenuItemListener
 
JmolPopup.MenuItemListener - Class in org.jmol.popup
 
JmolPopup.MenuItemListener() - Constructor for class org.jmol.popup.JmolPopup.MenuItemListener
 
JmolPopupAwt - Class in org.jmol.popup
 
JmolPopupAwt(JmolViewer, boolean) - Constructor for class org.jmol.popup.JmolPopupAwt
 
JmolPopupSwing - Class in org.jmol.popup
 
JmolPopupSwing(JmolViewer, boolean) - Constructor for class org.jmol.popup.JmolPopupSwing
 
jmolRenderer - Variable in class org.jmol.export._Exporter
 
JmolRendererInterface - Interface in org.jmol.api
 
JmolResourceHandler - Class in org.openscience.jmol.app
Provides access to resources (for example, strings and images).
JmolResourceHandler() - Constructor for class org.openscience.jmol.app.JmolResourceHandler
 
JmolSelectionListener - Interface in org.jmol.api
listen to atom selections in a Jmol Viewer
JmolSimpleViewer - Class in org.jmol.api
This is the high-level API for the JmolViewer for simple access.
JmolSimpleViewer() - Constructor for class org.jmol.api.JmolSimpleViewer
 
JmolStatusListener - Interface in org.jmol.api
 
jmolStatusListener - Variable in class org.jmol.viewer.StatusManager
 
JmolViewer - Class in org.jmol.api
This is the high-level API for the JmolViewer for simple access.
JmolViewer() - Constructor for class org.jmol.api.JmolViewer
 
join - Static variable in class org.jmol.viewer.Token
 
JpegEncoder - Class in org.jmol.util
 
JpegEncoder(Image, int, OutputStream) - Constructor for class org.jmol.util.JpegEncoder
 
JpegInfo - Class in org.jmol.util
 
JpegInfo(Image) - Constructor for class org.jmol.util.JpegInfo
 
jpegNaturalOrder - Static variable in class org.jmol.util.Huffman
 
JpegObj - Variable in class org.jmol.util.JpegEncoder
 
justifyMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
jvm11orGreater - Variable in class org.jmol.viewer.Viewer
 
jvm12 - Variable in class org.jmol.applet.Console
 
jvm12 - Variable in class org.jmol.applet.Jmol
 
Jvm12 - Class in org.jmol.applet
 
Jvm12(Component, JmolViewer, JmolAdapter, String) - Constructor for class org.jmol.applet.Jvm12
 
jvm12orGreater - Variable in class org.jmol.applet.Jmol
 
jvm12orGreater - Variable in class org.jmol.viewer.Viewer
 
jvm14orGreater - Variable in class org.jmol.viewer.Viewer
 
Jvxl - Class in org.openscience.jvxl
 
Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
 
JVXL_VERSION - Static variable in class org.jmol.jvxl.readers.JvxlReader
 
jvxlAddDummyAtomList(VolumeData, StringBuffer) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlCheckAtomLine(boolean, boolean, String, String, StringBuffer) - Static method in class org.jmol.jvxl.readers.JvxlReader
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlCompressionRatio - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlCompressString(String) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlCreateHeader(VolumeData, int, Point3f[], int[], StringBuffer) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, StringBuffer) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlCreateSurfaceData(JvxlData, float[][][], float, boolean, int, int, int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlCutoff - Variable in class org.jmol.jvxl.readers.VoxelReader
 
JvxlData - Class in org.jmol.jvxl.data
 
JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
jvxlData - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlData - Variable in class org.jmol.shapesurface.Isosurface
 
jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlDefinitionLine - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlExtraLine - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlExtraLine(JvxlData, int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlFileHeader - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFractionAsCharacter(float, int, int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlGetDefinitionLine(JvxlData, boolean) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlGetFile(JvxlData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlGetNextFraction(int, int, float) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlInfoLine - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.VoxelReader
 
jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlReadAtoms(BufferedReader, StringBuffer, int, VolumeData) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadDefinitionLine(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
JvxlReader - Class in org.jmol.jvxl.readers
 
JvxlReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.JvxlReader
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSkipDataBlock(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlUncompressString(String) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlUpdateInfo(JvxlData, String[], int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlUpdateInfo() - Method in class org.jmol.jvxl.readers.VoxelReader
 
jvxlUpdateInfoLines(JvxlData) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlUpdateSurfaceData(JvxlData, float[], int, int, char) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlValueAsCharacter2(float, float, float, int, int, char[]) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.readers.JvxlReader
 

K

kb - Variable in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
KCAL22 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL332 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL44 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL6 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL644 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL_TO_KJ - Static variable in class org.jmol.minimize.forcefield.Calculations
 
keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
keepCharsList - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
keepRunning - Variable in class org.jmol.appletwrapper.TickerThread
 
keepRunning - Variable in class org.openscience.jmol.app.LoopedStreams
 
key - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
key - Variable in class org.jmol.applet.GuiMap.KeyJMenu
 
key - Variable in class org.jmol.applet.GuiMap.KeyJMenuItem
 
key - Variable in class org.jmol.util.Int2IntHash.Entry
 
key - Variable in class org.openscience.jmol.app.GuiMap.KeyJCheckBox
 
key - Variable in class org.openscience.jmol.app.GuiMap.KeyJCheckBoxMenuItem
 
key - Variable in class org.openscience.jmol.app.GuiMap.KeyJMenu
 
key - Variable in class org.openscience.jmol.app.GuiMap.KeyJMenuItem
 
key - Variable in class org.openscience.jmol.app.GuiMap.KeyJRadioButtonMenuItem
 
keyDown(Event, int) - Method in class org.jmol.jcamp.SaisieDlg
 
keyPressed(KeyEvent) - Method in class org.jmol.viewer.MouseManager
 
keyReleased(KeyEvent) - Method in class org.jmol.viewer.MouseManager
 
keyTyped(KeyEvent) - Method in class org.jmol.viewer.MouseManager
 
keyword - Static variable in class org.jmol.viewer.Token
 

L

LABEL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
label(int) - Method in class org.jmol.viewer.Eval
 
label - Static variable in class org.jmol.viewer.Token
 
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
labelFormat - Variable in class org.jmol.shape.Hover
 
labels - Variable in class org.jmol.applet.GuiMap
 
Labels - Class in org.jmol.shape
 
Labels() - Constructor for class org.jmol.shape.Labels
 
labels - Variable in class org.openscience.jmol.app.GuiMap
 
LabelsGenerator - Class in org.jmol.export
 
LabelsGenerator() - Constructor for class org.jmol.export.LabelsGenerator
 
LabelsRenderer - Class in org.jmol.shape
 
LabelsRenderer() - Constructor for class org.jmol.shape.LabelsRenderer
 
language - Variable in class org.jmol.applet.Jmol
 
language - Variable in class org.jmol.i18n.GT
 
language - Variable in class org.jmol.i18n.GT.Language
 
language - Variable in class org.openscience.jmol.app.Jmol
 
languageList - Static variable in class org.jmol.i18n.GT
 
largeur - Variable in class org.jmol.jcamp.ZoneVisu
 
largeur_gfx - Variable in class org.jmol.jcamp.ZoneVisu
 
last - Static variable in class org.jmol.viewer.Token
 
Last_Firstx - Variable in class org.jmol.jcamp.ZoneVisu
 
Last_Lastx - Variable in class org.jmol.jcamp.ZoneVisu
 
Last_RealFirstx - Variable in class org.jmol.jcamp.ZoneVisu
 
Last_RealLastx - Variable in class org.jmol.jcamp.ZoneVisu
 
lastAtomData - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastAtomIndex - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lastAtomIndex - Variable in class org.jmol.modelset.Group
 
lastColumnIsDummy - Variable in class org.jmol.util.JpegInfo
 
lastConnections - Variable in class org.jmol.viewer.StateManager
 
lastCoordinates - Variable in class org.jmol.viewer.StateManager
 
lastFirstX - Variable in class org.jmol.jcamp.data.GraphControlData
 
lastFrameDelay - Variable in class org.jmol.viewer.RepaintManager
 
lastFrameDelayMs - Variable in class org.jmol.viewer.RepaintManager
 
lastLastX - Variable in class org.jmol.jcamp.data.GraphControlData
 
lastModelIndex - Variable in class org.jmol.atomdata.AtomData
 
lastModelIndex - Variable in class org.jmol.viewer.RepaintManager
 
lastMoNumber - Variable in class org.jmol.viewer.Eval
 
lastMotionEventNumber - Variable in class org.jmol.applet.Jmol
 
lastMotionEventNumber - Variable in class org.openscience.jmol.app.DisplayPanel
 
lastOrientation - Variable in class org.jmol.viewer.StateManager
 
lastRealFirstX - Variable in class org.jmol.jcamp.data.GraphControlData
 
lastRealLastX - Variable in class org.jmol.jcamp.data.GraphControlData
 
lastRowIsDummy - Variable in class org.jmol.util.JpegInfo
 
lastSelected - Variable in class org.jmol.viewer.StateManager
 
lastSequenceNumber - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
lastShape - Variable in class org.jmol.viewer.StateManager
 
lastSize - Variable in class org.jmol.shape.Dots
 
lastSolventRadius - Variable in class org.jmol.shape.Dots
 
lastState - Variable in class org.jmol.viewer.StateManager
 
lastToken - Variable in class org.jmol.viewer.Compiler
 
Lastx - Variable in class org.jmol.jcamp.Visua
 
Lastx - Variable in class org.jmol.jcamp.ZoneVisu
 
LATTICE_VECTOR - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
latticeCode - Variable in class org.jmol.symmetry.HallInfo
 
latticeCode - Variable in class org.jmol.symmetry.SpaceGroup
 
latticeExtension - Variable in class org.jmol.symmetry.HallInfo
 
latticeParameter - Variable in class org.jmol.symmetry.SpaceGroup
 
latticeTranslationData - Static variable in class org.jmol.symmetry.Translation
 
latticeVectorPtr - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
layoutWindow(Container) - Method in class org.openscience.jmol.app.AtomSetChooser
 
layoutWindow(Container) - Method in class org.openscience.jmol.app.ScriptWindow
 
LcaoCartoon - Class in org.jmol.shapesurface
 
LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
 
lcaoCartoon() - Method in class org.jmol.viewer.Eval
 
lcaocartoon - Static variable in class org.jmol.viewer.Token
 
LcaoCartoonGenerator - Class in org.jmol.export
 
LcaoCartoonGenerator() - Constructor for class org.jmol.export.LcaoCartoonGenerator
 
LcaoCartoonRenderer - Class in org.jmol.shapesurface
 
LcaoCartoonRenderer() - Constructor for class org.jmol.shapesurface.LcaoCartoonRenderer
 
lcaoColorNeg - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoColorPos - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoDir - Variable in class org.jmol.shapesurface.Isosurface
 
lcaoID - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoScale - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoType - Variable in class org.jmol.jvxl.readers.Parameters
 
leadAtomIndices - Variable in class org.jmol.modelset.Polymer
 
leadAtomIndices - Variable in class org.jmol.shapebio.BioShape
 
leadAtomIndices - Variable in class org.jmol.shapebio.BioShapeRenderer
 
LEADER_CHAR_MAX - Static variable in class org.jmol.adapter.smarter.Resolver
 
leadMidpoints - Variable in class org.jmol.modelset.Polymer
 
leadPoints - Variable in class org.jmol.modelset.Polymer
 
leaf - Variable in class org.jmol.bspt.CubeIterator
 
Leaf - Class in org.jmol.bspt
A leaf of Point3f objects in the bsp tree
Leaf(Bspt) - Constructor for class org.jmol.bspt.Leaf
 
Leaf(Bspt, Leaf, int) - Constructor for class org.jmol.bspt.Leaf
 
leafCountMax - Static variable in class org.jmol.bspt.Bspt
 
leafIndex - Variable in class org.jmol.bspt.CubeIterator
 
LEFT - Static variable in class org.jmol.viewer.MouseManager
 
left - Static variable in class org.jmol.viewer.Token
 
LEFT_MIDDLE_RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
leftAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
leftbrace - Static variable in class org.jmol.viewer.Token
 
leftBytes - Variable in class org.jmol.export.image.PngEncoder
 
leftDifference(Quaternion) - Method in class org.jmol.util.Quaternion
 
leftdivide - Static variable in class org.jmol.viewer.Token
 
leftparen - Static variable in class org.jmol.viewer.Token
 
leftsquare - Static variable in class org.jmol.viewer.Token
 
length - Variable in class org.jmol.shapespecial.Draw
 
length(BitSet) - Static method in class org.jmol.util.BitSetUtil
length = "last set bit plus one"
length - Variable in class org.jmol.viewer.MonitorInputStream
 
length - Static variable in class org.jmol.viewer.Token
 
length - Variable in class org.openscience.jvxl.MonitorInputStream
 
lengths - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
lengthsFreeBytes - Variable in class org.jmol.util.TempArray
 
lengthsFreePoints - Variable in class org.jmol.util.TempArray
 
lengthsFreeScreens - Variable in class org.jmol.util.TempArray
 
lengthVector - Variable in class org.jmol.shapebio.RocketsRenderer
 
lenStream - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
 
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
 
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
 
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
 
LEVEL_INFO - Static variable in class org.jmol.util.Logger
 
LEVEL_MAX - Static variable in class org.jmol.util.Logger
 
LEVEL_WARN - Static variable in class org.jmol.util.Logger
 
lFill(StringBuffer, String, String) - Static method in class org.jmol.util.TextFormat
 
lighting - Static variable in class org.jmol.g3d.Graphics3D
 
lighting - Static variable in class org.jmol.g3d.Shade3D
 
lighting - Variable in class org.jmol.shape.Mesh
 
lighting - Variable in class org.jmol.shapesurface.Isosurface
 
LIME - Static variable in class org.jmol.g3d.Graphics3D
 
LimitedLineReader - Class in org.jmol.adapter.smarter
 
LimitedLineReader(BufferedReader, int) - Constructor for class org.jmol.adapter.smarter.LimitedLineReader
 
LimitedLineReader - Class in org.jmol.jvxl.readers
 
LimitedLineReader(BufferedReader, int) - Constructor for class org.jmol.jvxl.readers.LimitedLineReader
 
line - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
line - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
line - Variable in class org.jmol.shapesurface.MeshFileCollection
 
line - Variable in class org.jmol.symmetry.SpaceGroup
 
line3d - Variable in class org.jmol.g3d.Cylinder3D
 
line3d - Variable in class org.jmol.g3d.Graphics3D
 
Line3D - Class in org.jmol.g3d
 
Line3D(Graphics3D) - Constructor for class org.jmol.g3d.Line3D
 
line3d - Variable in class org.jmol.g3d.Triangle3D
 
linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
linearSearch() - Method in class org.jmol.minimize.forcefield.ForceField
 
linearTolerance - Variable in class org.jmol.symmetry.PointGroup
 
lineBits - Variable in class org.jmol.g3d.Line3D
 
lineBond - Variable in class org.jmol.shape.SticksRenderer
 
lineCache - Variable in class org.jmol.g3d.Line3D
 
lineCurrent - Variable in class org.jmol.viewer.Compiler
 
lineEnd - Variable in class org.jmol.viewer.Eval.Context
 
lineEnd - Variable in class org.jmol.viewer.Eval
 
lineHeight - Variable in class org.jmol.shape.Text
 
lineIndices - Variable in class org.jmol.viewer.Compiler
 
lineIndices - Variable in class org.jmol.viewer.Eval.Context
 
lineIndices - Variable in class org.jmol.viewer.Eval
 
lineIndices - Variable in class org.jmol.viewer.Function
 
lineLength - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
lineNumbers - Variable in class org.jmol.viewer.Compiler
 
lineNumbers - Variable in class org.jmol.viewer.Eval.Context
 
lineNumbers - Variable in class org.jmol.viewer.Eval
 
lineNumbers - Variable in class org.jmol.viewer.Function
 
lineOptions - Static variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
linePt - Variable in class org.jmol.jvxl.readers.XplorReader
 
lines - Variable in class org.jmol.shape.Text
 
lines - Static variable in class org.jmol.viewer.Token
 
lineStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
lineTypeX - Variable in class org.jmol.g3d.Line3D
 
linkActivated(URL) - Method in class org.openscience.jmol.app.AboutDialog
Follows the reference in an link.
linkActivated(URL) - Method in class org.openscience.jmol.app.HelpDialog
Follows the reference in an link.
linkActivated(URL) - Method in class org.openscience.jmol.app.WhatsNewDialog
Follows the reference in an link.
linkedMesh - Variable in class org.jmol.shape.Mesh
 
linkedMesh - Variable in class org.jmol.shape.MeshCollection
 
lisSaisie() - Method in class org.jmol.jcamp.SaisieDlg
 
list - Static variable in class org.jmol.viewer.Token
 
listCommands - Variable in class org.jmol.viewer.Viewer
 
listeners - Variable in class org.jmol.viewer.SelectionManager
 
listIsosurface(int) - Method in class org.jmol.viewer.Eval
 
listLabel - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
listSavedStates() - Method in class org.jmol.viewer.StateManager
 
listSavedStates() - Method in class org.jmol.viewer.Viewer
 
listVariables - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
load() - Method in class org.jmol.export.dialog.HistoryFile
Loads properties from the history file.
load() - Method in class org.jmol.viewer.Eval
 
load - Static variable in class org.jmol.viewer.Token
 
Load_Clickable_Peaks_Source_File(String) - Method in class org.jmol.jcamp.Visua
 
Load_File - Variable in class org.jmol.jcamp.Visua
 
loadButton - Variable in class org.jmol.applet.Console
 
loadCoordinates(String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
loadData(int, String, String) - Method in class org.jmol.modelset.AtomCollection
 
loadData(int, String, String) - Method in class org.jmol.viewer.Viewer
 
loadDOMNode(JSObject) - Method in interface org.jmol.api.JmolAppletInterface
 
loadDOMNode(JSObject) - Method in class org.jmol.applet.Jmol
 
loadError(String) - Method in class org.jmol.viewer.Eval
 
loadFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
loadFormats - Static variable in class org.jmol.viewer.Compiler
 
loadFunction(String, Vector) - Method in class org.jmol.viewer.Eval
 
loading - Variable in class org.jmol.applet.Jmol
 
loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated.  
loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated.  
loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated.  
loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated.  
loadInline(String) - Method in class org.jmol.api.JmolViewer
 
loadInline(String, boolean) - Method in class org.jmol.api.JmolViewer
 
loadInline(String, char) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[]) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
 
loadInline(String) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String, String) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String[]) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String[], String) - Method in class org.jmol.applet.Jmol
Deprecated.  
loadInline(String) - Method in class org.jmol.viewer.Viewer
 
loadInline(String, boolean) - Method in class org.jmol.viewer.Viewer
 
loadInline(String, char) - Method in class org.jmol.viewer.Viewer
 
loadInline(String, char, boolean) - Method in class org.jmol.viewer.Viewer
 
loadInline(String[]) - Method in class org.jmol.viewer.Viewer
 
loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
 
loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
loadInlineArray(String[], String, boolean) - Method in class org.jmol.applet.Jmol
 
loadInlineSeparated(String, String) - Method in class org.jmol.applet.Jmol
 
loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
loadInlineString(String, String, boolean) - Method in class org.jmol.applet.Jmol
 
loadNodeId(String) - Method in interface org.jmol.api.JmolAppletInterface
 
loadNodeId(String) - Method in class org.jmol.applet.Jmol
 
loadPixelData(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
loadScript(String, String, boolean) - Method in class org.jmol.viewer.Eval
 
loadScript - Variable in class org.jmol.viewer.FileManager
 
loadScriptFile(String, boolean) - Method in class org.jmol.viewer.Eval
 
loadScriptFileInternal(String) - Method in class org.jmol.viewer.Eval
 
loadScriptString(String, boolean) - Method in class org.jmol.viewer.Eval
 
loadShape(int) - Method in class org.jmol.modelset.ModelSet
 
loadShape(int) - Method in class org.jmol.viewer.Viewer
 
localAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
localAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
localArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
localArrayListType - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
localFunctions - Variable in class org.jmol.viewer.Compiler
 
localize(boolean, Properties) - Method in class org.jmol.popup.PopupResourceBundle
 
localizeFileReferences(String, String[], String[]) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
localSpaceGroupName - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
locatePixel(Point3f) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
location_textetitre - Variable in class org.jmol.jcamp.ZoneVisu
 
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
Method to output a log.
log(String) - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
logArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
logCompression - Variable in class org.jmol.jvxl.readers.Parameters
 
logCube - Variable in class org.jmol.jvxl.readers.Parameters
 
logData - Variable in class org.jmol.minimize.forcefield.Calculations
 
logDebugScript(int) - Method in class org.jmol.viewer.Eval
 
Logger - Class in org.jmol.util
Logger mechanism.
Logger() - Constructor for class org.jmol.util.Logger
 
LoggerInterface - Interface in org.jmol.util
Interface used for the logging mechanism.
logging - Variable in class org.jmol.minimize.forcefield.Calculations
 
loggingEnabled - Variable in class org.jmol.minimize.forcefield.Calculations
 
logLevel() - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
logLevel(boolean) - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
logMessages - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
logMessages - Variable in class org.jmol.jvxl.readers.Parameters
 
logMessages - Variable in class org.jmol.viewer.Compiler
 
logMessages - Variable in class org.jmol.viewer.Eval
 
LogPanel - Class in org.openscience.jmol.app.webexport
 
LogPanel() - Constructor for class org.openscience.jmol.app.webexport.LogPanel
 
logTime - Variable in class org.jmol.viewer.FrameRenderer
 
lookForHbonds(NucleicPolymer, BitSet, BitSet) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
lookingAtBitset() - Method in class org.jmol.viewer.Compiler
 
lookingAtComment() - Method in class org.jmol.viewer.Compiler
 
lookingAtDecimal() - Method in class org.jmol.viewer.Compiler
 
lookingAtEndOfLine() - Method in class org.jmol.viewer.Compiler
 
lookingAtEndOfStatement() - Method in class org.jmol.viewer.Compiler
 
lookingAtExponential() - Method in class org.jmol.viewer.Compiler
 
lookingAtInteger() - Method in class org.jmol.viewer.Compiler
 
lookingAtLeadingWhitespace() - Method in class org.jmol.viewer.Compiler
 
lookingAtLoadFormat() - Method in class org.jmol.viewer.Compiler
 
lookingAtLookupToken() - Method in class org.jmol.viewer.Compiler
 
lookingAtObjectID(boolean) - Method in class org.jmol.viewer.Compiler
 
lookingAtSeqcode() - Method in class org.jmol.viewer.Compiler
 
lookingAtSpecialString() - Method in class org.jmol.viewer.Compiler
 
lookingAtString() - Method in class org.jmol.viewer.Compiler
 
lookup(String) - Static method in class org.jmol.symmetry.Rotation
 
lookupCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
lookupGroupID(String) - Static method in class org.jmol.api.JmolAdapter
 
lookupGroupID(String) - Static method in class org.jmol.modelset.Group
 
lookupIdentifierValue(String) - Method in class org.jmol.viewer.Eval
 
lookupInterpolatedVoxelValue(Point3f) - Method in interface org.jmol.api.VolumeDataInterface
 
lookupInterpolatedVoxelValue(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
lookupSpecialAtomID(String) - Static method in class org.jmol.modelset.ModelLoader
 
lookupValue(String, boolean) - Method in class org.jmol.viewer.Eval
 
loop - Static variable in class org.jmol.viewer.Token
 
loopData - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
LoopedStreams - Class in org.openscience.jmol.app
 
LoopedStreams() - Constructor for class org.openscience.jmol.app.LoopedStreams
 
LOW - Static variable in class org.jmol.util.ColorEncoder
 
lowerNeighborIsHelixOrSheet() - Method in class org.jmol.modelsetbio.ProteinStructure
 
ltoken - Variable in class org.jmol.viewer.Compiler
 
ltokenPostfix - Variable in class org.jmol.viewer.Compiler
 
lumoEnergy - Variable in class org.jmol.adapter.readers.more.JaguarReader
 

M

mad - Variable in class org.jmol.modelset.Bond
 
mad - Variable in class org.jmol.shape.Bbcage
 
mad - Variable in class org.jmol.shape.Measures
 
mad - Variable in class org.jmol.shape.ShapeRenderer
 
mad - Variable in class org.jmol.shapespecial.Dipole
 
mad - Variable in class org.jmol.viewer.StateManager.Connection
 
madAtom - Variable in class org.jmol.modelset.Atom
 
madBeg - Variable in class org.jmol.shape.ShapeRenderer
 
madDnaRna - Variable in class org.jmol.shapebio.BioShapeCollection
 
madEnd - Variable in class org.jmol.shape.ShapeRenderer
 
madHelixSheet - Variable in class org.jmol.shapebio.BioShapeCollection
 
madMid - Variable in class org.jmol.shape.ShapeRenderer
 
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JmolConstants
 
madOn - Variable in class org.jmol.shapebio.BioShapeCollection
 
mads - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
mads - Variable in class org.jmol.shape.AtomShape
 
mads - Variable in class org.jmol.shapebio.BioShape
 
mads - Variable in class org.jmol.shapebio.BioShapeRenderer
 
madTurnRandom - Variable in class org.jmol.shapebio.BioShapeCollection
 
mag2d - Variable in class org.jmol.shape.SticksRenderer
 
MAGENTA - Static variable in class org.jmol.g3d.Graphics3D
 
magicNumbers - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
magnitudeLight - Static variable in class org.jmol.g3d.Shade3D
 
main(String[]) - Static method in class org.openscience.jmol.app.Jmol
 
main(String[]) - Static method in class org.openscience.jmol.app.webexport.WebMaker
 
main(String[]) - Static method in class org.openscience.jvxl.Jvxl
 
mainMenu - Variable in class org.jmol.popup.JmolPopupAwt
 
mainMenu - Variable in class org.jmol.popup.JmolPopupSwing
 
makeColorScheme(String, int[], boolean) - Static method in class org.jmol.util.ColorEncoder
 
makeConnections(float, float, short, int, BitSet, BitSet, BitSet, boolean) - Method in class org.jmol.modelset.ModelCollection
 
makeConnections(float, float, short, int, BitSet, BitSet, BitSet, boolean) - Method in class org.jmol.modelset.ModelSet
 
makeConnections(float, float, short, int, BitSet, BitSet, BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
makePoints - Variable in class org.jmol.shapespecial.Draw
 
map - Variable in class org.jmol.applet.GuiMap
 
map - Static variable in class org.jmol.viewer.Token
 
map - Variable in class org.openscience.jmol.app.GuiMap
 
mapAtomName(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mapJavaScriptColors - Static variable in class org.jmol.g3d.Graphics3D
 
mapMostRecentAtomName() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mapMostRecentAtomSerialNumber() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mapNull - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMax - Variable in class org.jmol.jvxl.readers.Parameters
 
mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMin - Variable in class org.jmol.jvxl.readers.Parameters
 
mapSurface(Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
mapT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
mapWidth - Variable in class org.jmol.g3d.Text3D
 
marBond - Variable in class org.openscience.jmol.app.PreferencesDialog
 
MarchingCubes - Class in org.jmol.jvxl.calc
 
MarchingCubes(VertexDataServer, VolumeData, boolean, int, float, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
marchingCubes - Variable in class org.jmol.jvxl.readers.VoxelReader
 
MarchingSquares - Class in org.jmol.jvxl.calc
 
MarchingSquares(VertexDataServer, VolumeData, Point4f, int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
marchingSquares - Variable in class org.jmol.jvxl.readers.VoxelReader
 
MarchingSquares.ContourVertex - Class in org.jmol.jvxl.calc
 
MarchingSquares.ContourVertex(int, int, int, Point3f, int) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
MarchingSquares.PlanarSquare - Class in org.jmol.jvxl.calc
 
MarchingSquares.PlanarSquare(int) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
mark(int) - Method in class org.jmol.viewer.MonitorInputStream
 
mark(int) - Method in class org.openscience.jvxl.MonitorInputStream
 
markLines(String, char) - Static method in class org.jmol.util.Parser
 
markPosition - Variable in class org.jmol.viewer.MonitorInputStream
 
markPosition - Variable in class org.openscience.jvxl.MonitorInputStream
 
MAROON - Static variable in class org.jmol.g3d.Graphics3D
 
masks - Variable in class org.jmol.export.image.GifEncoder
 
mat - Variable in class org.jmol.g3d.Sphere3D
 
mat - Variable in class org.jmol.shapebio.BioShapeRenderer
 
mat - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mat - Variable in class org.jmol.util.Quaternion
 
matchingAtom - Variable in class org.jmol.smiles.SmilesAtom
 
matEllipsoidToScreen - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mathExpressionCommand - Static variable in class org.jmol.viewer.Token
 
mathfunc - Static variable in class org.jmol.viewer.Token
 
mathop - Static variable in class org.jmol.viewer.Token
 
mathproperty - Static variable in class org.jmol.viewer.Token
 
matInv - Variable in class org.jmol.modelset.ModelCollection
 
matrixCartesianToFractional - Variable in class org.jmol.symmetry.UnitCell
 
matrixEnd - Variable in class org.jmol.viewer.TransformManager
 
matrixFractionalToCartesian - Variable in class org.jmol.symmetry.UnitCell
 
matrixRotate - Variable in class org.jmol.viewer.TransformManager
 
matrixStart - Variable in class org.jmol.viewer.TransformManager
 
matrixStartInv - Variable in class org.jmol.viewer.TransformManager
 
matrixStep - Variable in class org.jmol.viewer.TransformManager
 
matrixStereo - Variable in class org.jmol.viewer.TransformManager
 
matrixT - Variable in class org.jmol.shape.MeasuresRenderer
 
matrixTemp - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp4 - Variable in class org.jmol.viewer.TransformManager
 
matrixTest - Variable in class org.jmol.viewer.TransformManager
 
matrixTransform - Variable in class org.jmol.viewer.TransformManager
 
matrixUnTransform(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
matScreenToCartesian - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
matScreenToEllipsoid - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
matTemp - Variable in class org.jmol.modelset.ModelCollection
 
matXyzToPlane - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
max - Static variable in class org.jmol.viewer.Token
 
MAX_ADJACENT_PHOSPHORUS_DISTANCE - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
MAX_BOND_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shape.Sticks
 
MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_DECIMALS - Static variable in class org.jmol.jcamp.GraphCharacteristics
 
MAX_DOUBLE_CLICK_MILLIS - Static variable in class org.jmol.viewer.MouseManager
 
MAX_FILES - Static variable in class org.openscience.jmol.app.RecentFilesDialog
 
MAX_GRID - Static variable in class org.jmol.quantum.MOCalculation
 
MAX_ITEMS - Static variable in class org.jmol.popup.JmolPopup
 
MAX_LEVEL - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
MAX_LEVEL - Static variable in class org.jmol.shape.Dots
 
MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Draw
 
max_squarable_double - Static variable in class org.jmol.minimize.Util
 
MAX_TREE_DEPTH - Static variable in class org.jmol.bspt.Bspt
 
MAX_VERTICES - Static variable in class org.jmol.shapespecial.Polyhedra
 
maxAxis - Static variable in class org.jmol.symmetry.PointGroup
 
maxbits - Variable in class org.jmol.export.image.GifEncoder
 
maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
 
maxcode - Variable in class org.jmol.export.image.GifEncoder
 
MAXCODE(int) - Method in class org.jmol.export.image.GifEncoder
 
maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
maxElement - Variable in class org.jmol.symmetry.PointGroup
 
maxGrid - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
maxHbondAlphaDistance - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
maxHbondAlphaDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
MaxHsampFactor - Variable in class org.jmol.util.JpegInfo
 
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JmolConstants
 
MAXIMUM_QUEUE_LENGTH - Static variable in class org.jmol.viewer.StatusManager
 
MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
 
MAXIMUM_ZOOM_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
 
maximumSize - Variable in class org.jmol.viewer.Viewer
 
Maxintegrate - Variable in class org.jmol.jcamp.ZoneVisu
 
maxLeft - Variable in class org.jmol.bspt.Node
 
maxLevel - Static variable in class org.jmol.geodesic.Geodesic
 
maxLevel - Variable in class org.jmol.viewer.Eval.Rpn
 
maxmaxcode - Variable in class org.jmol.export.image.GifEncoder
 
maxMemoryForNewerJvm() - Method in class org.jmol.popup.JmolPopup
 
maxMemoryForNewerJvm() - Method in class org.jmol.popup.JmolPopupSwing
 
maxOddSizeSphere - Static variable in class org.jmol.g3d.Sphere3D
 
maxPos - Variable in class org.jmol.export.image.PngEncoder
 
maxRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
maxRight - Variable in class org.jmol.bspt.Node
 
maxSerial - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
 
maxSet - Variable in class org.jmol.jvxl.readers.Parameters
 
maxSize - Variable in class org.jmol.util.CommandHistory
 
maxSphereCache - Static variable in class org.jmol.g3d.Sphere3D
 
maxSphereDiameter - Static variable in class org.jmol.g3d.Sphere3D
 
maxSphereDiameter2 - Static variable in class org.jmol.g3d.Sphere3D
 
MAXUNDO - Static variable in class org.openscience.jmol.app.ScriptWindow
 
maxVanderwaalsRadius - Variable in class org.jmol.modelset.AtomCollection
 
MaxVsampFactor - Variable in class org.jmol.util.JpegInfo
 
maxX - Variable in class org.jmol.g3d.Sphere3D
 
maxY - Variable in class org.jmol.g3d.Sphere3D
 
Maxy - Variable in class org.jmol.jcamp.ZoneVisu
 
maxZ - Variable in class org.jmol.g3d.Sphere3D
 
maxZ - Variable in class org.jmol.shape.BallsRenderer
 
maybeGetBaseRing5Points(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
mayScript - Variable in class org.jmol.applet.Jmol
 
mDeriv - Variable in class org.jmol.g3d.Sphere3D
 
mDeriv - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mdlRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
Measure - Class in org.jmol.util
 
Measure() - Constructor for class org.jmol.util.Measure
 
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
 
measureAllModels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
measureDistanceUnits - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Measurement - Class in org.jmol.modelset
 
Measurement(ModelSet, int[], Point3fi[], float, short, String, int) - Constructor for class org.jmol.modelset.Measurement
 
Measurement(ModelSet, int[], Point3fi[]) - Constructor for class org.jmol.modelset.Measurement
 
measurement - Variable in class org.jmol.shape.MeasuresRenderer
 
measurementCount - Variable in class org.jmol.shape.Measures
 
measurementGrowthIncrement - Static variable in class org.jmol.shape.Measures
 
measurementHeaders - Variable in class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
measurementLabels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
measurementMad - Variable in class org.jmol.shape.MeasuresRenderer
 
MeasurementPending - Class in org.jmol.modelset
 
MeasurementPending(ModelSet) - Constructor for class org.jmol.modelset.MeasurementPending
 
measurementPending - Variable in class org.jmol.shape.Measures
 
measurementPending - Variable in class org.jmol.viewer.MouseManager
 
measurementQueued - Variable in class org.jmol.viewer.PickingManager
 
measurements - Variable in class org.jmol.shape.Measures
 
measurementsAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
measurementTable - Variable in class org.openscience.jmol.app.Jmol
 
MeasurementTable - Class in org.openscience.jmol.app
 
MeasurementTable(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.MeasurementTable
Constructor
measurementTable - Variable in class org.openscience.jmol.app.MeasurementTable
 
MeasurementTable.MeasurementListWindowListener - Class in org.openscience.jmol.app
 
MeasurementTable.MeasurementListWindowListener() - Constructor for class org.openscience.jmol.app.MeasurementTable.MeasurementListWindowListener
 
MeasurementTable.MeasurementTableModel - Class in org.openscience.jmol.app
 
MeasurementTable.MeasurementTableModel() - Constructor for class org.openscience.jmol.app.MeasurementTable.MeasurementTableModel
 
measurementTableModel - Variable in class org.openscience.jmol.app.MeasurementTable
 
Measures - Class in org.jmol.shape
 
Measures() - Constructor for class org.jmol.shape.Measures
 
measuresEnabled - Variable in class org.jmol.viewer.MouseManager
 
MeasuresGenerator - Class in org.jmol.export
 
MeasuresGenerator() - Constructor for class org.jmol.export.MeasuresGenerator
 
MeasuresRenderer - Class in org.jmol.shape
 
MeasuresRenderer() - Constructor for class org.jmol.shape.MeasuresRenderer
 
mediaTracker - Variable in class org.jmol.appletwrapper.AppletWrapper
 
menubar - Variable in class org.jmol.applet.Console
 
menubar - Variable in class org.openscience.jmol.app.Jmol
 
menuContents - Static variable in class org.jmol.popup.PopupResourceBundle
 
menuFile - Static variable in class org.openscience.jmol.app.Jmol
 
MENUITEM_HEIGHT - Static variable in class org.jmol.popup.JmolPopupAwt
 
MENUITEM_HEIGHT - Static variable in class org.jmol.popup.JmolPopupSwing
 
menuItems - Variable in class org.openscience.jmol.app.Jmol
 
menuListener - Variable in class org.openscience.jmol.app.DisplayPanel
 
menuStructure - Variable in class org.jmol.applet.Jmol
 
menuStructure - Static variable in class org.jmol.popup.JmolPopup
 
menuStructure - Static variable in class org.openscience.jmol.app.Jmol
 
menuText - Variable in class org.jmol.popup.JmolPopup
 
mep - Static variable in class org.jmol.viewer.Token
 
mep_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
mep_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
mep_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
MepCalculation - Class in org.jmol.quantum
 
MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
 
MepCalculationInterface - Interface in org.jmol.api
 
merge(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
 
merge(ModelSet) - Method in class org.jmol.modelset.BondCollection
 
merge(ModelSet) - Method in class org.jmol.modelset.ModelCollection
initial transfer of model data from old to new model set.
merge(JmolAdapter, Object) - Method in class org.jmol.viewer.ModelManager
 
mergeBufferPixel(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
mergeModelArrays() - Method in class org.jmol.modelset.ModelLoader
 
mergeModelSet - Variable in class org.jmol.modelset.ModelLoader
 
mergeOpaqueAndTranslucentBuffers() - Method in class org.jmol.g3d.Graphics3D
 
mergeSets(int, int) - Method in class org.jmol.jvxl.data.MeshData
 
merging - Variable in class org.jmol.modelset.ModelLoader
 
Mesh - Class in org.jmol.shape
 
Mesh() - Constructor for class org.jmol.shape.Mesh
 
Mesh(String, JmolRendererInterface, short) - Constructor for class org.jmol.shape.Mesh
 
mesh - Variable in class org.jmol.shape.MeshRenderer
 
mesh - Static variable in class org.jmol.viewer.Token
 
MeshCollection - Class in org.jmol.shape
 
MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
 
meshCount - Variable in class org.jmol.shape.MeshCollection
 
MeshData - Class in org.jmol.jvxl.data
 
MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshData - Variable in class org.jmol.jvxl.readers.VoxelReader
 
MeshDataServer - Interface in org.jmol.jvxl.api
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshDataServer - Variable in class org.jmol.jvxl.readers.VoxelReader
 
meshes - Variable in class org.jmol.shape.MeshCollection
 
meshes - Variable in class org.jmol.shapebio.BioShape
 
meshes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
MeshFileCollection - Class in org.jmol.shapesurface
 
MeshFileCollection() - Constructor for class org.jmol.shapesurface.MeshFileCollection
 
meshReady - Variable in class org.jmol.shapebio.BioShape
 
meshReady - Variable in class org.jmol.shapebio.BioShapeRenderer
 
MeshRenderer - Class in org.jmol.shape
 
MeshRenderer() - Constructor for class org.jmol.shape.MeshRenderer
 
MeshRibbon - Class in org.jmol.shapebio
 
MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
 
meshRibbon - Static variable in class org.jmol.viewer.Token
 
MeshRibbonGenerator - Class in org.jmol.export
 
MeshRibbonGenerator() - Constructor for class org.jmol.export.MeshRibbonGenerator
 
MeshRibbonRenderer - Class in org.jmol.shapebio
 
MeshRibbonRenderer() - Constructor for class org.jmol.shapebio.MeshRibbonRenderer
 
meshType - Variable in class org.jmol.shape.Mesh
 
message() - Method in class org.jmol.viewer.Eval
 
message - Variable in exception org.jmol.viewer.Eval.ScriptException
 
message - Static variable in class org.jmol.viewer.Token
 
messageQueue - Variable in class org.jmol.viewer.StatusManager
 
messageStyleChime - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
mf - Variable in class org.jmol.modelset.Molecule
 
MIDDLE - Static variable in class org.jmol.viewer.MouseManager
 
MIDDLE_RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
mil - Variable in class org.jmol.popup.JmolPopup
 
min - Static variable in class org.jmol.viewer.Token
 
MIN_AXIS_LEN - Static variable in class org.jmol.shape.Axes
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.more.MopacDataReader
 
MIN_CONE_HEIGHT - Static variable in class org.jmol.shapebio.RocketsRenderer
 
MIN_MESH_RENDER_SIZE - Static variable in class org.jmol.shapebio.BioShapeRenderer
 
min_squarable_double - Static variable in class org.jmol.minimize.Util
 
MinAtom - Class in org.jmol.minimize
 
MinAtom(int, Atom, double[], String) - Constructor for class org.jmol.minimize.MinAtom
 
minAtoms - Variable in class org.jmol.minimize.Minimizer
 
MinBond - Class in org.jmol.minimize
 
MinBond(int[], boolean, boolean) - Constructor for class org.jmol.minimize.MinBond
 
minBondDistance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minBondDistance - Variable in class org.openscience.jmol.app.PreferencesDialog
 
minBonds - Variable in class org.jmol.minimize.Minimizer
 
minBytesStandardStream - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
minDistanceForPlanarity - Static variable in class org.jmol.shapespecial.Polyhedra
 
miniLogArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
minimizationCriterion - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationOn - Variable in class org.jmol.minimize.Minimizer
 
minimizationRefresh - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationSteps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
minimizationThread - Variable in class org.jmol.minimize.Minimizer
 
minimize(int, double, BitSet) - Method in interface org.jmol.api.MinimizerInterface
 
minimize(int, double, BitSet) - Method in class org.jmol.minimize.Minimizer
 
minimize() - Method in class org.jmol.viewer.Eval
 
minimize - Static variable in class org.jmol.viewer.Token
 
Minimizer - Class in org.jmol.minimize
 
Minimizer() - Constructor for class org.jmol.minimize.Minimizer
 
minimizer - Variable in class org.jmol.viewer.Viewer
 
Minimizer.MinimizationThread - Class in org.jmol.minimize
 
Minimizer.MinimizationThread() - Constructor for class org.jmol.minimize.Minimizer.MinimizationThread
 
MinimizerInterface - Interface in org.jmol.api
 
minimizeWithoutThread() - Method in class org.jmol.minimize.Minimizer
 
MINIMUM_ELAPSED_SECONDS - Static variable in class org.jmol.appletwrapper.AppletWrapper
 
minimumHbondDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
minimumLoadSeconds - Static variable in class org.jmol.appletwrapper.WrappedAppletLoader
 
minimumPixelSelectionRadius - Static variable in class org.jmol.modelset.AtomCollection
 
minLeft - Variable in class org.jmol.bspt.Node
 
minmaxmask - Static variable in class org.jmol.viewer.Token
 
minRight - Variable in class org.jmol.bspt.Node
 
minSet - Variable in class org.jmol.jvxl.readers.Parameters
 
minSyncRepeatMs - Variable in class org.jmol.viewer.StatusManager
 
minus - Static variable in class org.jmol.viewer.Token
 
minX - Variable in class org.jmol.g3d.Sphere3D
 
minY - Variable in class org.jmol.g3d.Sphere3D
 
Miny - Variable in class org.jmol.jcamp.ZoneVisu
 
minZ - Variable in class org.jmol.g3d.Sphere3D
 
minZ - Variable in class org.jmol.modelset.Group
 
minZ - Variable in class org.jmol.shape.BallsRenderer
 
misc - Static variable in class org.jmol.viewer.Token
 
mo - Variable in class org.jmol.jvxl.readers.Parameters
 
mo(boolean) - Method in class org.jmol.viewer.Eval
 
mo - Static variable in class org.jmol.viewer.Token
 
MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
mo_occ - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
MOCalculation - Class in org.jmol.quantum
 
MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
 
MOCalculationInterface - Interface in org.jmol.api
 
moCoeff - Variable in class org.jmol.quantum.MOCalculation
 
moCoefficients - Variable in class org.jmol.jvxl.readers.Parameters
 
moCoefficients - Variable in class org.jmol.quantum.MOCalculation
 
moColorNeg - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moColorPos - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moCount - Variable in class org.jmol.adapter.readers.more.JaguarReader
 
moCount - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
moCutoff - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moData - Variable in class org.jmol.adapter.readers.more.GamessReader
 
moData - Variable in class org.jmol.adapter.readers.more.GaussianReader
 
moData - Variable in class org.jmol.adapter.readers.more.JaguarReader
 
moData - Variable in class org.jmol.adapter.readers.more.MopacDataReader
 
moData - Variable in class org.jmol.adapter.readers.more.PsiReader
 
moData - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
moData - Variable in class org.jmol.adapter.readers.more.SpartanReader
 
moData - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
moData - Variable in class org.jmol.jvxl.readers.Parameters
 
mode - Static variable in class org.jmol.viewer.Token
 
MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_COORDS_AND_RADII - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
 
moDebug - Variable in class org.jmol.shapesurface.MolecularOrbital
 
model(int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
model - Variable in class org.jmol.modelset.Chain
 
Model - Class in org.jmol.modelset
 
Model(ModelSet, int, int, String, Properties, Hashtable) - Constructor for class org.jmol.modelset.Model
 
model - Variable in class org.jmol.modelsetbio.BioPolymer
 
model - Static variable in class org.jmol.viewer.Token
 
MODEL_NO - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
modelAdapter - Variable in class org.jmol.applet.Jmol
 
modelAdapter - Variable in class org.jmol.applet.Jvm12
 
modelAdapter - Variable in class org.jmol.viewer.FileManager
 
modelAdapter - Variable in class org.jmol.viewer.Viewer
 
modelAdapter - Variable in class org.openscience.jmol.app.Jmol
 
modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
 
ModelCollection - Class in org.jmol.modelset
 
ModelCollection() - Constructor for class org.jmol.modelset.ModelCollection
 
ModelCollection.StateScript - Class in org.jmol.modelset
 
ModelCollection.StateScript(int, String, BitSet, BitSet, BitSet, String, boolean) - Constructor for class org.jmol.modelset.ModelCollection.StateScript
 
ModelCollection.Structure - Class in org.jmol.modelset
 
ModelCollection.Structure(int, String, char, int, char, int) - Constructor for class org.jmol.modelset.ModelCollection.Structure
 
modelCount - Variable in class org.jmol.modelset.ModelCollection
 
modelCount - Variable in class org.jmol.popup.JmolPopup
 
modelCount - Variable in class org.jmol.shape.MeshCollection
 
modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelCollection
 
modelFileNumbers - Variable in class org.jmol.modelset.ModelCollection
 
modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
 
modelHasVibrationVectors(int) - Method in class org.jmol.api.JmolViewer
 
modelHasVibrationVectors(int) - Method in class org.jmol.modelset.ModelCollection
 
modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
 
modelIndex - Variable in class org.jmol.adapter.smarter.Structure
 
modelIndex - Variable in class org.jmol.atomdata.AtomData
 
modelIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
modelIndex - Variable in class org.jmol.modelset.Atom
 
modelIndex - Variable in class org.jmol.modelset.Model
 
modelIndex - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
modelIndex - Variable in class org.jmol.modelset.ModelCollection.Structure
 
modelIndex - Variable in class org.jmol.modelset.Molecule
 
modelIndex - Variable in class org.jmol.popup.JmolPopup
 
modelIndex - Variable in class org.jmol.shape.Mesh
 
modelIndex - Variable in class org.jmol.shape.MeshCollection
 
modelIndex - Variable in class org.jmol.shape.Object2d
 
modelIndex - Variable in class org.jmol.shapebio.BioShape
 
modelIndex - Variable in class org.jmol.shapespecial.Dipole
 
modelIndex - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
modelIndex - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
modelIndex - Variable in class org.jmol.symmetry.SymmetryInfo
 
modelInfo - Variable in class org.jmol.popup.JmolPopup
 
modelInfo - Variable in class org.jmol.shapespecial.Draw
 
ModelLoader - Class in org.jmol.modelset
 
ModelLoader(Viewer, String) - Constructor for class org.jmol.modelset.ModelLoader
 
ModelLoader(Viewer, JmolAdapter, Object, ModelLoader, String) - Constructor for class org.jmol.modelset.ModelLoader
 
modelLoader - Variable in class org.jmol.viewer.ModelManager
 
ModelManager - Class in org.jmol.viewer
 
ModelManager(Viewer) - Constructor for class org.jmol.viewer.ModelManager
 
modelManager - Variable in class org.jmol.viewer.Viewer
 
modelName - Variable in class org.jmol.adapter.readers.more.OdysseyReader
 
modelName - Variable in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
modelName - Variable in class org.jmol.adapter.readers.more.SpartanReader
 
modelName - Variable in class org.jmol.adapter.readers.more.SpartanSmolReader
 
modelName - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
modelName - Variable in class org.jmol.atomdata.AtomData
 
modelNames - Variable in class org.jmol.modelset.ModelCollection
 
modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
modelNumberParameter(int) - Method in class org.jmol.viewer.Eval
 
modelNumbers - Variable in class org.jmol.modelset.ModelCollection
 
modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelCollection
 
modelRadius - Variable in class org.jmol.viewer.TransformManager
 
modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
 
models - Variable in class org.jmol.modelset.ModelCollection
 
modelSet - Variable in class org.jmol.modelset.Chain
 
modelSet - Variable in class org.jmol.modelset.Measurement
 
modelSet - Variable in class org.jmol.modelset.Model
 
ModelSet - Class in org.jmol.modelset
 
ModelSet() - Constructor for class org.jmol.modelset.ModelSet
 
modelSet - Variable in class org.jmol.modelset.Molecule
 
modelSet - Variable in class org.jmol.shape.Shape
 
modelSet - Variable in class org.jmol.shape.ShapeRenderer
 
modelSet - Variable in class org.jmol.smiles.PatternMatcher
 
modelSet - Variable in class org.jmol.viewer.FrameExportJmolAdapter
 
modelSet - Variable in class org.jmol.viewer.Viewer
 
modelSetAuxiliaryInfo - Variable in class org.jmol.modelset.ModelCollection
 
modelSetFileName - Variable in class org.jmol.popup.JmolPopup
 
modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
 
modelSetHasVibrationVectors() - Method in class org.jmol.viewer.Viewer
 
modelSetInfo - Variable in class org.jmol.popup.JmolPopup
 
modelSetName - Variable in class org.jmol.modelset.ModelCollection
 
modelSetName - Variable in class org.jmol.popup.JmolPopup
 
modelSetProperties - Variable in class org.jmol.modelset.ModelCollection
 
modelSetRoot - Variable in class org.jmol.popup.JmolPopup
 
modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
 
modelsOf(BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
 
modelValue(String) - Static method in class org.jmol.viewer.Compiler
 
modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
 
modelZeroBased - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
modeMultipleBond - Variable in class org.jmol.shape.SticksRenderer
 
modeMultipleBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
modifiersWhenPressed10 - Variable in class org.jmol.viewer.MouseManager10
 
moDots - Variable in class org.jmol.shapesurface.MolecularOrbital
 
MODULE - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moduleNestingLevel - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
moFieldMap - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
moFields - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
moFill - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moFrontOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moIsPositiveOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
 
Mol2Reader - Class in org.jmol.adapter.readers.more
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
 
mol2Records - Static variable in class org.jmol.adapter.smarter.Resolver
 
MoldenReader - Class in org.jmol.adapter.readers.more
A molecular structure and orbital reader for MolDen files.
MoldenReader() - Constructor for class org.jmol.adapter.readers.more.MoldenReader
 
moldenRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MolecdeleteButton - Variable in class org.openscience.jmol.app.webexport.Molecules
 
MolecList - Variable in class org.openscience.jmol.app.webexport.Molecules
 
MolecopenButton - Variable in class org.openscience.jmol.app.webexport.Molecules
 
molectohtml(int, int, File, JList, String) - Method in class org.openscience.jmol.app.webexport.Molecules
 
MolecularOrbital - Class in org.jmol.shapesurface
 
MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
 
MolecularOrbitalGenerator - Class in org.jmol.export
 
MolecularOrbitalGenerator() - Constructor for class org.jmol.export.MolecularOrbitalGenerator
 
MolecularOrbitalRenderer - Class in org.jmol.shapesurface
 
MolecularOrbitalRenderer() - Constructor for class org.jmol.shapesurface.MolecularOrbitalRenderer
 
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
MOLECULE - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
Molecule - Class in org.jmol.modelset
 
Molecule(ModelSet, int, BitSet, int, int) - Constructor for class org.jmol.modelset.Molecule
 
molecule - Static variable in class org.jmol.viewer.Token
 
MOLECULE_ATOM - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_ARRAY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_BUILTIN - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_SCALAR - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_ARRAY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_BUILTIN - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_FORMULA - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moleculeCount - Variable in class org.jmol.modelset.Model
 
moleculeCount - Variable in class org.jmol.modelset.ModelCollection
 
moleculeIndex - Variable in class org.jmol.modelset.Molecule
 
moleculeNesting - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
molecules - Variable in class org.jmol.modelset.ModelCollection
 
Molecules - Class in org.openscience.jmol.app.webexport
 
Molecules() - Constructor for class org.openscience.jmol.app.webexport.Molecules
 
molProImplementedAttributes - Static variable in class org.jmol.adapter.readers.xml.XmlMolproReader
 
MolReader - Class in org.jmol.adapter.readers.molxyz
A reader for MDLI mol and sdf files.
MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
 
moMesh - Variable in class org.jmol.shapesurface.MolecularOrbital
 
monitor() - Method in class org.jmol.viewer.Eval
 
monitor - Static variable in class org.jmol.viewer.Token
 
MonitorInputStream - Class in org.jmol.viewer
 
MonitorInputStream(InputStream, int) - Constructor for class org.jmol.viewer.MonitorInputStream
 
MonitorInputStream - Class in org.openscience.jvxl
 
MonitorInputStream(InputStream, int) - Constructor for class org.openscience.jvxl.MonitorInputStream
 
Monomer - Class in org.jmol.modelsetbio
 
Monomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.Monomer
 
monomer - Static variable in class org.jmol.viewer.Token
 
monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomerCount - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomerCount - Variable in class org.jmol.shapebio.BioShape
 
monomerCount - Variable in class org.jmol.shapebio.BioShapeRenderer
 
monomerIndex - Variable in class org.jmol.modelsetbio.Monomer
 
monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomerIndexLast - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomers - Variable in class org.jmol.shapebio.BioShape
 
monomers - Variable in class org.jmol.shapebio.BioShapeRenderer
 
moNumber - Variable in class org.jmol.shapesurface.Isosurface
 
moNumber - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moOffset(int) - Method in class org.jmol.viewer.Eval
 
MopacData - Class in org.jmol.adapter.readers.more
 
MopacData() - Constructor for class org.jmol.adapter.readers.more.MopacData
 
MopacDataReader - Class in org.jmol.adapter.readers.more
 
MopacDataReader() - Constructor for class org.jmol.adapter.readers.more.MopacDataReader
 
MopacGraphfReader - Class in org.jmol.adapter.readers.more
Reads Mopac 2007 GRAPHF output files
MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.more.MopacGraphfReader
 
MopacReader - Class in org.jmol.adapter.readers.more
Reads Mopac 93, 97 or 2002 output files, but was tested only for Mopac 93 files yet.
MopacReader() - Constructor for class org.jmol.adapter.readers.more.MopacReader
 
mopacRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
moPlane - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moResolution - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moreTokens() - Method in class org.jmol.viewer.Compiler
 
mosaicPreviewChanged() - Method in class org.openscience.jmol.app.PovrayDialog
Called when the MosaicPreview check box is modified
mosaicPreviewCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
mosaicPreviewComboEnd - Variable in class org.openscience.jmol.app.PovrayDialog
 
mosaicPreviewComboStart - Variable in class org.openscience.jmol.app.PovrayDialog
 
mosaicPreviewEnd - Variable in class org.openscience.jmol.app.PovrayDialog
 
mosaicPreviewStart - Variable in class org.openscience.jmol.app.PovrayDialog
 
moScale - Variable in class org.jmol.shapesurface.MolecularOrbital
 
motionEventNumber - Variable in class org.jmol.viewer.Viewer
 
moTitleFormat - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTranslucency - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTranslucentLevel - Variable in class org.jmol.shapesurface.MolecularOrbital
 
MOUSE_DELETE - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_MEASURE - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_NONE - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_PICK - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_POPUP_MENU - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_ROTATE - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_ROTATE_Z - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_SLAB_PLANE - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_XLATE - Static variable in class org.jmol.viewer.JmolConstants
 
MOUSE_ZOOM - Static variable in class org.jmol.viewer.JmolConstants
 
mouseClicked(long, int, int, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseClicked(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
mouseDown(Event, int, int) - Method in class org.jmol.jcamp.ZoneVisu
 
mouseDrag(Event, int, int) - Method in class org.jmol.jcamp.ZoneVisu
 
mouseDragged(long, int, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseDragged(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
mouseEntered(long, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseEntered(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
mouseExited(long, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseExited(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
MouseManager - Class in org.jmol.viewer
 
MouseManager(Viewer) - Constructor for class org.jmol.viewer.MouseManager
 
mouseManager - Variable in class org.jmol.viewer.Viewer
 
MouseManager.HoverWatcher - Class in org.jmol.viewer
 
MouseManager.HoverWatcher() - Constructor for class org.jmol.viewer.MouseManager.HoverWatcher
 
MouseManager10 - Class in org.jmol.viewer
 
MouseManager10(Component, Viewer) - Constructor for class org.jmol.viewer.MouseManager10
 
MouseManager11 - Class in org.jmol.viewer
 
MouseManager11(Component, Viewer) - Constructor for class org.jmol.viewer.MouseManager11
 
MouseManager14 - Class in org.jmol.viewer
 
MouseManager14(Component, Viewer) - Constructor for class org.jmol.viewer.MouseManager14
 
mouseMoved(long, int, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseMoved(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
mouseMovedTime - Variable in class org.jmol.viewer.MouseManager
 
mouseMovedX - Variable in class org.jmol.viewer.MouseManager
 
mouseMovedY - Variable in class org.jmol.viewer.MouseManager
 
mousePressed(long, int, int, int, boolean) - Method in class org.jmol.viewer.MouseManager
 
mousePressed(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
mouseReleased(long, int, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseReleased(MouseEvent) - Method in class org.jmol.viewer.MouseManager11
 
mouseWheel(long, int, int) - Method in class org.jmol.viewer.MouseManager
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.viewer.MouseManager14
 
MouseWrapper11 - Class in org.jmol.viewer
 
MouseWrapper11() - Constructor for class org.jmol.viewer.MouseWrapper11
 
MouseWrapper14 - Class in org.jmol.viewer
 
MouseWrapper14() - Constructor for class org.jmol.viewer.MouseWrapper14
 
movableX - Variable in class org.jmol.shape.Object2d
 
movableXPercent - Variable in class org.jmol.shape.Object2d
 
movableY - Variable in class org.jmol.shape.Object2d
 
movableYPercent - Variable in class org.jmol.shape.Object2d
 
movableZ - Variable in class org.jmol.shape.Object2d
 
movableZPercent - Variable in class org.jmol.shape.Object2d
 
move() - Method in class org.jmol.viewer.Eval
 
move - Static variable in class org.jmol.viewer.Token
 
move(Vector3f, float, Vector3f, float, float, int) - Method in class org.jmol.viewer.TransformManager
 
move(Vector3f, float, Vector3f, float, float, int) - Method in class org.jmol.viewer.Viewer
 
move2D(DrawMesh, int[], int, int, int, boolean) - Method in class org.jmol.shapespecial.Draw
 
Move_Points_To_Tableau() - Method in class org.jmol.jcamp.Visua
 
movepict(String) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
moveRotationCenter(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
 
moveto() - Method in class org.jmol.viewer.Eval
 
moveto - Static variable in class org.jmol.viewer.Token
 
moveTo(float, Point3f, Point3f, float, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager
 
moveTo(float, Matrix3f, Point3f, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager
 
moveTo(float, Point3f, Point3f, float, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.Viewer
 
moveTo(float, Matrix3f, Point3f, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.Viewer
 
moveToText - Variable in class org.jmol.viewer.StateManager.Orientation
 
movetoTime - Variable in class org.openscience.jmol.app.webexport.Test
 
moveUpdate(float) - Method in class org.jmol.viewer.Viewer
 
MSAT0 - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
mTemp - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
mul(float) - Method in class org.jmol.util.Quaternion
 
mul(Quaternion) - Method in class org.jmol.util.Quaternion
 
mul - Static variable in class org.jmol.viewer.Token
 
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JmolConstants
 
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JmolConstants
 
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JmolConstants
 
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JmolConstants
 
multiplier - Variable in class org.jmol.viewer.TransformManager11
 
Multx - Variable in class org.jmol.jcamp.ZoneVisu
 
Multy - Variable in class org.jmol.jcamp.ZoneVisu
 
mustRender - Variable in class org.jmol.viewer.Viewer
 
mustRenderFlag() - Method in class org.jmol.viewer.Viewer
 
My_Thread - Variable in class org.jmol.jcamp.Visua
 
My_ZoneVisu - Variable in class org.jmol.jcamp.Visua
 
myAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
myColorPt - Variable in class org.jmol.shapesurface.LcaoCartoon
 
myColorPt - Variable in class org.jmol.shapesurface.MolecularOrbital
 
myDistanceFactor - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
myFaceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
myIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
myMask - Variable in class org.jmol.shape.Sticks
 
myStatusListener - Variable in class org.jmol.applet.Jmol
 
myType - Variable in class org.jmol.shape.FontLineShape
 
myType - Variable in class org.jmol.shape.MeshCollection
 
myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
 
myVisibilityFlag - Variable in class org.jmol.shape.Shape
 
myVisibilityFlag - Variable in class org.jmol.shape.ShapeRenderer
 

N

N - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
N - Static variable in class org.jmol.util.DCT
DCT Block Size - default 8
N1 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N3 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N7 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N9 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
n_bits - Variable in class org.jmol.export.image.GifEncoder
 
nada - Static variable in class org.jmol.viewer.Token
 
nAdditionalMATsectors - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
nAltLocs - Variable in class org.jmol.modelset.Model
 
name - Variable in class org.jmol.export._MayaExporter
 
name - Variable in class org.jmol.symmetry.PointGroup
 
name - Variable in class org.jmol.viewer.Function
 
name - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
Name_Load_Now_Html - Variable in class org.jmol.jcamp.ZoneVisu
 
nameAsGiven - Variable in class org.jmol.viewer.FileManager
 
nameAsGivenInThread - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
nameOf(int) - Static method in class org.jmol.viewer.Token
 
names - Variable in class org.jmol.viewer.Function
 
namesAsGivenInThread - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
nAtoms - Variable in class org.jmol.adapter.readers.more.CsfReader
 
nAtoms - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
nAtoms - Variable in class org.jmol.modelset.Molecule
 
nAtoms - Variable in class org.jmol.symmetry.PointGroup
 
naturalIsotopes - Static variable in class org.jmol.viewer.JmolConstants
 
NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager11
 
NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager11
 
navCenter - Variable in class org.jmol.viewer.StateManager.Orientation
 
navDepth - Variable in class org.jmol.viewer.StateManager.Orientation
 
navigate() - Method in class org.jmol.viewer.Eval
 
navigate - Static variable in class org.jmol.viewer.Token
 
navigate(int, int) - Method in class org.jmol.viewer.TransformManager
entry point for keyboard-based navigation
navigate(float, Point3f) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navigate(float, Vector3f, float) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navigate(float, Point3f[], float[], int, int) - Method in class org.jmol.viewer.TransformManager
scripted navigation
navigate(float, Point3f[][]) - Method in class org.jmol.viewer.TransformManager
follows a path guided by orientation and offset vectors (as Point3fs)
navigate(int, int) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Vector3f, float) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f[][]) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f[], float[], int, int) - Method in class org.jmol.viewer.TransformManager11
 
navigate(float, Point3f[][], Point3f[], float[], int, int) - Method in class org.jmol.viewer.TransformManager11
 
navigate(int, int) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Point3f[], float[], int, int) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Point3f) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Point3f[][]) - Method in class org.jmol.viewer.Viewer
 
navigate(float, Vector3f, float) - Method in class org.jmol.viewer.Viewer
 
navigateTo(float, Vector3f, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager11
 
navigating - Variable in class org.jmol.viewer.TransformManager
 
navigationCenter - Variable in class org.jmol.viewer.TransformManager
 
navigationMode - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navigationMode - Variable in class org.jmol.viewer.StateManager.Orientation
 
navigationOffset - Variable in class org.jmol.viewer.TransformManager
 
navigationPeriodic - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
 
navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager11
 
navigationSpeed - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
navMode - Variable in class org.jmol.viewer.TransformManager11
 
navTranslate(float, Point3f) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navTranslate(float, Point3f) - Method in class org.jmol.viewer.TransformManager11
 
navTranslate(float, Point3f) - Method in class org.jmol.viewer.Viewer
 
navTranslatePercent(float, float, float) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navTranslatePercent(float, float, float) - Method in class org.jmol.viewer.TransformManager11
 
navTranslatePercent(float, float, float) - Method in class org.jmol.viewer.Viewer
 
NAVY - Static variable in class org.jmol.g3d.Graphics3D
 
nAxes - Variable in class org.jmol.symmetry.PointGroup
 
Nb_Clickable_Peaks - Variable in class org.jmol.jcamp.ZoneVisu
 
nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
 
nBalls - Variable in class org.jmol.export._MayaExporter
 
nBits - Variable in class org.jmol.g3d.Line3D
 
nbitsets - Variable in class org.jmol.shapespecial.Draw
 
nbLignes - Variable in class org.jmol.jcamp.Visua
 
nbLignes - Variable in class org.jmol.jcamp.ZoneVisu
 
nBlock - Variable in class org.jmol.jvxl.readers.XplorReader
 
nBonds - Variable in class org.jmol.adapter.readers.more.CsfReader
 
nBonds - Variable in class org.jmol.minimize.MinAtom
 
nBondsDisplayed - Variable in class org.jmol.modelset.Atom
 
Nbpoints - Variable in class org.jmol.jcamp.Visua
 
Nbpoints - Variable in class org.jmol.jcamp.ZoneVisu
 
Nbpoints_a_tracer - Variable in class org.jmol.jcamp.ZoneVisu
 
nBytes - Variable in class org.jmol.export._PovrayExporter
 
nBytes - Variable in class org.jmol.jvxl.data.JvxlData
 
nBytes - Variable in class org.jmol.jvxl.readers.VoxelReader
 
nBytesUnicodeName - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
nCached - Variable in class org.jmol.g3d.Line3D
 
nContourMax - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
nContourMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
nContours - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
nContours - Variable in class org.jmol.jvxl.data.JvxlData
 
nContours - Variable in class org.jmol.jvxl.readers.Parameters
 
nContoursSpecified - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
nCyl - Variable in class org.jmol.export._MayaExporter
 
nDataPoints - Variable in class org.jmol.jvxl.readers.VoxelReader
 
nDegrees - Variable in class org.jmol.viewer.TransformManager.SpinThread
 
nDirEntriesperSector - Variable in class org.jmol.util.CompoundDocument
 
nearbyAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
nEdges - Variable in class org.jmol.jvxl.data.JvxlData
 
needPopupMenu - Variable in class org.jmol.applet.Jmol
 
needToApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
needToCompleteInitialization - Variable in class org.jmol.appletwrapper.AppletWrapper
 
needToFill - Variable in class org.jmol.g3d.Hermite3D
 
negate() - Method in class org.jmol.util.Quaternion
 
negativeAtomCount - Variable in class org.jmol.adapter.readers.more.CubeReader
 
negativeAtomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
neighborCenters - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborIndices - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborPlusProbeRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborVertexesArrays - Static variable in class org.jmol.g3d.Normix3D
 
neighborVertexesArrays - Static variable in class org.jmol.geodesic.Geodesic
 
neighborVertexesIcosahedron - Static variable in class org.jmol.geodesic.Geodesic
 
nElements - Variable in class org.jmol.modelset.Molecule
 
nError - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
nEscape - Static variable in class org.jmol.util.Escape
 
newAction - Static variable in class org.openscience.jmol.app.Jmol
 
newAntialiasing - Variable in class org.jmol.g3d.Graphics3D
 
newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newComputedMenu(String, String) - Method in class org.jmol.popup.JmolPopupAwt
 
newComputedMenu(String, String) - Method in class org.jmol.popup.JmolPopupSwing
 
newDialog(boolean) - Static method in class org.jmol.applet.Jvm12
 
newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.GuiMap
 
newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.GuiMap
 
newJMenu(String) - Method in class org.jmol.applet.GuiMap
 
newJMenu(String) - Method in class org.openscience.jmol.app.GuiMap
 
newJMenuItem(String) - Method in class org.jmol.applet.GuiMap
 
newJMenuItem(String) - Method in class org.openscience.jmol.app.GuiMap
 
newJmolPopup(JmolViewer, boolean, String, boolean) - Static method in class org.jmol.popup.JmolPopup
 
newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.GuiMap
 
newline - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
newMenu(String, String) - Method in class org.jmol.popup.JmolPopup
 
newMenu(String, String) - Method in class org.jmol.popup.JmolPopupAwt
 
newMenu(String, String) - Method in class org.jmol.popup.JmolPopupSwing
 
newNavigationCenter() - Method in class org.jmol.viewer.TransformManager11
We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
newPoint(int, Point3f, Point3f, int, int, int) - Method in class org.jmol.symmetry.SpaceGroup
 
newPoint(Point3f, Point3f, int, int, int) - Method in class org.jmol.symmetry.SymmetryOperation
 
newRockets - Variable in class org.jmol.shapebio.CartoonRenderer
 
newScale - Variable in class org.jmol.shapespecial.Draw
 
newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
newSpaceGroupPoint(int, Point3f, Point3f, int, int, int) - Method in interface org.jmol.api.SymmetryInterface
 
newSpaceGroupPoint(int, Point3f, Point3f, int, int, int) - Method in class org.jmol.symmetry.Symmetry
 
newSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
newVolumeData() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newwinAction - Static variable in class org.openscience.jmol.app.Jmol
 
newWindowHeight - Variable in class org.jmol.g3d.Graphics3D
 
newWindowWidth - Variable in class org.jmol.g3d.Graphics3D
 
next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
next - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
next() - Method in interface org.jmol.modelset.AtomIndexIterator
 
next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
next() - Method in class org.jmol.modelset.AtomIteratorWithinSet
 
next() - Method in interface org.jmol.modelset.BondIterator
 
next() - Method in class org.jmol.modelset.BondIteratorSelected
 
next - Variable in class org.jmol.shapesurface.MeshFileCollection
 
next - Variable in class org.jmol.util.Int2IntHash.Entry
 
next - Static variable in class org.jmol.viewer.Token
 
NEXT - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
nextCommand - Variable in class org.jmol.util.CommandHistory
Position of the next command.
nextElement() - Method in class org.jmol.bspt.CubeIterator
normal iterator method
nextIndex() - Method in interface org.jmol.modelset.BondIterator
 
nextIndex() - Method in class org.jmol.modelset.BondIteratorSelected
 
nextMeasure(int, int, Vector, Measurement, int, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
 
nextRandom8Bit() - Static method in class org.jmol.g3d.Shade3D
Implements RANDU algorithm for random noise in lighting/shading.
nextToken() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
assume that hasMoreTokens() has been called and that ich is pointing at a non-white character.
nextVoxel() - Method in class org.jmol.jvxl.readers.JaguarReader
read one value per line
nextVoxel() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.XplorReader
 
nf - Variable in class org.jmol.shape.UccageRenderer
 
nf - Variable in class org.jmol.shapesurface.MolecularOrbitalRenderer
 
nfformat(float) - Method in class org.jmol.shape.UccageRenderer
 
nFound - Variable in class org.jmol.g3d.Line3D
 
nFrankList - Variable in class org.jmol.popup.JmolPopup
 
nGaussians - Variable in class org.jmol.adapter.readers.more.CsfReader
 
nhChecked - Variable in class org.jmol.modelsetbio.AminoMonomer
 
nHits - Variable in class org.jmol.viewer.TransformManager11
 
nidentifiers - Variable in class org.jmol.shapespecial.Draw
 
nImage - Variable in class org.jmol.export._PovrayExporter
 
nIn - Static variable in class org.jmol.g3d.Sphere3D
 
nInsertions - Variable in class org.jmol.modelset.Model
 
nInside - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
nIntPerSector - Variable in class org.jmol.util.CompoundDocument
 
nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
nLatticeTypes - Static variable in class org.jmol.symmetry.Translation
 
nLCAO - Variable in class org.jmol.shapesurface.Isosurface
 
nMatrixElements - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
nModules - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
nmr_observe_frequency - Variable in class org.jmol.jcamp.Visua
 
NN - Static variable in class org.jmol.util.DCT
 
NO_ALPHA - Static variable in class org.jmol.export.image.PngEncoder
Constant specifying that alpha channel should not be encoded.
NO_ANISOTROPY - Static variable in class org.jmol.jvxl.readers.Parameters
 
noArgs - Static variable in class org.jmol.viewer.Token
 
noAutoBond - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
noCross - Variable in class org.jmol.shapespecial.Dipole
 
Node - Class in org.jmol.bspt
Nodes of the bspt.
Node(Bspt, int, Leaf) - Constructor for class org.jmol.bspt.Node
 
nodots - Static variable in class org.jmol.viewer.Token
 
noeval - Static variable in class org.jmol.viewer.Token
 
nofill - Static variable in class org.jmol.viewer.Token
 
noHead - Variable in class org.jmol.shapespecial.Draw
 
nohead - Variable in class org.jmol.shapespecial.DrawMesh
 
NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
 
NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
 
nomesh - Static variable in class org.jmol.viewer.Token
 
NONE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
none - Static variable in class org.jmol.viewer.Token
 
noneSelected - Variable in class org.jmol.viewer.Viewer
 
NONPOLY_COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
NONPOLY_ENTITY_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
NONPOLY_NAME - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
nonpolyFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
nOps - Variable in class org.jmol.symmetry.PointGroup
 
nOrbitals - Variable in class org.jmol.adapter.readers.more.MopacDataReader
 
norm - Variable in class org.jmol.shapebio.BioShapeRenderer
 
normal - Static variable in class org.jmol.viewer.Token
 
normalizeTwelfths(float) - Method in class org.jmol.symmetry.SymmetryOperation
 
normalMode - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
normalOrAxis - Variable in class org.jmol.symmetry.PointGroup.Operation
 
normix3d - Variable in class org.jmol.g3d.Graphics3D
 
Normix3D - Class in org.jmol.g3d
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix3D() - Constructor for class org.jmol.g3d.Normix3D
 
NORMIX_GEODESIC_LEVEL - Static variable in class org.jmol.g3d.Normix3D
 
normixCount - Static variable in class org.jmol.g3d.Normix3D
 
normixes - Variable in class org.jmol.shape.Mesh
 
normixes - Variable in class org.jmol.shape.MeshRenderer
 
normixes - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
normixesT - Variable in class org.jmol.shapespecial.Polyhedra
 
notClipped - Variable in class org.jmol.g3d.Cylinder3D
 
notfrontonly - Static variable in class org.jmol.viewer.Token
 
notifyAtomPicked(String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
notifyBackgroundChange(int) - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
notifyBufferReady() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
notifyCallback(int, Object[]) - Method in interface org.jmol.api.JmolStatusListener
 
notifyCallback(int, Object[]) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyCallback(int, Object[]) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
notifyEnabled(int) - Method in interface org.jmol.api.JmolStatusListener
 
notifyEnabled(int) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyEnabled(int) - Method in class org.jmol.viewer.StatusManager
 
notifyEnabled(int) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
notifyEndOfRendering() - Method in class org.jmol.g3d.Awt3D
 
notifyEndOfRendering() - Method in class org.jmol.g3d.Platform3D
 
notifyFileLoaded(String, String, String, String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
notifyFileOpen(String) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
notifyFrameChanged(int, int, int) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
notifyMinimizationStatus(String) - Method in class org.jmol.viewer.StatusManager
 
notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
 
notifyScriptStart() - Method in class org.openscience.jmol.app.ScriptWindow
 
notifyScriptTermination() - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notifyScriptTermination() - Method in class org.openscience.jmol.app.ScriptWindow
 
notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySync(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
notionalUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
notionalUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
notionalUnitcell - Variable in class org.jmol.symmetry.UnitCell
 
notionalUnitcellTags - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
notriangles - Static variable in class org.jmol.viewer.Token
 
nOut - Static variable in class org.jmol.g3d.Sphere3D
 
nOutside - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
NP - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
nParameters - Variable in class org.jmol.viewer.Function
 
nPoints - Variable in class org.jmol.shapespecial.Draw
 
nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsX - Variable in class org.jmol.jvxl.readers.VoxelReader
 
nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsY - Variable in class org.jmol.jvxl.readers.VoxelReader
 
nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsZ - Variable in class org.jmol.jvxl.readers.VoxelReader
 
nRead - Variable in class org.jmol.jvxl.readers.XplorReader
 
nRotations - Variable in class org.jmol.symmetry.HallInfo
 
nSATsectors - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
nSemiSkip - Variable in class org.jmol.viewer.Compiler
 
nSets - Variable in class org.jmol.jvxl.data.MeshData
 
nSets - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
nShortSectorsPerStandardSector - Variable in class org.jmol.util.CompoundDocument
 
nSlaters - Variable in class org.jmol.adapter.readers.more.CsfReader
 
nSquares - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
nSurfaceAtoms - Variable in class org.jmol.modelset.AtomCollection
 
nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
 
nSurfaces - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nText - Variable in class org.jmol.export._PovrayExporter
 
nThisValue - Variable in class org.jmol.jvxl.readers.JvxlReader
 
nThrough - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
nTrajectories - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
nucleic - Static variable in class org.jmol.viewer.Token
 
NucleicMonomer - Class in org.jmol.modelsetbio
 
NucleicMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.NucleicMonomer
 
NucleicPolymer - Class in org.jmol.modelsetbio
 
NucleicPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.NucleicPolymer
 
nullGroup - Variable in class org.jmol.modelset.ModelLoader
 
nullModelSetName - Variable in class org.jmol.popup.JmolPopup
 
nullNeighbor - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
number - Variable in class org.jmol.smiles.SmilesAtom
 
numberOfClickablePeaks - Variable in class org.jmol.jcamp.data.GraphControlData
 
NumberOfComponents - Variable in class org.jmol.util.JpegInfo
 
numberOutOfRange(float, float) - Method in class org.jmol.viewer.Eval
 
numCached - Variable in class org.jmol.modelset.BondCollection
 
NumericDataUtils - Class in org.jmol.jcamp.utils
 
NumericDataUtils() - Constructor for class org.jmol.jcamp.utils.NumericDataUtils
 
NumOfACTables - Variable in class org.jmol.util.Huffman
 
NumOfDCTables - Variable in class org.jmol.util.Huffman
 
numSet - Variable in class org.jmol.modelset.MeasurementPending
 
numWindows - Static variable in class org.openscience.jmol.app.Jmol
 
nUnique - Static variable in class org.jmol.symmetry.PointGroup
 
nUnnamed - Variable in class org.jmol.shape.MeshCollection
 
nValue(Token) - Static method in class org.jmol.viewer.Token
 
nVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
nVibrations - Variable in class org.jmol.adapter.readers.more.CsfReader
 
NWChemReader - Class in org.jmol.adapter.readers.more
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
NWChemReader() - Constructor for class org.jmol.adapter.readers.more.NWChemReader
 
nwchemRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 

O

O - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
O1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O3Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O5Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
 
OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
 
objCls1 - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
objCls2 - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
objColors - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Object2d - Class in org.jmol.shape
 
Object2d() - Constructor for class org.jmol.shape.Object2d
 
Object2d(Viewer, Graphics3D, String, short, int, int, float) - Constructor for class org.jmol.shape.Object2d
 
Object2dShape - Class in org.jmol.shape
 
Object2dShape() - Constructor for class org.jmol.shape.Object2dShape
 
objectNameList - Static variable in class org.jmol.viewer.StateManager
 
objectNameParameter(int) - Method in class org.jmol.viewer.Eval
 
objectOf(DefaultListModel, Object) - Static method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
objects - Variable in class org.jmol.shape.Object2dShape
 
objID1 - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
objID2 - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
objMad - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
objStateOn - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
obtainBufferForClient() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
obtainScreenBuffer() - Method in class org.jmol.g3d.Platform3D
 
occupancies - Variable in class org.jmol.adapter.readers.more.GamessUKReader
 
occupancies - Variable in class org.jmol.modelset.AtomCollection
 
OCCUPANCY - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
occupancy - Variable in class org.jmol.adapter.smarter.Atom
 
occupancy - Static variable in class org.jmol.viewer.Token
 
octantPoints - Variable in class org.jmol.g3d.Sphere3D
 
octants - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
odysseyImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
OdysseyReader - Class in org.jmol.adapter.readers.more
 
OdysseyReader() - Constructor for class org.jmol.adapter.readers.more.OdysseyReader
 
OdysseyXMLReader - Class in org.jmol.adapter.readers.more
 
OdysseyXMLReader() - Constructor for class org.jmol.adapter.readers.more.OdysseyXMLReader
 
off - Static variable in class org.jmol.viewer.Token
 
officialRelease - Static variable in class org.jmol.viewer.JmolConstants
 
offset - Variable in class org.jmol.shapespecial.DipolesRenderer
 
offset - Variable in class org.jmol.shapespecial.Draw
 
offset(Vector3f) - Method in class org.jmol.shapespecial.DrawMesh
 
offsetAfterPrompt - Variable in class org.openscience.jmol.app.ConsoleDocument
 
offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
 
offsetCenter(Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
offsetPbufBeginLine - Variable in class org.jmol.g3d.Sphere3D
 
offsetPercent - Variable in class org.jmol.shapespecial.Dipole
 
offsets - Variable in class org.jmol.modelsetbio.Monomer
 
offsets - Variable in class org.jmol.shape.Labels
 
offsetSide - Variable in class org.jmol.shapespecial.Dipole
 
offsetX - Variable in class org.jmol.shape.Object2d
 
offsetY - Variable in class org.jmol.shape.Object2d
 
Ok - Variable in class org.jmol.jcamp.SaisieDlg
 
ok() - Method in class org.openscience.jmol.app.PreferencesDialog
 
okButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
okButton - Variable in class org.openscience.jmol.app.RecentFilesDialog
 
OKPressed() - Method in class org.openscience.jmol.app.AboutDialog
 
OKPressed() - Method in class org.openscience.jmol.app.HelpDialog
 
OKPressed() - Method in class org.openscience.jmol.app.WhatsNewDialog
 
OkStatus - Variable in class org.jmol.jcamp.SaisieDlg
 
OLIVE - Static variable in class org.jmol.g3d.Graphics3D
 
omega - Variable in class org.jmol.modelset.Group
 
on - Static variable in class org.jmol.viewer.Token
 
oneFifth - Static variable in class org.jmol.geodesic.Geodesic
 
oneTenth - Static variable in class org.jmol.geodesic.Geodesic
 
only - Static variable in class org.jmol.viewer.Token
 
oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
opAnd - Static variable in class org.jmol.viewer.Token
 
opaque - Static variable in class org.jmol.viewer.Token
 
OPAQUE_MASK - Static variable in class org.jmol.g3d.Graphics3D
 
openAction - Static variable in class org.openscience.jmol.app.Jmol
 
openBufferedReader(String, String, BufferedReader, Hashtable) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
openBufferedReader(String, String, BufferedReader, Hashtable) - Method in class org.jmol.api.JmolAdapter
Associate a clientFile object with a bufferedReader.
openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, BufferedReader, Hashtable) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader() - Method in class org.jmol.viewer.FileManager.FileOpenThread
 
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.viewer.FileManager
 
openBufferedReaders(JmolFileReaderInterface, String[], String[], Hashtable[]) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
openBufferedReaders(JmolFileReaderInterface, String[], String[], Hashtable[]) - Method in class org.jmol.api.JmolAdapter
Associate a clientFile object with an array of BufferedReader.
openChooser - Static variable in class org.jmol.export.dialog.Dialog
 
openClientFile(String, String, Object) - Method in class org.jmol.api.JmolViewer
 
openClientFile(String, String, Object) - Method in class org.jmol.viewer.Viewer
 
openDialog - Variable in class org.jmol.jcamp.Visua
 
openDOM(Object) - Method in class org.jmol.api.JmolSimpleViewer
 
openDOM(Object) - Method in class org.jmol.viewer.FileManager
 
openDOM(Object) - Method in class org.jmol.viewer.Viewer
 
openDOMReader(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
openDOMReader(Object) - Method in class org.jmol.api.JmolAdapter
 
openErrorMessage - Variable in class org.jmol.viewer.FileManager
 
openFile(String) - Method in class org.jmol.api.JmolSimpleViewer
 
openFile(String, Hashtable, String, boolean) - Method in class org.jmol.viewer.FileManager
 
openFile(String) - Method in class org.jmol.viewer.Viewer
 
openFile(String, Hashtable, String, boolean) - Method in class org.jmol.viewer.Viewer
 
openFilePreview - Variable in class org.openscience.jmol.app.PreferencesDialog
 
openFiles(String, String[], String, boolean) - Method in class org.jmol.viewer.FileManager
 
openFiles(String, String[]) - Method in class org.jmol.viewer.Viewer
 
openFiles(String, String[], String, boolean) - Method in class org.jmol.viewer.Viewer
 
openPreview - Variable in class org.jmol.export.dialog.Dialog
 
openReader(String, String, Reader) - Method in class org.jmol.api.JmolViewer
 
openReader(String, String, Reader) - Method in class org.jmol.viewer.FileManager
not used in Jmol project
openReader(String, String, Reader) - Method in class org.jmol.viewer.Viewer
Opens the file, given the reader.
openStringInline(String) - Method in class org.jmol.api.JmolSimpleViewer
 
openStringInline(String, Hashtable, boolean) - Method in class org.jmol.viewer.FileManager
 
openStringInline(String) - Method in class org.jmol.viewer.Viewer
 
openStringInline(String, Hashtable, boolean) - Method in class org.jmol.viewer.Viewer
 
openStringReaders() - Method in class org.jmol.viewer.FileManager.FilesOpenThread
 
openStringsInline(String[], Hashtable, boolean) - Method in class org.jmol.viewer.FileManager
 
openStringsInline(String[], Hashtable, boolean) - Method in class org.jmol.viewer.Viewer
 
openurlAction - Static variable in class org.openscience.jmol.app.Jmol
 
openZipFiles(InputStream, String, String[], Hashtable, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
openZipFiles(InputStream, String, String[], Hashtable, boolean) - Method in class org.jmol.api.JmolAdapter
 
openZipStream(String, ZipInputStream) - Method in class org.jmol.viewer.FileManager.FileOpenThread
 
opEQ - Static variable in class org.jmol.viewer.Token
 
operate() - Method in class org.jmol.viewer.Eval.Rpn
 
OPERATION_IMPROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_INVERSION_CENTER - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_PLANE - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_PROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
 
operationCount - Variable in class org.jmol.symmetry.SpaceGroup
 
operations - Variable in class org.jmol.symmetry.SpaceGroup
 
opGE - Static variable in class org.jmol.viewer.Token
 
opGT - Static variable in class org.jmol.viewer.Token
 
opLE - Static variable in class org.jmol.viewer.Token
 
opLT - Static variable in class org.jmol.viewer.Token
 
opNE - Static variable in class org.jmol.viewer.Token
 
opNot - Static variable in class org.jmol.viewer.Token
 
opOr - Static variable in class org.jmol.viewer.Token
 
oPt - Variable in class org.jmol.viewer.Eval.Rpn
 
opToggle - Static variable in class org.jmol.viewer.Token
 
optParameterAsString(int) - Method in class org.jmol.viewer.Eval
 
opXor - Static variable in class org.jmol.viewer.Token
 
ORANGE - Static variable in class org.jmol.g3d.Graphics3D
 
OrbdeleteButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
orbitals - Variable in class org.jmol.adapter.readers.more.GamessReader
 
orbitals - Variable in class org.jmol.adapter.readers.more.GaussianReader
 
orbitals - Variable in class org.jmol.adapter.readers.more.JaguarReader
 
orbitals - Variable in class org.jmol.adapter.readers.more.MopacDataReader
 
orbitals - Variable in class org.jmol.adapter.readers.more.PsiReader
 
orbitals - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
Orbitals - Class in org.openscience.jmol.app.webexport
 
Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
 
OrbList - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
OrbopenButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
orbtohtml(int, int, File, String, JList, String) - Method in class org.openscience.jmol.app.webexport.Orbitals
 
order - Variable in class org.jmol.adapter.smarter.Bond
 
order - Variable in class org.jmol.modelset.Bond
 
order - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
order - Variable in class org.jmol.symmetry.PointGroup.Operation
 
order - Variable in class org.jmol.viewer.StateManager.Connection
 
ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
 
org.jmol.adapter.readers.cifpdb - package org.jmol.adapter.readers.cifpdb
 
org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
 
org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
 
org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
 
org.jmol.adapter.smarter - package org.jmol.adapter.smarter
 
org.jmol.api - package org.jmol.api
 
org.jmol.applet - package org.jmol.applet
 
org.jmol.appletwrapper - package org.jmol.appletwrapper
 
org.jmol.atomdata - package org.jmol.atomdata
 
org.jmol.bspt - package org.jmol.bspt
Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
org.jmol.export - package org.jmol.export
 
org.jmol.export.dialog - package org.jmol.export.dialog
 
org.jmol.export.image - package org.jmol.export.image
 
org.jmol.g3d - package org.jmol.g3d
Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
org.jmol.geodesic - package org.jmol.geodesic
 
org.jmol.i18n - package org.jmol.i18n
 
org.jmol.jcamp - package org.jmol.jcamp
 
org.jmol.jcamp.data - package org.jmol.jcamp.data
 
org.jmol.jcamp.utils - package org.jmol.jcamp.utils
 
org.jmol.jvxl.api - package org.jmol.jvxl.api
 
org.jmol.jvxl.calc - package org.jmol.jvxl.calc
 
org.jmol.jvxl.data - package org.jmol.jvxl.data
 
org.jmol.jvxl.readers - package org.jmol.jvxl.readers
 
org.jmol.minimize - package org.jmol.minimize
 
org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
 
org.jmol.modelset - package org.jmol.modelset
 
org.jmol.modelsetbio - package org.jmol.modelsetbio
 
org.jmol.popup - package org.jmol.popup
 
org.jmol.quantum - package org.jmol.quantum
 
org.jmol.shape - package org.jmol.shape
 
org.jmol.shapebio - package org.jmol.shapebio
 
org.jmol.shapespecial - package org.jmol.shapespecial
 
org.jmol.shapesurface - package org.jmol.shapesurface
 
org.jmol.smiles - package org.jmol.smiles
Provides SMILES parsing Functionality.
org.jmol.symmetry - package org.jmol.symmetry
 
org.jmol.util - package org.jmol.util
 
org.jmol.viewer - package org.jmol.viewer
 
org.openscience.jmol.app - package org.openscience.jmol.app
 
org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
 
org.openscience.jvxl - package org.openscience.jvxl
 
orientation - Variable in class org.jmol.modelset.Model
 
orientation - Static variable in class org.jmol.viewer.Token
 
origin - Variable in class org.jmol.adapter.readers.more.CubeReader
 
origin - Variable in class org.jmol.jvxl.data.VolumeData
 
origin - Variable in class org.jmol.shapespecial.Dipole
 
originalSystemProperties - Variable in class org.openscience.jmol.app.PreferencesDialog
 
originBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
originPoint - Variable in class org.jmol.shape.Axes
 
originScreen - Variable in class org.jmol.shape.AxesRenderer
 
os - Variable in class org.jmol.export._Exporter
 
oStack - Variable in class org.jmol.viewer.Eval.Rpn
 
OT - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
otherAtoms - Variable in class org.jmol.shapespecial.Polyhedra
 
out - Variable in class org.jmol.export.image.ImageEncoder
 
output - Variable in class org.jmol.applet.Console
 
output(String) - Method in class org.jmol.applet.Console
 
output(String, AttributeSet) - Method in class org.jmol.applet.Console
 
output - Variable in class org.jmol.export._Exporter
 
output(String) - Method in class org.jmol.export._PovrayExporter
 
output(String) - Method in class org.jmol.export._VrmlExporter
 
output(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
outputAlphaCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
outputBeforePrompt(String, SimpleAttributeSet) - Method in class org.openscience.jmol.app.ConsoleDocument
 
outputBuffer - Variable in class org.jmol.viewer.Eval.Context
 
outputBuffer - Variable in class org.jmol.viewer.Eval
 
outputBuffer - Variable in class org.jmol.viewer.StatusManager
 
outputDocument - Variable in class org.jmol.applet.Console
 
outputEcho(String) - Method in class org.openscience.jmol.app.ConsoleDocument
 
outputEcho(String) - Method in class org.openscience.jmol.app.ConsoleTextPane
 
outputError(String) - Method in class org.openscience.jmol.app.ConsoleDocument
 
outputError(String) - Method in class org.openscience.jmol.app.ConsoleTextPane
 
outputErrorForeground(String) - Method in class org.openscience.jmol.app.ConsoleDocument
 
outputErrorForeground(String) - Method in class org.openscience.jmol.app.ConsoleTextPane
 
outputExtension - Variable in class org.openscience.jmol.app.PovrayDialog
 
outputFileName - Variable in class org.jmol.applet.Jvm12
 
outputFileType - Variable in class org.openscience.jmol.app.PovrayDialog
 
outputFormatChanged() - Method in class org.openscience.jmol.app.PovrayDialog
Called when the OutputFormat check box is modified
outputFormatCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
outputFormatCombo - Variable in class org.openscience.jmol.app.PovrayDialog
 
outputHeight - Variable in class org.openscience.jmol.app.PovrayDialog
 
outputStatus(String) - Method in class org.openscience.jmol.app.ConsoleDocument
 
outputStatus(String) - Method in class org.openscience.jmol.app.ConsoleTextPane
 
outputWidth - Variable in class org.openscience.jmol.app.PovrayDialog
 
outStream - Variable in class org.jmol.util.JpegEncoder
 
oValue(Token) - Static method in class org.jmol.viewer.Token
 

P

packageJSON(String, StringBuffer) - Static method in class org.jmol.util.Escape
 
packageJSON(String, String) - Static method in class org.jmol.util.Escape
 
packageReadable(String, String, StringBuffer) - Static method in class org.jmol.util.Escape
 
packageReadable(String, String, String) - Static method in class org.jmol.util.Escape
 
pageAuthorName - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
pageAuthorName - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
paint(Graphics) - Method in class org.jmol.applet.Jmol
 
paint(Graphics) - Method in class org.jmol.appletwrapper.AppletWrapper
 
paint(Graphics) - Method in interface org.jmol.appletwrapper.WrappedApplet
 
paint(Graphics) - Method in class org.jmol.export.dialog.FilePreview.JmolPanel
 
paint(Graphics) - Method in class org.jmol.jcamp.ZoneVisu
 
paint(Graphics) - Method in class org.openscience.jmol.app.DisplayPanel
 
paint(Graphics) - Method in class org.openscience.jmol.app.Splash
 
paintCounter - Variable in class org.jmol.applet.Jmol
 
paintMeasurementString(int, int, int, int, boolean, int) - Method in class org.jmol.shape.MeasuresRenderer
 
pairSearch(Vector, CalculationsUFF.PairCalc) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
palette - Variable in class org.jmol.util.ColorEncoder
 
palette - Variable in class org.jmol.viewer.ColorManager
 
PALETTE_ALTLOC - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_AMINO - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_CHAIN - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_CPK - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_FIXEDTEMP - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_FORMAL_CHARGE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_GROUP - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_INSERTION - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_JMOL - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_MOLECULE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_MONOMER - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_NONE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_PARTIAL_CHARGE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_PROPERTY - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_RASMOL - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_SHAPELY - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_STATIC - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_STRAIGHTNESS - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_STRUCTURE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_TEMP - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_TYPE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_UNKNOWN - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_VARIABLE - Static variable in class org.jmol.viewer.JmolConstants
 
PALETTE_VOLATILE - Static variable in class org.jmol.viewer.JmolConstants
 
paletteCount - Static variable in class org.jmol.viewer.JmolConstants
 
paletteID - Variable in class org.jmol.modelset.Atom
 
paletteIDs - Variable in class org.jmol.shape.AtomShape
 
paletteIDs - Variable in class org.jmol.shapebio.BioShape
 
paletteIDs - Static variable in class org.jmol.viewer.JmolConstants
 
paletteNames - Static variable in class org.jmol.viewer.JmolConstants
 
panel() - Method in class org.openscience.jmol.app.webexport.Test
 
panelIndex - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
panelName - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
PAR_D - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_HARD - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_R - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_RADIUS - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_THETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_U - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_V - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_X - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_XI - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_Z - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_ZETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
parA - Variable in class org.jmol.minimize.forcefield.Calculation
 
parameterAsString(int) - Method in class org.jmol.viewer.Eval
 
parameterExpression(int, int, String, boolean) - Method in class org.jmol.viewer.Eval
 
parameterExpression(int, int, String, boolean, int, Hashtable, String) - Method in class org.jmol.viewer.Eval
 
Parameters - Class in org.jmol.jvxl.readers
 
Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
 
params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
params - Variable in class org.jmol.jvxl.readers.VoxelReader
 
parB - Variable in class org.jmol.minimize.forcefield.Calculation
 
parC - Variable in class org.jmol.minimize.forcefield.Calculation
 
parenCount - Variable in class org.jmol.viewer.Eval.Rpn
 
parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
parent - Variable in class org.jmol.viewer.Compiler.FlowContext
 
parseAtom(SmilesMolecule, String, SmilesAtom, int, boolean) - Method in class org.jmol.smiles.SmilesParser
Parses an atom definition
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
parseFloat(String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseFloat(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseFloat() - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseFloat(String) - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseFloat(String) - Static method in class org.jmol.util.Parser
 
parseFloat(String, int[]) - Static method in class org.jmol.util.Parser
 
parseFloat(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseFloatArray(String, BitSet, float[]) - Static method in class org.jmol.util.Parser
parses a "dirty" string for floats.
parseFloatArray(String[], BitSet, float[]) - Static method in class org.jmol.util.Parser
 
parseFloatArray(String[], float[]) - Static method in class org.jmol.util.Parser
parses a string array for floats.
parseFloatArray(String[], float[], int) - Static method in class org.jmol.util.Parser
parses a string array for floats.
parseFloatArray2d(String) - Static method in class org.jmol.util.Parser
 
parseFloatArrayFromMatchAndField(String, BitSet, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
the major lifter here.
parseFloatChecked(String, int, int[], boolean) - Static method in class org.jmol.util.Parser
 
parseFloatNext(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseFloatNext(String) - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseFloatStrict(String) - Static method in class org.jmol.util.Parser
 
parseInt(String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseInt(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseInt(String, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseInt() - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseInt(String) - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseInt(String, int) - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseInt(String) - Static method in class org.jmol.util.Parser
 
parseInt(String, int[]) - Static method in class org.jmol.util.Parser
 
parseInt(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseIntChecked(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseIntNext(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
parseIntNext(String) - Method in class org.jmol.shapesurface.MeshFileCollection
 
parseLattRecord() - Method in class org.jmol.adapter.readers.more.ShelxReader
 
parseLineParameters(String[], byte[]) - Method in class org.jmol.adapter.readers.more.CsfReader
 
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
sets up arrays and variables for tokenizer.getData()
Parser - Class in org.jmol.util
 
Parser() - Constructor for class org.jmol.util.Parser
 
parseReaderXML(XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
parseRing(SmilesMolecule, String, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesParser
Parses a ring definition
parseSfacCoefficients(String[]) - Method in class org.jmol.adapter.readers.more.ShelxReader
 
parseSfacElementSymbols(String[]) - Method in class org.jmol.adapter.readers.more.ShelxReader
 
parseSfacRecord() - Method in class org.jmol.adapter.readers.more.ShelxReader
 
parseSmiles(String) - Method in class org.jmol.smiles.SmilesParser
Parses a SMILES String
parseSmiles(SmilesMolecule, String, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
Parses a part of a SMILES String
parseSymmRecord() - Method in class org.jmol.adapter.readers.more.ShelxReader
 
parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String) - Static method in class org.jmol.util.Parser
 
parseToken(String, int[]) - Static method in class org.jmol.util.Parser
 
parseToken(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseTokenChecked(String, int, int[]) - Static method in class org.jmol.util.Parser
 
parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String) - Static method in class org.jmol.util.Parser
 
parseTrimmed(String, int) - Static method in class org.jmol.util.Parser
 
parseTrimmed(String, int, int) - Static method in class org.jmol.util.Parser
 
parseTrimmedChecked(String, int, int) - Static method in class org.jmol.util.Parser
 
PARTIAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
 
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
 
PARTIAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
 
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
 
partialCharge - Variable in class org.jmol.adapter.smarter.Atom
 
partialCharge - Static variable in class org.jmol.viewer.Token
 
partialCharges - Variable in class org.jmol.minimize.forcefield.Calculations
 
partialCharges - Variable in class org.jmol.minimize.Minimizer
 
partialCharges - Variable in class org.jmol.modelset.AtomCollection
 
Pass - Variable in class org.jmol.export.image.GifEncoder
 
pasteClipboardAction - Variable in class org.openscience.jmol.app.Jmol
 
pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
PathButton - Variable in class org.openscience.jmol.app.webexport.Test
 
PatternMatcher - Class in org.jmol.smiles
A class to match a SMILES pattern with a Jmol molecule.
PatternMatcher() - Constructor for class org.jmol.smiles.PatternMatcher
Constructs a PatternMatcher.
pause() - Method in class org.jmol.viewer.Eval
 
pause - Static variable in class org.jmol.viewer.Token
 
PAUSE - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
pauseAnimation() - Method in class org.jmol.viewer.RepaintManager
 
pauseAnimation() - Method in class org.jmol.viewer.Viewer
 
pauseExecution() - Method in class org.jmol.viewer.Eval
 
pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
 
pBotLeft - Variable in class org.jmol.g3d.Hermite3D
 
pBotRight - Variable in class org.jmol.g3d.Hermite3D
 
pbuf - Variable in class org.jmol.g3d.Graphics3D
 
pBuffer - Variable in class org.jmol.g3d.Platform3D
 
pBufferT - Variable in class org.jmol.g3d.Platform3D
 
pbufT - Variable in class org.jmol.g3d.Graphics3D
 
pButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
pc - Variable in class org.jmol.viewer.Eval.Context
 
pc - Variable in class org.jmol.viewer.Eval
 
pcEnd - Variable in class org.jmol.viewer.Eval.Context
 
pcEnd - Variable in class org.jmol.viewer.Eval
 
pchrg - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
pcs - Variable in class org.openscience.jmol.app.Jmol
 
pdbGetHeader - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pdbheader - Static variable in class org.jmol.viewer.Token
 
PDBOnly - Variable in class org.jmol.popup.JmolPopup
 
PdbReader - Class in org.jmol.adapter.readers.cifpdb
PDB file reader.
PdbReader() - Constructor for class org.jmol.adapter.readers.cifpdb.PdbReader
 
pdbRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
pdbRecords - Static variable in class org.jmol.modelset.ModelCollection
 
pdbSequential - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Peak_Html - Variable in class org.jmol.jcamp.ZoneVisu
 
Peak_Start - Variable in class org.jmol.jcamp.ZoneVisu
 
Peak_Stop - Variable in class org.jmol.jcamp.ZoneVisu
 
peakHtml - Variable in class org.jmol.jcamp.data.GraphControlData
 
peakStart - Variable in class org.jmol.jcamp.data.GraphControlData
 
peakStop - Variable in class org.jmol.jcamp.data.GraphControlData
 
peekToken() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
just look at the next token.
pending(MeasurementPending) - Method in class org.jmol.shape.Measures
 
percent - Static variable in class org.jmol.viewer.Token
 
percentVdwAtom - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
percentVdwAtom - Variable in class org.openscience.jmol.app.PreferencesDialog
 
PERIOD_MAX - Static variable in class org.openscience.jmol.app.AtomSetChooser
Maximum value for the vibration period in seconds.
PERIOD_PRECISION - Static variable in class org.openscience.jmol.app.AtomSetChooser
Precision of the vibration period slider in seconds.
PERIOD_VALUE - Static variable in class org.openscience.jmol.app.AtomSetChooser
Initial value for the vibration period in seconds.
periodicOriginXyz - Variable in class org.jmol.symmetry.SymmetryInfo
 
periodSlider - Variable in class org.openscience.jmol.app.AtomSetChooser
 
perspectiveAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
perspectiveDepth - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
 
perspectiveDepth - Variable in class org.openscience.jmol.app.PreferencesDialog
 
perspectiveFactor - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
perspectiveModel - Variable in class org.jmol.viewer.TransformManager
 
pfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
pFF - Variable in class org.jmol.minimize.Minimizer
 
phase - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
phi - Variable in class org.jmol.modelset.Group
 
phi - Static variable in class org.jmol.viewer.Token
 
PhosphorusMonomer - Class in org.jmol.modelsetbio
 
PhosphorusMonomer(Chain, String, int, int, int, byte[]) - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
 
phosphorusOffsets - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
PhosphorusPolymer - Class in org.jmol.modelsetbio
 
PhosphorusPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.PhosphorusPolymer
 
PI_OVER_2 - Static variable in class org.jmol.minimize.forcefield.Calculations
 
pickedMesh - Variable in class org.jmol.shapespecial.Draw
 
pickedModel - Variable in class org.jmol.shapespecial.Draw
 
pickedVertex - Variable in class org.jmol.shapespecial.Draw
 
picking - Static variable in class org.jmol.viewer.Token
 
PICKING_CENTER - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_DRAW - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_IDENT - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_LABEL - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_MEASURE - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_NAVIGATE - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_OFF - Static variable in class org.jmol.viewer.JmolConstants
picking modes
PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SELECT_DRAG - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.JmolConstants
 
PICKING_SPIN - Static variable in class org.jmol.viewer.JmolConstants
 
PickingManager - Class in org.jmol.viewer
 
PickingManager(Viewer) - Constructor for class org.jmol.viewer.PickingManager
 
pickingManager - Variable in class org.jmol.viewer.Viewer
 
pickingMode - Variable in class org.jmol.viewer.PickingManager
 
pickingModeNames - Static variable in class org.jmol.viewer.JmolConstants
 
pickingSpinRate - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pickingStyle - Variable in class org.jmol.viewer.PickingManager
 
pickingStyle - Static variable in class org.jmol.viewer.Token
 
PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.JmolConstants
 
PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.JmolConstants
 
PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.JmolConstants
 
PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.JmolConstants
 
PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.JmolConstants
picking styles
PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.JmolConstants
 
PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.JmolConstants
 
pickingStyleMeasure - Variable in class org.jmol.viewer.PickingManager
 
pickingStyleNames - Static variable in class org.jmol.viewer.JmolConstants
 
pickingStyleSelect - Variable in class org.jmol.viewer.PickingManager
 
pickLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pickSelected(String, int) - Method in class org.jmol.viewer.PickingManager
 
pictFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
pictIsScratchFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
pidOf(Object) - Static method in class org.jmol.viewer.JmolConstants
 
PINK - Static variable in class org.jmol.g3d.Graphics3D
 
pipedIS - Variable in class org.openscience.jmol.app.LoopedStreams
 
pipedOS - Variable in class org.openscience.jmol.app.LoopedStreams
 
pixelCounts - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pixelData - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pixelLocation - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
pixelOrigin - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pixelPtToXYZ(int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
pixelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
planarMatrix - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
planarOrigin - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
planarSquares - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
planarVectorLengths - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
planarVectors - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
plane - Variable in class org.jmol.shapespecial.Draw
 
plane - Static variable in class org.jmol.viewer.Token
 
planeExpected() - Method in class org.jmol.viewer.Eval
 
planeParameter(int) - Method in class org.jmol.viewer.Eval
 
planes - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
planeShade - Variable in class org.jmol.g3d.Sphere3D
 
planeShades - Variable in class org.jmol.g3d.Sphere3D
 
planesT - Variable in class org.jmol.shapespecial.Polyhedra
 
planeValue(Token) - Method in class org.jmol.viewer.Eval.Rpn
 
platform - Variable in class org.jmol.g3d.Graphics3D
 
Platform3D - Class in org.jmol.g3d
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() - Constructor for class org.jmol.g3d.Platform3D
 
Platform3D.ClearingThread - Class in org.jmol.g3d
 
Platform3D.ClearingThread() - Constructor for class org.jmol.g3d.Platform3D.ClearingThread
 
play - Static variable in class org.jmol.viewer.Token
 
PLAY - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
playrev - Static variable in class org.jmol.viewer.Token
 
pLeft - Variable in class org.jmol.g3d.Hermite3D
 
plot(int, int, int, int, String, Font3D, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.Text3D
 
plot8CircleCenteredClipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plot8CircleCenteredUnclipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plot8FilledCircleCenteredClipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plot8FilledCircleCenteredUnclipped(int, int) - Method in class org.jmol.g3d.Circle3D
 
plotByCharacter(int, int, int, int, String, Font3D, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.Text3D
 
plotCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotClipped(int, int, int, int, Graphics3D, JmolRendererInterface, int, int, int[]) - Static method in class org.jmol.g3d.Text3D
 
plotDashedLine(int, boolean, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotFilledCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotFilledCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Circle3D
 
plotImage(int, int, int, Image, short, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
plotImage(int, int, int, Image, short, int, int) - Method in class org.jmol.export._MayaExporter
 
plotImage(int, int, int, Image, short, int, int) - Method in class org.jmol.export._PovrayExporter
 
plotImage(int, int, int, Image, short, int, int) - Method in class org.jmol.export._VrmlExporter
 
plotImage(int, int, int, Image, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotImage(int, int, int, Image, Graphics3D, JmolRendererInterface, boolean, int, int, int) - Static method in class org.jmol.g3d.Text3D
 
plotImageClipped(int, int, int, Graphics3D, JmolRendererInterface, int, int, int[], int) - Static method in class org.jmol.g3d.Text3D
 
plotImageUnClipped(int, int, int, Graphics3D, int, int, int[], int) - Static method in class org.jmol.g3d.Text3D
 
plotLine(int, boolean, int, boolean, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotLineClipped(int, boolean, int, boolean, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.Line3D
 
plotLineClipped(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.Line3D
 
plotLineClippedBits(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.Line3D
 
plotLineDelta(int, boolean, int, boolean, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotLineDelta(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotLineDeltaBits(int[], boolean, int[], boolean, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.Line3D
 
plotPixelClipped(Point3i) - Method in interface org.jmol.api.JmolRendererInterface
 
plotPixelClipped(int, int, int) - Method in class org.jmol.export.Export3D
 
plotPixelClipped(Point3i) - Method in class org.jmol.export.Export3D
 
plotPixelClipped(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClipped(Point3i) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClipped(int, boolean, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClippedNoSlab(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
plotPixelClippedNoSlab(int, int, int, int) - Method in class org.jmol.export.Export3D
 
plotPixelClippedNoSlab(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsClipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsClipped(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsUnclipped(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelUnclipped(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelUnclipped(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPoints(int, int[]) - Method in class org.jmol.g3d.Graphics3D
 
plotRaster(int) - Method in class org.jmol.g3d.Cylinder3D
 
plotRasterBits(int) - Method in class org.jmol.g3d.Cylinder3D
 
plotRasterCone(int, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
plotText(int, int, int, int, String, Font3D) - Method in interface org.jmol.api.JmolExportInterface
 
plotText(int, int, int, int, String, Font3D) - Method in class org.jmol.export._MayaExporter
 
plotText(int, int, int, int, String, Font3D) - Method in class org.jmol.export._PovrayExporter
 
plotText(int, int, int, int, String, Font3D) - Method in class org.jmol.export._VrmlExporter
 
plotText(int, int, int, int, String, Font3D, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
plotUnclipped(int, int, int, int, Graphics3D, int, int, int[]) - Static method in class org.jmol.g3d.Text3D
 
PltFormattedReader - Class in org.jmol.jvxl.readers
 
PltFormattedReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PltFormattedReader
 
plus - Static variable in class org.jmol.viewer.Token
 
Pmesh - Class in org.jmol.shapesurface
 
Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
 
pmesh() - Method in class org.jmol.viewer.Eval
 
pmesh - Static variable in class org.jmol.viewer.Token
 
Pmesh.PmeshBinaryDocument - Class in org.jmol.shapesurface
 
Pmesh.PmeshBinaryDocument(BufferedInputStream) - Constructor for class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.shapesurface.Pmesh
 
pmeshError - Variable in class org.jmol.shapesurface.Pmesh
 
PmeshGenerator - Class in org.jmol.export
 
PmeshGenerator() - Constructor for class org.jmol.export.PmeshGenerator
 
PmeshRenderer - Class in org.jmol.shapesurface
 
PmeshRenderer() - Constructor for class org.jmol.shapesurface.PmeshRenderer
 
pngBytes - Variable in class org.jmol.export.image.PngEncoder
 
pngEncode(boolean) - Method in class org.jmol.export.image.PngEncoder
Creates an array of bytes that is the PNG equivalent of the current image, specifying whether to encode alpha or not.
pngEncode() - Method in class org.jmol.export.image.PngEncoder
Creates an array of bytes that is the PNG equivalent of the current image.
PngEncoder - Class in org.jmol.export.image
PngEncoder takes a Java Image object and creates a byte string which can be saved as a PNG file.
PngEncoder() - Constructor for class org.jmol.export.image.PngEncoder
Class constructor
PngEncoder(Image) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image to encode, with no alpha channel encoding.
PngEncoder(Image, boolean) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image to encode, and whether to encode alpha.
PngEncoder(Image, boolean, int) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image to encode, whether to encode alpha, and filter to use.
PngEncoder(Image, boolean, int, int) - Constructor for class org.jmol.export.image.PngEncoder
Class constructor specifying Image source to encode, whether to encode alpha, filter to use, and compression level.
pnqD - Static variable in class org.jmol.adapter.readers.more.MopacData
 
pocket - Variable in class org.jmol.jvxl.readers.Parameters
 
point - Variable in class org.jmol.jvxl.readers.Parameters
 
point - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
point - Static variable in class org.jmol.viewer.Token
 
point3f - Static variable in class org.jmol.viewer.Token
 
Point3fi - Class in org.jmol.util
 
Point3fi() - Constructor for class org.jmol.util.Point3fi
 
point3fScreenTemp - Variable in class org.jmol.viewer.TransformManager
 
point3fVibrationTemp - Variable in class org.jmol.viewer.TransformManager
 
point3iScreenTemp - Variable in class org.jmol.viewer.TransformManager
 
point4f - Static variable in class org.jmol.viewer.Token
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointArc - Variable in class org.jmol.modelset.Measurement
 
pointArrowHead - Variable in class org.jmol.shapespecial.VectorsRenderer
 
pointB - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointCorner - Variable in class org.jmol.shapebio.RocketsRenderer
 
pointer - Variable in class org.jmol.shape.Object2d
 
POINTER_BACKGROUND - Static variable in class org.jmol.shape.Object2d
 
POINTER_FLAGS - Static variable in class org.jmol.shape.Labels
 
POINTER_NONE - Static variable in class org.jmol.shape.Object2d
 
POINTER_ON - Static variable in class org.jmol.shape.Object2d
 
pointGroup - Variable in class org.jmol.modelset.ModelSet
 
PointGroup - Class in org.jmol.symmetry
 
PointGroup() - Constructor for class org.jmol.symmetry.PointGroup
 
pointGroup - Variable in class org.jmol.symmetry.Symmetry
 
pointGroup() - Method in class org.jmol.viewer.Eval
 
pointgroup - Static variable in class org.jmol.viewer.Token
 
PointGroup.Operation - Class in org.jmol.symmetry
 
PointGroup.Operation() - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
PointGroup.Operation(Vector3f, int) - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
PointGroup.Operation(Vector3f) - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
pointGroupDistanceTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pointGroupLinearTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
pointPlaneAngleRadians(Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
points - Variable in class org.jmol.modelset.Measurement
 
points - Variable in class org.jmol.shapespecial.DipolesRenderer
 
points - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
 
pointT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
pointT - Variable in class org.jmol.shape.MeasuresRenderer
 
pointT - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pointT - Variable in class org.jmol.viewer.TransformManager
 
pointT2 - Variable in class org.jmol.viewer.TransformManager
 
pointTipOffset - Variable in class org.jmol.shapebio.RocketsRenderer
 
pointVector - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointVector - Variable in class org.jmol.jvxl.data.VolumeData
 
pointVectorEnd - Variable in class org.jmol.shapespecial.VectorsRenderer
 
polygonCount - Variable in class org.jmol.jvxl.data.MeshData
 
polygonCount - Variable in class org.jmol.shape.Mesh
 
polygonCount - Variable in class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
polygonIndexes - Variable in class org.jmol.jvxl.data.MeshData
 
polygonIndexes - Variable in class org.jmol.shape.Mesh
 
Polyhedra - Class in org.jmol.shapespecial
 
Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
 
polyhedra() - Method in class org.jmol.viewer.Eval
 
polyhedra - Static variable in class org.jmol.viewer.Token
 
Polyhedra.Polyhedron - Class in org.jmol.shapespecial
 
Polyhedra.Polyhedron(Atom, int, int, int, Atom[], short[], byte[]) - Constructor for class org.jmol.shapespecial.Polyhedra.Polyhedron
 
PolyhedraGenerator - Class in org.jmol.export
 
PolyhedraGenerator() - Constructor for class org.jmol.export.PolyhedraGenerator
 
PolyhedraRenderer - Class in org.jmol.shapespecial
 
PolyhedraRenderer() - Constructor for class org.jmol.shapespecial.PolyhedraRenderer
 
polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
 
polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
 
Polymer - Class in org.jmol.modelset
 
Polymer() - Constructor for class org.jmol.modelset.Polymer
 
polymer - Static variable in class org.jmol.viewer.Token
 
polymerLength - Static variable in class org.jmol.viewer.Token
 
popContext() - Method in class org.jmol.viewer.Eval
 
popHoldRepaint() - Method in class org.jmol.api.JmolViewer
 
popHoldRepaint() - Method in class org.jmol.viewer.RepaintManager
 
popHoldRepaint() - Method in class org.jmol.viewer.Viewer
 
PopInJmol - Class in org.openscience.jmol.app.webexport
 
PopInJmol(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.PopInJmol
 
popupMenu(int, int) - Method in class org.jmol.viewer.StatusManager
 
popupMenu(int, int) - Method in class org.jmol.viewer.Viewer
 
popupMenuAllowed - Variable in class org.jmol.applet.Jmol
 
PopupResourceBundle - Class in org.jmol.popup
 
PopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.PopupResourceBundle
 
position - Variable in class org.jmol.viewer.MonitorInputStream
 
position - Variable in class org.openscience.jvxl.MonitorInputStream
 
positionAfterPrompt - Variable in class org.openscience.jmol.app.ConsoleDocument
 
positionBeforePrompt - Variable in class org.openscience.jmol.app.ConsoleDocument
 
postDefinitions - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
povrayAction - Variable in class org.openscience.jmol.app.Jmol
 
povrayActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
PovrayDialog - Class in org.openscience.jmol.app
A dialog for controling the creation of a povray input file from a Chemframe and a display.
PovrayDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.PovrayDialog
Creates a dialog for getting info related to output frames in povray format.
PovrayDialog.PovrayWindowListener - Class in org.openscience.jmol.app
Listener for responding to dialog window events.
PovrayDialog.PovrayWindowListener() - Constructor for class org.openscience.jmol.app.PovrayDialog.PovrayWindowListener
 
povrayPathButton - Variable in class org.openscience.jmol.app.PovrayDialog
 
povrayPathLabel - Variable in class org.openscience.jmol.app.PovrayDialog
 
PovraySaver - Class in org.openscience.jmol.app
 
PovraySaver() - Constructor for class org.openscience.jmol.app.PovraySaver
 
power4 - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
ppa - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
PpmEncoder - Class in org.jmol.export.image
 
PpmEncoder(Image, OutputStream) - Constructor for class org.jmol.export.image.PpmEncoder
 
PpmEncoder(ImageProducer, OutputStream) - Constructor for class org.jmol.export.image.PpmEncoder
 
PqrReader - Class in org.jmol.adapter.readers.more
PQR file reader.
PqrReader() - Constructor for class org.jmol.adapter.readers.more.PqrReader
 
pqrRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
precalculateVoxelData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
Precision - Variable in class org.jmol.util.JpegInfo
 
predefine(String) - Method in class org.jmol.viewer.Eval
 
predefinedArgbs - Static variable in class org.jmol.g3d.Colix3D
 
predefinedGroup1Names - Static variable in class org.jmol.viewer.JmolConstants
 
predefinedGroup3Names - Static variable in class org.jmol.viewer.JmolConstants
 
predefinedset - Static variable in class org.jmol.viewer.Token
 
predefinedStatic - Static variable in class org.jmol.viewer.JmolConstants
 
predefinedVariable - Static variable in class org.jmol.viewer.JmolConstants
 
preDefining - Variable in class org.jmol.viewer.Compiler
 
preferencesDialog - Variable in class org.openscience.jmol.app.Jmol
 
PreferencesDialog - Class in org.openscience.jmol.app
 
PreferencesDialog(JFrame, GuiMap, JmolViewer) - Constructor for class org.openscience.jmol.app.PreferencesDialog
 
PreferencesDialog.PrefsAction - Class in org.openscience.jmol.app
 
PreferencesDialog.PrefsAction() - Constructor for class org.openscience.jmol.app.PreferencesDialog.PrefsAction
 
prefsAction - Variable in class org.openscience.jmol.app.PreferencesDialog
 
preloadClassIndex - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadClassNames - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadImage - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadImageName - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadImagePainted - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadImageReadyForDisplay - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadTextMessage - Variable in class org.jmol.appletwrapper.AppletWrapper
 
preloadThreadCount - Variable in class org.jmol.appletwrapper.AppletWrapper
 
prempoint - Variable in class org.jmol.jcamp.ZoneVisu
 
pressedCount - Variable in class org.jmol.viewer.MouseManager
 
prev - Static variable in class org.jmol.viewer.Token
 
prevFrame - Variable in class org.jmol.viewer.Viewer
 
PREVIOUS - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.viewer.JmolConstants
 
previousClassName - Variable in class org.jmol.appletwrapper.AppletWrapper
 
previousClickCount - Variable in class org.jmol.viewer.MouseManager
 
previousClickModifiers - Variable in class org.jmol.viewer.MouseManager
 
previousClickTime - Variable in class org.jmol.viewer.MouseManager
 
previousClickX - Variable in class org.jmol.viewer.MouseManager
 
previousClickY - Variable in class org.jmol.viewer.MouseManager
 
previousDragX - Variable in class org.jmol.viewer.MouseManager
 
previousDragY - Variable in class org.jmol.viewer.MouseManager
 
previousMeshID - Variable in class org.jmol.shape.MeshCollection
 
previousPressedModifiers - Variable in class org.jmol.viewer.MouseManager
 
previousPressedTime - Variable in class org.jmol.viewer.MouseManager
 
previousPressedX - Variable in class org.jmol.viewer.MouseManager
 
previousPressedY - Variable in class org.jmol.viewer.MouseManager
 
previousX - Variable in class org.jmol.viewer.TransformManager11
 
previousY - Variable in class org.jmol.viewer.TransformManager11
 
prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
prevZoomSetting - Variable in class org.jmol.viewer.TransformManager11
 
pRight - Variable in class org.jmol.g3d.Hermite3D
 
primitiveCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
primitiveHallSymbol - Variable in class org.jmol.symmetry.HallInfo
 
primitiveLatticeVectors - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
principalAxis - Variable in class org.jmol.symmetry.PointGroup
 
principalPlane - Variable in class org.jmol.symmetry.PointGroup
 
principalQuantumNumber - Static variable in class org.jmol.adapter.readers.more.MopacData
 
print() - Method in class org.jmol.viewer.Eval
 
print - Static variable in class org.jmol.viewer.Token
 
print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.DisplayPanel
 
print() - Method in class org.openscience.jmol.app.Jmol
added print command, so that it can be used by RasmolScriptHandler
printAction - Variable in class org.openscience.jmol.app.Jmol
 
printActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
printProgressbarMessage(Graphics) - Method in class org.jmol.applet.Jmol
 
priorRow - Variable in class org.jmol.export.image.PngEncoder
 
processAtom() - Method in class org.jmol.adapter.readers.more.HinReader
 
processAtomBlock() - Method in class org.jmol.adapter.readers.more.V3000Reader
 
processAtomicCharges() - Method in class org.jmol.adapter.readers.more.MopacReader
Reads the section in MOPAC files with atomic charges.
processAtomObject() - Method in class org.jmol.adapter.readers.more.CsfReader
 
processAtoms() - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
processAtomSiteLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads atom data in any order
processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
processBasisObject(String) - Method in class org.jmol.adapter.readers.more.CsfReader
 
processBondBlock() - Method in class org.jmol.adapter.readers.more.V3000Reader
 
processBondObject() - Method in class org.jmol.adapter.readers.more.CsfReader
 
processBonds() - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
processCellParameter() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
unit cell parameters -- two options, so we use MOD 6
processCharges() - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
a general name definition field.
processChemicalInfo(String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads some of the more interesting info into specific atomSetAuxiliaryInfo elements
processCmdfAtoms() - Method in class org.jmol.adapter.readers.more.ShelxReader
 
processComponentKeyEvent(KeyEvent) - Method in class org.jmol.applet.Console.ControlEnterTextArea
 
processConnectorObject() - Method in class org.jmol.adapter.readers.more.CsfReader
 
processCoord() - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
processCoordinates() - Method in class org.jmol.adapter.readers.more.MopacReader
Reads the section in MOPAC files with cartesian coordinates.
processCtab() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processCtab() - Method in class org.jmol.adapter.readers.more.V3000Reader
 
processDataParameter() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
initialize a new atom set
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processEndElement2(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processEndmol() - Method in class org.jmol.adapter.readers.more.HinReader
 
processGeomBondLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms.
processHeader() - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
processInfo() - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processKeyEvent(KeyEvent) - Method in class org.jmol.viewer.MouseManager
 
processKeyEvent(KeyEvent) - Method in class org.openscience.jmol.app.ConsoleTextPane
Custom key event processing for command 0 implementation.
processLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
processes loop_ blocks of interest or skips the data
processMep() - Method in class org.jmol.quantum.MepCalculation
 
processMol() - Method in class org.jmol.adapter.readers.more.HinReader
 
processMolecularOrbitalObject() - Method in class org.jmol.adapter.readers.more.CsfReader
 
processMolecule() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
processMolSdHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processNonpolyData() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
processNonpolyLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
a HETERO name definition field.
processObjectClass() - Method in class org.jmol.adapter.readers.more.CsfReader
 
processOneCubical(int, int[], int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processOneQuadrilateral(int, float, int[], int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
processRgHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processShell(int) - Method in class org.jmol.quantum.MOCalculation
 
processSlater(int) - Method in class org.jmol.quantum.MOCalculation
 
processStartElement(String, String, String, HashMap) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processStartElement(String, String, String, HashMap) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processStartElement(String, String, String, HashMap) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processStartElement(String, String, String, HashMap) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processStartElement(String, String, String, HashMap) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processStartElement2(String, String, String, HashMap) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
identifies ranges for HELIX and TURN
processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
identifies sheet ranges
processStructSiteBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
identifies structure sites
processSupportedRecord(int) - Method in class org.jmol.adapter.readers.more.ShelxReader
 
processSymmetryOperationsLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
retrieves symmetry operations
processSymmetrySpaceGroupName() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
done by AtomSetCollectionReader
processTotalEnergy() - Method in class org.jmol.adapter.readers.more.MopacReader
 
processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
the PDB transformation matrix cartesian --> fractional
processVibrationObject() - Method in class org.jmol.adapter.readers.more.CsfReader
 
processXml(XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
producer - Variable in class org.jmol.export.image.ImageEncoder
 
programInfo - Variable in class org.jmol.atomdata.AtomData
 
progressbarMsgs - Static variable in class org.jmol.applet.Jmol
 
projectOntoAxis(Point3f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.g3d.Graphics3D
 
prompt - Variable in class org.openscience.jmol.app.Jmol.OpenUrlAction
 
prop - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
PROP_ANIMATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_APPLET_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ATOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ATOM_LIST - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_AUXILIARY_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_BOND_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_BOUNDBOX_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CENTER_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CHAIN_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_COUNT - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_DATA_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_EVALUATE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_EXTRACT_MODEL - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILECONTENTS - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILECONTENTS_PATH - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILEHEADER - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILENAME - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_IMAGE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JMOL_STATUS - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JMOL_VIEWER - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MEASUREMENT_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MENU - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MESSAGE_QUEUE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MINIMIZATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MODEL_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MOLECULE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ORIENTATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_POINTGROUP_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_POLYMER_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_SHAPE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_STATE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_TRANSFORM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
propagateNeighborPointIndexes(int, int, int, int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
propagateNeighborPointIndexes2d(int, int, int[][], float[][]) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
propagateSecondaryStructure() - Method in class org.jmol.modelset.ModelCollection
 
properties - Variable in class org.jmol.export.dialog.HistoryFile
The data stored in the history file.
properties - Variable in class org.jmol.modelset.Model
 
propertiesTextArea - Variable in class org.openscience.jmol.app.AtomSetChooser
 
property - Static variable in class org.jmol.viewer.Token
 
propertyChange(PropertyChangeEvent) - Method in class org.jmol.export.dialog.FilePreview
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.AtomSetChooser
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.FileTyper
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.Jmol.ActionChangedListener
 
propertyColorScheme - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
propertyCount - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
propertyItemCounts - Variable in class org.jmol.adapter.readers.more.CsfReader
 
PropertyManager - Class in org.jmol.viewer
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
 
propertyOf - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
propertySmoothing - Variable in class org.jmol.jvxl.readers.Parameters
 
propertyTypes - Static variable in class org.jmol.viewer.PropertyManager
 
props - Variable in class org.openscience.jmol.app.RecentFilesDialog
 
propselector - Static variable in class org.jmol.viewer.Token
 
protein - Static variable in class org.jmol.viewer.Token
 
PROTEIN_STRUCTURE_DNA - Static variable in class org.jmol.viewer.JmolConstants
 
PROTEIN_STRUCTURE_HELIX - Static variable in class org.jmol.viewer.JmolConstants
 
PROTEIN_STRUCTURE_NONE - Static variable in class org.jmol.viewer.JmolConstants
Default table of PdbStructure colors
PROTEIN_STRUCTURE_RNA - Static variable in class org.jmol.viewer.JmolConstants
 
PROTEIN_STRUCTURE_SHEET - Static variable in class org.jmol.viewer.JmolConstants
 
PROTEIN_STRUCTURE_TURN - Static variable in class org.jmol.viewer.JmolConstants
 
proteinShape(int) - Method in class org.jmol.viewer.Eval
 
proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
ProteinStructure - Class in org.jmol.modelsetbio
 
ProteinStructure(AlphaPolymer, byte, int, int) - Constructor for class org.jmol.modelsetbio.ProteinStructure
 
proteinStructureNames - Static variable in class org.jmol.viewer.JmolConstants
 
proteinstructurePending - Variable in class org.jmol.shapebio.RocketsRenderer
 
proteinStructureTainted - Variable in class org.jmol.modelset.ModelCollection
 
psi - Variable in class org.jmol.modelset.Group
 
psi - Static variable in class org.jmol.viewer.Token
 
psi_l - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_l - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_m - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_m - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_n - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_n - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_Znuc - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_Znuc - Variable in class org.jmol.jvxl.readers.Parameters
 
PsiReader - Class in org.jmol.adapter.readers.more
Reader for Psi3 output files.
PsiReader() - Constructor for class org.jmol.adapter.readers.more.PsiReader
 
psiRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
pt - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pt - Variable in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pt0 - Static variable in class org.jmol.shape.Axes
 
pt0 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pt0 - Variable in class org.jmol.viewer.Compiler.FlowContext
 
pt0 - Variable in class org.jmol.viewer.Function
 
pt0 - Static variable in class org.jmol.viewer.Token
 
pt0f - Variable in class org.jmol.shapespecial.DrawRenderer
 
pt0i - Variable in class org.jmol.shapespecial.DrawRenderer
 
pt1 - Variable in class org.jmol.shape.FontLineShapeRenderer
 
pt1 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pt1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
pt1f - Variable in class org.jmol.shape.MeshRenderer
 
pt1i - Variable in class org.jmol.shape.MeshRenderer
 
pt2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
pt2f - Variable in class org.jmol.shape.MeshRenderer
 
pt2i - Variable in class org.jmol.shape.MeshRenderer
 
PT_BITSET - Static variable in class org.jmol.shapespecial.Draw
 
PT_CHARGE - Static variable in class org.jmol.minimize.Minimizer
 
PT_CONNECT - Static variable in class org.jmol.minimize.Minimizer
 
PT_COORD - Static variable in class org.jmol.shapespecial.Draw
 
PT_ELEMENT - Static variable in class org.jmol.minimize.Minimizer
 
PT_IDENTIFIER - Static variable in class org.jmol.shapespecial.Draw
 
PT_MODEL_BASED_POINTS - Static variable in class org.jmol.shapespecial.Draw
 
PT_MODEL_INDEX - Static variable in class org.jmol.shapespecial.Draw
 
ptA - Variable in class org.jmol.export.Export3D
 
ptA - Variable in class org.jmol.shape.MeasuresRenderer
 
ptAi - Variable in class org.jmol.export.Export3D
 
ptB - Variable in class org.jmol.export.Export3D
 
ptB - Variable in class org.jmol.shape.MeasuresRenderer
 
ptBi - Variable in class org.jmol.export.Export3D
 
ptC - Variable in class org.jmol.export.Export3D
 
ptCenter - Variable in class org.jmol.shape.Mesh
 
ptCenter - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
ptCenters - Variable in class org.jmol.shapespecial.DrawMesh
 
ptConnect - Variable in class org.jmol.shapebio.CartoonRenderer
 
ptD - Variable in class org.jmol.export.Export3D
 
ptDefaultLattice - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ptiTemp - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ptList - Variable in class org.jmol.shapespecial.Draw
 
ptMoveToCenter - Variable in class org.jmol.viewer.TransformManager
 
ptNewSetModifier - Variable in class org.jmol.viewer.Compiler
 
ptNext - Variable in class org.jmol.shapebio.BioShapeRenderer
 
pTopLeft - Variable in class org.jmol.g3d.Hermite3D
 
pTopRight - Variable in class org.jmol.g3d.Hermite3D
 
ptPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
ptPsi - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
ptRef - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
ptS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptTemp - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptTemp - Variable in class org.jmol.g3d.Sphere3D
 
ptTemp - Variable in class org.jmol.jvxl.readers.VoxelReader
 
ptTemp - Variable in class org.jmol.modelset.ModelCollection
 
ptTemp - Variable in class org.jmol.modelsetbio.AminoMonomer
 
ptTemp - Variable in class org.jmol.shape.Axes
 
ptTemp - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
ptTemp1 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptTemp2 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ptTempi - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
ptTest1 - Variable in class org.jmol.viewer.TransformManager
 
ptTest2 - Variable in class org.jmol.viewer.TransformManager
 
ptTest3 - Variable in class org.jmol.viewer.TransformManager
 
ptValue(Token) - Method in class org.jmol.viewer.Eval.Rpn
 
ptXY - Variable in class org.jmol.shape.Sticks
 
ptXY - Variable in class org.jmol.shapespecial.Draw
 
ptXyzTemp - Variable in class org.jmol.jvxl.data.VolumeData
 
ptXyzTemp - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
purine - Static variable in class org.jmol.viewer.Token
 
PURPLE - Static variable in class org.jmol.g3d.Graphics3D
 
pushContext(Function) - Method in class org.jmol.viewer.Eval
 
pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
 
pushHoldRepaint() - Method in class org.jmol.viewer.RepaintManager
 
pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
 
put(int, int) - Method in class org.jmol.util.Int2IntHash
 
Putbyte(byte, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
putCoord(Vector3d, double[]) - Static method in class org.jmol.minimize.Util
 
putLabel(int, Text) - Method in class org.jmol.shape.Labels
 
Putword(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
 
pyrimidine - Static variable in class org.jmol.viewer.Token
 

Q

q0 - Variable in class org.jmol.util.Quaternion
 
q1 - Variable in class org.jmol.util.Quaternion
 
q2 - Variable in class org.jmol.util.Quaternion
 
q3 - Variable in class org.jmol.util.Quaternion
 
QchemReader - Class in org.jmol.adapter.readers.more
A reader for Q-Chem 2.1 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QchemReader() - Constructor for class org.jmol.adapter.readers.more.QchemReader
 
qchemRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
qColor - Static variable in class org.jmol.modelsetbio.BioPolymer
 
QConst - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
qm_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_moNumber - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_nAtoms - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_GAUSSIAN - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_SLATER - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_UNKNOWN - Static variable in class org.jmol.jvxl.readers.Parameters
 
qmOrbitalCount - Variable in class org.jmol.jvxl.readers.Parameters
 
qmOrbitalType - Variable in class org.jmol.jvxl.readers.Parameters
 
qPanelJPEG - Variable in class org.jmol.export.dialog.Dialog
 
qPanelPNG - Variable in class org.jmol.export.dialog.Dialog
 
qSliderJPEG - Variable in class org.jmol.export.dialog.Dialog
 
qSliderPNG - Variable in class org.jmol.export.dialog.Dialog
 
QtableNumber - Variable in class org.jmol.util.JpegInfo
 
qTemp - Static variable in class org.jmol.util.Quaternion
 
Quadric - Class in org.jmol.util
 
Quadric() - Constructor for class org.jmol.util.Quadric
 
quadruple(int, short[]) - Static method in class org.jmol.geodesic.Geodesic
 
Quality - Variable in class org.jmol.util.JpegEncoder
 
qualityJPG - Variable in class org.jmol.applet.Jvm12
 
qualityJPG - Static variable in class org.jmol.export.dialog.Dialog
 
qualityJPG - Variable in class org.openscience.jmol.app.Jmol
 
qualityPNG - Variable in class org.jmol.applet.Jvm12
 
qualityPNG - Static variable in class org.jmol.export.dialog.Dialog
 
qualityPNG - Variable in class org.openscience.jmol.app.Jmol
 
quantize(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
 
quantizeBlock(double[][], double[]) - Static method in class org.jmol.util.DCT
 
quantum - Variable in class org.jmol.util.DCT
Image Quality (0-100) - default 80 (good image / good compression)
quantum_chrominance - Variable in class org.jmol.util.DCT
Quantitization Matrix for chrominance.
quantum_luminance - Variable in class org.jmol.util.DCT
Quantitization Matrix for luminace.
QuantumCalculation - Class in org.jmol.quantum
 
QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
 
quantumShellIDs - Static variable in class org.jmol.viewer.JmolConstants
 
quantumShellTags - Static variable in class org.jmol.viewer.JmolConstants
 
Quaternion - Class in org.jmol.util
 
Quaternion(Quaternion) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(float, float, float, float) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Point4f) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Tuple3f, float) - Constructor for class org.jmol.util.Quaternion
 
Quaternion(Matrix3f) - Constructor for class org.jmol.util.Quaternion
 
quaternion - Static variable in class org.jmol.viewer.Token
 
quaternionFrame - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
query - Static variable in class org.jmol.symmetry.SpaceGroup
 
queueAtom(int, Point3f) - Method in class org.jmol.viewer.PickingManager
 
queueThreads - Variable in class org.jmol.viewer.ScriptManager
 
quit - Static variable in class org.jmol.viewer.Token
 
qw - Static variable in class org.jmol.viewer.Token
 

R

r - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
r0 - Variable in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
rab - Variable in class org.jmol.minimize.forcefield.Calculation
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.forcefield.Calculations
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
 
radiansPerDegree - Static variable in class org.jmol.util.Measure
 
radiansPerDegree - Static variable in class org.jmol.viewer.TransformManager
 
radiiIP2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radius - Variable in class org.jmol.adapter.smarter.Atom
 
radius - Variable in class org.jmol.bspt.CubeIterator
 
radius - Variable in class org.jmol.g3d.Cylinder3D
 
radius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
radius - Variable in class org.jmol.shapespecial.Polyhedra
 
radius - Variable in class org.jmol.symmetry.PointGroup
 
radius - Static variable in class org.jmol.viewer.Token
 
radius2 - Variable in class org.jmol.g3d.Cylinder3D
 
RADIUS_MAX - Static variable in class org.openscience.jmol.app.AtomSetChooser
Maximum value for vector radius.
RADIUS_VALUE - Static variable in class org.openscience.jmol.app.AtomSetChooser
Initial value of vector radius.
radiusHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
 
radiusI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radiusP - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radiusParameter(int, float) - Method in class org.jmol.viewer.Eval
Based on the form of the parameters, returns and encoded radius as follows: script meaning range encoded +1.2 offset [0 - 10] x -1.2 offset 0) x 1.2 absolute (0 - 10] x + 10 -30% 70% (-100 - 0) x + 200 +30% 130% (0 x + 200 80% percent (0 x + 100 in each case, numbers can be integer or float
radiusSlider - Variable in class org.openscience.jmol.app.AtomSetChooser
 
ramachandran - Static variable in class org.jmol.viewer.Token
 
random - Static variable in class org.jmol.viewer.Token
 
randomizeUnitVector(Vector3d) - Static method in class org.jmol.minimize.Util
 
randomPoint - Static variable in class org.jmol.shapespecial.Polyhedra
 
range - Variable in class org.jmol.shapebio.BioShape
 
range - Static variable in class org.jmol.viewer.Token
 
rangeAll - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeDefined - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
rangeMinMax - Variable in class org.jmol.shape.Measures
 
rangeSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
rasmol - Static variable in class org.jmol.viewer.Token
 
rasmolDefaultsButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
rasmolHeteroSetting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
rasmolHydrogenSetting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
rasmolOverrides - Static variable in class org.openscience.jmol.app.PreferencesDialog
 
rasmolScale - Static variable in class org.jmol.util.ColorEncoder
 
rasterCount - Variable in class org.jmol.g3d.Cylinder3D
 
rasterize(Platform3D, boolean) - Method in class org.jmol.g3d.Text3D
 
read() - Method in class org.jmol.viewer.MonitorInputStream
 
read(byte[]) - Method in class org.jmol.viewer.MonitorInputStream
 
read(byte[], int, int) - Method in class org.jmol.viewer.MonitorInputStream
 
read() - Method in class org.openscience.jvxl.MonitorInputStream
 
read(byte[]) - Method in class org.openscience.jvxl.MonitorInputStream
 
read(byte[], int, int) - Method in class org.openscience.jvxl.MonitorInputStream
 
readableTypes - Static variable in class org.jmol.viewer.PropertyManager
 
readArchive(String, boolean) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readArchiveHeader() - Method in class org.jmol.adapter.readers.more.SpartanSmolReader
 
readAtomCount() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
readAtomCountAndOrigin() - Method in class org.jmol.adapter.readers.more.CubeReader
 
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.ApbsReader
 
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.CubeReader
 
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.JaguarReader
skip initial stuff and read the origin= line
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readAtomCountAndOrigin() - Method in class org.jmol.jvxl.readers.XplorReader
 
readAtomicOrbitalOrder() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readAtomNames() - Method in class org.jmol.adapter.readers.more.OdysseyReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.CubeReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.more.FoldingXyzReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.GaussianReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.HinReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.more.JmeReader
 
readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.MoldenReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.MopacGraphfReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.NWChemReader
Reads the output coordinates section into a new AtomSet.
readAtoms() - Method in class org.jmol.adapter.readers.more.OdysseyReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
readAtoms(boolean) - Method in class org.jmol.adapter.readers.more.PsiReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.QchemReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readAtoms() - Method in class org.jmol.adapter.readers.more.SpartanReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.AdfReader
Read the ADF output.
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.CsfReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.CubeReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.FoldingXyzReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.GamessReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.GamessUKReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.GamessUSReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.GaussianReader
Reads a Collection of AtomSets from a BufferedReader.
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.GhemicalMMReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.HinReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.JmeReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.MoldenReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.MopacDataReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.MopacGraphfReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.MopacReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.NWChemReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.OdysseyReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.PsiReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.QchemReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.ShelxReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.SpartanReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.SpartanSmolReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.V3000Reader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
readAtomSetCollection(BufferedReader) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readAtomSetCollectionFromDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
readAtomSetCollectionFromDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readAtomSetName() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
readAtomsInAngstromCoordinates() - Method in class org.jmol.adapter.readers.more.GamessUSReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.more.GamessReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.more.GamessUKReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.more.GamessUSReader
 
readAtSign() - Method in class org.jmol.adapter.readers.more.NWChemReader
 
readBasis() - Method in class org.jmol.adapter.readers.more.GaussianReader
 
readBasis() - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readBasis() - Method in class org.jmol.adapter.readers.more.PsiReader
 
readBasis() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readBasisNormalized() - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readBFactor() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
readBFactor() - Method in class org.jmol.adapter.readers.more.PqrReader
 
readBonds(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.more.JmeReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readBonds() - Method in class org.jmol.adapter.readers.more.OdysseyReader
 
readBonds() - Method in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
readBonds() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readByte() - Method in class org.jmol.util.BinaryDocument
 
readByteArray(byte[]) - Method in class org.jmol.util.BinaryDocument
 
readByteArray(byte[], int, int) - Method in class org.jmol.util.BinaryDocument
 
readCharges() - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readColorData() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readColorData() - Method in class org.jmol.jvxl.readers.VoxelReader
 
readComponents(int, float[]) - Method in class org.jmol.adapter.readers.more.GamessReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.more.AdfReader
Reads a set of coordinates
readCrystalInfo() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readData() - Method in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
readData() - Method in class org.jmol.util.CompoundDocument.CmpDocHeader
 
readDescription() - Method in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
readDipole() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.more.GaussianReader
 
reader - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
reader - Variable in class org.jmol.viewer.FileManager.FileOpenThread
 
readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readerSets - Static variable in class org.jmol.adapter.smarter.Resolver
 
readEventCount - Variable in class org.jmol.viewer.MonitorInputStream
 
readEventCount - Variable in class org.openscience.jvxl.MonitorInputStream
 
readExtraLine() - Method in class org.jmol.adapter.readers.more.CubeReader
 
readExtraLine() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readExtraLine() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readFloat() - Method in class org.jmol.util.BinaryDocument
 
readFreqsAndModes() - Method in class org.jmol.adapter.readers.more.MoldenReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.more.AdfReader
Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.more.GamessReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.more.GaussianReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.more.MopacReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.more.NWChemReader
Reads the AtomSet and projected frequencies in the frequency section.
readFrequencies() - Method in class org.jmol.adapter.readers.more.QchemReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.more.SpartanReader
 
readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.more.GamessReader
 
readGaussianBasis() - Method in class org.jmol.adapter.readers.more.MoldenReader
 
readGaussianBasis() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readGradients() - Method in class org.jmol.adapter.readers.more.NWChemReader
Reads the energy gradients section into a new AtomSet.
readHeader() - Method in class org.jmol.adapter.readers.more.OdysseyReader
 
readHeader() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readHeader() - Method in class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
readHeader() - Method in class org.jmol.util.CompoundDocument
 
readInt() - Method in class org.jmol.util.BinaryDocument
 
readKeywords() - Method in class org.jmol.adapter.readers.more.MopacGraphfReader
 
readLEInt() - Method in class org.jmol.util.BinaryDocument
 
readLine() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readLineTrimmed() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readLineWithContinuation() - Method in class org.jmol.adapter.readers.more.V3000Reader
 
readLineWithNewline() - Method in class org.jmol.adapter.smarter.LimitedLineReader
 
readLong() - Method in class org.jmol.util.BinaryDocument
 
readMolecularOrbital() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readMolecularOrbital() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.more.GamessReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.more.GaussianReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.more.JaguarReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.more.MoldenReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.more.PsiReader
 
readMOs(boolean) - Method in class org.jmol.adapter.readers.more.MopacGraphfReader
 
readNonCommentLine() - Method in class org.jmol.jvxl.readers.LimitedLineReader
 
readNWChemLine() - Method in class org.jmol.adapter.readers.more.NWChemReader
 
readOccupancy() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
readOccupancy() - Method in class org.jmol.adapter.readers.more.PqrReader
 
readOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.more.GamessUKReader
 
readPartialCharge() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
readPartialCharge() - Method in class org.jmol.adapter.readers.more.PqrReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.more.GaussianReader
Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.more.NWChemReader
Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.more.QchemReader
 
readPmesh() - Method in class org.jmol.shapesurface.Pmesh
 
readPoint3fArray(Point3f[]) - Method in class org.jmol.util.BinaryDocument
 
readPolygon(int) - Method in class org.jmol.shapesurface.Pmesh
 
readPolygonCount() - Method in class org.jmol.shapesurface.Pmesh
 
readPolygonIndexes() - Method in class org.jmol.shapesurface.Pmesh
 
readProperties() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readProperty() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readRadius() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
readRadius() - Method in class org.jmol.adapter.readers.more.PqrReader
 
readResInfo(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readSCFDone() - Method in class org.jmol.adapter.readers.more.GaussianReader
Interprets the SCF Done: section.
readSCFDone() - Method in class org.jmol.adapter.readers.more.PsiReader
Interprets the SCF Done: section.
readShort() - Method in class org.jmol.util.BinaryDocument
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.more.MopacGraphfReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.more.WebMOReader
 
readSurfacePoint(float, boolean, float, float, Point3f, Vector3f, float[], Point3f) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readSurfacePoint(float, boolean, float, float, Point3f, Vector3f, float[], Point3f) - Method in class org.jmol.jvxl.readers.VoxelReader
 
readSymmetry() - Method in class org.jmol.adapter.readers.more.NWChemReader
Read the symmetry information and set the property.
readTitleLines() - Method in class org.jmol.adapter.readers.more.CubeReader
 
readTitleLines() - Method in class org.jmol.jvxl.readers.ApbsReader
 
readTitleLines() - Method in class org.jmol.jvxl.readers.CubeReader
 
readTitleLines() - Method in class org.jmol.jvxl.readers.JaguarReader
nothing much here
readTitleLines() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readTitleLines() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
readTitleLines() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readTitleLines() - Method in class org.jmol.jvxl.readers.XplorReader
 
readTotal() - Method in class org.jmol.adapter.readers.more.NWChemReader
Interpret a line starting with a line with "Total" in it.
readUniqueAtoms() - Method in class org.jmol.adapter.readers.more.PsiReader
 
readVertexCount() - Method in class org.jmol.shapesurface.Pmesh
 
readVertices() - Method in class org.jmol.shapesurface.Pmesh
 
readVibFreqs() - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
readVolumeParameters() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVolumeParameters() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumeParameters() - Method in class org.jmol.jvxl.readers.VoxelReader
 
readVolumetricHeader() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
readVolumetricHeader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumetricHeader() - Method in class org.jmol.jvxl.readers.XplorReader
 
readVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readVoxelData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVoxelData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVoxelData(boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
readVoxelDataIndividually(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVoxelVector(int) - Method in class org.jmol.adapter.readers.more.CubeReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.ApbsReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JaguarReader
read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVoxelVectors() - Method in class org.jmol.adapter.readers.more.CubeReader
 
readVoxelVectors() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
readVoxelVectors() - Method in class org.jmol.jvxl.readers.XplorReader
 
readXML(String) - Method in class org.jmol.adapter.readers.more.OdysseyXMLReader
 
RealFirstx - Variable in class org.jmol.jcamp.ZoneVisu
 
realFistX - Variable in class org.jmol.jcamp.data.GraphControlData
 
realLastX - Variable in class org.jmol.jcamp.data.GraphControlData
 
RealLastx - Variable in class org.jmol.jcamp.ZoneVisu
 
realloc(int[]) - Method in class org.jmol.g3d.Cylinder3D
 
realloc(float[]) - Method in class org.jmol.g3d.Cylinder3D
 
reallocRasterArrays(int) - Method in class org.jmol.g3d.Triangle3D
 
reallocRgb16s(Rgb16[], int) - Method in class org.jmol.g3d.Triangle3D
 
Really_Load_File(String) - Method in class org.jmol.jcamp.Visua
 
realVertexCount - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
rebond() - Method in class org.jmol.api.JmolViewer
 
rebond() - Method in class org.jmol.viewer.Viewer
 
recalc() - Method in class org.jmol.shape.Object2d
 
recalc() - Method in class org.jmol.shape.Text
 
recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelCollection
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelset.Polymer
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
recallCommand(boolean) - Method in class org.jmol.applet.Console.ControlEnterTextArea
 
recallCommand(boolean) - Method in class org.openscience.jmol.app.ConsoleTextPane
Recall command history.
recentFiles - Variable in class org.openscience.jmol.app.Jmol
 
recentFilesAction - Static variable in class org.openscience.jmol.app.Jmol
 
RecentFilesDialog - Class in org.openscience.jmol.app
Manages a list of recently opened files.
RecentFilesDialog(Frame) - Constructor for class org.openscience.jmol.app.RecentFilesDialog
Creates a hidden recent files dialog
recordAtomVector(int, int, float, float, float) - Method in class org.jmol.adapter.readers.more.QchemReader
 
recordTime(int) - Method in class org.openscience.jmol.app.DisplayPanel
 
rectClip - Variable in class org.jmol.applet.Jvm12
 
rectClip - Variable in class org.openscience.jmol.app.DisplayPanel
 
rectRubber - Static variable in class org.jmol.viewer.MouseManager
 
red - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
RED - Static variable in class org.jmol.g3d.Graphics3D
 
redoButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
Redraw() - Method in class org.jmol.jcamp.ZoneVisu
 
Reduce_String_0(String) - Method in class org.jmol.jcamp.ZoneVisu
 
Reduce_String_EndBlanks(String) - Method in class org.jmol.jcamp.ZoneVisu
 
reduceDataPrecision(String) - Static method in class org.jmol.jcamp.utils.StringDataUtils
Reduces the precision of numerical data strings provided
reduceFilename(String) - Static method in class org.jmol.viewer.ModelManager
 
referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
 
reformatDistanceIfSelected() - Method in class org.jmol.modelset.Measurement
 
reformatDistances() - Method in class org.jmol.shape.Measures
 
refresh(int, String) - Method in class org.jmol.api.JmolViewer
 
refresh() - Method in class org.jmol.modelset.Measurement
 
refresh() - Method in class org.jmol.viewer.Eval
 
refresh() - Method in class org.jmol.viewer.RepaintManager
 
refresh - Static variable in class org.jmol.viewer.Token
 
refresh(int, String) - Method in class org.jmol.viewer.Viewer
initiate a repaint/update sequence if it has not already been requested.
refreshing - Variable in class org.jmol.viewer.Viewer
 
refreshMeasures() - Method in class org.jmol.viewer.Viewer
 
registerAllValues(StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
rehash() - Method in class org.jmol.util.Int2IntHash
 
release() - Method in class org.jmol.bspt.CubeIterator
nulls internal references
release() - Method in interface org.jmol.modelset.AtomIndexIterator
 
release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
release() - Method in class org.jmol.modelset.AtomIteratorWithinSet
 
releaseBufferForClearing() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
releaseBuffers() - Method in class org.jmol.g3d.Graphics3D
 
releaseBuffers() - Method in class org.jmol.g3d.Platform3D
 
releaseModelSet() - Method in class org.jmol.modelset.AtomCollection
 
releaseModelSet() - Method in class org.jmol.modelset.BondCollection
 
releaseModelSet() - Method in class org.jmol.modelset.ModelCollection
 
releaseModelSet() - Method in class org.jmol.modelset.ModelLoader
 
releaseModelSet() - Method in class org.jmol.modelset.ModelSet
 
releaseScreenImage() - Method in class org.jmol.api.JmolViewer
 
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
 
releaseScreenImage() - Method in class org.jmol.viewer.Viewer
 
remapColors() - Method in class org.jmol.shape.Shape
 
remapColors() - Method in class org.jmol.shapesurface.Isosurface
 
remappable - Variable in class org.jmol.jvxl.readers.Parameters
 
remark350() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
rememberCheckbox(String, Object) - Method in class org.jmol.popup.JmolPopup
 
remoteAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
remoteAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
remove(int, int) - Method in class org.openscience.jmol.app.ConsoleDocument
 
removeAll(Object) - Method in class org.jmol.popup.JmolPopup
 
removeAll(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
removeAll(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
removeAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
removeCommand() - Method in class org.jmol.util.CommandHistory
 
removeCommand(int) - Method in class org.jmol.util.CommandHistory
 
removeCommand() - Method in class org.jmol.viewer.Viewer
Removes one command from the command history
removeConsumer(ImageConsumer) - Method in class org.jmol.g3d.Awt3D
 
removeJmolParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
removeMenuItem(Object, int) - Method in class org.jmol.popup.JmolPopup
 
removeMenuItem(Object, int) - Method in class org.jmol.popup.JmolPopupAwt
 
removeMenuItem(Object, int) - Method in class org.jmol.popup.JmolPopupSwing
 
removeMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
removeMouseListeners11() - Method in class org.jmol.viewer.MouseManager
 
removeMouseListeners11() - Method in class org.jmol.viewer.MouseManager11
 
removeMouseListeners14() - Method in class org.jmol.viewer.MouseManager
 
removeMouseListeners14() - Method in class org.jmol.viewer.MouseManager14
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.openscience.jmol.app.FileDropper
 
removeProteinStructure(int, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
removeUserVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
 
renameMenu(Object, String) - Method in class org.jmol.popup.JmolPopup
 
renameMenu(Object, String) - Method in class org.jmol.popup.JmolPopupAwt
 
renameMenu(Object, String) - Method in class org.jmol.popup.JmolPopupSwing
 
render(short, short, boolean, boolean, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Cylinder3D
 
render(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Hermite3D
 
render(int[], boolean, int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.g3d.Sphere3D
 
render() - Method in class org.jmol.shape.AxesRenderer
 
render() - Method in class org.jmol.shape.BallsRenderer
 
render() - Method in class org.jmol.shape.BbcageRenderer
 
render() - Method in class org.jmol.shape.DotsRenderer
 
render() - Method in class org.jmol.shape.EchoRenderer
 
render(int, Point3f[], Point3f[], Point3f[], int) - Method in class org.jmol.shape.FontLineShapeRenderer
 
render() - Method in class org.jmol.shape.FrankRenderer
 
render() - Method in class org.jmol.shape.HalosRenderer
 
render() - Method in class org.jmol.shape.HoverRenderer
 
render() - Method in class org.jmol.shape.LabelsRenderer
 
render() - Method in class org.jmol.shape.MeasuresRenderer
 
render() - Method in class org.jmol.shape.MeshRenderer
 
render(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.shape.ShapeRenderer
 
render() - Method in class org.jmol.shape.ShapeRenderer
 
render() - Method in class org.jmol.shape.StarsRenderer
 
render() - Method in class org.jmol.shape.SticksRenderer
 
render(JmolRendererInterface, float, float) - Method in class org.jmol.shape.Text
 
render() - Method in class org.jmol.shape.UccageRenderer
 
render() - Method in class org.jmol.shapebio.BioShapeRenderer
 
render() - Method in class org.jmol.shapespecial.DipolesRenderer
 
render() - Method in class org.jmol.shapespecial.DrawRenderer
 
render() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
render() - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
 
render() - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
render() - Method in class org.jmol.shapespecial.VectorsRenderer
 
render() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
render() - Method in class org.jmol.shapesurface.MolecularOrbitalRenderer
 
render(Graphics3D, ModelSet) - Method in class org.jmol.viewer.FrameRenderer
 
render(Graphics3D, ModelSet) - Method in class org.jmol.viewer.RepaintManager
 
render() - Method in class org.jmol.viewer.Viewer
 
render1(Dots) - Method in class org.jmol.shape.DotsRenderer
 
render1(Atom, short, short) - Method in class org.jmol.shape.HalosRenderer
 
render1(Mesh) - Method in class org.jmol.shape.MeshRenderer
 
render1(Atom, short) - Method in class org.jmol.shape.StarsRenderer
 
render1(int) - Method in class org.jmol.shape.UccageRenderer
 
render1() - Method in class org.jmol.shapebio.CartoonRenderer
 
render1() - Method in class org.jmol.shapebio.RocketsRenderer
 
render1() - Method in class org.jmol.shapebio.StrandsRenderer
 
render1(Atom, Object[]) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
render1(Polyhedra.Polyhedron, short) - Method in class org.jmol.shapespecial.PolyhedraRenderer
 
render1(Graphics, Image, int, int) - Method in class org.jmol.viewer.Viewer
 
render1Strand(Point3i[]) - Method in class org.jmol.shapebio.StrandsRenderer
 
render2(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Hermite3D
 
render2() - Method in class org.jmol.shape.MeshRenderer
 
render2() - Method in class org.jmol.shapespecial.DrawRenderer
 
render2() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
render2Strand(boolean, float, float) - Method in class org.jmol.shapebio.MeshRibbonRenderer
 
render2x(boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Hermite3D
 
renderAngle(boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderArc(Point3f, int, int) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderArcs(Point3f) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderArrowHead(Point3f, Point3f, float, boolean, boolean) - Method in class org.jmol.shapespecial.DrawRenderer
 
renderAsBarrels - Variable in class org.jmol.shapebio.RocketsRenderer
 
renderAsRockets - Variable in class org.jmol.shapebio.CartoonRenderer
 
renderAtom(Atom, short) - Method in interface org.jmol.api.JmolExportInterface
 
renderAtom(Atom, short) - Method in class org.jmol.export._MayaExporter
 
renderAtom(Atom, short) - Method in class org.jmol.export._PovrayExporter
 
renderAtom(Atom, short) - Method in class org.jmol.export._VrmlExporter
 
renderAxes() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderBackground() - Method in interface org.jmol.api.JmolExportInterface
 
renderBackground() - Method in class org.jmol.export._MayaExporter
 
renderBackground() - Method in class org.jmol.export._PovrayExporter
 
renderBackground() - Method in class org.jmol.export._VrmlExporter
 
renderBackground() - Method in class org.jmol.export.Export3D
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
renderBall(Atom) - Method in class org.jmol.export.BallsGenerator
 
renderBall(Atom) - Method in class org.jmol.shape.BallsRenderer
 
renderBall() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.BackboneRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.CartoonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.MeshRibbonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.RibbonsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.StrandsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.shapebio.TraceRenderer
 
renderBits(short, short, boolean, boolean, byte, int, float, float, float, float, float, float) - Method in class org.jmol.g3d.Cylinder3D
 
renderBond(int) - Method in class org.jmol.export.SticksGenerator
 
renderBond() - Method in class org.jmol.shape.SticksRenderer
 
renderBond(int) - Method in class org.jmol.shape.SticksRenderer
 
renderCone(short, boolean, byte, int, float, float, float, float, float, float, boolean) - Method in class org.jmol.g3d.Cylinder3D
 
renderCone(int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderConvex(short, int[], int) - Method in class org.jmol.shape.DotsRenderer
generic renderer -- dots and geosurface
renderConvex(short, int[], int) - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
 
renderCylinder(Point3f, Point3f, short, byte, int) - Method in class org.jmol.export._MayaExporter
 
renderCylinder(Point3f, Point3f, short, byte, int) - Method in class org.jmol.export._PovrayExporter
 
renderCylinder(Point3f, Point3f, short, byte, int) - Method in class org.jmol.export._VrmlExporter
 
renderDipoleVector(Dipole) - Method in class org.jmol.shapespecial.DipolesRenderer
 
renderDistance(boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderDots(int) - Method in class org.jmol.shape.DotsRenderer
also called by GeoSurface when in motion
renderDots(Point3f) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderEllipsoid(short, int, int, int, int, double[], Point3i[]) - Method in interface org.jmol.api.JmolExportInterface
 
renderEllipsoid(int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in interface org.jmol.api.JmolRendererInterface
 
renderEllipsoid(short, int, int, int, int, double[], Point3i[]) - Method in class org.jmol.export._MayaExporter
 
renderEllipsoid(short, int, int, int, int, double[], Point3i[]) - Method in class org.jmol.export._PovrayExporter
 
renderEllipsoid(short, int, int, int, int, double[], Point3i[]) - Method in class org.jmol.export._VrmlExporter
 
renderEllipsoid(int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.export.Export3D
 
renderEllipsoid(int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.g3d.Graphics3D
 
renderEllipsoid(Ellipsoids.Ellipsoid) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
renderers - Variable in class org.jmol.viewer.FrameRenderer
 
renderExport() - Method in class org.jmol.export.IsosurfaceGenerator
 
renderExport() - Method in class org.jmol.export.LcaoCartoonGenerator
 
renderExport() - Method in class org.jmol.export.MolecularOrbitalGenerator
 
renderExport() - Method in class org.jmol.export.PmeshGenerator
 
renderExport() - Method in class org.jmol.shape.MeshRenderer
 
renderFlatEndcap(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
renderFlatEndcapPrecisely(boolean) - Method in class org.jmol.g3d.Cylinder3D
 
renderFrameTitle(String) - Method in class org.jmol.shape.EchoRenderer
 
renderHandles() - Method in class org.jmol.shapespecial.DrawRenderer
 
renderHbondDashed() - Method in class org.jmol.shape.SticksRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteConic(int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteCylinder(Point3i[], int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
 
renderInfo(SymmetryInterface) - Method in class org.jmol.shape.UccageRenderer
 
renderInfo() - Method in class org.jmol.shapespecial.DrawRenderer
 
renderInfo() - Method in class org.jmol.shapesurface.MolecularOrbitalRenderer
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in interface org.jmol.api.JmolExportInterface
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in class org.jmol.export._MayaExporter
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in class org.jmol.export._PovrayExporter
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in class org.jmol.export._VrmlExporter
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in class org.jmol.export.Export3D
 
renderIsosurface(Point3f[], short, short[], Vector3f[], int[][], BitSet, int, int) - Method in class org.jmol.g3d.Graphics3D
 
renderJoint(Point3f, short, byte, int) - Method in class org.jmol.export._PovrayExporter
 
renderLabel(String, Font3D, float, float, float, float, float) - Method in class org.jmol.shape.AxesRenderer
 
renderLarge() - Method in class org.jmol.g3d.Sphere3D
 
renderLine(Point3f, Point3f, int, byte, Point3i, Point3i) - Method in class org.jmol.shape.ShapeRenderer
 
renderMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
RenderMode - Variable in class org.openscience.jmol.app.webexport.Molecules
 
RenderMode - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
renderNormals() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderNucleic() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderNucleicBaseStep(NucleicMonomer, short, Point3i) - Method in class org.jmol.shapebio.CartoonRenderer
 
renderOffscreen(String, Font3D, Platform3D, boolean) - Method in class org.jmol.g3d.Text3D
 
renderPending() - Method in class org.jmol.shapebio.RocketsRenderer
 
renderPendingMeasurement(MeasurementPending) - Method in class org.jmol.shape.MeasuresRenderer
 
renderPendingRocketSegment(int, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderPendingSheet(Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderPendingWithCursor(int, MeasurementPending) - Method in class org.jmol.shape.MeasuresRenderer
 
renderPoints() - Method in class org.jmol.shape.MeshRenderer
 
renderPoints() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderQuadrant(int, int) - Method in class org.jmol.g3d.Sphere3D
 
renderQuadrantClipped(int, int, int) - Method in class org.jmol.g3d.Sphere3D
 
renderQuadrantUnclipped(int, int, int) - Method in class org.jmol.g3d.Sphere3D
 
renderRing5() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderRing6() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderRockets() - Method in class org.jmol.shapebio.CartoonRenderer
 
renderScreenImage(Graphics, Dimension, Rectangle) - Method in class org.jmol.api.JmolSimpleViewer
 
renderScreenImage(Graphics, Dimension, Rectangle) - Method in class org.jmol.viewer.Viewer
 
renderShapeClipped(int[]) - Method in class org.jmol.g3d.Sphere3D
 
renderShapeUnclipped(int[]) - Method in class org.jmol.g3d.Sphere3D
 
renderSimpleLabel(JmolRendererInterface, Font3D, String, short, short, float[], int, int, int, int, float, int, boolean, short) - Static method in class org.jmol.shape.Text
 
renderSpecialSegment(Monomer, short, short) - Method in class org.jmol.shapebio.RocketsRenderer
 
renderSphericalEndcaps() - Method in class org.jmol.g3d.Cylinder3D
 
renderSurface(int[]) - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
 
renderText(Text) - Method in interface org.jmol.api.JmolExportInterface
 
renderText(Text) - Method in class org.jmol.export._MayaExporter
 
renderText(Text) - Method in class org.jmol.export._PovrayExporter
 
renderText(Text) - Method in class org.jmol.export._VrmlExporter
 
renderTorsion(boolean) - Method in class org.jmol.shape.MeasuresRenderer
 
renderTriangle(Bond) - Method in class org.jmol.shape.SticksRenderer
 
renderTriangles(boolean, boolean) - Method in class org.jmol.shape.MeshRenderer
 
renderTriangles(boolean, boolean) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
renderVector(Atom) - Method in class org.jmol.shapespecial.VectorsRenderer
 
renderWireframe - Variable in class org.jmol.shape.SticksRenderer
 
renderXyArrow(int) - Method in class org.jmol.shapespecial.DrawRenderer
 
repaint() - Method in class org.jmol.viewer.Viewer
 
repaintClock() - Method in class org.jmol.appletwrapper.AppletWrapper
 
repaintDone() - Method in class org.jmol.viewer.RepaintManager
 
RepaintManager - Class in org.jmol.viewer
 
RepaintManager(Viewer) - Constructor for class org.jmol.viewer.RepaintManager
 
repaintManager - Variable in class org.jmol.viewer.Viewer
 
RepaintManager.AnimationThread - Class in org.jmol.viewer
 
RepaintManager.AnimationThread(int, int, int) - Constructor for class org.jmol.viewer.RepaintManager.AnimationThread
 
repaintPending - Variable in class org.jmol.viewer.RepaintManager
 
repaintView() - Method in class org.jmol.api.JmolViewer
 
repaintView() - Method in class org.jmol.viewer.Viewer
 
repeatCheckBox - Variable in class org.openscience.jmol.app.AtomSetChooser
 
replace - Static variable in class org.jmol.viewer.Token
 
replace(int, int, String, AttributeSet) - Method in class org.openscience.jmol.app.ConsoleDocument
 
replaceAllCharacters(String, String, String) - Static method in class org.jmol.util.TextFormat
Does a clean replace of any of the characters in str with strTo If strTo contains strFrom, then only a single pass is done.
replaceAllCharacters(String, String, char) - Static method in class org.jmol.util.TextFormat
Does a clean replace of any of the characters in str with chrTo If strTo contains strFrom, then only a single pass is done.
replaceCommand(String, boolean) - Method in class org.openscience.jmol.app.ConsoleDocument
Replaces current command on script.
report(String) - Static method in class org.openscience.jmol.app.Jmol
 
reportAll - Variable in class org.jmol.shape.Sticks
 
reportSelection(String) - Method in class org.jmol.viewer.Viewer
 
repositionWindow(String, Component, int, int) - Method in class org.jmol.export.dialog.HistoryFile
Uses the informations in the history to reposition the window.
repositionWindow(String, Component) - Method in class org.jmol.export.dialog.HistoryFile
Uses the informations in the history to reposition the window.
requestRepaintAndWait() - Method in class org.jmol.viewer.RepaintManager
 
requestRepaintAndWait() - Method in class org.jmol.viewer.Viewer
 
requestTopDownLeftRightResend(ImageConsumer) - Method in class org.jmol.g3d.Awt3D
 
REQUIRE_PROGRESSBAR - Static variable in class org.jmol.applet.Jmol
 
reset() - Method in class org.jmol.modelset.BoxInfo
 
reset(int) - Method in class org.jmol.util.CommandHistory
Resets instance.
reset() - Method in class org.jmol.viewer.Eval
 
reset() - Method in class org.jmol.viewer.MonitorInputStream
 
reset - Static variable in class org.jmol.viewer.Token
 
reset() - Method in class org.jmol.viewer.Viewer
 
reset() - Method in class org.openscience.jvxl.MonitorInputStream
 
resetAromatic() - Method in class org.jmol.modelset.BondCollection
 
resetAromatic() - Method in class org.jmol.viewer.Viewer
 
resetAxes() - Method in class org.jmol.modelsetbio.ProteinStructure
 
resetAxisCoordinates() - Method in class org.jmol.shape.SticksRenderer
 
resetDefaults(String[]) - Method in class org.openscience.jmol.app.PreferencesDialog
 
resetElementColors() - Method in class org.jmol.viewer.ColorManager
 
resetFlag - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
resetFrankMenu() - Method in class org.jmol.popup.JmolPopup
 
resetFrankMenu() - Method in class org.jmol.popup.JmolPopupAwt
 
resetFrankMenu() - Method in class org.jmol.popup.JmolPopupSwing
 
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.Monomer
 
resetIsosurface() - Method in class org.jmol.jvxl.readers.VoxelReader
 
resetMeasurement() - Method in class org.jmol.viewer.PickingManager
 
resetMessageQueue(String) - Method in class org.jmol.viewer.StatusManager
 
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
something has arisen that requires resetting of the navigation point.
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager11
 
resetParameterStringValue(String, StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
resetTimes() - Method in class org.openscience.jmol.app.DisplayPanel
 
residue - Static variable in class org.jmol.viewer.Token
 
residueSpecCodeGenerated - Variable in class org.jmol.viewer.Compiler
 
resizeByteArray(byte[], int) - Method in class org.jmol.export.image.PngEncoder
Increase or decrease the length of a byte array.
resizeImage(int, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
resno - Static variable in class org.jmol.viewer.Token
 
resolution - Variable in class org.jmol.jvxl.readers.Parameters
 
resolve(String, String, BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
 
resolve(String, String, BufferedReader, Hashtable) - Static method in class org.jmol.adapter.smarter.Resolver
 
resolveEntity(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.DummyResolver
 
resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
resolveEntity(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
Resolver - Class in org.jmol.adapter.smarter
 
Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
 
Resolver - Class in org.jmol.modelsetbio
 
Resolver() - Constructor for class org.jmol.modelsetbio.Resolver
 
restorativeForceAndAngleRadians(Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndDistance(Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndOutOfPlaneAngleRadians(Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndTorsionAngleRadians(Vector3d, Vector3d, Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
restore() - Method in class org.jmol.viewer.Eval
 
restore() - Method in class org.jmol.viewer.StateManager.Connections
 
restore(float, boolean) - Method in class org.jmol.viewer.StateManager.Orientation
 
restore - Static variable in class org.jmol.viewer.Token
 
restoreBonds(String) - Method in class org.jmol.viewer.StateManager
 
restoreBonds(String) - Method in class org.jmol.viewer.Viewer
 
restoreCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
 
restoreCoordinates() - Method in class org.jmol.minimize.Minimizer
 
restoreModelOrientation(int) - Method in class org.jmol.viewer.Viewer
 
restoreModelRotation(int) - Method in class org.jmol.viewer.Viewer
 
restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
 
restoreOrientation(String, float) - Method in class org.jmol.viewer.Viewer
 
restorePopupMenu() - Method in class org.jmol.popup.JmolPopup
 
restoreRotation(String, float) - Method in class org.jmol.viewer.Viewer
 
restoreSelection(String) - Method in class org.jmol.viewer.StateManager
 
restoreSelection(String) - Method in class org.jmol.viewer.Viewer
 
restrict() - Method in class org.jmol.viewer.Eval
 
restrict - Static variable in class org.jmol.viewer.Token
 
restrictSelected(boolean) - Method in class org.jmol.viewer.Eval
 
RESU - Static variable in class org.jmol.util.ColorEncoder
 
resume - Static variable in class org.jmol.viewer.Token
 
resumeAnimation() - Method in class org.jmol.viewer.RepaintManager
 
resumeAnimation() - Method in class org.jmol.viewer.Viewer
 
resumePausedExecution() - Method in class org.jmol.viewer.Eval
 
resumeScriptExecution() - Method in class org.jmol.viewer.Viewer
 
returnCmd() - Method in class org.jmol.viewer.Eval
 
returncmd - Static variable in class org.jmol.viewer.Token
 
returnToken() - Method in class org.jmol.viewer.Compiler
 
returnValue - Variable in class org.jmol.viewer.Function
 
Reverse - Variable in class org.jmol.jcamp.Visua
 
reverse - Variable in class org.jmol.jcamp.ZoneVisu
 
Reverse() - Method in class org.jmol.jcamp.ZoneVisu
 
reverseAnimation() - Method in class org.jmol.viewer.RepaintManager
 
reverseAnimation() - Method in class org.jmol.viewer.Viewer
 
revNumber - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
rewind - Static variable in class org.jmol.viewer.Token
 
REWIND - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
rewindAnimation() - Method in class org.jmol.viewer.RepaintManager
 
rewindAnimation() - Method in class org.jmol.viewer.Viewer
 
rfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
rFill(StringBuffer, String, String) - Static method in class org.jmol.util.TextFormat
 
rgb - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
rgb - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
rgb(int, int, int) - Static method in class org.jmol.g3d.Shade3D
 
Rgb16 - Class in org.jmol.g3d
 
Rgb16() - Constructor for class org.jmol.g3d.Rgb16
 
Rgb16(int) - Constructor for class org.jmol.g3d.Rgb16
 
rgb16sE - Variable in class org.jmol.g3d.Triangle3D
 
rgb16sGouraud - Variable in class org.jmol.g3d.Triangle3D
 
rgb16sW - Variable in class org.jmol.g3d.Triangle3D
 
rgb16t1 - Variable in class org.jmol.g3d.Triangle3D
 
rgb16t2 - Variable in class org.jmol.g3d.Triangle3D
 
rgb2 - Variable in class org.jmol.export.image.GifEncoder.ColorItem
 
rgbColorModel - Static variable in class org.jmol.g3d.Swing3D
 
rgbColorModelT - Static variable in class org.jmol.g3d.Swing3D
 
rgbFractionalFromArgb(int, char) - Method in class org.jmol.export._Exporter
 
rgbFractionalFromColix(short, char) - Method in class org.jmol.export._Exporter
 
rgbFromColix(short, char) - Method in class org.jmol.export._Exporter
 
rgbModel - Static variable in class org.jmol.export.image.ImageEncoder
 
rgbPixels - Variable in class org.jmol.export.image.GifEncoder
 
ribbon - Static variable in class org.jmol.viewer.Token
 
ribbonAspectRatio - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ribbonBorder - Variable in class org.jmol.shapebio.BioShapeRenderer
 
ribbonBorder - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
ribbonBottomScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
Ribbons - Class in org.jmol.shapebio
 
Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
 
RibbonsGenerator - Class in org.jmol.export
 
RibbonsGenerator() - Constructor for class org.jmol.export.RibbonsGenerator
 
RibbonsRenderer - Class in org.jmol.shapebio
 
RibbonsRenderer() - Constructor for class org.jmol.shapebio.RibbonsRenderer
 
ribbonTopScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
 
RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
right - Static variable in class org.jmol.viewer.Token
 
rightAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
rightbrace - Static variable in class org.jmol.viewer.Token
 
rightDifference(Quaternion) - Method in class org.jmol.util.Quaternion
 
rightparen - Static variable in class org.jmol.viewer.Token
 
rightsquare - Static variable in class org.jmol.viewer.Token
 
ring5OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
ring5Points - Variable in class org.jmol.shapebio.CartoonRenderer
 
ring5Screens - Variable in class org.jmol.shapebio.CartoonRenderer
 
ring6OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
ring6Points - Variable in class org.jmol.shapebio.CartoonRenderer
 
ring6Screens - Variable in class org.jmol.shapebio.CartoonRenderer
 
ringBonds - Variable in class org.jmol.smiles.SmilesParser
 
rmaxx - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rmaxy - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rmaxz - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rminx - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rminy - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rminz - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
rna - Static variable in class org.jmol.viewer.Token
 
rocket - Static variable in class org.jmol.viewer.Token
 
rocketBarrels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Rockets - Class in org.jmol.shapebio
 
Rockets() - Constructor for class org.jmol.shapebio.Rockets
 
RocketsGenerator - Class in org.jmol.export
 
RocketsGenerator() - Constructor for class org.jmol.export.RocketsGenerator
 
RocketsRenderer - Class in org.jmol.shapebio
 
RocketsRenderer() - Constructor for class org.jmol.shapebio.RocketsRenderer
 
ROOT2 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
 
rootEntry - Variable in class org.jmol.util.CompoundDocument
 
rotate(boolean, boolean) - Method in class org.jmol.viewer.Eval
 
rotate - Static variable in class org.jmol.viewer.Token
 
rotateAboutPointsInternal(Point3f, Point3f, float, float, boolean, boolean, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAboutPointsInternal(Point3f, Point3f, float, float, boolean, BitSet) - Method in class org.jmol.viewer.Viewer
 
rotateAtoms(Matrix3f, Matrix3f, BitSet, boolean, Point3f, boolean) - Method in class org.jmol.modelset.ModelCollection
 
rotateAtoms(Matrix3f, Matrix3f, boolean, Point3f, boolean, BitSet) - Method in class org.jmol.viewer.Viewer
 
rotateAxisAngle(Vector3f, float) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngle(AxisAngle4f, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(Point3f, Vector3f, float, float, boolean, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(Point3f, Vector3f, float, float, boolean, BitSet) - Method in class org.jmol.viewer.Viewer
 
rotateAxisAngleRadiansFixed(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleRadiansInternal(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateEllipsoid(int, Point3f, Vector3f[], Point3f, Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
rotateEllipsoid(int, Point3f, Vector3f[], UnitCell, Point3f, Point3f) - Method in class org.jmol.symmetry.SpaceGroup
 
rotateEllipsoid(int, Point3f, Vector3f[], Point3f, Point3f) - Method in class org.jmol.symmetry.Symmetry
 
rotateEllipsoid(Point3f, Vector3f[], UnitCell, Point3f, Point3f) - Method in class org.jmol.symmetry.SymmetryOperation
 
rotateFront() - Method in class org.jmol.api.JmolViewer
 
rotateFront() - Method in class org.jmol.viewer.TransformManager
 
rotateFront() - Method in class org.jmol.viewer.Viewer
 
rotateMolecule - Variable in class org.jmol.viewer.TransformManager
 
rotateMolecule(int, int) - Method in class org.jmol.viewer.Viewer
 
rotatePoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
rotatePoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
rotateSelected - Static variable in class org.jmol.viewer.Token
 
rotateX(int) - Method in class org.jmol.api.JmolViewer
 
rotateX(float) - Method in class org.jmol.api.JmolViewer
 
rotateX(float) - Method in class org.jmol.viewer.TransformManager
 
rotateX(float) - Method in class org.jmol.viewer.Viewer
 
rotateX(int) - Method in class org.jmol.viewer.Viewer
 
rotateXRadians(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(int, int, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
 
rotateY(int) - Method in class org.jmol.api.JmolViewer
 
rotateY(float) - Method in class org.jmol.api.JmolViewer
 
rotateY(float) - Method in class org.jmol.viewer.TransformManager
 
rotateY(float) - Method in class org.jmol.viewer.Viewer
 
rotateY(int) - Method in class org.jmol.viewer.Viewer
 
rotateYRadians(float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
rotateZ(float) - Method in class org.jmol.api.JmolViewer
 
rotateZ(float) - Method in class org.jmol.viewer.TransformManager
 
rotateZ(float) - Method in class org.jmol.viewer.Viewer
 
rotateZBy(int) - Method in class org.jmol.viewer.TransformManager
 
rotateZBy(int) - Method in class org.jmol.viewer.Viewer
 
rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
 
rotation - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
Rotation - Class in org.jmol.symmetry
 
Rotation() - Constructor for class org.jmol.symmetry.Rotation
 
Rotation(String, String) - Constructor for class org.jmol.symmetry.Rotation
 
rotation - Static variable in class org.jmol.viewer.Token
 
rotationAxis - Variable in class org.jmol.shapesurface.LcaoCartoon
 
rotationAxis - Variable in class org.jmol.viewer.TransformManager
 
rotationCenterDefault - Variable in class org.jmol.viewer.TransformManager
 
rotationMatrix - Variable in class org.jmol.g3d.Normix3D
 
rotationMatrix - Variable in class org.jmol.viewer.StateManager.Orientation
 
rotationOrder - Variable in class org.jmol.symmetry.Translation
 
rotationRadius - Variable in class org.jmol.viewer.StateManager.Orientation
 
rotationRadiusDefault - Variable in class org.jmol.viewer.TransformManager
 
rotationRate - Variable in class org.jmol.viewer.TransformManager
 
rotationShift12ths - Variable in class org.jmol.symmetry.Translation
 
rotationTerms - Variable in class org.jmol.symmetry.HallInfo
 
rotCode - Variable in class org.jmol.symmetry.Rotation
 
ROYGB - Static variable in class org.jmol.util.ColorEncoder
 
rScaled - Variable in class org.jmol.g3d.Rgb16
 
rubberband - Static variable in class org.jmol.viewer.Token
 
rubberbandSelectionMode - Variable in class org.jmol.viewer.MouseManager
 
run() - Method in class org.jmol.appletwrapper.ClassPreloader
 
run() - Method in class org.jmol.appletwrapper.TickerThread
 
run() - Method in class org.jmol.appletwrapper.WrappedAppletLoader
 
run() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
run() - Method in class org.jmol.jcamp.Visua
 
run() - Method in class org.jmol.minimize.Minimizer.MinimizationThread
 
run() - Method in class org.jmol.viewer.FileManager.DOMOpenThread
 
run() - Method in class org.jmol.viewer.FileManager.FileOpenThread
 
run() - Method in class org.jmol.viewer.FileManager.FilesOpenThread
 
run() - Method in class org.jmol.viewer.MouseManager.HoverWatcher
 
run() - Method in class org.jmol.viewer.RepaintManager.AnimationThread
 
run() - Method in class org.jmol.viewer.ScriptManager.CommandWatcher
 
run() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
run() - Method in class org.jmol.viewer.TransformManager.SpinThread
 
run() - Method in class org.jmol.viewer.TransformManager.VibrationThread
 
run() - Method in class org.openscience.jmol.app.AboutDialog.PageLoader
 
run() - Method in class org.openscience.jmol.app.AtomSetChooser
 
run() - Method in class org.openscience.jmol.app.HelpDialog.PageLoader
 
run() - Method in class org.openscience.jmol.app.ScriptWindow.ExecuteCommandThread
 
run() - Method in class org.openscience.jmol.app.WhatsNewDialog.PageLoader
 
runButton - Variable in class org.jmol.applet.Console
 
runButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
runEval(boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Eval
 
runNextScript() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
runPovCheck - Variable in class org.openscience.jmol.app.PovrayDialog
 
runScript(String) - Method in class org.jmol.viewer.Eval
 
runScript(String, StringBuffer) - Method in class org.jmol.viewer.Eval
 
runScript(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
runStatus - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
RWB - Static variable in class org.jmol.util.ColorEncoder
 

S

s0 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
s1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
s10 - Static variable in class org.jmol.symmetry.PointGroup
 
s12 - Static variable in class org.jmol.symmetry.PointGroup
 
s2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
s3 - Static variable in class org.jmol.symmetry.PointGroup
 
s4 - Static variable in class org.jmol.symmetry.PointGroup
 
s5 - Static variable in class org.jmol.symmetry.PointGroup
 
s6 - Static variable in class org.jmol.symmetry.PointGroup
 
s8 - Static variable in class org.jmol.symmetry.PointGroup
 
safeTruncate(float, int) - Static method in class org.jmol.util.TextFormat
 
Saisie - Variable in class org.jmol.jcamp.SaisieDlg
 
SaisieDlg - Class in org.jmol.jcamp
 
SaisieDlg(Frame, String, String) - Constructor for class org.jmol.jcamp.SaisieDlg
 
sameAs(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
sameAs(int[], Point3fi[], int, int) - Method in class org.jmol.modelset.Measurement
 
sameAs(int, int) - Method in class org.jmol.modelset.Measurement
 
sampleModelBitMasks - Static variable in class org.jmol.g3d.Swing3D
 
sampleModelBitMasksT - Static variable in class org.jmol.g3d.Swing3D
 
sasurface - Static variable in class org.jmol.viewer.Token
 
SAT - Variable in class org.jmol.util.CompoundDocument
 
Sav_Firstx - Variable in class org.jmol.jcamp.ZoneVisu
 
Sav_Lastx - Variable in class org.jmol.jcamp.ZoneVisu
 
Sav_Nbpoints_a_tracer - Variable in class org.jmol.jcamp.ZoneVisu
 
SavBufGra - Variable in class org.jmol.jcamp.ZoneVisu
 
SavBufImg - Variable in class org.jmol.jcamp.ZoneVisu
 
save() - Method in class org.jmol.export.dialog.HistoryFile
Saves properties to the history file.
save() - Method in class org.jmol.viewer.Eval
 
save - Static variable in class org.jmol.viewer.Token
 
SAVE - Static variable in class org.openscience.jmol.app.AtomSetChooser
 
save() - Method in class org.openscience.jmol.app.PreferencesDialog
 
saveBonds(String) - Method in class org.jmol.viewer.StateManager
 
saveBonds(String) - Method in class org.jmol.viewer.Viewer
 
saveButton - Variable in class org.openscience.jmol.app.webexport.Molecules
 
saveButton - Variable in class org.openscience.jmol.app.webexport.Orbitals
 
saveButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
saveChooser - Static variable in class org.jmol.export.dialog.Dialog
 
saveChooser - Variable in class org.openscience.jmol.app.AtomSetChooser
 
saveCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
 
saveCoordinates() - Method in class org.jmol.minimize.Minimizer
 
saveCoordinates(String, BitSet) - Method in class org.jmol.viewer.StateManager
 
saveCoordinates(String, BitSet) - Method in class org.jmol.viewer.Viewer
 
saved - Variable in class org.jmol.viewer.StateManager
 
saveDialog - Variable in class org.jmol.jcamp.Visua
 
saveField - Variable in class org.openscience.jmol.app.PovrayDialog
 
saveHistory() - Method in class org.openscience.jmol.app.PovrayDialog
Just saves the path settings from this session.
saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
saveList() - Method in class org.openscience.jmol.app.RecentFilesDialog
Saves the list to the history file.
saveModelOrientation(int, StateManager.Orientation) - Method in class org.jmol.modelset.ModelCollection
 
saveModelOrientation() - Method in class org.jmol.viewer.Viewer
 
saveName - Variable in class org.jmol.viewer.StateManager.Connections
 
saveName - Variable in class org.jmol.viewer.StateManager.Orientation
 
saveOrientation(String) - Method in class org.jmol.viewer.StateManager
 
saveOrientation(String) - Method in class org.jmol.viewer.Viewer
 
savePathLabel - Variable in class org.openscience.jmol.app.PovrayDialog
 
saveSelection(String, BitSet) - Method in class org.jmol.viewer.StateManager
 
saveSelection(String) - Method in class org.jmol.viewer.Viewer
 
saveState(String) - Method in class org.jmol.viewer.StateManager
 
saveState(String) - Method in class org.jmol.viewer.Viewer
 
saveStructure(String) - Method in class org.jmol.viewer.StateManager
 
saveStructure(String) - Method in class org.jmol.viewer.Viewer
 
saveXYZCollection() - Method in class org.openscience.jmol.app.AtomSetChooser
Saves the currently active collection as a multistep XYZ file.
savFirstX - Variable in class org.jmol.jcamp.data.GraphControlData
 
savLastX - Variable in class org.jmol.jcamp.data.GraphControlData
 
say(String) - Method in class org.openscience.jmol.app.Jmol
 
scalarDictRef - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scalarDictValue - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scalarTitle - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scale(int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
scale - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
scale - Variable in class org.jmol.jvxl.readers.Parameters
 
scale - Variable in class org.jmol.shape.Axes
 
scale - Variable in class org.jmol.shape.Mesh
 
scale - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
scale - Static variable in class org.jmol.viewer.Token
 
scale3d - Static variable in class org.jmol.viewer.Token
 
scale3D - Variable in class org.jmol.viewer.TransformManager
 
scale3DAngstromsPerInch - Variable in class org.jmol.viewer.TransformManager
 
SCALE_FLAG - Static variable in class org.jmol.shape.Labels
 
SCALE_MAX - Static variable in class org.openscience.jmol.app.AtomSetChooser
Maximum value for vector scale.
SCALE_PRECISION - Static variable in class org.openscience.jmol.app.AtomSetChooser
Precision of the vector scale slider
SCALE_VALUE - Static variable in class org.openscience.jmol.app.AtomSetChooser
Initial value of vector scale.
scaleByVoxelVector(Vector3f, int) - Method in class org.jmol.jvxl.data.VolumeData
 
scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scaledHeightVector - Variable in class org.jmol.shapebio.RocketsRenderer
 
scaleDrawing(DrawMesh, float) - Static method in class org.jmol.shapespecial.Draw
 
scaledWidthVector - Variable in class org.jmol.shapebio.RocketsRenderer
 
scaleFitToScreen(boolean) - Method in class org.jmol.viewer.TransformManager
 
scaleFitToScreen(boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
scalePixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scalePixelsPerMicron - Variable in class org.jmol.shape.MeshRenderer
 
scalePixelsPerMicron - Variable in class org.jmol.shape.Object2d
 
scaleSlider - Variable in class org.openscience.jmol.app.AtomSetChooser
 
scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
 
scaleToPerspective(int, float) - Method in class org.jmol.viewer.Viewer
 
scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
 
scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
 
scaleToScreen(int, int) - Method in class org.jmol.viewer.Viewer
 
scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
 
scanPoint - Variable in class org.jmol.adapter.readers.more.GaussianReader
The scan point, where -1 denotes no scan information.
schemeIndex(String) - Static method in class org.jmol.util.ColorEncoder
 
schemes - Static variable in class org.jmol.util.ColorEncoder
 
screenA - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenArrowBot - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenArrowBotPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenArrowHead - Variable in class org.jmol.shapespecial.VectorsRenderer
 
screenArrowTop - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenArrowTopPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
 
screenB - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenC - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenCoordinates - Variable in class org.jmol.shape.DotsRenderer
 
screenCorners - Variable in class org.jmol.shapebio.RocketsRenderer
 
screenDiameter - Variable in class org.jmol.util.Point3fi
 
screenDotCount - Variable in class org.jmol.shape.DotsRenderer
 
screenHeight - Variable in class org.jmol.export._Exporter
 
screenHeight - Variable in class org.jmol.viewer.TransformManager
 
screenLevel - Variable in class org.jmol.shape.DotsRenderer
 
screenPixelCount - Variable in class org.jmol.viewer.TransformManager
 
screens - Variable in class org.jmol.shape.BbcageRenderer
 
screens - Variable in class org.jmol.shape.MeshRenderer
 
screens - Variable in class org.jmol.shape.UccageRenderer
 
screens - Variable in class org.jmol.shapespecial.DipolesRenderer
 
screens - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
screenSize - Static variable in class org.openscience.jmol.app.Jmol
 
screenVectorEnd - Variable in class org.jmol.shapespecial.VectorsRenderer
 
screenWidth - Variable in class org.jmol.export._Exporter
 
screenWidth - Variable in class org.jmol.viewer.TransformManager
 
screenX - Variable in class org.jmol.util.Point3fi
 
screenY - Variable in class org.jmol.util.Point3fi
 
screenZ - Variable in class org.jmol.util.Point3fi
 
script(String) - Method in interface org.jmol.api.JmolAppletInterface
 
script(String) - Method in class org.jmol.api.JmolViewer
 
script(String) - Method in class org.jmol.applet.Jmol
 
script - Variable in class org.jmol.jvxl.readers.Parameters
 
script - Variable in class org.jmol.shape.MeshCollection
 
script - Variable in class org.jmol.shape.Object2d
 
script - Variable in class org.jmol.viewer.Compiler
 
script - Variable in class org.jmol.viewer.Eval.Context
 
script - Variable in class org.jmol.viewer.Eval
 
script(int) - Method in class org.jmol.viewer.Eval
 
script - Variable in class org.jmol.viewer.Function
 
script - Static variable in class org.jmol.viewer.Token
 
script(String) - Method in class org.jmol.viewer.Viewer
 
script - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
script1 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
script2 - Variable in class org.jmol.modelset.ModelCollection.StateScript
 
SCRIPT_CHECK - Static variable in class org.jmol.applet.Jmol
 
SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.Eval
 
SCRIPT_NOWAIT - Static variable in class org.jmol.applet.Jmol
 
SCRIPT_WAIT - Static variable in class org.jmol.applet.Jmol
 
SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.Jmol
 
scriptAction - Static variable in class org.openscience.jmol.app.Jmol
 
ScriptButtons - Class in org.openscience.jmol.app.webexport
 
ScriptButtons(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.ScriptButtons
 
scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptCheck(String) - Method in class org.jmol.api.JmolViewer
 
scriptCheck(String) - Method in class org.jmol.applet.Jmol
 
scriptCheck(String) - Method in class org.jmol.viewer.Viewer
 
scriptCommand - Variable in class org.jmol.shape.Mesh
 
scriptDelay - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
scriptEcho(String) - Method in class org.jmol.viewer.Viewer
 
scriptError(String) - Method in class org.jmol.viewer.Viewer
 
scriptIndex - Variable in class org.jmol.viewer.Viewer
 
scriptLevel - Variable in class org.jmol.viewer.Eval
 
scriptLevelMax - Static variable in class org.jmol.viewer.Eval
 
ScriptManager - Class in org.jmol.viewer
 
ScriptManager(Viewer) - Constructor for class org.jmol.viewer.ScriptManager
 
scriptManager - Variable in class org.jmol.viewer.Viewer
 
ScriptManager.CommandWatcher - Class in org.jmol.viewer
 
ScriptManager.CommandWatcher() - Constructor for class org.jmol.viewer.ScriptManager.CommandWatcher
 
ScriptManager.ScriptQueueRunnable - Class in org.jmol.viewer
 
ScriptManager.ScriptQueueRunnable(boolean, int) - Constructor for class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptNoWait(String) - Method in class org.jmol.applet.Jmol
 
scriptProcessor(String, String, int) - Method in class org.jmol.applet.Jmol
 
scriptQueue - Variable in class org.jmol.viewer.ScriptManager
 
scriptQueueRunning - Variable in class org.jmol.viewer.ScriptManager
 
scriptReportingLevel - Variable in class org.jmol.viewer.Eval
 
scriptStatus(String) - Method in class org.jmol.viewer.Eval
 
scriptStatus(String) - Method in class org.jmol.viewer.Viewer
 
scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWait(String) - Method in class org.jmol.api.JmolViewer
 
scriptWait(String) - Method in class org.jmol.applet.Jmol
 
scriptWait(String, String) - Method in class org.jmol.applet.Jmol
 
scriptWait(String) - Method in class org.jmol.viewer.Viewer
 
scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
 
scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
 
scriptWindow - Variable in class org.openscience.jmol.app.Jmol
 
ScriptWindow - Class in org.openscience.jmol.app
 
ScriptWindow(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.ScriptWindow
 
ScriptWindow.ExecuteCommandThread - Class in org.openscience.jmol.app
 
ScriptWindow.ExecuteCommandThread(String) - Constructor for class org.openscience.jmol.app.ScriptWindow.ExecuteCommandThread
 
SDIM - Static variable in class org.jmol.g3d.Sphere3D
 
Se - Variable in class org.jmol.util.JpegInfo
 
searchForTurns(byte[], float[], byte[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
searchMatch(BitSet, SmilesMolecule, int) - Method in class org.jmol.smiles.PatternMatcher
Recursively search matches.
searchMatch(BitSet, SmilesMolecule, SmilesAtom, int, int) - Method in class org.jmol.smiles.PatternMatcher
Recursively search matches.
sectorPower - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
sectorSize - Variable in class org.jmol.util.CompoundDocument
 
seed - Static variable in class org.jmol.g3d.Shade3D
 
SEED_COUNT - Static variable in class org.jmol.jvxl.data.MeshData
 
SEED_COUNT - Static variable in class org.jmol.shape.Mesh
 
seek(long) - Method in class org.jmol.util.BinaryDocument
 
segments - Variable in class org.jmol.modelsetbio.ProteinStructure
 
seitzMatrix - Variable in class org.jmol.symmetry.Rotation
 
seitzMatrix12ths - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
seitzMatrixInv - Variable in class org.jmol.symmetry.Rotation
 
select() - Method in class org.jmol.viewer.Eval
 
select(BitSet, boolean) - Method in class org.jmol.viewer.SelectionManager
 
select - Static variable in class org.jmol.viewer.Token
 
select(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
selectAll() - Method in class org.jmol.api.JmolViewer
 
selectAll(boolean) - Method in class org.jmol.viewer.SelectionManager
 
selectAll() - Method in class org.jmol.viewer.Viewer
 
selectAllModels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
selectAtoms(BitSet) - Method in class org.jmol.modelset.Group
 
selectBonds(BitSet) - Method in class org.jmol.viewer.Viewer
 
selectDisplayedTrajectories(BitSet) - Method in class org.jmol.modelset.ModelCollection
 
selected - Static variable in class org.jmol.viewer.Token
 
selectedBonds - Variable in class org.jmol.shape.Sticks
 
selectedFileName - Variable in class org.openscience.jmol.app.RecentFilesDialog
 
selectedGroupCount - Variable in class org.jmol.modelset.Chain
 
selectedIndex - Variable in class org.jmol.modelset.Group
 
selectedMeasurementRow - Variable in class org.openscience.jmol.app.MeasurementTable
 
selectedMoleculeCount - Variable in class org.jmol.modelset.ModelCollection
 
selectedMolecules - Variable in class org.jmol.modelset.ModelCollection
 
selectedMonomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
 
selectedOctant - Variable in class org.jmol.g3d.Sphere3D
 
selectedOctant - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
selectedPoints - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
selectedTrajectory - Variable in class org.jmol.modelset.Model
 
selectionChanged(BitSet) - Method in interface org.jmol.api.JmolSelectionListener
Called when the selected atoms change
selectionChanged(boolean) - Method in class org.jmol.viewer.SelectionManager
 
selectionHalo(int) - Method in class org.jmol.viewer.Eval
 
selectionHalo - Static variable in class org.jmol.viewer.Token
 
selectionHaloEnabled - Variable in class org.jmol.modelset.ModelSet
 
SelectionManager - Class in org.jmol.viewer
 
SelectionManager(Viewer) - Constructor for class org.jmol.viewer.SelectionManager
 
selectionManager - Variable in class org.jmol.viewer.Viewer
 
selectItem(Token) - Static method in class org.jmol.viewer.Token
 
selectItem(Token, int) - Static method in class org.jmol.viewer.Token
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.VoxelReader
 
selectRectangle(Rectangle, int) - Method in class org.jmol.viewer.Viewer
 
selectSeqcodeRange(int, int, int, BitSet) - Method in class org.jmol.modelset.Chain
 
selectSeqcodeRange(int, int, char, BitSet, boolean) - Method in class org.jmol.modelset.Model
 
selectSlider - Variable in class org.openscience.jmol.app.AtomSetChooser
 
semicolon - Static variable in class org.jmol.viewer.Token
 
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.ScriptWindow
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.ScriptWindow
 
sendJsTextareaStatus(String) - Method in class org.jmol.applet.Jmol
 
sendJsTextStatus(String) - Method in class org.jmol.applet.Jmol
 
sendScript(String, String, boolean, boolean) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
seqcode - Variable in class org.jmol.modelset.Group
 
seqcode - Static variable in class org.jmol.viewer.Token
 
seqcodes - Variable in class org.jmol.modelset.ModelLoader
 
sequence - Static variable in class org.jmol.viewer.Token
 
SEQUENCE_NUMBER_FLAG - Static variable in class org.jmol.modelset.Group
 
SEQUENCE_NUMBER_SHIFT - Static variable in class org.jmol.modelset.Group
 
sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
 
serialArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Test
 
set(Point3f, Point3i) - Static method in class org.jmol.g3d.Hermite3D
 
set(int) - Method in class org.jmol.g3d.Rgb16
 
set(Rgb16) - Method in class org.jmol.g3d.Rgb16
 
set() - Method in class org.jmol.minimize.MinAtom
 
set(String, String, Atom[], float, short, float, int, float, Point3f, Vector3f) - Method in class org.jmol.shapespecial.Dipole
 
set(Point3f, Point3f) - Method in class org.jmol.shapespecial.Dipole
 
set(float) - Method in class org.jmol.shapespecial.Dipole
 
set(Point3f, Point3f, float) - Method in class org.jmol.shapespecial.Dipole
 
set(Point3f, Vector3f) - Method in class org.jmol.shapespecial.Dipole
 
set(Atom, Atom, float) - Method in class org.jmol.shapespecial.Dipole
 
set(PointGroup, Atom[], BitSet, boolean, float, float) - Method in class org.jmol.symmetry.PointGroup
 
set() - Method in class org.jmol.viewer.Eval
 
set - Static variable in class org.jmol.viewer.Token
 
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
Changes the activation state for a logging level.
setAdjustForWindow(boolean) - Method in class org.jmol.shape.Object2d
 
setAlignment(int, int) - Method in class org.jmol.shape.Labels
 
setAlignment(String) - Method in class org.jmol.shape.Object2d
 
setAlignment(int) - Method in class org.jmol.shape.Object2d
 
setAll(int) - Static method in class org.jmol.util.BitSetUtil
 
setAllBits(int[], int) - Static method in class org.jmol.geodesic.EnvelopeCalculation
 
setAllowRotateSelected(boolean) - Method in class org.jmol.viewer.Viewer
 
setAllowStatusReporting(boolean) - Method in class org.jmol.viewer.StatusManager
 
setAmbientPercent(int) - Static method in class org.jmol.g3d.Graphics3D
 
setAmbientPercent(int) - Static method in class org.jmol.viewer.ColorManager
 
setAmbientPercent(int) - Static method in class org.jmol.viewer.Viewer
 
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.g3d.Rgb16
 
setAnimationDirection(int) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationDirection(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
 
setAnimationFps(int) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationLast() - Method in class org.jmol.viewer.RepaintManager
 
setAnimationLast() - Method in class org.jmol.viewer.Viewer
 
setAnimationNext() - Method in class org.jmol.viewer.RepaintManager
 
setAnimationNext() - Method in class org.jmol.viewer.Viewer
 
setAnimationOff(boolean) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setAnimationPrevious() - Method in class org.jmol.viewer.RepaintManager
 
setAnimationPrevious() - Method in class org.jmol.viewer.Viewer
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
 
setAnimationRelative(int) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.RepaintManager
 
setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.Viewer
 
setAnisotropy(Point3f) - Method in class org.jmol.jvxl.readers.Parameters
 
setAntialias(boolean) - Method in class org.jmol.viewer.TransformManager
 
setAntialias(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setAppendNew(boolean) - Method in class org.jmol.viewer.Viewer
 
setAppletContext(String, URL, URL, String) - Method in class org.jmol.api.JmolViewer
 
setAppletContext(URL, URL, String) - Method in class org.jmol.viewer.FileManager
 
setAppletContext(String, URL, URL, String) - Method in class org.jmol.viewer.Viewer
 
setAppletPath(String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setAppletProxy(String) - Method in class org.jmol.viewer.FileManager
 
setAppletWrapper(AppletWrapper) - Method in class org.jmol.applet.Jmol
 
setAppletWrapper(AppletWrapper) - Method in interface org.jmol.appletwrapper.WrappedApplet
 
setApplySymmetryToBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setApplySymmetryToBonds(boolean) - Method in class org.jmol.viewer.Viewer
 
setAtom1(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
setAtom2(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
setAtomCoord(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoord(BitSet, int, Object) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoord(BitSet, int, Object) - Method in class org.jmol.modelset.ModelCollection
 
setAtomCoord(int, float, float, float) - Method in class org.jmol.viewer.Viewer
 
setAtomCoord(BitSet, int, Object) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoordRelative(BitSet, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoordRelative(Point3f, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordRelative(Point3f) - Method in class org.jmol.viewer.Viewer
 
setAtomI(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the atomic mass of the atom.
setAtomicOrbital(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setAtomNames(Properties) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomNamesAndNumbers() - Method in class org.jmol.modelset.ModelLoader
 
setAtomPositions() - Method in class org.jmol.minimize.Minimizer
 
setAtomProperty(BitSet, int, int, float, float[]) - Method in class org.jmol.modelset.AtomCollection
 
setAtomProperty(BitSet, int, int, float, float[]) - Method in class org.jmol.modelset.ModelCollection
 
setAtomProperty(BitSet, int, int, float, float[]) - Method in class org.jmol.viewer.Viewer
 
setAtomSetAuxiliaryInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for the AtomSet
setAtomSetAuxiliaryInfo(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for the an AtomSet
setAtomSetCollectionAuxiliaryInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on atomSetCollection auxiliary info
setAtomSetCollectionProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets a property for the AtomSetCollection
setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the name for the current AtomSet
setAtomSetName(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the name for an AtomSet
setAtomSetNames(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the atom set names of the last n atomSets
setAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the number for the current AtomSet
setAtomSetPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on atomSet auxiliary info
setAtomSetProperties(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the same properties for the last n atomSets.
setAtomSetProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets a property for the AtomSet
setAtomSetProperty(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the a property for the an AtomSet
setAtomSetSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomShapeSize(int, int) - Method in class org.jmol.viewer.Eval
 
setAtomVibrationVector(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAttr(String, float) - Method in class org.jmol.export._MayaExporter
 
setAttr(String, int) - Method in class org.jmol.export._MayaExporter
 
setAttr(String, Tuple3f) - Method in class org.jmol.export._MayaExporter
 
setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
 
setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
 
setAutoscrolls(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
setAutoscrolls(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
setAxes(DrawMesh) - Static method in class org.jmol.shapespecial.Draw
 
setAxes(Point3f, float) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
setAxesModeMolecular(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesModeUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesScale(float) - Method in class org.jmol.viewer.Viewer
 
setAxisColor(String) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Axis Color' option
setAxisTextColor(String) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Axis Text Color' option
setBackgroundArgb(int) - Method in class org.jmol.g3d.Graphics3D
sets background color to the specified argb value
setBackgroundColor(int) - Method in class org.jmol.g3d.Platform3D
 
setBackgroundImage(Image) - Method in class org.jmol.g3d.Graphics3D
 
setBackgroundImage(String, Image) - Method in class org.jmol.viewer.Viewer
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.RepaintManager
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Platform3D
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Swing3D
 
setBbcage() - Method in class org.jmol.modelset.BoxInfo
 
setBFactor(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setBgcolix(int, short) - Method in class org.jmol.shape.Labels
 
setBgColix(short) - Method in class org.jmol.shape.Object2d
 
setBgColix(Object) - Method in class org.jmol.shape.Object2d
 
setBiomoleculeAtomCounts() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
setBioPolymer(BioPolymer, int) - Method in class org.jmol.modelsetbio.Monomer
 
setBit(int[], int) - Static method in class org.jmol.geodesic.EnvelopeCalculation
 
setBitsetProperty(BitSet, int, int, float, Token) - Method in class org.jmol.viewer.Eval
 
setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
 
setBondmode() - Method in class org.jmol.viewer.Eval
 
setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
 
setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
 
setBondType(int) - Method in class org.jmol.smiles.SmilesBond
 
setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
 
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Eval
 
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setBooleanProperty(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
setBorder() - Method in class org.openscience.jmol.app.DisplayPanel
 
setBoundBox(Point3f, Point3f, boolean) - Method in class org.jmol.modelset.BoxInfo
 
setBoundBox(Point3f, Point3f, boolean) - Method in class org.jmol.modelset.ModelCollection
 
setBoundBox(Point3f, Point3f, boolean) - Method in class org.jmol.viewer.Viewer
 
setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.shape.Object2d
 
setBsHidden(BitSet) - Method in class org.jmol.modelset.AtomCollection
 
setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolStatusListener
 
setCallbackFunction(String, String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
setCallbackFunction(String, String) - Method in class org.jmol.viewer.StatusManager
 
setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
setCameraDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
setCE(float, float, float, float, float) - Method in class org.jmol.quantum.MOCalculation
 
setCenter(int) - Method in class org.jmol.shapespecial.DrawMesh
 
setCenter() - Method in class org.jmol.viewer.TransformManager
 
setCenterAt(String, Point3f) - Method in class org.jmol.viewer.TransformManager
 
setCenterAt(String, Point3f) - Method in class org.jmol.viewer.Viewer
 
setCenterBitSet(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
 
setCenterSelected() - Method in class org.jmol.api.JmolViewer
 
setCenterSelected() - Method in class org.jmol.viewer.Viewer
 
setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the charge of the atom.
setCheckBoxState(Object, boolean) - Method in class org.jmol.popup.JmolPopup
 
setCheckBoxState(Object, boolean) - Method in class org.jmol.popup.JmolPopupAwt
 
setCheckBoxState(Object, boolean) - Method in class org.jmol.popup.JmolPopupSwing
 
setCheckBoxValue(String, boolean) - Method in class org.jmol.popup.JmolPopup
(1) setOption --> set setOption true or set setOption false
setCheckBoxValue(Object) - Method in class org.jmol.popup.JmolPopup
 
setCheckBoxValue(Object) - Method in class org.jmol.popup.JmolPopupAwt
 
setCheckBoxValue(Object) - Method in class org.jmol.popup.JmolPopupSwing
 
setCheckSpecial(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setChiralClass(String) - Method in class org.jmol.smiles.SmilesAtom
Sets the chiral class of the atom.
setChiralOrder(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the chiral order of the atom.
setClickable(int) - Method in class org.jmol.modelset.Atom
 
setClientFile(String, String, JmolAdapter, Object) - Method in class org.jmol.viewer.ModelManager
 
setClipboard(Image) - Static method in class org.jmol.export.image.ImageSelection
Transfers image into the clipboard.
setClipboard(String) - Static method in class org.jmol.export.image.ImageSelection
Transfers text into the clipboard.
setColix(short) - Method in interface org.jmol.api.JmolRendererInterface
sets current color from colix color index
setColix(short) - Method in class org.jmol.export.Export3D
sets current color from colix color index
setColix(short) - Method in class org.jmol.g3d.Graphics3D
sets current color from colix color index
setColix(short) - Method in class org.jmol.modelset.Bond
 
setColix(short) - Method in class org.jmol.modelset.Measurement
 
setColix(int, short, byte) - Method in class org.jmol.shape.Labels
 
setColix(short) - Method in class org.jmol.shape.Mesh
 
setColix(short) - Method in class org.jmol.shape.Object2d
 
setColix(Object) - Method in class org.jmol.shape.Object2d
 
setColix(short, byte, int) - Method in class org.jmol.shape.Shape
 
setColix(short, byte, Atom) - Method in class org.jmol.shape.Shape
 
setColix(short, byte, BitSet) - Method in class org.jmol.shapebio.BioShape
 
setColixAndIntensity(short, int) - Method in class org.jmol.g3d.Graphics3D
 
setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
 
setColixAtom(short) - Method in class org.jmol.modelset.Atom
 
setColixBackgroundContrast(int) - Method in class org.jmol.viewer.ColorManager
 
setColixDipole(short, short, BitSet) - Method in class org.jmol.shapespecial.Dipoles
 
setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setColorBackground(String) - Method in class org.jmol.api.JmolViewer
 
setColorBackground(String) - Method in class org.jmol.viewer.Viewer
 
setColorModel(ColorModel) - Method in class org.jmol.export.image.ImageEncoder
 
setColorNoisy(int) - Method in class org.jmol.g3d.Graphics3D
 
setColorOptions(int, int, int) - Method in class org.jmol.viewer.Eval
 
setColorScheme(String) - Method in class org.jmol.util.ColorEncoder
 
setColorScheme(String, boolean) - Method in class org.jmol.viewer.ColorManager
 
setColorSchemeSets() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setCommonDefaults() - Method in class org.jmol.viewer.StateManager
 
setCompressionLevel(int) - Method in class org.jmol.export.image.PngEncoder
Set the compression level to use
setConformation(BitSet) - Method in class org.jmol.modelset.Model
 
setConformation(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
 
setConformation(int, int) - Method in class org.jmol.modelset.ModelCollection
 
setConformation(BitSet, int) - Method in class org.jmol.modelset.Polymer
 
setConformation(BitSet, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
setConformation() - Method in class org.jmol.viewer.Viewer
 
setConformation(int) - Method in class org.jmol.viewer.Viewer
 
setConnected(boolean) - Method in class org.jmol.shape.Measures
 
setConsoleTextPane(ConsoleTextPane) - Method in class org.openscience.jmol.app.ConsoleDocument
 
setConstraints(Vector) - Method in class org.jmol.minimize.forcefield.Calculations
 
setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
 
setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setContourType() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setCount(int) - Method in class org.jmol.modelset.Measurement
 
setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelCollection
 
setCrystallographicDefaults() - Method in class org.jmol.viewer.StateManager
 
setCurrentColorRange(float[], BitSet, String) - Method in class org.jmol.viewer.ColorManager
 
setCurrentColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
 
setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentColorRange(float[], BitSet) - Method in class org.jmol.viewer.Viewer
 
setCurrentColorRange(float, float) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndex(int) - Method in class org.jmol.viewer.RepaintManager
 
setCurrentModelIndex(int, boolean) - Method in class org.jmol.viewer.RepaintManager
 
setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndex(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setCurrentUnitCellOffset(int) - Method in class org.jmol.viewer.Viewer
 
setCurrentUnitCellOffset(Point3f) - Method in class org.jmol.viewer.Viewer
 
setCursor(int) - Method in class org.jmol.viewer.Viewer
 
setData(Vector, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
 
setData(Vector, int, int, double) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
 
setData(Vector, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
 
setData(Vector, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
 
setData(Vector, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.PairCalc
 
setData(Vector, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
 
setData(Vector, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
 
setData(Viewer, String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
 
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
setDataDistanceToPlane(Point4f) - Method in interface org.jmol.api.VolumeDataInterface
 
setDataDistanceToPlane(Point4f) - Method in class org.jmol.jvxl.data.VolumeData
 
setDebugging() - Method in class org.jmol.viewer.Eval
 
setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
 
setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
 
setDefaultColors(String) - Method in class org.jmol.viewer.ColorManager
 
setDefaultColors(String) - Method in class org.jmol.viewer.Viewer
 
setDefaultDrawArrowScale(float) - Method in class org.jmol.viewer.Viewer
 
setDefaultLattice(Point3f) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setDefaultLattice(Point3f) - Method in class org.jmol.viewer.Viewer
 
setDefaults - Variable in class org.jmol.shape.Labels
 
setDefaults(String) - Method in class org.jmol.viewer.Viewer
 
setDefaultVdw(String) - Method in class org.jmol.viewer.DataManager
 
setDefaultVdw(String) - Method in class org.jmol.viewer.Viewer
 
setDepth(Vector3f, Point3f, Point3f, Point3f, float) - Method in class org.jmol.g3d.Hermite3D
 
setDialogLocation(Point) - Method in class org.jmol.export.dialog.FileChooser
 
setDialogSize(Dimension) - Method in class org.jmol.export.dialog.FileChooser
 
setDiffusePercent(int) - Static method in class org.jmol.g3d.Graphics3D
 
setDiffusePercent(int) - Static method in class org.jmol.viewer.ColorManager
 
setDiffusePercent(int) - Static method in class org.jmol.viewer.Viewer
 
setDimensions(int, int) - Method in class org.jmol.export.image.ImageEncoder
 
setDipole() - Method in class org.jmol.shapespecial.Dipoles
 
setDipole(Atom, Atom, float, float) - Method in class org.jmol.shapespecial.Dipoles
 
setDisplayMenuState() - Method in class org.openscience.jmol.app.DisplayPanel
 
setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
 
setDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setDrawHover(boolean) - Method in class org.jmol.viewer.PickingManager
 
setDrawing() - Method in class org.jmol.shapespecial.Draw
 
setDynamic(boolean) - Method in class org.jmol.modelset.Measurement
 
setDynamicMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
setEccentricity(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setEcho() - Method in class org.jmol.viewer.Eval
 
setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
 
setEchoStateActive(boolean) - Method in class org.jmol.viewer.Viewer
 
setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
 
setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
 
setEllipsoid(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setEllipsoid(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setEllipsoid(int, Object[]) - Method in class org.jmol.modelset.AtomCollection
 
setEllipsoidMatrix(Vector3f[], float[], Vector3f, Matrix3f) - Static method in class org.jmol.util.Quadric
 
setEncodeAlpha(boolean) - Method in class org.jmol.export.image.PngEncoder
Set the alpha encoding on or off.
setEndCheck(String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
setEnergies(String, String, int) - Method in class org.jmol.adapter.readers.more.NWChemReader
 
setEnergy() - Method in class org.jmol.adapter.readers.more.GaussianReader
Interpret the Energy= line for non SCF type energy output
setEnergy(String, String) - Method in class org.jmol.adapter.readers.more.NWChemReader
 
setError(Exception) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setError(boolean) - Method in class org.openscience.jmol.app.ScriptWindow
 
setErrorLineMessage(String, int, int, String) - Static method in class org.jmol.viewer.Eval
 
setErrorMessage(String) - Method in class org.jmol.viewer.Eval
 
setErrorMessages() - Static method in class org.jmol.viewer.Compiler
 
setErrorMessages() - Static method in class org.jmol.viewer.Eval
 
setFid(byte) - Method in class org.jmol.shape.Text
 
setFileData(Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
 
setFileInfo(String[]) - Method in class org.jmol.viewer.Viewer
 
setFileTypeName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Just sets the overall file type after the fact.
setFilter(int) - Method in class org.jmol.export.image.PngEncoder
Set the filter to use
setFinalOperations(Point3f[], int, int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setFinalOperations(Point3f[], int, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
setFinalOperations(Point3f[], int, int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
setFixedRotationCenter(Point3f) - Method in class org.jmol.viewer.TransformManager
 
setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
 
setFloatProperty(String, float) - Method in class org.jmol.viewer.Eval
 
setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
 
setFloatProperty(String, float, boolean) - Method in class org.jmol.viewer.Viewer
 
setFont(byte) - Method in interface org.jmol.api.JmolRendererInterface
 
setFont(byte) - Method in class org.jmol.export.Export3D
 
setFont(byte) - Method in class org.jmol.g3d.Graphics3D
 
setFont(Font3D) - Method in class org.jmol.g3d.Graphics3D
 
setFont(int, byte) - Method in class org.jmol.shape.Labels
 
setFont(Font3D) - Method in class org.jmol.shape.Text
 
setFontScale(float) - Method in class org.jmol.shape.Text
 
setForcesUsingNumericalDerivative(MinAtom, int) - Method in class org.jmol.minimize.forcefield.ForceField
 
setFormalCharge(int) - Method in class org.jmol.modelset.Atom
 
setFormalCharges(BitSet, int) - Method in class org.jmol.modelset.AtomCollection
 
setFormalCharges(int) - Method in class org.jmol.viewer.Viewer
 
setFormats(String) - Method in class org.jmol.shape.Measures
 
setFractionalCoord(int, float) - Method in class org.jmol.modelset.Atom
 
setFractionalCoord(Point3f) - Method in class org.jmol.modelset.Atom
 
setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFrameRangeVisible() - Method in class org.jmol.viewer.RepaintManager
 
setFrameTitle(int, String) - Method in class org.jmol.modelset.ModelCollection
 
setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
 
setFrameTitle(String) - Method in class org.jmol.viewer.Viewer
 
setFrameVariables(int, int) - Method in class org.jmol.viewer.Viewer
 
setFrankMenu(String) - Method in class org.jmol.popup.JmolPopup
 
setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
 
setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setFromBits(int, BitSet) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setFront(int, boolean) - Method in class org.jmol.shape.Labels
 
setFunction(Function) - Method in class org.jmol.viewer.Compiler.FlowContext
 
setFunction(String, int, int, short[], int[], Vector) - Method in class org.jmol.viewer.Compiler.FlowContext
 
setFunctionXY(Vector) - Method in class org.jmol.jvxl.readers.Parameters
 
setg3dExporter(Graphics3D, JmolExportInterface) - Method in interface org.jmol.api.JmolRendererInterface
 
setg3dExporter(Graphics3D, JmolExportInterface) - Method in class org.jmol.export.Export3D
 
setg3dExporter(Graphics3D, JmolExportInterface) - Method in class org.jmol.g3d.Graphics3D
 
setGenerator(boolean) - Method in class org.jmol.export.DrawGenerator
 
setGenerator(boolean) - Method in class org.jmol.shape.ShapeRenderer
 
setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setGouraud(int, int, int) - Method in class org.jmol.g3d.Triangle3D
 
setGraphCurveColor(String) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Graph Curve Color' option
setGraphDataUtils(GraphCharacteristics) - Method in class org.jmol.jcamp.ZoneVisu
 
setGraphicsColor(String) - Method in class org.jmol.jcamp.ZoneVisu
Method to set the color of the graphics output
setGreyscaleMode(boolean) - Method in class org.jmol.g3d.Graphics3D
controls greyscale rendering
setGrid(boolean) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Grid' option
setGridLimitsForAtom(Point3f, float, Point3i, Point3i) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
setGroup(Group) - Method in class org.jmol.modelset.Atom
 
setGroup(int, boolean) - Method in class org.jmol.shape.Labels
 
setHandler(XMLReader, XmlReader.JmolXmlHandler) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
setHbond() - Method in class org.jmol.viewer.Eval
 
setHeader(String, String) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setHeader(String) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setHidden(boolean) - Method in class org.jmol.modelset.Measurement
 
setHideNotSelected(boolean) - Method in class org.jmol.viewer.SelectionManager
 
setHints(int) - Method in class org.jmol.export.image.ImageEncoder
 
setHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of hydrogen atoms bonded with this atom.
setImage(Image) - Method in class org.jmol.export.image.PngEncoder
Set the image to be encoded
setImage(Image) - Method in class org.jmol.shape.Text
 
setImageDimensions(int, int) - Method in class org.openscience.jmol.app.PovrayDialog
Sets the output image dimensions.
setImageFontScaling(int, int) - Method in class org.jmol.viewer.Viewer
 
setIndex(int) - Method in class org.jmol.modelset.Bond
 
setIndex(int) - Method in class org.jmol.modelset.Measurement
 
setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.AtomSetChooser
Sets the indexes to the atomSetIndex values of each leaf of the node.
setIndices() - Method in class org.jmol.shape.Measures
 
setInfo(String) - Method in class org.jmol.adapter.readers.more.SpartanArchive
 
setInMotion(boolean) - Method in class org.jmol.viewer.RepaintManager
 
setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
 
setIntegrate(boolean) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Integrate' option
setIntegrateCurveColor(String) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Integrate Curve Color' option
setIntegrateTextColor(String) - Method in class org.jmol.jcamp.GraphCharacteristics
 
setIntegrationValues(ArrayList) - Method in class org.jmol.jcamp.GraphCharacteristics
Method to create a HashTable of integration curve area relationship to the concerned points
setIntegrationValues() - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Integration Values' option
setIntersectionPoints(int, int[], float[]) - Method in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
 
setIntProperty(String, int) - Method in class org.jmol.viewer.Eval
 
setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
 
setIntProperty(String, int, boolean) - Method in class org.jmol.viewer.Viewer
 
setIsDna(boolean) - Method in class org.jmol.modelset.Chain
 
setIsRna(boolean) - Method in class org.jmol.modelset.Chain
 
setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelCollection
 
setJmolDataFrame(String, int, int) - Method in class org.jmol.viewer.Viewer
 
setJmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setJmolDefaults() - Method in class org.jmol.viewer.StateManager
 
setJmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.StatusManager
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
 
setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setJvxlInfo() - Method in class org.jmol.shapesurface.Isosurface
 
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
setLabel(Object, String) - Method in class org.jmol.popup.JmolPopup
 
setLabel(Object, String) - Method in class org.jmol.popup.JmolPopupAwt
 
setLabel(Object, String) - Method in class org.jmol.popup.JmolPopupSwing
 
setLabel(String) - Method in class org.jmol.viewer.Eval
 
setLabel(String) - Method in class org.jmol.viewer.Viewer
 
setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
 
setLattice(int) - Method in class org.jmol.symmetry.SpaceGroup
 
setLattice(char, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
setLattice(int) - Method in class org.jmol.symmetry.Symmetry
 
setLatticeCells(int[], boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setLcao(String, int) - Method in class org.jmol.jvxl.readers.Parameters
 
setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setLcaoOn(boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setLcaoOn(int, boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setLength(Object, int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(String[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(float[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(int[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(short[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(byte[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLength(boolean[], int) - Static method in class org.jmol.util.ArrayUtil
 
setLighting(int) - Method in class org.jmol.shape.Mesh
 
setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setLineBits(float, float) - Method in class org.jmol.g3d.Line3D
 
setListVariable(String, Token) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setListVariable(String, Token) - Method in class org.jmol.viewer.Viewer
 
setLoadScript(String, boolean) - Method in class org.jmol.viewer.FileManager
 
setLobe(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
Replaces the current logger implementation by a new one.
setLogging() - Method in class org.jmol.applet.Jmol
 
setLoggingEnabled(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setLogLevel(int) - Static method in class org.jmol.util.Logger
Activates all logging levels up through a given level.
setMad(short) - Method in class org.jmol.modelset.Bond
 
setMad(short, BitSet) - Method in class org.jmol.shapebio.BioShape
 
setMad(int, short) - Method in class org.jmol.shapebio.BioShape
 
setMadAtom(Viewer, int) - Method in class org.jmol.modelset.Atom
 
setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setMads(int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
 
setMapRanges(VoxelReader) - Method in class org.jmol.jvxl.readers.Parameters
 
setMarBond(short) - Method in class org.jmol.api.JmolViewer
 
setMarBond(short) - Method in class org.jmol.viewer.Viewer
 
setMarchingSquares(MarchingSquares) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setMatchingAtom(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of a matching atom in a molecule.
setMatrices() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
setMatrix() - Method in interface org.jmol.api.VolumeDataInterface
 
setMatrix() - Method in class org.jmol.jvxl.data.VolumeData
 
setMatrix() - Method in class org.jmol.util.Quaternion
 
setMatrixFromXYZ(String) - Method in class org.jmol.symmetry.SymmetryOperation
 
setMaximumSize(int) - Method in class org.jmol.viewer.Viewer
 
setMaxSize(int) - Method in class org.jmol.util.CommandHistory
Resets maximum size of command queue.
setMeasureDistanceUnits(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setMeasureDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
 
setMeasurementFormats(String) - Method in class org.jmol.viewer.Viewer
 
setMeasurementUnits(String) - Method in class org.jmol.viewer.Eval
 
setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setMep(float[], boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setMesh(String) - Method in class org.jmol.shape.MeshCollection
 
setMeshDisplayProperty(int, int, int) - Method in class org.jmol.viewer.Eval
 
setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
 
setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
 
setMinimizationOn(boolean) - Method in class org.jmol.minimize.Minimizer
 
setMinimizer(MinimizerInterface) - Method in class org.jmol.viewer.Viewer
 
setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setMinMax() - Method in class org.jmol.quantum.QuantumCalculation
 
setMinZ(int) - Method in class org.jmol.modelset.Group
 
setMO(int) - Method in class org.jmol.jvxl.readers.Parameters
 
setMOData(Hashtable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setMoData(int, int, int, int, String) - Method in class org.jmol.viewer.Eval
 
setModel(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
 
setModel(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
setModel(int) - Method in class org.jmol.shape.Object2d
 
setModelAuxiliaryInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelCollection
 
setModelClickability() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setModelClickability() - Method in class org.jmol.shape.AtomShape
 
setModelClickability() - Method in class org.jmol.shape.Balls
 
setModelClickability() - Method in class org.jmol.shape.Dots
 
setModelClickability() - Method in class org.jmol.shape.Labels
 
setModelClickability() - Method in class org.jmol.shape.Shape
 
setModelClickability() - Method in class org.jmol.shape.Sticks
 
setModelClickability() - Method in class org.jmol.shapebio.Backbone
 
setModelClickability() - Method in class org.jmol.shapebio.BioShape
 
setModelClickability() - Method in class org.jmol.shapebio.BioShapeCollection
 
setModelIndex(int) - Method in interface org.jmol.api.SymmetryInterface
 
setModelIndex(int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setModelIndex(int, int) - Method in class org.jmol.shape.MeshCollection
 
setModelIndex() - Method in class org.jmol.shapespecial.Dipoles
 
setModelIndex() - Method in class org.jmol.shapesurface.Isosurface
 
setModelIndex(int) - Method in class org.jmol.symmetry.Symmetry
 
setModelNameNumberProperties(int, int, String, int, Properties, Hashtable, boolean, String) - Method in class org.jmol.modelset.ModelLoader
 
setModelSet(ModelSet) - Method in class org.jmol.modelset.Chain
 
setModelSet(ModelSet) - Method in class org.jmol.modelset.Group
 
setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
 
setModelSetAuxiliaryInfo(Hashtable) - Method in class org.jmol.modelset.ModelCollection
 
setModelSetProperties(Properties) - Method in class org.jmol.modelset.ModelCollection
 
setModelVisibility() - Method in class org.jmol.modelset.ModelSet
 
setModelVisibility() - Method in class org.jmol.viewer.Viewer
 
setModeMouse(int) - Method in class org.jmol.api.JmolViewer
 
setModeMouse(int) - Method in class org.jmol.viewer.MouseManager
 
setModeMouse(int) - Method in class org.jmol.viewer.Viewer
 
setMonitor() - Method in class org.jmol.viewer.Eval
 
setMOs(String) - Method in class org.jmol.adapter.readers.more.MopacDataReader
 
setMouseMode() - Method in class org.jmol.viewer.MouseManager
 
setMovableX(int) - Method in class org.jmol.shape.Object2d
 
setMovableXPercent(int) - Method in class org.jmol.shape.Object2d
 
setMovableY(int) - Method in class org.jmol.shape.Object2d
 
setMovableYPercent(int) - Method in class org.jmol.shape.Object2d
 
setMovableZ(int) - Method in class org.jmol.shape.Object2d
 
setMovableZPercent(int) - Method in class org.jmol.shape.Object2d
 
setNAltLocs(int) - Method in class org.jmol.modelset.Model
 
setNames(String[]) - Method in class org.jmol.viewer.FileManager
 
setNavigationDepthPercent(float, float) - Method in class org.jmol.viewer.TransformManager
sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)
setNavigationDepthPercent(float, float) - Method in class org.jmol.viewer.TransformManager11
 
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager11
 
setNavigationDepthPercent(float, float) - Method in class org.jmol.viewer.Viewer
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
 
setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager
 
setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager11
 
setNeighbors(int) - Method in class org.jmol.shapebio.BioShapeRenderer
 
setNewRotationCenter(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
 
setNewRotationCenter(Point3f) - Method in class org.jmol.viewer.Viewer
 
setNInsertions(int) - Method in class org.jmol.modelset.Model
 
setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setNoneSelected(boolean) - Method in class org.jmol.viewer.Viewer
 
setNoPrompt() - Method in class org.openscience.jmol.app.ConsoleDocument
 
setNotionalUnitCell(float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectColor(String, String) - Method in class org.jmol.viewer.Viewer
 
setObjectMad(int, String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectProperty() - Method in class org.jmol.viewer.Eval
 
setOccupancy(int, int) - Method in class org.jmol.modelset.AtomCollection
 
setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
 
setOffset(int) - Method in class org.jmol.shape.Object2d
 
setOffset(int) - Method in class org.jmol.symmetry.Symmetry
 
setOffset(Point3f[], int, int) - Method in class org.jmol.symmetry.SymmetryOperation
 
setOffset(Point3f) - Method in class org.jmol.symmetry.UnitCell
 
setOffset(int) - Method in class org.jmol.symmetry.UnitCell
 
setOffsetPositions() - Method in class org.openscience.jmol.app.ConsoleDocument
 
setOffsets(int, int) - Method in class org.jmol.shape.Labels
 
setOmega(float) - Method in class org.jmol.modelset.Group
 
setOrbital(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.more.GamessUKReader
 
setOrder(short) - Method in class org.jmol.modelset.Bond
 
setPaletteID(byte) - Method in class org.jmol.modelset.Atom
 
setparam - Static variable in class org.jmol.viewer.Token
 
setParameter(String, Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setParameter is the main interface for surface generation.
setParameter(String, Object, BitSet) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setParameter(String, int, boolean, boolean) - Method in class org.jmol.viewer.Eval
 
setParameterValue(String, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParameterValue(String, int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParameterValue(String, float) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParameterValue(String, String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setParams(Hashtable) - Method in class org.jmol.minimize.forcefield.Calculations
 
setPartialCharge(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setPdbConectBonding(int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
setPdbConectBonding(boolean) - Method in class org.jmol.viewer.Viewer
 
setPendingMeasurement(MeasurementPending) - Method in class org.jmol.viewer.Viewer
 
setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
 
setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.TransformManager
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
 
setPerspectiveModel(int) - Method in class org.jmol.viewer.Viewer
 
setPhi(float) - Method in class org.jmol.modelset.Group
 
setPicking() - Method in class org.jmol.viewer.Eval
 
setPickingMode(int) - Method in class org.jmol.viewer.PickingManager
 
setPickingMode(String) - Method in class org.jmol.viewer.Viewer
 
setPickingStyle() - Method in class org.jmol.viewer.Eval
 
setPickingStyle(int) - Method in class org.jmol.viewer.PickingManager
 
setPickingStyle(String) - Method in class org.jmol.viewer.Viewer
 
setPixelLocation(Point3i) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
setPixels(int, int, int, int, ColorModel, byte[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
setPixels(int, int, int, int, ColorModel, int[], int, int) - Method in class org.jmol.export.image.ImageEncoder
 
setPlanarTransform() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setPlane(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
 
setPlaneDerivatives() - Method in class org.jmol.g3d.Sphere3D
 
setPlaneParameters(Point4f) - Method in interface org.jmol.api.VolumeDataInterface
 
setPlaneParameters(Point4f) - Method in class org.jmol.jvxl.data.VolumeData
 
setPoint(Point3f, Point3f, Vector3f, int) - Method in class org.jmol.g3d.Hermite3D
 
setPointer(int, int) - Method in class org.jmol.shape.Labels
 
setPointer(int) - Method in class org.jmol.shape.Object2d
 
setPointGroup(SymmetryInterface, Atom[], BitSet, boolean, float, float) - Method in interface org.jmol.api.SymmetryInterface
 
setPointGroup(SymmetryInterface, Atom[], BitSet, boolean, float, float) - Method in class org.jmol.symmetry.Symmetry
 
setPoints(int, int) - Method in class org.jmol.shapespecial.Draw
 
setPolygon(int) - Method in class org.jmol.shapespecial.Draw
 
setPolygonCount(int) - Method in class org.jmol.shape.Mesh
 
setPosition(float) - Method in class org.jmol.shape.Text
 
setPosition(float, float, float, float, float[]) - Static method in class org.jmol.shape.Text
 
setPreliminary(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setPrincipalAxis(int, int) - Method in class org.jmol.symmetry.PointGroup
 
setPrincipalPlane(int, int) - Method in class org.jmol.symmetry.PointGroup
 
setPrompt() - Method in class org.openscience.jmol.app.ConsoleDocument
 
setPrompt() - Method in class org.openscience.jmol.app.ConsoleTextPane
 
setProperties(Hashtable) - Method in class org.jmol.export.image.ImageEncoder
 
setProperty(String, Object) - Method in interface org.jmol.api.MinimizerInterface
 
setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.AtomShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Axes
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Balls
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Dots
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Echo
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.FontLineShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Halos
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Hover
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Labels
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Measures
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.MeshCollection
 
setProperty(int, boolean) - Method in class org.jmol.shape.MeshCollection
 
setProperty(String, Object, Object2d) - Static method in class org.jmol.shape.Object2d
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Object2dShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Shape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.Sticks
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shape.TextShape
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapebio.Backbone
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(int, boolean, int, float) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(int, Dipole, int, float) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Draw
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Ellipsoids
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Polyhedra
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapespecial.Vectors
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setProperty(String, Object, BitSet) - Method in class org.jmol.shapesurface.Pmesh
 
setProperty() - Method in class org.jmol.viewer.Eval
 
setPropertyColorScheme(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setPropertySuper(String, Object, BitSet) - Method in class org.jmol.shapespecial.Draw
 
setPropertySuper(String, Object, BitSet) - Method in class org.jmol.shapesurface.Isosurface
 
setProteinStructureType(byte, int) - Method in class org.jmol.modelset.Group
 
setProteinStructureType(byte, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setProteinType(BitSet, byte) - Method in class org.jmol.modelset.ModelCollection
 
setProteinType(byte, BitSet) - Method in class org.jmol.viewer.Viewer
 
setPsi(float) - Method in class org.jmol.modelset.Group
 
setQuality(int) - Method in class org.jmol.util.JpegEncoder
 
setQueue(boolean) - Method in class org.jmol.viewer.ScriptManager
 
setRadii(boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
setRadius(boolean, float) - Method in class org.jmol.jvxl.readers.Parameters
 
setRadius(float) - Method in class org.jmol.modelset.Atom
 
setRandom(boolean) - Method in class org.jmol.util.BinaryDocument
 
setRange(float[]) - Method in class org.jmol.shape.Measures
 
setRangesAndAddAtoms(float, int, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setRasMolDefaults() - Method in class org.jmol.viewer.StateManager
 
setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setReader() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setRef(Quaternion) - Method in class org.jmol.util.Quaternion
 
setRefreshing(boolean) - Method in class org.jmol.viewer.Viewer
 
setRenderer(JmolRendererInterface) - Method in interface org.jmol.api.JmolExportInterface
 
setRenderer(ShapeRenderer) - Method in interface org.jmol.api.JmolRendererInterface
 
setRenderer(JmolRendererInterface) - Method in class org.jmol.export._Exporter
 
setRenderer(ShapeRenderer) - Method in class org.jmol.export.Export3D
 
setRenderer(ShapeRenderer) - Method in class org.jmol.g3d.Graphics3D
 
setReverse(boolean) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Reverse' option
setRgb(byte[], byte[], byte[]) - Method in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
 
setRotateButton() - Static method in class org.openscience.jmol.app.Jmol
 
setRotateFixed(Point3f, Vector3f, float) - Method in class org.jmol.viewer.TransformManager
 
setRotateInternal(Point3f, Vector3f, float) - Method in class org.jmol.viewer.TransformManager
 
setRotateMode() - Method in class org.openscience.jmol.app.DisplayPanel
 
setRotateMolecule(boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotation(Matrix3f) - Method in class org.jmol.viewer.TransformManager
 
setRotationCenterAndRadiusXYZ(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationCenterAndRadiusXYZ(String, Point3f) - Method in class org.jmol.viewer.TransformManager
 
setRotationMatrix(Matrix3f) - Method in class org.jmol.g3d.Normix3D
 
setRotationPointXY(Point3f) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelCollection
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
 
setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
 
setRubberbandArgb(int) - Method in class org.jmol.viewer.Viewer
 
setScale(float) - Method in class org.jmol.shape.Axes
 
setScaleAngstromsPerInch(float) - Method in class org.jmol.viewer.TransformManager
 
setScalePixelsPerMicron(float) - Method in class org.jmol.shape.Object2d
 
setScalePixelsPerMicron(float) - Method in class org.jmol.shape.Text
 
setScreenDimension(Dimension) - Method in class org.jmol.api.JmolViewer
 
setScreenDimension(Dimension) - Method in class org.jmol.viewer.Viewer
 
setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager11
 
setScript(String) - Method in class org.jmol.shape.Object2d
 
setScriptEcho(String, boolean) - Method in class org.jmol.viewer.StatusManager
 
setScriptInfo() - Method in class org.jmol.shapesurface.Isosurface
 
setScriptStatus(String, String, int) - Method in class org.jmol.viewer.StatusManager
 
setSelected(String, boolean) - Method in class org.jmol.applet.GuiMap
 
setSelected(String, boolean) - Method in class org.openscience.jmol.app.GuiMap
 
setSelectedFloats(float, BitSet, float[]) - Static method in class org.jmol.util.Parser
 
setSelectedOctant() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
 
setSelectionHaloEnabled(boolean) - Method in class org.jmol.modelset.ModelSet
 
setSelectionHalos(boolean) - Method in class org.jmol.api.JmolViewer
 
setSelectionHalos(boolean) - Method in class org.jmol.viewer.Viewer
 
setSelectionSet(BitSet) - Method in class org.jmol.api.JmolViewer
 
setSelectionSet(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
setSelectionSet(BitSet) - Method in class org.jmol.viewer.Viewer
 
setSelectionSubset(BitSet) - Method in class org.jmol.viewer.SelectionManager
 
setSelectionSubset(BitSet) - Method in class org.jmol.viewer.Viewer
 
setShapeId(int, int, boolean) - Method in class org.jmol.viewer.Eval
 
setShapeProperty(int, String, Object, BitSet) - Method in class org.jmol.modelset.ModelSet
 
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Eval
 
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
 
setShapeProperty(int, String, Object, BitSet) - Method in class org.jmol.viewer.Viewer
 
setShapePropertyArgb(int, String, int) - Method in class org.jmol.viewer.Viewer
 
setShapeSize(int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
 
setShapeSize(int, int) - Method in class org.jmol.viewer.Eval
 
setShapeSize(int, int) - Method in class org.jmol.viewer.Viewer
 
setShapeSize(int, int, BitSet) - Method in class org.jmol.viewer.Viewer
 
setShapeState(Hashtable, Hashtable) - Method in class org.jmol.shapebio.BioShape
 
setShapeTranslucency(int, String, String, float, BitSet) - Method in class org.jmol.viewer.Eval
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Bond
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
 
setShapeVisibilityFlags(int) - Method in class org.jmol.modelset.Atom
 
setShapeVisibilityFlags(int) - Method in class org.jmol.modelset.Bond
 
setShowAxes(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowBbcage(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
 
setSilent(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setSingleItem(Vector) - Method in class org.jmol.shape.Measures
 
setSize(int, BitSet) - Method in class org.jmol.shape.AtomShape
 
setSize(int, BitSet) - Method in class org.jmol.shape.Balls
 
setSize(int, BitSet) - Method in class org.jmol.shape.Dots
 
setSize(int, BitSet) - Method in class org.jmol.shape.Measures
 
setSize(int, BitSet) - Method in class org.jmol.shape.Shape
 
setSize(int, BitSet) - Method in class org.jmol.shape.Sticks
sets the size of a bond, or sets the selectedBonds set
setSize(int, BitSet) - Method in class org.jmol.shapebio.Backbone
 
setSize(int, BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
setSize(int, BitSet) - Method in class org.jmol.shapespecial.Ellipsoids
 
setSlab(int) - Method in interface org.jmol.api.JmolRendererInterface
 
setSlab(int) - Method in class org.jmol.export.Export3D
 
setSlab(int) - Method in class org.jmol.g3d.Graphics3D
 
setSlabAndDepthValues(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
clipping from the front and the back
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
set internal slab or depth from screen-based slab or depth
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.Viewer
 
setSlabEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setSlaters() - Method in class org.jmol.adapter.readers.more.MopacDataReader
 
setSolvent(String, float) - Method in class org.jmol.jvxl.readers.Parameters
 
setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroup(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroup(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSpecular(boolean) - Static method in class org.jmol.g3d.Graphics3D
 
setSpecular(boolean) - Static method in class org.jmol.viewer.ColorManager
 
setSpecular(boolean) - Static method in class org.jmol.viewer.Viewer
 
setSpecularExponent(int) - Static method in class org.jmol.g3d.Graphics3D
 
setSpecularExponent(int) - Static method in class org.jmol.viewer.Viewer
 
setSpecularPercent(int) - Static method in class org.jmol.g3d.Graphics3D
 
setSpecularPercent(int) - Static method in class org.jmol.viewer.ColorManager
 
setSpecularPercent(int) - Static method in class org.jmol.viewer.Viewer
 
setSpecularPower(int) - Static method in class org.jmol.g3d.Graphics3D
 
setSpecularPower(int) - Static method in class org.jmol.viewer.ColorManager
 
setSpecularPower(int) - Static method in class org.jmol.viewer.Viewer
 
setSphere(float) - Method in class org.jmol.jvxl.readers.Parameters
 
setSpin(String, int) - Method in class org.jmol.viewer.Eval
 
setSpin(String, int) - Method in class org.jmol.viewer.Viewer
 
setSpinFps(int) - Method in class org.jmol.viewer.TransformManager
 
setSpinOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setSpinOn(boolean, float, BitSet) - Method in class org.jmol.viewer.TransformManager
 
setSpinOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setSpinX(float) - Method in class org.jmol.viewer.TransformManager
 
setSpinY(float) - Method in class org.jmol.viewer.TransformManager
 
setSpinZ(float) - Method in class org.jmol.viewer.TransformManager
 
setSsbond() - Method in class org.jmol.viewer.Eval
 
setsSuccessful - Variable in class org.jmol.jvxl.data.MeshData
 
setStateInfo(Hashtable, int, String) - Static method in class org.jmol.shape.Shape
 
setStateInfo(Hashtable, int, int, String) - Static method in class org.jmol.shape.Shape
 
setStateInfo(Hashtable, int, int, String) - Static method in class org.jmol.viewer.StateManager
 
setStatement(int) - Method in class org.jmol.viewer.Eval
 
setStatus(int, String) - Method in class org.openscience.jmol.app.StatusBar
 
setStatusAtomHovered(String, int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusAtomPicked(String, int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomPicked(int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusChanged(String, int, Object, boolean) - Method in class org.jmol.viewer.StatusManager
 
setStatusFileLoaded(String, String, String, String, String, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusFileLoaded(int, String, String, String, String) - Method in class org.jmol.viewer.Viewer
 
setStatusFileNotLoaded(String, String) - Method in class org.jmol.viewer.Viewer
 
setStatusFrameChanged() - Method in class org.jmol.viewer.RepaintManager
 
setStatusFrameChanged(String, int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusFrameChanged(int) - Method in class org.jmol.viewer.Viewer
 
setStatusList(String) - Method in class org.jmol.viewer.StatusManager
 
setStatusMeasurePicked(int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusMeasurePicked(int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusMeasuring(String, int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusMeasuring(String, int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusResized(String, int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
 
setStatusScriptStarted(int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusScriptStarted(int, String) - Method in class org.jmol.viewer.Viewer
 
setStereoDegrees(float) - Method in class org.jmol.viewer.TransformManager
 
setStereoMode(int[]) - Method in class org.jmol.viewer.TransformManager
 
setStereoMode(int) - Method in class org.jmol.viewer.TransformManager
 
setStereoMode(int[], int, float) - Method in class org.jmol.viewer.Viewer
 
setStraightness(float) - Method in class org.jmol.modelset.Group
 
setStrandCount() - Method in class org.jmol.shapebio.StrandsRenderer
 
setStrandCount(int, int) - Method in class org.jmol.viewer.Viewer
 
setStream(DataInputStream) - Method in class org.jmol.util.BinaryDocument
 
setString(String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
sets a string to be parsed from the beginning
setStringNextLine() - Method in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
sets the string for parsing to be from the next line when the token buffer is empty, and if ';' is at the beginning of that line, extends the string to include that full multiline string.
setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
 
setStringProperty(String, String) - Method in class org.jmol.applet.Jmol
 
setStringProperty(String, String) - Method in class org.jmol.viewer.Eval
 
setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
 
setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.Monomer
 
setStructure(String) - Method in class org.jmol.popup.PopupResourceBundle
 
setStructureTypes() - Method in class org.jmol.shapebio.BioShapeRenderer
 
setSurfaceInfo(JvxlData, Point4f, int, StringBuffer) - Static method in class org.jmol.jvxl.readers.JvxlReader
 
setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
Sets the symbol of the atm.
setSymmetryInfo(int, Hashtable) - Method in interface org.jmol.api.SymmetryInterface
 
setSymmetryInfo(int, Hashtable) - Method in class org.jmol.symmetry.Symmetry
 
setSymmetryInfo(int, Hashtable) - Method in class org.jmol.symmetry.SymmetryInfo
 
setSymmetryMinMax(Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSymmetryRange(float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSync(String) - Method in class org.jmol.viewer.StatusManager
 
setSync() - Method in class org.jmol.viewer.Viewer
 
setSyncDriver(int) - Method in class org.jmol.viewer.StatusManager
 
setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
 
setSyncTarget(int, boolean) - Method in class org.jmol.viewer.Viewer
 
settable - Static variable in class org.jmol.viewer.Token
 
setTainted(boolean) - Method in class org.jmol.viewer.Viewer
 
setTaintedAtoms(BitSet, byte) - Method in class org.jmol.modelset.AtomCollection
 
setTaintedAtoms(BitSet, byte) - Method in class org.jmol.viewer.Viewer
 
setText(String) - Method in class org.jmol.shape.Text
 
setTextColor(String) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Graph Text Color' option
setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTrajectory(BitSet) - Method in class org.jmol.modelset.ModelSet
 
setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
 
setTrajectory(int) - Method in class org.jmol.viewer.Viewer
 
setTrajectory(BitSet) - Method in class org.jmol.viewer.Viewer
 
setTransformManagerDefaults() - Method in class org.jmol.viewer.Viewer
 
setTranslationFractions() - Method in class org.jmol.viewer.TransformManager
 
setTranslations() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
 
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
 
setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
 
setTranslucent(float, boolean) - Method in class org.jmol.shape.Object2d
 
setTranslucent(boolean, BitSet, float) - Method in class org.jmol.shapebio.BioShape
 
setTranslucent(boolean, float) - Method in class org.jmol.shapespecial.Dipole
 
setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCell(float[]) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCell(float[]) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCell(float[]) - Method in class org.jmol.symmetry.UnitCell
 
setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCellOffset(Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCellOffset(int, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
setUnitCellOffset(int, int) - Method in class org.jmol.modelset.ModelCollection
 
setUnitCellOffset(Point3f) - Method in class org.jmol.symmetry.Symmetry
 
setUnitVectors() - Method in interface org.jmol.api.VolumeDataInterface
 
setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
 
setUnsortedIntegrationValues(String) - Method in class org.jmol.jcamp.GraphCharacteristics
Method to split and create an ArrayList of Integration relationship values
setup() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setup() - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setup() - Method in class org.jmol.jvxl.readers.IsoMepReader
 
setup() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
setup() - Method in class org.jmol.jvxl.readers.IsoPlaneReader
 
setup() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setup() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
setup(AtomDataServer, MeshDataServer, ColorEncoder, MeshData, JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setup() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setup() - Method in class org.jmol.minimize.forcefield.ForceField
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.Calculations
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
setupCoordinates(float[], float[]) - Method in class org.jmol.quantum.QuantumCalculation
 
setupElectrostatics() - Method in class org.jmol.minimize.forcefield.Calculations
 
setupElectrostatics() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
setupInput() - Method in class org.jmol.applet.Console
 
setupLabels() - Method in class org.jmol.applet.GuiMap
 
setupLabels() - Method in class org.openscience.jmol.app.GuiMap
 
setupMatrix(Matrix3f, Vector3f[]) - Static method in class org.jmol.jvxl.calc.MarchingSquares
 
setupMinimization() - Method in class org.jmol.minimize.Minimizer
 
setupNewFrame(String) - Method in class org.openscience.jmol.app.Jmol
 
setupOutput() - Method in class org.jmol.applet.Console
 
setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
setupUI(boolean) - Method in class org.jmol.export.dialog.Dialog
 
setupUIManager() - Static method in class org.jmol.export.dialog.Dialog
Setup the UIManager (for i18n)
setUseFileExtension(boolean) - Method in class org.openscience.jmol.app.FileTyper
 
setUseNumberLocalization(boolean) - Static method in class org.jmol.util.TextFormat
 
setUserColors() - Method in class org.jmol.viewer.Eval
 
setUserScale(int[]) - Static method in class org.jmol.util.ColorEncoder
 
setUserScale(int[]) - Static method in class org.jmol.viewer.ColorManager
 
setUserScale(int[]) - Static method in class org.jmol.viewer.Viewer
 
setUserVariable(String, Token) - Method in class org.jmol.viewer.StateManager.GlobalSettings
 
setUserVdw(int) - Method in class org.jmol.viewer.DataManager
 
setValence(int) - Method in class org.jmol.modelset.Atom
 
setValue(String, String) - Method in class org.jmol.applet.Jmol
 
setValue(float, VolumeData) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
setVariable(int, int, String, boolean) - Method in class org.jmol.viewer.Eval
 
setVariables() - Method in class org.jmol.shape.MeshRenderer
 
setVariables(Hashtable, Vector) - Method in class org.jmol.viewer.Function
 
setVectorScale(float) - Method in class org.jmol.api.JmolViewer
 
setVectorScale(float) - Method in class org.jmol.viewer.Viewer
 
setVertex(int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
setVibrationOff() - Method in class org.jmol.viewer.Viewer
 
setVibrationOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationScale(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationVector() - Method in class org.jmol.modelset.Atom
 
setVibrationVector(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setVibrationVector(int, int, float) - Method in class org.jmol.modelset.AtomCollection
 
setViewer(JmolViewer) - Method in interface org.jmol.api.JmolImageCreatorInterface
 
setViewer(Viewer) - Method in interface org.jmol.api.SmilesMatcherInterface
 
setViewer(JmolViewer) - Method in class org.jmol.export.image.ImageCreator
 
setViewer(Viewer) - Method in class org.jmol.smiles.PatternMatcher
 
setViewer(Viewer, int, int) - Method in class org.jmol.viewer.TransformManager
 
setViewer(JmolViewer) - Method in class org.openscience.jmol.app.DisplayPanel
 
setViewerG3dShapeID(Viewer, JmolRendererInterface, int) - Method in class org.jmol.shape.ShapeRenderer
 
setVisibility(boolean) - Method in class org.jmol.shape.Object2d
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Balls
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Bbcage
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Halos
 
setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.MeshCollection
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Object2dShape
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shape.Shape
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Dipoles
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Draw
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Ellipsoids
 
setVisibilityFlags(BitSet) - Method in class org.jmol.shapespecial.Polyhedra
 
setVisibilityInfo() - Method in class org.jmol.shape.Measures
 
setVisible(boolean) - Method in class org.jmol.applet.Console
 
setVisible(boolean) - Method in class org.jmol.modelset.Measurement
 
setVisible(boolean) - Method in class org.jmol.shapespecial.Polyhedra
 
setVisualRange(float) - Method in class org.jmol.viewer.TransformManager
 
setVisualRange(float) - Method in class org.jmol.viewer.Viewer
 
setVolume(VolumeDataInterface, BitSet) - Method in class org.jmol.quantum.QuantumCalculation
 
setVolumeData(VolumeData) - Method in class org.jmol.jvxl.readers.VoxelReader
 
setVolumetricOrigin(float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setVolumetricOrigin(float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
 
setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setVolumetricVector(int, float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
 
setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelCounts(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setVoxelCounts(int, int, int) - Method in interface org.jmol.api.VolumeDataInterface
 
setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelData(float[][][]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setVoxelData(float[][][]) - Method in interface org.jmol.api.VolumeDataInterface
 
setVoxelData(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelPoint() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelRange(int, float, float, float, int) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setWebPageAuthor(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setWidthHeight(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setWindow(JmolRendererInterface, float) - Method in class org.jmol.shape.Object2d
 
setWindowCentered(boolean) - Method in class org.jmol.viewer.TransformManager
 
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
 
setXY(int, int) - Method in class org.jmol.shape.Object2d
 
setXYZ(Point3f) - Method in class org.jmol.shape.Object2d
 
setXYZs(int, int, int, int) - Method in class org.jmol.shape.Object2d
 
setZMargin(int) - Method in class org.jmol.g3d.Graphics3D
 
setZoomEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setZoomIn(boolean) - Method in class org.jmol.jcamp.GraphCharacteristics
Setter and Getter methods for the 'Zoom In' option
setZs(int, int) - Method in class org.jmol.shape.Object2d
 
sfacElementSymbols - Variable in class org.jmol.adapter.readers.more.ShelxReader
 
sg - Variable in class org.jmol.jvxl.readers.VoxelReader
 
sg - Variable in class org.jmol.shapesurface.Isosurface
 
sgIndex - Static variable in class org.jmol.symmetry.SpaceGroup
 
Shade3D - Class in org.jmol.g3d
Implements the shading of RGB values to support shadow and lighting highlights.
Shade3D() - Constructor for class org.jmol.g3d.Shade3D
 
SHADE_SLAB_CLIPPED - Static variable in class org.jmol.g3d.Sphere3D
 
shadeLast - Static variable in class org.jmol.g3d.Graphics3D
 
shadeLast - Static variable in class org.jmol.g3d.Shade3D
 
shadeMax - Static variable in class org.jmol.g3d.Graphics3D
 
shadeMax - Static variable in class org.jmol.g3d.Shade3D
 
shadeNormal - Static variable in class org.jmol.g3d.Graphics3D
 
shadeNormal - Static variable in class org.jmol.g3d.Shade3D
 
shades - Variable in class org.jmol.g3d.Sphere3D
 
shadesA - Variable in class org.jmol.g3d.Cylinder3D
 
shadesB - Variable in class org.jmol.g3d.Cylinder3D
 
shadesCurrent - Variable in class org.jmol.g3d.Graphics3D
 
Shape - Class in org.jmol.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
Shape() - Constructor for class org.jmol.shape.Shape
 
shape - Variable in class org.jmol.shape.ShapeRenderer
 
shape - Variable in class org.jmol.shapebio.BioShape
 
shape - Static variable in class org.jmol.viewer.Token
 
SHAPE_AXES - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_BALLS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_DOTS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_DRAW - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ECHO - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_FRANK - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_HALOS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_HOVER - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_LABELS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_MO - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_PMESH - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STARS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STICKS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_TRACE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JmolConstants
 
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JmolConstants
 
shapeClassBases - Static variable in class org.jmol.viewer.JmolConstants
 
shapeID - Variable in class org.jmol.shape.Shape
 
shapeID - Variable in class org.jmol.shape.ShapeRenderer
 
SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
shapely - Static variable in class org.jmol.viewer.Token
 
ShapeRenderer - Class in org.jmol.shape
 
ShapeRenderer() - Constructor for class org.jmol.shape.ShapeRenderer
 
shapes - Variable in class org.jmol.modelset.ModelSet
 
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JmolConstants
 
shapeToks - Static variable in class org.jmol.viewer.JmolConstants
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
 
shapeVisibilityFlags - Variable in class org.jmol.viewer.StateManager.Connection
 
Sheet - Class in org.jmol.modelsetbio
 
Sheet(AlphaPolymer, int, int) - Constructor for class org.jmol.modelsetbio.Sheet
 
sheetPoints - Variable in class org.jmol.modelset.Polymer
 
sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
 
sheetSmoothing - Variable in class org.jmol.shapebio.BioShapeRenderer
 
sheetSmoothing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
shell - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
SHELL_D_CARTESIAN - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_D_CARTESIAN - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_D_SPHERICAL - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_D_SPHERICAL - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_F_CARTESIAN - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_F_CARTESIAN - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_F_SPHERICAL - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_F_SPHERICAL - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_L - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_L - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_P - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_P - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_S - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_S - Static variable in class org.jmol.viewer.JmolConstants
 
SHELL_SP - Static variable in class org.jmol.api.JmolAdapter
 
SHELL_SP - Static variable in class org.jmol.viewer.JmolConstants
 
shellCount - Variable in class org.jmol.adapter.readers.more.GamessReader
 
shellCount - Variable in class org.jmol.adapter.readers.more.GaussianReader
 
shellCount - Variable in class org.jmol.adapter.readers.more.PsiReader
 
shellCount - Variable in class org.jmol.adapter.readers.more.SpartanArchive
 
shellOrder - Static variable in class org.jmol.viewer.JmolConstants
 
shells - Variable in class org.jmol.quantum.MOCalculation
 
shellsByUniqueAtom - Variable in class org.jmol.adapter.readers.more.PsiReader
 
ShelxReader - Class in org.jmol.adapter.readers.more
A reader for SHELX output (RES) files.
ShelxReader() - Constructor for class org.jmol.adapter.readers.more.ShelxReader
 
shelxRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SHIFT - Static variable in class org.jmol.viewer.MouseManager
 
SHIFT_LEFT - Static variable in class org.jmol.viewer.MouseManager
 
SHIFT_MIDDLE - Static variable in class org.jmol.viewer.MouseManager
 
SHIFT_RIGHT - Static variable in class org.jmol.viewer.MouseManager
 
shitty_starting_constant - Variable in class org.jmol.jcamp.Visua
 
shitty_starting_constant - Variable in class org.jmol.jcamp.ZoneVisu
 
shortSectorPower - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
shortSectorSize - Variable in class org.jmol.util.CompoundDocument
 
show() - Method in class org.jmol.jcamp.SaisieDlg
 
show(int, int) - Method in class org.jmol.popup.JmolPopup
 
show() - Method in class org.jmol.viewer.Eval
 
show - Static variable in class org.jmol.viewer.Token
 
showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.AtomSetChooser
Show an atom set from the indexes array
showAuxiliaryInfo(Hashtable) - Method in class org.openscience.jmol.app.AtomSetChooser
Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
showAxes - Variable in class org.openscience.jmol.app.PreferencesDialog
 
showBoundingBox - Variable in class org.openscience.jmol.app.PreferencesDialog
 
showBox(JmolRendererInterface, short, short, int, int, int, int, int, int, float, boolean) - Static method in class org.jmol.shape.Text
 
showConsole(boolean) - Method in interface org.jmol.api.JmolStatusListener
 
showConsole(boolean) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
showConsole(boolean) - Method in class org.jmol.applet.Jvm12
 
showConsole(boolean) - Method in class org.jmol.viewer.StatusManager
 
showConsole(boolean) - Method in class org.jmol.viewer.Viewer
 
showConsole(boolean) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
showFrankMenu(int, int) - Method in class org.jmol.popup.JmolPopup
 
showFrankMenu(int, int) - Method in class org.jmol.popup.JmolPopupAwt
 
showFrankMenu(int, int) - Method in class org.jmol.popup.JmolPopupSwing
 
showHiddenSelectionHalos - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showHide(Measurement, boolean) - Method in class org.jmol.shape.Measures
 
showHide(boolean) - Method in class org.jmol.shape.Measures
 
showHydrogens - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showHydrogens - Variable in class org.openscience.jmol.app.PreferencesDialog
 
showInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
showMeasurement(int[], boolean) - Method in class org.jmol.viewer.Viewer
 
showMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showMeasurements - Variable in class org.openscience.jmol.app.PreferencesDialog
 
showModelSetDownload() - Method in class org.jmol.api.JmolViewer
 
showModelSetDownload() - Method in class org.jmol.viewer.Viewer
 
showMoleculesAndOrbitals - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
showMultipleBonds - Variable in class org.jmol.shape.SticksRenderer
 
showMultipleBonds - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showNavigationPointAlways - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
showPaintTime - Variable in class org.jmol.applet.Jmol
 
showPaintTime - Variable in class org.openscience.jmol.app.DisplayPanel
 
showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
 
showPoints - Variable in class org.jmol.shape.Mesh
 
showPopupMenu(int, int) - Method in class org.jmol.popup.JmolPopup
 
showPopupMenu(int, int) - Method in class org.jmol.popup.JmolPopupAwt
 
showPopupMenu(int, int) - Method in class org.jmol.popup.JmolPopupSwing
 
showPovrayPathDialog() - Method in class org.openscience.jmol.app.PovrayDialog
Show a file selector when the savePath button is pressed.
showProperties(Properties) - Method in class org.openscience.jmol.app.AtomSetChooser
Shows the properties in the propertiesPane of the AtomSetChooser window
showRebondTimes - Static variable in class org.jmol.modelset.AtomCollection
 
showSaveDialog(Dialog, Component, JFileChooser, File) - Method in class org.jmol.export.dialog.Dialog
 
showSavePathDialog() - Method in class org.openscience.jmol.app.PovrayDialog
Show a file selector when the savePath button is pressed.
showSplashScreen() - Method in class org.openscience.jmol.app.Splash
 
showStatus(String) - Method in class org.openscience.jmol.app.Splash
 
showStatusAndConsole(String, boolean) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
showString(String) - Method in class org.jmol.viewer.Eval
 
showString(String) - Method in class org.jmol.viewer.Viewer
 
showTimes(int, int, Graphics) - Method in class org.jmol.applet.Jmol
 
showTimes() - Method in class org.openscience.jmol.app.DisplayPanel
 
ShowTitle - Variable in class org.jmol.jcamp.ZoneVisu
 
showTriangles - Variable in class org.jmol.shape.Mesh
 
showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
 
showUrl(String) - Method in class org.jmol.api.JmolViewer
 
showUrl(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
 
showUrl(String) - Method in class org.jmol.viewer.StatusManager
 
showUrl(String) - Method in class org.jmol.viewer.Viewer
 
showUrl(String) - Method in class org.openscience.jmol.app.Jmol.MyStatusListener
 
SID_DIR_start - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
SID_MSAT_next - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
SID_SSAT_start - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
sidechain - Static variable in class org.jmol.viewer.Token
 
SIDfirstSector - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
SignedOnly - Variable in class org.jmol.popup.JmolPopup
 
silent - Variable in class org.jmol.minimize.forcefield.Calculations
 
SILVER - Static variable in class org.jmol.g3d.Graphics3D
 
simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.PovrayDialog
 
simpleReplace(String, String, String) - Static method in class org.jmol.util.TextFormat
Does a clean replace of strFrom in str with strTo If strTo contains strFrom, then only a single pass is done.
sin - Static variable in class org.jmol.viewer.Token
 
sinAlpha - Variable in class org.jmol.symmetry.UnitCell.Data
 
sinBeta - Variable in class org.jmol.symmetry.UnitCell.Data
 
sinGamma - Variable in class org.jmol.symmetry.UnitCell.Data
 
sinPhi - Variable in class org.jmol.g3d.Cylinder3D
 
site() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
site - Static variable in class org.jmol.viewer.Token
 
SITE_ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
SITE_SEQ_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
siteNum - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
size - Variable in class org.jmol.g3d.Text3D
 
size - Static variable in class org.jmol.viewer.Token
 
sizeCorrection - Variable in class org.jmol.g3d.Circle3D
 
sizeOf(Token) - Static method in class org.jmol.viewer.Token
 
skip(long) - Method in class org.jmol.viewer.MonitorInputStream
 
skip(long) - Method in class org.openscience.jvxl.MonitorInputStream
 
skipAtomSet(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
skipComments(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipLoop() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
skips all associated loop data
skipVoxels(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
slab - Variable in class org.jmol.export.Export3D
 
slab - Variable in class org.jmol.g3d.Graphics3D
 
slab - Variable in class org.jmol.g3d.Sphere3D
 
slab(boolean) - Method in class org.jmol.viewer.Eval
 
slab - Static variable in class org.jmol.viewer.Token
 
slabbing - Variable in class org.jmol.shape.ShapeRenderer
 
slabByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
slabByPixels(int) - Method in class org.jmol.viewer.Viewer
 
slabDepthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
slabDepthByPixels(int) - Method in class org.jmol.viewer.Viewer
 
slabEnabled - Variable in class org.jmol.viewer.TransformManager
 
slabInternal(Point4f, boolean) - Method in class org.jmol.viewer.TransformManager
 
slabInternal(Point4f, boolean) - Method in class org.jmol.viewer.Viewer
 
slabPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
slabPlane - Variable in class org.jmol.viewer.TransformManager
 
slabReset() - Method in class org.jmol.viewer.TransformManager
 
slabReset() - Method in class org.jmol.viewer.Viewer
 
slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
slabToPercent(int) - Method in class org.jmol.viewer.Viewer
 
slabValue - Variable in class org.jmol.viewer.TransformManager
 
slabZ - Variable in class org.jmol.export._Exporter
 
slaterData - Variable in class org.jmol.quantum.MOCalculation
 
slaterInfo - Variable in class org.jmol.quantum.MOCalculation
 
sLeft - Variable in class org.jmol.g3d.Hermite3D
 
slider - Variable in class org.jmol.export.dialog.Dialog.QualityListener
 
SLIM - Static variable in class org.jmol.g3d.Sphere3D
 
slope - Variable in class org.jmol.g3d.Line3D
 
slopeKey - Variable in class org.jmol.g3d.Line3D
 
SmallAtomDot - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
smartAromatic - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
SmarterJmolAdapter - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
 
SmarterJmolAdapter.AtomIterator - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter.AtomIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
 
SmarterJmolAdapter.BondIterator - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter.BondIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
 
SmarterJmolAdapter.StructureIterator - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter.StructureIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
SmilesAtom - Class in org.jmol.smiles
This class represents an atom in a SmilesMolecule.
SmilesAtom(int) - Constructor for class org.jmol.smiles.SmilesAtom
Constructs a SmilesAtom.
SmilesBond - Class in org.jmol.smiles
Bond in a SmilesMolecule
SmilesBond(SmilesAtom, SmilesAtom, int) - Constructor for class org.jmol.smiles.SmilesBond
SmilesBond constructor
SmilesMatcherInterface - Interface in org.jmol.api
 
SmilesMolecule - Class in org.jmol.smiles
Molecule created from a SMILES String
SmilesMolecule() - Constructor for class org.jmol.smiles.SmilesMolecule
SmilesMolecule constructor
SmilesParser - Class in org.jmol.smiles
Parses a SMILES String to create a SmilesMolecule.
SmilesParser() - Constructor for class org.jmol.smiles.SmilesParser
Constructs a SmilesParser.
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
 
solid - Static variable in class org.jmol.viewer.Token
 
solvent - Static variable in class org.jmol.viewer.Token
 
solvent_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
solvent_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
solventAtomRadiusAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
 
solventAtomRadiusFactor - Variable in class org.jmol.jvxl.readers.Parameters
 
solventAtomRadiusOffset - Variable in class org.jmol.jvxl.readers.Parameters
 
solventDistance(Point3f, Point3f, Point3f, float, float, float, float, float) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
solventExtendedAtomRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
solventOn - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
solventProbeRadius - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
solventRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
solventRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelCollection
 
someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelCollection
 
someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelCollection
 
someModelsHaveUnitcells - Variable in class org.jmol.modelset.ModelLoader
 
sort(int) - Method in class org.jmol.bspt.Leaf
 
sort() - Method in class org.jmol.export.image.GifEncoder.ColorVector
 
source - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
sourceIndices - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
sp - Variable in class org.jmol.bspt.CubeIterator
 
sp - Variable in class org.jmol.g3d.Hermite3D
 
SPACE_GROUP_QUERY - Static variable in class org.jmol.symmetry.SpaceGroup
 
spacefill - Static variable in class org.jmol.viewer.Token
 
Spacefilling - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
spaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
SpaceGroup - Class in org.jmol.symmetry
 
SpaceGroup(boolean) - Constructor for class org.jmol.symmetry.SpaceGroup
 
SpaceGroup(String) - Constructor for class org.jmol.symmetry.SpaceGroup
 
spaceGroup - Variable in class org.jmol.symmetry.Symmetry
 
spaceGroup - Variable in class org.jmol.symmetry.SymmetryInfo
 
spacegroup - Static variable in class org.jmol.viewer.Token
 
spaceGroupDefinitions - Static variable in class org.jmol.symmetry.SpaceGroup
 
SpartanArchive - Class in org.jmol.adapter.readers.more
 
SpartanArchive(AtomSetCollectionReader, AtomSetCollection, Hashtable) - Constructor for class org.jmol.adapter.readers.more.SpartanArchive
 
SpartanArchive(AtomSetCollectionReader, AtomSetCollection, Hashtable, String, String) - Constructor for class org.jmol.adapter.readers.more.SpartanArchive
 
spartanBinaryRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SpartanReader - Class in org.jmol.adapter.readers.more
 
SpartanReader() - Constructor for class org.jmol.adapter.readers.more.SpartanReader
 
spartanRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SpartanSmolReader - Class in org.jmol.adapter.readers.more
 
SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.more.SpartanSmolReader
 
spartanSmolRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
spec_alternate - Static variable in class org.jmol.viewer.Token
 
spec_atom - Static variable in class org.jmol.viewer.Token
 
spec_chain - Static variable in class org.jmol.viewer.Token
 
spec_model - Static variable in class org.jmol.viewer.Token
 
spec_model2 - Static variable in class org.jmol.viewer.Token
 
spec_name_pattern - Static variable in class org.jmol.viewer.Token
 
spec_resid - Static variable in class org.jmol.viewer.Token
 
spec_seqcode - Static variable in class org.jmol.viewer.Token
 
spec_seqcode_range - Static variable in class org.jmol.viewer.Token
 
specexponent - Static variable in class org.jmol.viewer.Token
 
SPECIAL_ARGUS_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ARGUS_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CHEM3D_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CHEM3D_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CML_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_CML_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_COLIX_MAX - Static variable in class org.jmol.g3d.Graphics3D
 
SPECIAL_CUBE - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_FOLDINGXYZ - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_JME - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOL - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOLPRO_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOLPRO_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_MOPACGRAPHF - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ODYSSEY - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ODYSSEY_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_ODYSSEY_XML - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_V3000 - Static variable in class org.jmol.adapter.smarter.Resolver
 
SPECIAL_XYZ - Static variable in class org.jmol.adapter.smarter.Resolver
 
specialAtomIDs - Variable in class org.jmol.modelset.AtomCollection
 
specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
specialAtomNames - Static variable in class org.jmol.viewer.JmolConstants
 
specialLoad(String, String) - Static method in class org.jmol.adapter.smarter.Resolver
In the case of spt files, no need to load them; here we are just checking for type In the case of .spardir directories, we need to provide a list of the critical files that need loading and concatenation for the SpartanSmolReader we return an array for which: [0] file type (class prefix) or null for SPT file [1] header to add for each BEGIN/END block [2...] files to load and concatenate
specialLoad(String, String) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
specialLoad(String, String) - Method in class org.jmol.api.JmolAdapter
 
specialposition - Static variable in class org.jmol.viewer.Token
 
specialTags - Static variable in class org.jmol.adapter.smarter.Resolver
 
specpercent - Static variable in class org.jmol.viewer.Token
 
specpower - Static variable in class org.jmol.viewer.Token
 
specular - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
specular - Static variable in class org.jmol.viewer.Token
 
SPECULAR_EXPONENT - Static variable in class org.jmol.g3d.Shade3D
 
SPECULAR_ON - Static variable in class org.jmol.g3d.Shade3D
 
SPECULAR_PERCENT - Static variable in class org.jmol.g3d.Shade3D
 
SPECULAR_POWER - Static variable in class org.jmol.g3d.Shade3D
 
specularExponent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
specularPercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
specularPower - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
sphere3d - Variable in class org.jmol.g3d.Graphics3D
 
Sphere3D - Class in org.jmol.g3d
Implements high performance rendering of shaded spheres.
Sphere3D(Graphics3D) - Constructor for class org.jmol.g3d.Sphere3D
 
sphere_radiusAngstroms - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
sphereIntensities - Static variable in class org.jmol.g3d.Shade3D
 
sphereShadingCalculated - Static variable in class org.jmol.g3d.Shade3D
 
sphereShapeCache - Static variable in class org.jmol.g3d.Sphere3D
 
spin - Static variable in class org.jmol.viewer.Token
 
spinFps - Variable in class org.jmol.viewer.TransformManager
 
spinOn - Variable in class org.jmol.viewer.TransformManager
 
spinThread - Variable in class org.jmol.viewer.TransformManager
 
spinX - Variable in class org.jmol.viewer.TransformManager
 
spinY - Variable in class org.jmol.viewer.TransformManager
 
spinZ - Variable in class org.jmol.viewer.TransformManager
 
splash - Variable in class org.openscience.jmol.app.Jmol
 
Splash - Class in org.openscience.jmol.app
 
Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.Splash
 
Splash.WindowListener - Class in org.openscience.jmol.app
 
Splash.WindowListener() - Constructor for class org.openscience.jmol.app.Splash.WindowListener
 
splashImage - Variable in class org.openscience.jmol.app.Splash
 
split(String, String) - Static method in class org.jmol.util.TextFormat
proper splitting, even for Java 1.3 -- if the text ends in the run, no new line is appended.
split(String, char) - Static method in class org.jmol.util.TextFormat
 
split - Static variable in class org.jmol.viewer.Token
 
splitKeyValue() - Method in class org.jmol.adapter.readers.more.MoldenReader
 
splitKeyValue(String) - Method in class org.jmol.adapter.readers.more.MoldenReader
 
splitKeyValue(String, String) - Method in class org.jmol.adapter.readers.more.MoldenReader
 
sprintf(String, Object[]) - Static method in class org.jmol.util.TextFormat
 
sprintf(String, String[], float[]) - Static method in class org.jmol.util.TextFormat
 
sprintf(String, String[], float[], int[]) - Static method in class org.jmol.util.TextFormat
 
sqrt - Static variable in class org.jmol.viewer.Token
 
squareCount - Variable in class org.jmol.viewer.Eval.Rpn
 
squareCountX - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
squareCountY - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
squareFractions - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
squareVertexOffsets - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
squareVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
sRight - Variable in class org.jmol.g3d.Hermite3D
 
Ss - Variable in class org.jmol.util.JpegInfo
 
SSAT - Variable in class org.jmol.util.CompoundDocument
 
ssbond() - Method in class org.jmol.viewer.Eval
 
ssbond - Static variable in class org.jmol.viewer.Token
 
ssbondsBackbone - Variable in class org.jmol.shape.SticksRenderer
 
ssbondsBackbone - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
stack - Variable in class org.jmol.bspt.CubeIterator
 
stack - Variable in class org.jmol.viewer.Eval
 
stackOverflow() - Method in class org.jmol.viewer.Eval.Rpn
 
STAND_ALONE - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
standardLevel - Static variable in class org.jmol.geodesic.Geodesic
5 levels, 0 through 4
star - Static variable in class org.jmol.viewer.Token
 
Stars - Class in org.jmol.shape
 
Stars() - Constructor for class org.jmol.shape.Stars
 
StarsGenerator - Class in org.jmol.export
 
StarsGenerator() - Constructor for class org.jmol.export.StarsGenerator
 
StarsRenderer - Class in org.jmol.shape
 
StarsRenderer() - Constructor for class org.jmol.shape.StarsRenderer
 
START - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
start() - Method in class org.jmol.jcamp.Visua
 
start() - Method in class org.openscience.jmol.app.DisplayPanel
 
startByteArrayReaderThread() - Method in class org.openscience.jmol.app.LoopedStreams
 
startChainID - Variable in class org.jmol.adapter.smarter.Structure
 
startChainID - Variable in class org.jmol.modelset.ModelCollection.Structure
 
startCommandWatcher(boolean) - Method in class org.jmol.viewer.ScriptManager
 
startConsoleReaderThread(InputStream) - Method in class org.openscience.jmol.app.ConsoleTextArea
 
startCoord - Variable in class org.jmol.shapespecial.Dipoles
 
startDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
started - Variable in class org.jmol.export.image.ImageEncoder
 
startedByCommandThread - Variable in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
startElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
startHoverWatcher(boolean) - Method in class org.jmol.viewer.MouseManager
 
startIndexPending - Variable in class org.jmol.shapebio.RocketsRenderer
 
startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
startMinimization() - Method in class org.jmol.minimize.Minimizer
 
startPaintClock() - Method in class org.jmol.applet.Jmol
 
startPaintClock() - Method in class org.openscience.jmol.app.DisplayPanel
 
startProduction(ImageConsumer) - Method in class org.jmol.g3d.Awt3D
 
startScriptQueue(boolean) - Method in class org.jmol.viewer.ScriptManager
 
startSeqcode - Variable in class org.jmol.modelset.ModelCollection.Structure
 
startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
startSpinningAxis(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
startSpinningAxis(Point3f, Point3f, boolean) - Method in class org.jmol.viewer.Viewer
 
startTime - Variable in class org.jmol.appletwrapper.AppletWrapper
 
startTime - Static variable in class org.jmol.util.Logger
 
startTimer() - Static method in class org.jmol.util.Logger
 
startupDimension - Variable in class org.openscience.jmol.app.DisplayPanel
 
startupHeight - Variable in class org.openscience.jmol.app.Jmol
 
startupWidth - Variable in class org.openscience.jmol.app.Jmol
 
state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
the current state
state - Variable in class org.jmol.jvxl.readers.Parameters
 
state - Static variable in class org.jmol.viewer.Token
 
STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.Viewer
 
stateButton - Variable in class org.jmol.applet.Console
 
stateButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
StateButton - Variable in class org.openscience.jmol.app.webexport.Test
 
stateChanged(ChangeEvent) - Method in class org.jmol.export.dialog.Dialog.QualityListener
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.AtomSetChooser
 
StateManager - Class in org.jmol.viewer
 
StateManager(Viewer) - Constructor for class org.jmol.viewer.StateManager
 
stateManager - Variable in class org.jmol.viewer.Viewer
 
StateManager.Connection - Class in org.jmol.viewer
 
StateManager.Connection(int, int, short, short, short, int) - Constructor for class org.jmol.viewer.StateManager.Connection
 
StateManager.Connections - Class in org.jmol.viewer
 
StateManager.Connections() - Constructor for class org.jmol.viewer.StateManager.Connections
 
StateManager.GlobalSettings - Class in org.jmol.viewer
 
StateManager.GlobalSettings() - Constructor for class org.jmol.viewer.StateManager.GlobalSettings
 
StateManager.Orientation - Class in org.jmol.viewer
 
StateManager.Orientation() - Constructor for class org.jmol.viewer.StateManager.Orientation
 
statement - Variable in class org.jmol.viewer.Eval.Context
 
statement - Variable in class org.jmol.viewer.Eval
 
statementAsString() - Method in class org.jmol.viewer.Eval
 
statementLength - Variable in class org.jmol.viewer.Eval.Context
 
statementLength - Variable in class org.jmol.viewer.Eval
 
stateScripts - Variable in class org.jmol.modelset.ModelCollection
 
staticGetFileTypeName(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
staticOpenBufferedReader(String, String, BufferedReader, Hashtable) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
staticOpenBufferedReaders(JmolFileReaderInterface, String[], String[], Hashtable[]) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
staticOpenDOMReader(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
staticOpenZipFiles(InputStream, String, String[], Hashtable, int, boolean) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
stats() - Method in class org.jmol.bspt.Bspf
 
stats() - Method in class org.jmol.bspt.Bspt
prints some simple stats to stdout
status - Variable in class org.openscience.jmol.app.DisplayPanel
 
status - Variable in class org.openscience.jmol.app.Jmol
 
status - Variable in class org.openscience.jmol.app.Splash
 
status - Variable in class org.openscience.jmol.app.StatusBar
 
StatusBar - Class in org.openscience.jmol.app
 
StatusBar() - Constructor for class org.openscience.jmol.app.StatusBar
 
statusForm - Variable in class org.jmol.applet.Jmol
 
statusList - Variable in class org.jmol.viewer.StatusManager
 
StatusManager - Class in org.jmol.viewer
The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
StatusManager(Viewer) - Constructor for class org.jmol.viewer.StatusManager
 
statusManager - Variable in class org.jmol.viewer.Viewer
 
statusPtr - Variable in class org.jmol.viewer.StatusManager
 
statusReporting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
STATUSSIZE - Static variable in class org.openscience.jmol.app.Splash
 
statusText - Variable in class org.jmol.applet.Jmol
 
statusText - Variable in class org.openscience.jmol.app.DisplayPanel.SetStatusAction
 
statusTextarea - Variable in class org.jmol.applet.Jmol
 
statusTop - Variable in class org.openscience.jmol.app.Splash
 
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET - Static variable in class org.jmol.adapter.readers.more.GaussianReader
Word index of atomic number in line with atom coordinates in an orientation block.
steepestDescentInitialize(int, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
steepestDescentTakeNSteps(int) - Method in class org.jmol.minimize.forcefield.ForceField
 
stepAxisCoordinates() - Method in class org.jmol.shape.SticksRenderer
 
stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
stepMax - Variable in class org.jmol.minimize.forcefield.ForceField
 
stepMinimization() - Method in class org.jmol.minimize.Minimizer
 
steps - Variable in class org.jmol.minimize.Minimizer
 
stereo() - Method in class org.jmol.viewer.Eval
 
stereo - Static variable in class org.jmol.viewer.Token
 
STEREO_CUSTOM - Static variable in class org.jmol.viewer.JmolConstants
 
STEREO_DOUBLE - Static variable in class org.jmol.viewer.JmolConstants
 
STEREO_NONE - Static variable in class org.jmol.viewer.JmolConstants
 
STEREO_REDBLUE - Static variable in class org.jmol.viewer.JmolConstants
 
STEREO_REDCYAN - Static variable in class org.jmol.viewer.JmolConstants
 
STEREO_REDGREEN - Static variable in class org.jmol.viewer.JmolConstants
 
STEREO_UNKNOWN - Static variable in class org.jmol.viewer.JmolConstants
 
stereoColors - Variable in class org.jmol.viewer.TransformManager
 
stereoDegrees - Variable in class org.jmol.viewer.TransformManager
 
stereoFrame - Variable in class org.jmol.viewer.TransformManager
 
stereoMode - Variable in class org.jmol.viewer.TransformManager
 
stereoModes - Static variable in class org.jmol.viewer.JmolConstants
 
stereoRadians - Variable in class org.jmol.viewer.TransformManager
 
Sticks - Class in org.jmol.shape
 
Sticks() - Constructor for class org.jmol.shape.Sticks
 
SticksGenerator - Class in org.jmol.export
 
SticksGenerator() - Constructor for class org.jmol.export.SticksGenerator
 
SticksRenderer - Class in org.jmol.shape
 
SticksRenderer() - Constructor for class org.jmol.shape.SticksRenderer
 
sto_exp - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
stop() - Method in class org.jmol.export.image.ImageEncoder
 
stop() - Method in class org.jmol.jcamp.Visua
 
stop() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
 
stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
 
stopPaintClock() - Method in class org.jmol.applet.Jmol
 
stopPaintClock() - Method in class org.openscience.jmol.app.DisplayPanel
 
str - Variable in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
straightness - Variable in class org.jmol.modelset.Group
 
straightness - Static variable in class org.jmol.viewer.Token
 
strandCount - Variable in class org.jmol.shapebio.StrandsRenderer
 
strandCountForMeshRibbon - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
strandCountForStrands - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Strands - Class in org.jmol.shapebio
 
Strands() - Constructor for class org.jmol.shapebio.Strands
 
strands - Static variable in class org.jmol.viewer.Token
 
strandSeparation - Variable in class org.jmol.shapebio.StrandsRenderer
 
StrandsGenerator - Class in org.jmol.export
 
StrandsGenerator() - Constructor for class org.jmol.export.StrandsGenerator
 
StrandsRenderer - Class in org.jmol.shapebio
 
StrandsRenderer() - Constructor for class org.jmol.shapebio.StrandsRenderer
 
strbufLog - Variable in class org.jmol.viewer.Eval
 
strCommand - Variable in class org.openscience.jmol.app.ScriptWindow.ExecuteCommandThread
 
stream - Variable in class org.jmol.util.BinaryDocument
 
strFormat - Variable in class org.jmol.modelset.Measurement
 
strFormat - Variable in class org.jmol.shape.Measures
 
strFractionTemp - Variable in class org.jmol.jvxl.readers.JvxlReader
 
strID - Variable in class org.jmol.shapesurface.MolecularOrbital
 
string - Static variable in class org.jmol.viewer.Token
 
stringClass - Variable in class org.openscience.jmol.app.MeasurementTable
 
StringDataUtils - Class in org.jmol.jcamp.utils
 
StringDataUtils() - Constructor for class org.jmol.jcamp.utils.StringDataUtils
 
stringParameter(int) - Method in class org.jmol.viewer.Eval
 
stringReaders - Variable in class org.jmol.viewer.FileManager.FilesOpenThread
 
strings - Variable in class org.jmol.shape.Labels
 
stringSetting(int, boolean) - Method in class org.jmol.viewer.Eval
 
stringsResourceBundle - Variable in class org.openscience.jmol.app.JmolResourceHandler
 
StringtoScriptButton - Variable in class org.openscience.jmol.app.webexport.Test
 
stringWidth(String) - Method in class org.jmol.shape.Text
 
strJavaVendor - Variable in class org.jmol.viewer.Viewer
 
strJavaVersion - Variable in class org.jmol.viewer.Viewer
 
strMeasurement - Variable in class org.jmol.modelset.Measurement
 
strOSName - Variable in class org.jmol.viewer.Viewer
 
strPeeked - Variable in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
structConfFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structSheetRangeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structSiteRangeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
structure() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
 
structure - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
Structure - Class in org.jmol.adapter.smarter
 
Structure() - Constructor for class org.jmol.adapter.smarter.Structure
 
Structure(int, String, char, int, char, char, int, char) - Constructor for class org.jmol.adapter.smarter.Structure
 
structure - Variable in class org.jmol.popup.PopupResourceBundle
 
structure() - Method in class org.jmol.viewer.Eval
 
structure - Static variable in class org.jmol.viewer.Token
 
structureContents - Static variable in class org.jmol.popup.PopupResourceBundle
 
structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structureCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
structureCount - Variable in class org.jmol.modelset.ModelCollection
 
structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structures - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
 
structures - Variable in class org.jmol.modelset.ModelCollection
 
structuresDefinedInFile - Variable in class org.jmol.modelset.ModelCollection
 
structureTainted - Variable in class org.jmol.modelset.Model
 
structureType - Variable in class org.jmol.adapter.smarter.Structure
 
structureTypes - Variable in class org.jmol.shapebio.BioShapeRenderer
 
sub(double[], double[], Vector3d) - Static method in class org.jmol.minimize.Util
 
sub - Static variable in class org.jmol.viewer.Token
 
subset() - Method in class org.jmol.viewer.Eval
 
subset - Static variable in class org.jmol.viewer.Token
 
substructure - Static variable in class org.jmol.viewer.Token
 
sumVertexNormals(Vector3f[]) - Method in class org.jmol.shape.Mesh
 
sumVertexNormals(Vector3f[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
supportedRecordTypes - Static variable in class org.jmol.adapter.readers.more.ShelxReader
 
surface - Static variable in class org.jmol.viewer.Token
 
SURFACE_ATOMICORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.shape.Dots
 
SURFACE_ELLIPSOID2 - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_ELLIPSOID3 - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_FILE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_FUNCTIONXY - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_INFO - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LCAOCARTOON - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LOBE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MEP - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MOLECULAR - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MOLECULARORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NOMAP - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NONE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_PROPERTY - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SASURFACE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SOLVENT - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SPHERE - Static variable in class org.jmol.jvxl.readers.Parameters
 
surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlReader
 
surfacedistance - Static variable in class org.jmol.viewer.Token
 
surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
 
surfaceDistanceMax - Variable in class org.jmol.modelset.AtomCollection
 
SurfaceGenerator - Class in org.jmol.jvxl.readers
 
SurfaceGenerator() - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
 
SurfaceGenerator(AtomDataServer, MeshDataServer, ColorEncoder, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
 
surfaceSet - Variable in class org.jmol.jvxl.data.MeshData
 
surfaceSet - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
surfaceType - Variable in class org.jmol.jvxl.readers.Parameters
 
sVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
sValue(Token) - Static method in class org.jmol.viewer.Token
 
swap(short[], int, int) - Static method in class org.jmol.util.ArrayUtil
 
swap(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
 
swap(float[], int, int) - Static method in class org.jmol.util.ArrayUtil
 
Swing3D - Class in org.jmol.g3d
Implementation of Platform3D when using Swing on JVMs >= 1.2
Swing3D() - Constructor for class org.jmol.g3d.Swing3D
 
swingPopup - Variable in class org.jmol.popup.JmolPopupSwing
 
sym - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
SYM_EQUIV_XYZ - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
symbol - Variable in class org.jmol.smiles.SmilesAtom
 
symmetries - Variable in class org.jmol.adapter.readers.more.GamessUKReader
 
SYMMETRY - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
Symmetry - Class in org.jmol.symmetry
 
Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
 
symmetry - Variable in class org.jmol.viewer.Eval
 
symmetry - Static variable in class org.jmol.viewer.Token
 
symmetryAddAtoms(int, int, int, int, int, int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
symmetryInfo - Variable in class org.jmol.symmetry.Symmetry
 
SymmetryInfo - Class in org.jmol.symmetry
 
SymmetryInfo() - Constructor for class org.jmol.symmetry.SymmetryInfo
 
symmetryInfoString - Variable in class org.jmol.symmetry.SymmetryInfo
 
SymmetryInterface - Interface in org.jmol.api
 
SymmetryOnly - Variable in class org.jmol.popup.JmolPopup
 
SymmetryOperation - Class in org.jmol.symmetry
 
SymmetryOperation() - Constructor for class org.jmol.symmetry.SymmetryOperation
 
SymmetryOperation(boolean) - Constructor for class org.jmol.symmetry.SymmetryOperation
 
SymmetryOperation(SymmetryOperation, Point3f[], int, int, boolean) - Constructor for class org.jmol.symmetry.SymmetryOperation
 
symmetryOperations - Variable in class org.jmol.symmetry.SymmetryInfo
 
symmetryOperationsFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
symop - Static variable in class org.jmol.viewer.Token
 
SYMOP_XYZ - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
symTemp - Variable in class org.jmol.modelset.ModelCollection
 
sync() - Method in class org.jmol.viewer.Eval
 
sync - Static variable in class org.jmol.viewer.Token
 
SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
 
syncDisabled - Variable in class org.jmol.viewer.StatusManager
 
syncId - Variable in class org.jmol.applet.Jmol
 
syncId - Variable in class org.jmol.viewer.Viewer
 
syncingMouse - Variable in class org.jmol.viewer.StatusManager
 
syncingScripts - Variable in class org.jmol.viewer.StatusManager
 
syncLists() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
syncScript(String) - Method in interface org.jmol.api.JmolAppletInterface
 
syncScript(String, String) - Method in class org.jmol.api.JmolViewer
 
syncScript(String) - Method in class org.jmol.applet.Jmol
 
syncScript(String, String) - Method in class org.jmol.viewer.Viewer
 
syncSend(String, String) - Method in class org.jmol.viewer.StatusManager
 

T

T1 - Variable in class org.jmol.g3d.Hermite3D
 
T2 - Variable in class org.jmol.g3d.Hermite3D
 
tableau_integrate - Variable in class org.jmol.jcamp.ZoneVisu
 
tableau_points - Variable in class org.jmol.jcamp.ZoneVisu
 
TAG_HELIX - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
TAG_NADA - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
TAG_SHEET - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
TAG_TURN - Static variable in class org.jmol.modelsetbio.AlphaPolymer
 
taint(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
 
tainted - Variable in class org.jmol.modelset.AtomCollection
 
target - Variable in class org.jmol.shape.Object2d
 
taskNumber - Variable in class org.jmol.adapter.readers.more.NWChemReader
The number of the task begin interpreted.
tButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
TEAL - Static variable in class org.jmol.g3d.Graphics3D
 
temp - Variable in class org.jmol.symmetry.SymmetryOperation
 
tempA - Variable in class org.jmol.export._Exporter
 
TempArray - Class in org.jmol.util
 
TempArray() - Constructor for class org.jmol.util.TempArray
 
tempDipole - Variable in class org.jmol.shapespecial.Dipoles
 
temperature - Static variable in class org.jmol.viewer.Token
 
TemperatureOnly - Variable in class org.jmol.popup.JmolPopup
 
tempManager - Variable in class org.jmol.viewer.Viewer
 
tempP1 - Variable in class org.jmol.export._Exporter
 
tempP2 - Variable in class org.jmol.export._Exporter
 
tempP3 - Variable in class org.jmol.export._Exporter
 
tempStatement - Variable in class org.jmol.viewer.Eval
 
tempV1 - Variable in class org.jmol.export._Exporter
 
tempV2 - Variable in class org.jmol.export._Exporter
 
tempV3 - Variable in class org.jmol.export._Exporter
 
tEndcapOpen - Variable in class org.jmol.g3d.Cylinder3D
 
tensScale - Static variable in class org.jmol.util.Parser
 
term - Variable in class org.jmol.symmetry.SpaceGroup
 
Test - Class in org.openscience.jmol.app.webexport
 
Test(Viewer) - Constructor for class org.openscience.jmol.app.webexport.Test
 
testData - Static variable in class org.jmol.viewer.Viewer
 
testData2 - Static variable in class org.jmol.viewer.Viewer
 
testFlag1 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testFlag2 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testFlag3 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
testFlag4 - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
tEvenDiameter - Variable in class org.jmol.g3d.Cylinder3D
 
text - Variable in class org.jmol.export.image.ImageSelection
 
text - Variable in class org.jmol.shape.Hover
 
text - Variable in class org.jmol.shape.Labels
 
Text - Class in org.jmol.shape
 
Text(JmolRendererInterface, Font3D, String, short, short, int, int, int, int, int, float) - Constructor for class org.jmol.shape.Text
 
Text(Viewer, Graphics3D, Font3D, String, short, int, int, float) - Constructor for class org.jmol.shape.Text
 
text - Variable in class org.jmol.shape.Text
 
Text3D - Class in org.jmol.g3d
implementation for text rendering
Text3D(String, Font3D, Platform3D, boolean) - Constructor for class org.jmol.g3d.Text3D
 
textColor - Variable in class org.jmol.appletwrapper.AppletWrapper
 
TEXTCOLOR - Static variable in class org.openscience.jmol.app.Splash
 
texte - Variable in class org.jmol.jcamp.Visua
 
TexteTitre - Variable in class org.jmol.jcamp.Visua
 
TexteTitre - Variable in class org.jmol.jcamp.ZoneVisu
 
TextFormat - Class in org.jmol.util
 
TextFormat() - Constructor for class org.jmol.util.TextFormat
 
textHeight - Variable in class org.jmol.shape.Text
 
textInfo - Variable in class org.jmol.symmetry.PointGroup
 
TextShape - Class in org.jmol.shape
 
TextShape() - Constructor for class org.jmol.shape.TextShape
 
textUnformatted - Variable in class org.jmol.shape.Text
 
textWidth - Variable in class org.jmol.shape.Text
 
textY - Variable in class org.openscience.jmol.app.Splash
 
tHemisphere - Variable in class org.jmol.bspt.CubeIterator
 
thePlane - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
thePlane - Variable in class org.jmol.jvxl.data.VolumeData
 
thePlane - Variable in class org.jmol.jvxl.readers.Parameters
 
thePlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
 
theProperty - Variable in class org.jmol.jvxl.readers.Parameters
 
theta - Variable in class org.jmol.minimize.forcefield.Calculation
 
theTok - Variable in class org.jmol.viewer.Eval
 
theToken - Variable in class org.jmol.viewer.Compiler
 
theToken - Variable in class org.jmol.viewer.Eval
 
theValue - Variable in class org.jmol.viewer.Compiler
 
thisArgb - Variable in class org.jmol.shape.Dots
 
thisAtom - Variable in class org.jmol.shape.Dots
 
thisCommand - Variable in class org.jmol.viewer.Eval
 
thisContour - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
thisContour - Variable in class org.jmol.jvxl.readers.Parameters
 
thisDataSetName - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
thisFormula - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
thisFunction - Variable in class org.jmol.viewer.Compiler
 
thisID - Variable in class org.jmol.shape.Mesh
 
thisID - Variable in class org.jmol.shape.Object2dShape
 
thisID - Variable in class org.jmol.shapespecial.Dipole
 
thisInside - Variable in class org.jmol.jvxl.readers.JvxlReader
 
thisMesh - Variable in class org.jmol.shapespecial.Draw
 
thisMesh - Variable in class org.jmol.shapesurface.Isosurface
 
thisModel - Variable in class org.jmol.shapesurface.MolecularOrbital
 
thismodel - Static variable in class org.jmol.viewer.Token
 
thisName - Static variable in class org.jmol.util.ColorEncoder
 
thisRadius - Variable in class org.jmol.shape.Dots
 
thisScale - Static variable in class org.jmol.util.ColorEncoder
 
thisSet - Variable in class org.jmol.shapesurface.LcaoCartoon
 
thisStateModel - Variable in class org.jmol.modelset.ModelCollection
 
thisStructuralFormula - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
thisType - Variable in class org.jmol.export.dialog.Dialog.TypeFilter
 
thisType - Variable in class org.jmol.shapesurface.LcaoCartoon
 
thisx - Variable in class org.jmol.popup.JmolPopup
 
thisy - Variable in class org.jmol.popup.JmolPopup
 
TickerThread - Class in org.jmol.appletwrapper
 
TickerThread(AppletWrapper) - Constructor for class org.jmol.appletwrapper.TickerThread
 
timeBegin - Variable in class org.jmol.applet.Jmol
 
timeBegin - Variable in class org.openscience.jmol.app.DisplayPanel
 
timeBegin - Variable in class org.openscience.jvxl.MonitorInputStream
 
timeBeginExecution - Variable in class org.jmol.viewer.Eval
 
timeCount - Variable in class org.jmol.applet.Jmol
 
timeCount - Static variable in class org.openscience.jmol.app.DisplayPanel
 
timeCurrent - Variable in class org.jmol.viewer.MouseManager
 
timeEndExecution - Variable in class org.jmol.viewer.Eval
 
timeLast - Variable in class org.jmol.applet.Jmol
 
timeLast - Static variable in class org.openscience.jmol.app.DisplayPanel
 
times - Static variable in class org.jmol.viewer.Token
 
TimeStamp_WebLink() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
timeTotal - Variable in class org.jmol.applet.Jmol
 
timeTotal - Static variable in class org.openscience.jmol.app.DisplayPanel
 
TIMINGS - Static variable in class org.jmol.g3d.Normix3D
 
title - Variable in class org.jmol.jvxl.data.JvxlData
 
title - Variable in class org.jmol.jvxl.readers.Parameters
 
title - Variable in class org.jmol.shape.Mesh
 
title - Variable in class org.jmol.shape.MeshCollection
 
title - Variable in class org.openscience.jmol.app.Jmol.OpenUrlAction
 
TITLE_MAX_WIDTH - Static variable in class org.jmol.popup.JmolPopup
 
toAxisAngle4f() - Method in class org.jmol.util.Quaternion
 
toBytes(StringBuffer) - Static method in class org.jmol.util.Base64
 
toCartesian(Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
toCartesian(int, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
toCartesian(Point3f) - Method in class org.jmol.symmetry.Symmetry
 
toCartesian(Point3f) - Method in class org.jmol.symmetry.UnitCell
 
toCartesian(Point3f) - Method in class org.jmol.viewer.Viewer
 
toFloat(double[]) - Static method in class org.jmol.util.Eigen
 
toFloat3x3(double[][]) - Static method in class org.jmol.util.Eigen
 
toFractional(Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
toFractional(int, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
toFractional(Point3f) - Method in class org.jmol.symmetry.Symmetry
 
toFractional(Point3f) - Method in class org.jmol.symmetry.UnitCell
 
toFractional(float) - Static method in class org.jmol.symmetry.UnitCell
 
toFractional(Point3f) - Method in class org.jmol.viewer.Viewer
 
toFractionalUnitCell(Point3f) - Method in class org.jmol.symmetry.UnitCell
 
toggle(Measurement) - Method in class org.jmol.shape.Measures
 
toggleInPlace(BitSet, BitSet, int) - Static method in class org.jmol.util.BitSetUtil
a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
toggleMeasurement() - Method in class org.jmol.viewer.MouseManager
 
toggleMeasurement(int[], String) - Method in class org.jmol.viewer.Viewer
 
toggleOn(int[]) - Method in class org.jmol.shape.Measures
 
togglePickingLabel(BitSet) - Method in class org.jmol.viewer.Viewer
 
toJSON(String, Object) - Static method in class org.jmol.util.Escape
 
tok - Variable in class org.jmol.viewer.Token
 
tokAt(int) - Method in class org.jmol.viewer.Compiler
 
tokAt(int) - Method in class org.jmol.viewer.Eval
 
tokAt(int, Token[]) - Method in class org.jmol.viewer.Eval
 
tokAttr(int, int) - Static method in class org.jmol.viewer.Compiler
 
tokAttrOr(int, int, int) - Static method in class org.jmol.viewer.Compiler
 
tokCommand - Variable in class org.jmol.viewer.Compiler
 
token - Variable in class org.jmol.viewer.Compiler.FlowContext
 
Token - Class in org.jmol.viewer
 
Token(int, int, Object) - Constructor for class org.jmol.viewer.Token
 
Token(int) - Constructor for class org.jmol.viewer.Token
 
Token(int, int) - Constructor for class org.jmol.viewer.Token
 
Token(int, Object) - Constructor for class org.jmol.viewer.Token
 
Token.Token2 - Class in org.jmol.viewer
 
Token.Token2(int, int, Object) - Constructor for class org.jmol.viewer.Token.Token2
 
TOKEN_ELEMENT_AROMATIC - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_CHARGED - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_CONNECTED - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_ONLY - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_SP - Static variable in class org.jmol.minimize.Minimizer
 
TOKEN_ELEMENT_SP2 - Static variable in class org.jmol.minimize.Minimizer
 
tokenAll - Static variable in class org.jmol.viewer.Token
 
tokenAnd - Static variable in class org.jmol.viewer.Token
 
tokenArraySelector - Static variable in class org.jmol.viewer.Token
 
tokenAt(int, Token[]) - Method in class org.jmol.viewer.Eval
 
tokenAttr(Token, int) - Static method in class org.jmol.viewer.Compiler
 
tokenComma - Static variable in class org.jmol.viewer.Token
 
tokenCommand - Variable in class org.jmol.viewer.Compiler
 
tokenCoordinateBegin - Static variable in class org.jmol.viewer.Token
 
tokenCoordinateEnd - Static variable in class org.jmol.viewer.Token
 
tokenCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokenDivide - Static variable in class org.jmol.viewer.Token
 
tokenExpressionBegin - Static variable in class org.jmol.viewer.Token
 
tokenExpressionEnd - Static variable in class org.jmol.viewer.Token
 
tokenize(String) - Method in class org.openscience.jmol.app.Jmol
Take the given string and chop it up into a series of strings on whitespace boundries.
tokenizer - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
tokenizer - Variable in class org.jmol.adapter.readers.more.JmeReader
 
tokenLeftParen - Static variable in class org.jmol.viewer.Token
 
tokenMinus - Static variable in class org.jmol.viewer.Token
 
tokenNext() - Method in class org.jmol.viewer.Compiler
increments the pointer; does NOT set theToken or theValue
tokenNext(int) - Method in class org.jmol.viewer.Compiler
 
tokenOff - Static variable in class org.jmol.viewer.Token
 
tokenOn - Static variable in class org.jmol.viewer.Token
 
tokenOr - Static variable in class org.jmol.viewer.Token
 
tokenPlus - Static variable in class org.jmol.viewer.Token
 
tokenRightParen - Static variable in class org.jmol.viewer.Token
 
tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokenSet - Static variable in class org.jmol.viewer.Token
 
tokenSetArray - Static variable in class org.jmol.viewer.Token
 
tokenSetProperty - Static variable in class org.jmol.viewer.Token
 
tokenSetting(int) - Method in class org.jmol.viewer.Eval
 
tokenSetVar - Static variable in class org.jmol.viewer.Token
 
tokenTimes - Static variable in class org.jmol.viewer.Token
 
tokenTypes - Static variable in class org.jmol.minimize.Minimizer
 
tokPeek() - Method in class org.jmol.viewer.Compiler
 
tokPeek(int) - Method in class org.jmol.viewer.Compiler
 
toolbar - Variable in class org.openscience.jmol.app.Jmol
 
toolbarButtonGroup - Static variable in class org.openscience.jmol.app.Jmol
 
top - Static variable in class org.jmol.viewer.Token
 
topAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
toPoint4f() - Method in class org.jmol.util.Quaternion
 
toRadians - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
toRadians - Static variable in class org.jmol.symmetry.UnitCell
 
toReadable(Object) - Static method in class org.jmol.util.Escape
 
toReadable(String, Object) - Static method in class org.jmol.util.Escape
 
torsion - Static variable in class org.jmol.viewer.Token
 
torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
torsions - Variable in class org.jmol.minimize.forcefield.Calculations
 
torsions - Variable in class org.jmol.minimize.Minimizer
 
toString() - Method in class org.jmol.g3d.Rgb16
 
toString() - Method in class org.jmol.modelset.Group
 
toString() - Method in class org.jmol.modelset.ModelCollection.StateScript
 
toString() - Method in class org.jmol.util.Quaternion
 
toString() - Method in exception org.jmol.viewer.Eval.ScriptException
 
toString() - Method in class org.jmol.viewer.Eval
 
toString() - Method in class org.jmol.viewer.Function
 
toString() - Method in class org.jmol.viewer.Token
 
toString() - Method in class org.openscience.jmol.app.AtomSetChooser.AtomSet
 
toUnitCell(Point3f, Point3f) - Method in interface org.jmol.api.SymmetryInterface
 
toUnitCell(int, Point3f, Point3f) - Method in class org.jmol.modelset.ModelCollection
 
toUnitCell(Point3f, Point3f) - Method in class org.jmol.symmetry.Symmetry
 
toUnitCell(Point3f, Point3f) - Method in class org.jmol.symmetry.UnitCell
 
toUnitCell(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
toVector() - Method in class org.jmol.modelset.Measurement
 
toWebAction - Variable in class org.openscience.jmol.app.Jmol
 
toWebActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
tPending - Variable in class org.jmol.shapebio.RocketsRenderer
 
tql2() - Method in class org.jmol.util.Eigen
 
tQuiet - Variable in class org.jmol.viewer.Eval
 
Trace - Class in org.jmol.shapebio
 
Trace() - Constructor for class org.jmol.shapebio.Trace
 
trace - Static variable in class org.jmol.viewer.Token
 
Trace_Integrate() - Method in class org.jmol.jcamp.ZoneVisu
 
Trace_PEAK_TABLE() - Method in class org.jmol.jcamp.ZoneVisu
 
Trace_XYDATA() - Method in class org.jmol.jcamp.ZoneVisu
 
traceAlpha - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
TraceGenerator - Class in org.jmol.export
 
TraceGenerator() - Constructor for class org.jmol.export.TraceGenerator
 
TraceRenderer - Class in org.jmol.shapebio
 
TraceRenderer() - Constructor for class org.jmol.shapebio.TraceRenderer
 
trajectories - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectories - Variable in class org.jmol.modelset.ModelCollection
 
trajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
 
transform(Vector3f, Vector3f) - Method in interface org.jmol.api.VolumeDataInterface
 
transform(Vector3f, Vector3f) - Method in class org.jmol.jvxl.data.VolumeData
 
transform(Viewer) - Method in class org.jmol.modelset.Atom
 
transform() - Method in class org.jmol.shape.MeshRenderer
 
transform(Dipole) - Method in class org.jmol.shapespecial.DipolesRenderer
 
transform(short, Atom, Vector3f) - Method in class org.jmol.shapespecial.VectorsRenderer
 
transform() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
 
transform(Point3f) - Method in class org.jmol.util.Quaternion
 
transform(Point3f, Point3f) - Method in class org.jmol.util.Quaternion
 
transform(Vector3f) - Method in class org.jmol.util.Quaternion
 
transform - Static variable in class org.jmol.viewer.Token
 
transformCartesian(UnitCell, Point3f) - Method in class org.jmol.symmetry.SymmetryOperation
 
transformedVectors - Variable in class org.jmol.g3d.Normix3D
 
transformedVectors - Variable in class org.jmol.shape.MeshRenderer
 
TransformFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
TransformManager - Class in org.jmol.viewer
 
TransformManager() - Constructor for class org.jmol.viewer.TransformManager
 
TransformManager(Viewer) - Constructor for class org.jmol.viewer.TransformManager
 
TransformManager(Viewer, int, int) - Constructor for class org.jmol.viewer.TransformManager
 
transformManager - Variable in class org.jmol.viewer.Viewer
 
TransformManager.SpinThread - Class in org.jmol.viewer
 
TransformManager.SpinThread(float, BitSet) - Constructor for class org.jmol.viewer.TransformManager.SpinThread
 
TransformManager.VibrationThread - Class in org.jmol.viewer
 
TransformManager.VibrationThread() - Constructor for class org.jmol.viewer.TransformManager.VibrationThread
 
TransformManager10 - Class in org.jmol.viewer
 
TransformManager10(Viewer) - Constructor for class org.jmol.viewer.TransformManager10
 
TransformManager10(Viewer, int, int) - Constructor for class org.jmol.viewer.TransformManager10
 
TransformManager11 - Class in org.jmol.viewer
 
TransformManager11() - Constructor for class org.jmol.viewer.TransformManager11
 
TransformManager11(Viewer) - Constructor for class org.jmol.viewer.TransformManager11
 
TransformManager11(Viewer, int, int) - Constructor for class org.jmol.viewer.TransformManager11
 
transformPoint(Point3f, Point3i) - Method in class org.jmol.viewer.TransformManager
 
transformPoint(Point3f) - Method in class org.jmol.viewer.TransformManager
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPoint(Point3f, Vector3f) - Method in class org.jmol.viewer.TransformManager
 
transformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
transformPoint(Point3f) - Method in class org.jmol.viewer.Viewer
 
transformPoint(Point3f, Vector3f) - Method in class org.jmol.viewer.Viewer
 
transformPoint(Point3f, Point3i) - Method in class org.jmol.viewer.Viewer
 
transformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
transformPointNoClip(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
transformPointNoClip(Point3f) - Method in class org.jmol.viewer.TransformManager
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPointNoClip(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
transformPoints(int, Point3f[], Point3i[]) - Method in class org.jmol.viewer.TransformManager
 
transformPoints(Point3f[], Point3i[]) - Method in class org.jmol.viewer.Viewer
 
transformScreenPoint(Point3f) - Method in class org.jmol.viewer.TransformManager
 
transformVector(Vector3f, Vector3f) - Method in class org.jmol.viewer.TransformManager
 
transformVector(Vector3f, Vector3f) - Method in class org.jmol.viewer.Viewer
 
transitionDipole - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
translate() - Method in class org.jmol.viewer.Eval
 
translate - Static variable in class org.jmol.viewer.Token
 
translate(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
translateSelected() - Method in class org.jmol.viewer.Eval
 
translateSelected - Static variable in class org.jmol.viewer.Token
 
translateToXPercent(float) - Method in class org.jmol.viewer.TransformManager
 
translateToXPercent(float) - Method in class org.jmol.viewer.Viewer
 
translateToYPercent(float) - Method in class org.jmol.viewer.TransformManager
 
translateToYPercent(float) - Method in class org.jmol.viewer.Viewer
 
translateToZPercent(float) - Method in class org.jmol.viewer.TransformManager
 
translateToZPercent(float) - Method in class org.jmol.viewer.Viewer
 
translateXYBy(int, int) - Method in class org.jmol.viewer.TransformManager
 
translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
 
translation - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
Translation - Class in org.jmol.symmetry
 
Translation() - Constructor for class org.jmol.symmetry.Translation
 
Translation(char, int) - Constructor for class org.jmol.symmetry.Translation
 
Translation(char, int, Point3i) - Constructor for class org.jmol.symmetry.Translation
 
Translation(char, int, int) - Constructor for class org.jmol.symmetry.Translation
 
translation - Static variable in class org.jmol.viewer.Token
 
translationCode - Variable in class org.jmol.symmetry.Translation
 
translationResources - Variable in class org.jmol.i18n.GT
 
translationResourcesCount - Variable in class org.jmol.i18n.GT
 
translations - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
translationString - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
 
translucencyFractionalFromColix(short) - Method in class org.jmol.export._Exporter
 
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
 
translucent - Static variable in class org.jmol.viewer.Token
 
TRANSLUCENT_50 - Static variable in class org.jmol.g3d.Graphics3D
 
TRANSLUCENT_MASK - Static variable in class org.jmol.g3d.Graphics3D
 
TRANSLUCENT_SCREENED - Static variable in class org.jmol.g3d.Graphics3D
 
TRANSLUCENT_SHIFT - Static variable in class org.jmol.g3d.Graphics3D
 
translucentAllowed - Variable in class org.jmol.shape.Shape
 
translucentLevel - Variable in class org.jmol.shape.Shape
 
translucentLevel - Variable in class org.jmol.shapesurface.LcaoCartoon
 
TRANSPARENT - Static variable in class org.jmol.g3d.Graphics3D
 
transparent - Static variable in class org.jmol.viewer.Token
 
tRaster - Variable in class org.jmol.g3d.Cylinder3D
 
tred2() - Method in class org.jmol.util.Eigen
 
tree - Variable in class org.openscience.jmol.app.AtomSetChooser
 
treeDepth - Variable in class org.jmol.bspt.Bspt
 
treeModel - Variable in class org.openscience.jmol.app.AtomSetChooser
 
triad(Tuple3f) - Method in class org.jmol.export._PovrayExporter
 
triad(int[]) - Method in class org.jmol.export._PovrayExporter
 
triangle3d - Variable in class org.jmol.g3d.Graphics3D
 
Triangle3D - Class in org.jmol.g3d
renders triangles
Triangle3D(Graphics3D) - Constructor for class org.jmol.g3d.Triangle3D
 
triangles - Static variable in class org.jmol.viewer.Token
 
triangleTable2 - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
triangleVertexList - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
triangulateContours(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
trim(String, String) - Static method in class org.jmol.util.TextFormat
 
trim - Static variable in class org.jmol.viewer.Token
 
trouve_f(double) - Method in class org.jmol.jcamp.ZoneVisu
 
TRUE - Static variable in class org.jmol.viewer.SelectionManager
 
truncate0(StringBuffer, float) - Static method in class org.jmol.viewer.TransformManager
 
truncate2(StringBuffer, float) - Static method in class org.jmol.viewer.TransformManager
 
truncateEndBlanks(String) - Static method in class org.jmol.jcamp.utils.StringDataUtils
Truncates blank spaces at the end of the string provided
tScreened - Variable in class org.jmol.g3d.Sphere3D
 
tuples - Variable in class org.jmol.bspt.Leaf
 
Turn - Class in org.jmol.modelsetbio
 
Turn(AlphaPolymer, int, int) - Constructor for class org.jmol.modelsetbio.Turn
 
tValue(String) - Static method in class org.jmol.viewer.Token
 
twelfths - Static variable in class org.jmol.symmetry.SymmetryOperation
 
twelfthsOf(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
TWO_PI - Static variable in class org.jmol.minimize.forcefield.Calculations
 
twoP2 - Static variable in class org.jmol.symmetry.UnitCell.Data
 
twoPass - Variable in class org.jmol.g3d.Graphics3D
 
twoPI - Static variable in class org.jmol.viewer.TransformManager
 
txRaster - Variable in class org.jmol.g3d.Cylinder3D
 
type - Variable in class org.jmol.minimize.MinAtom
 
type - Variable in class org.jmol.modelset.ModelCollection.Structure
 
type - Variable in class org.jmol.modelset.Polymer
 
type - Variable in class org.jmol.modelsetbio.ProteinStructure
 
type - Variable in class org.jmol.shapespecial.Dipole
 
type - Variable in class org.jmol.symmetry.PointGroup.Operation
 
type - Static variable in class org.jmol.viewer.Token
 
TYPE_AMINO - Static variable in class org.jmol.modelset.Polymer
 
TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelset.Polymer
 
TYPE_DIRECTIONAL_1 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_DIRECTIONAL_2 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_DOUBLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NUCLEIC - Static variable in class org.jmol.modelset.Polymer
 
TYPE_OTHER - Static variable in class org.jmol.modelset.Polymer
 
TYPE_SINGLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
TYPE_TRIPLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_UNKOWN - Static variable in class org.jmol.smiles.SmilesBond
 
typedata - Variable in class org.jmol.jcamp.ZoneVisu
 
typeIndex - Variable in class org.jmol.symmetry.PointGroup.Operation
 
typeName - Variable in class org.jmol.modelset.ModelCollection.Structure
 
typeNames - Static variable in class org.jmol.symmetry.PointGroup
 
typeOf(Token) - Static method in class org.jmol.viewer.Token
 
tyRaster - Variable in class org.jmol.g3d.Cylinder3D
 
tzRaster - Variable in class org.jmol.g3d.Cylinder3D
 

U

U_ISO_OR_EQUIV - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
 
Uccage - Class in org.jmol.shape
 
Uccage() - Constructor for class org.jmol.shape.Uccage
 
UccageGenerator - Class in org.jmol.export
 
UccageGenerator() - Constructor for class org.jmol.export.UccageGenerator
 
UccageRenderer - Class in org.jmol.shape
 
UccageRenderer() - Constructor for class org.jmol.shape.UccageRenderer
 
uguideAction - Static variable in class org.openscience.jmol.app.Jmol
 
uicrcifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
Un_Nombre - Variable in class org.jmol.jcamp.ZoneVisu
 
unaryMinus - Static variable in class org.jmol.viewer.Token
 
undoButton - Variable in class org.openscience.jmol.app.ScriptWindow
 
undoClear() - Method in class org.openscience.jmol.app.ScriptWindow
 
undoPointer - Variable in class org.openscience.jmol.app.ScriptWindow
 
undoRedo(boolean) - Method in class org.openscience.jmol.app.ScriptWindow
 
undoSave() - Method in class org.openscience.jmol.app.ScriptWindow
 
undoSaved - Variable in class org.openscience.jmol.app.ScriptWindow
 
undoSetEnabled() - Method in class org.openscience.jmol.app.ScriptWindow
 
undoStack - Variable in class org.openscience.jmol.app.ScriptWindow
 
unescapeBitset(String) - Static method in class org.jmol.util.Escape
 
unescapePoint(String) - Static method in class org.jmol.util.Escape
 
unescapePointOrBitsetAsToken(String) - Static method in class org.jmol.viewer.Token
 
unicode(char) - Static method in class org.jmol.util.Escape
 
unicodeName - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
uniqueAtomMap - Variable in class org.jmol.adapter.readers.more.PsiReader
 
uniqueAxis - Variable in class org.jmol.symmetry.SpaceGroup
 
uniqueID - Variable in class org.jmol.modelsetbio.ProteinStructure
 
uniqueID - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
uniqueID - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
unitAxisPoints - Static variable in class org.jmol.shape.Axes
 
unitAxisPoints - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
unitBboxPoints - Static variable in class org.jmol.modelset.BoxInfo
 
unitCell - Variable in class org.jmol.symmetry.Symmetry
 
UnitCell - Class in org.jmol.symmetry
 
UnitCell(float[]) - Constructor for class org.jmol.symmetry.UnitCell
 
unitcell(int) - Method in class org.jmol.viewer.Eval
 
unitcell - Static variable in class org.jmol.viewer.Token
 
UnitCell.Data - Class in org.jmol.symmetry
 
UnitCell.Data() - Constructor for class org.jmol.symmetry.UnitCell.Data
 
UnitcellOnly - Variable in class org.jmol.popup.JmolPopup
 
unitCells - Variable in class org.jmol.modelset.ModelCollection
 
unitCubePoints - Static variable in class org.jmol.symmetry.UnitCell
 
unitPlanarVectors - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
unitVectors - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
unitVectorX - Variable in class org.jmol.modelsetbio.BioPolymer
 
unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
UNKNOWN - Static variable in class org.jmol.viewer.SelectionManager
 
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.g3d.Graphics3D
 
unreportedProperties - Static variable in class org.jmol.viewer.StateManager.GlobalSettings
 
UNSET - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
unsetProperty(String) - Method in class org.jmol.viewer.Viewer
 
unsupportedRecordTypes - Static variable in class org.jmol.adapter.readers.more.ShelxReader
 
untaint(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
unTransformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
 
unTransformPoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
 
unused - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
unused - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
unused2 - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
UNUSED_OPTION3 - Static variable in class org.jmol.g3d.Graphics3D
 
update(Graphics) - Method in class org.jmol.applet.Jmol
 
update(Graphics, String) - Method in class org.jmol.applet.Jmol
 
update(Graphics) - Method in class org.jmol.appletwrapper.AppletWrapper
 
update(Graphics) - Method in interface org.jmol.appletwrapper.WrappedApplet
 
update(Graphics) - Method in class org.jmol.jcamp.ZoneVisu
 
UPDATE_ALL - Static variable in class org.jmol.popup.JmolPopup
 
UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolPopup
 
UPDATE_SHOW - Static variable in class org.jmol.popup.JmolPopup
 
updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
 
updateAtomXYZ() - Method in class org.jmol.minimize.Minimizer
 
updateCommandLine() - Method in class org.openscience.jmol.app.PovrayDialog
 
updateComponents() - Method in class org.openscience.jmol.app.PreferencesDialog
 
updateComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateElementsComputedMenu(BitSet) - Method in class org.jmol.popup.JmolPopup
 
updateEquation(Ellipsoids.Ellipsoid) - Method in class org.jmol.shapespecial.Ellipsoids
 
updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolPopup
 
updateForShow() - Method in class org.jmol.popup.JmolPopup
 
updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateGroup3List(Object, String) - Method in class org.jmol.popup.JmolPopup
 
updateHeteroComputedMenu(Hashtable) - Method in class org.jmol.popup.JmolPopup
 
updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
 
updateMeasurementTableData() - Method in class org.openscience.jmol.app.MeasurementTable
 
updateMenuItem(Object, String, String) - Method in class org.jmol.popup.JmolPopup
 
updateMenuItem(Object, String, String) - Method in class org.jmol.popup.JmolPopupAwt
 
updateMenuItem(Object, String, String) - Method in class org.jmol.popup.JmolPopupSwing
 
updateMode - Variable in class org.jmol.popup.JmolPopup
 
updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateOffsetsForAlternativeLocations(BitSet, int, byte[], int, int) - Method in class org.jmol.modelset.Chain
 
updateOffsetsForAlternativeLocations(BitSet, int) - Method in class org.jmol.modelsetbio.Monomer
 
updatePDBComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updatePreview(File) - Method in class org.jmol.export.dialog.FilePreview
Update preview
updateScreen() - Method in class org.openscience.jmol.app.PovrayDialog
Update screen informations
updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
 
updateSize() - Method in class org.openscience.jmol.app.DisplayPanel
 
updateSurfaceData() - Method in class org.jmol.jvxl.readers.VoxelReader
 
updateSurfMoComputedMenu(Hashtable) - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateTables() - Method in class org.openscience.jmol.app.MeasurementTable
 
updateTriangles() - Method in class org.jmol.jvxl.readers.VoxelReader
 
updateWriteMenu() - Method in class org.jmol.popup.JmolPopup
 
upperNeighborIsHelixOrSheet() - Method in class org.jmol.modelsetbio.ProteinStructure
 
url - Static variable in class org.jmol.viewer.Token
 
url - Variable in class org.openscience.jmol.app.AboutDialog.PageLoader
 
url - Variable in class org.openscience.jmol.app.HelpDialog.PageLoader
 
url - Variable in class org.openscience.jmol.app.WhatsNewDialog.PageLoader
 
URL_LOCAL - Static variable in class org.jmol.viewer.FileManager
 
urlPrefixes - Static variable in class org.jmol.export.dialog.Dialog
 
urlPrefixes - Static variable in class org.jmol.viewer.FileManager
 
urlTypeIndex(String) - Static method in class org.jmol.viewer.FileManager
 
use2dBondOrderCalculation - Variable in class org.jmol.export._Exporter
 
USE_PALETTE - Static variable in class org.jmol.g3d.Graphics3D
 
useAppletJS - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
useAutoBond - Static variable in class org.jmol.adapter.readers.more.FoldingXyzReader
 
useClearingThread - Variable in class org.jmol.g3d.Platform3D
 
useCommandThread - Variable in class org.jmol.viewer.Viewer
 
useCommandWatcherThread - Variable in class org.jmol.viewer.ScriptManager
 
useFileExtension - Variable in class org.openscience.jmol.app.FileTyper
 
useFileExtensionCheckBox - Variable in class org.openscience.jmol.app.FileTyper
 
useIonic - Variable in class org.jmol.atomdata.AtomData
 
useIonic - Variable in class org.jmol.jvxl.readers.Parameters
 
useMinimizationThread() - Method in class org.jmol.viewer.Viewer
 
useNumberLocalization - Static variable in class org.jmol.util.TextFormat
 
useNumberLocalization - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
useQueue - Variable in class org.jmol.viewer.ScriptManager
 
USER - Static variable in class org.jmol.util.ColorEncoder
 
user - Static variable in class org.jmol.viewer.Token
 
useRasMolHbondsCalculation - Static variable in class org.jmol.modelset.ModelSet
 
userDefinedVanDerWaalRadius - Variable in class org.jmol.modelset.Atom
 
userflags - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
 
UserPropsFile - Static variable in class org.openscience.jmol.app.Jmol
 
userScale - Static variable in class org.jmol.util.ColorEncoder
 
userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
 
userVdwMars - Variable in class org.jmol.viewer.DataManager
 
userVdws - Variable in class org.jmol.viewer.DataManager
 
useZoomLarge - Variable in class org.jmol.viewer.TransformManager
 
usingScriptQueue() - Method in class org.jmol.viewer.Viewer
 
Util - Class in org.jmol.minimize
 
Util() - Constructor for class org.jmol.minimize.Util
 

V

v1 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
v2 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
v3 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v3 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
V3000Reader - Class in org.jmol.adapter.readers.more
A reader for MDL V3000 files
V3000Reader() - Constructor for class org.jmol.adapter.readers.more.V3000Reader
 
vAB - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vAB - Variable in class org.jmol.shape.Mesh
 
vAB - Variable in class org.jmol.shapespecial.Draw
 
vAB - Variable in class org.jmol.shapespecial.Polyhedra
 
vAC - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vAC - Variable in class org.jmol.shape.Mesh
 
vAC - Variable in class org.jmol.shapespecial.Draw
 
vAC - Variable in class org.jmol.shapespecial.Polyhedra
 
valACchrominance - Static variable in class org.jmol.util.Huffman
 
valACluminance - Static variable in class org.jmol.util.Huffman
 
valDCchrominance - Static variable in class org.jmol.util.Huffman
 
valDCluminance - Static variable in class org.jmol.util.Huffman
 
valence - Variable in class org.jmol.modelset.Atom
 
valence - Static variable in class org.jmol.viewer.Token
 
VALIDATE - Static variable in class org.jmol.geodesic.Geodesic
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.AlphaMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.PhosphorusMonomer
 
validatePolyhedronNew(Atom, int, Atom[]) - Method in class org.jmol.shapespecial.Polyhedra
 
valign - Variable in class org.jmol.shape.Object2d
 
VALIGN_BOTTOM - Static variable in class org.jmol.shape.Object2d
 
VALIGN_MIDDLE - Static variable in class org.jmol.shape.Object2d
 
VALIGN_TOP - Static variable in class org.jmol.shape.Object2d
 
VALIGN_XY - Static variable in class org.jmol.shape.Object2d
 
VALIGN_XYZ - Static variable in class org.jmol.shape.Object2d
 
vAlignNames - Static variable in class org.jmol.shape.Object2d
 
value - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
value - Variable in class org.jmol.modelset.Measurement
 
value - Variable in class org.jmol.util.Int2IntHash.Entry
 
value - Variable in class org.jmol.viewer.Token
 
valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.AtomSetChooser
 
valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToBlue - Variable in class org.jmol.jvxl.readers.Parameters
 
valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToRed - Variable in class org.jmol.jvxl.readers.Parameters
 
valueMax - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
valueMin - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
valuePeek() - Method in class org.jmol.viewer.Compiler
 
vanderwaals - Static variable in class org.jmol.viewer.Token
 
vanderwaalsMars - Static variable in class org.jmol.viewer.JmolConstants
Default table of van der Waals Radii.
var - Static variable in class org.jmol.viewer.Token
 
variables - Variable in class org.jmol.viewer.Eval
 
vButton - Variable in class org.openscience.jmol.app.PreferencesDialog
 
vConnect - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vd - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vData - Variable in class org.jmol.shapespecial.Draw
 
VDW_BABEL - Static variable in class org.jmol.viewer.JmolConstants
 
VDW_JMOL - Static variable in class org.jmol.viewer.JmolConstants
 
VDW_RASMOL - Static variable in class org.jmol.viewer.JmolConstants
 
VDW_USER - Static variable in class org.jmol.viewer.JmolConstants
 
vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
vdwLabels - Static variable in class org.jmol.viewer.JmolConstants
 
vdwPercentSlider - Variable in class org.openscience.jmol.app.PreferencesDialog
 
vector - Variable in class org.jmol.shapespecial.Dipole
 
vector() - Method in class org.jmol.viewer.Eval
 
vector - Static variable in class org.jmol.viewer.Token
 
VECTOR - Static variable in class org.openscience.jmol.app.AtomSetChooser
String for prefix/resource identifier for the vector area.
vector12ths - Variable in class org.jmol.symmetry.HallInfo
 
vectorAB - Variable in class org.jmol.g3d.Graphics3D
 
vectorAC - Variable in class org.jmol.g3d.Graphics3D
 
vectorAngleRadians(Vector3d, Vector3d) - Static method in class org.jmol.minimize.Util
 
vectorCode - Variable in class org.jmol.symmetry.HallInfo
 
vectorNormal - Variable in class org.jmol.g3d.Graphics3D
 
vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
 
Vectors - Class in org.jmol.shapespecial
 
Vectors() - Constructor for class org.jmol.shapespecial.Vectors
 
vectorScale - Variable in class org.jmol.shapespecial.VectorsRenderer
 
vectorScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
VectorsGenerator - Class in org.jmol.export
 
VectorsGenerator() - Constructor for class org.jmol.export.VectorsGenerator
 
vectorShift12ths - Variable in class org.jmol.symmetry.Translation
 
VectorsRenderer - Class in org.jmol.shapespecial
 
VectorsRenderer() - Constructor for class org.jmol.shapespecial.VectorsRenderer
 
vectorT - Variable in class org.jmol.viewer.TransformManager
 
vectorT2 - Variable in class org.jmol.viewer.TransformManager
 
vectorTemp - Variable in class org.jmol.viewer.TransformManager
 
vectorX - Variable in class org.jmol.adapter.smarter.Atom
 
vectorY - Variable in class org.jmol.adapter.smarter.Atom
 
vectorZ - Variable in class org.jmol.adapter.smarter.Atom
 
VERIFY - Static variable in class org.jmol.g3d.Triangle3D
 
verNumber - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
 
version - Static variable in class org.jmol.viewer.JmolConstants
 
VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
vertexColixes - Variable in class org.jmol.jvxl.data.MeshData
 
vertexColixes - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexCount - Variable in class org.jmol.jvxl.data.MeshData
 
vertexCount - Variable in class org.jmol.shape.Mesh
 
vertexCount - Variable in class org.jmol.shape.MeshRenderer
 
vertexCount - Variable in class org.jmol.shapesurface.Pmesh.PmeshBinaryDocument
 
vertexCounts - Static variable in class org.jmol.geodesic.Geodesic
 
VertexDataServer - Interface in org.jmol.jvxl.api
 
vertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares.PlanarSquare
 
vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
 
vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
vertexNext - Static variable in class org.jmol.geodesic.Geodesic
 
vertexPoints - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
vertexSets - Variable in class org.jmol.jvxl.data.MeshData
 
vertexSets - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexTest - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
vertexValues - Variable in class org.jmol.jvxl.data.MeshData
 
vertexValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexValues - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
 
vertexValues2d - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
vertexVectors - Static variable in class org.jmol.g3d.Normix3D
 
vertexVectors - Static variable in class org.jmol.geodesic.Geodesic
 
vertexXYZ - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
vertices - Variable in class org.jmol.jvxl.data.MeshData
 
vertices - Variable in class org.jmol.shape.Mesh
 
vertices - Variable in class org.jmol.shape.MeshRenderer
 
vertices - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
vertices - Variable in class org.jmol.symmetry.UnitCell
 
verticesT - Variable in class org.jmol.shape.UccageRenderer
 
verticesTransformed - Variable in class org.jmol.shape.DotsRenderer
 
vibEnergy - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
vibFieldMap - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
vibFields - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
vibration() - Method in class org.jmol.viewer.Eval
 
vibration - Static variable in class org.jmol.viewer.Token
 
VIBRATION_VECTOR_FLAG - Static variable in class org.jmol.modelset.Atom
 
vibrationAmplitude - Variable in class org.jmol.viewer.TransformManager
 
vibrationOn - Variable in class org.jmol.viewer.TransformManager
 
VibrationOnly - Variable in class org.jmol.popup.JmolPopup
 
vibrationPeriod - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
vibrationPeriod - Variable in class org.jmol.viewer.TransformManager
 
vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
 
vibrationRadians - Variable in class org.jmol.viewer.TransformManager
 
vibrationScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
vibrationScale - Variable in class org.jmol.viewer.TransformManager
 
vibrationThread - Variable in class org.jmol.viewer.TransformManager
 
vibrationVectors - Variable in class org.jmol.modelset.AtomCollection
 
vibX - Static variable in class org.jmol.viewer.Token
 
vibXyz - Static variable in class org.jmol.viewer.Token
 
vibY - Static variable in class org.jmol.viewer.Token
 
vibZ - Static variable in class org.jmol.viewer.Token
 
viewer - Variable in class org.jmol.applet.Console
 
viewer - Variable in class org.jmol.applet.Jmol
 
viewer - Variable in class org.jmol.applet.Jvm12
 
viewer - Variable in class org.jmol.export._Exporter
 
viewer - Variable in class org.jmol.export.dialog.FilePreview.JmolPanel
 
viewer - Variable in class org.jmol.export.image.ImageCreator
 
viewer - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
viewer - Variable in class org.jmol.minimize.forcefield.ForceField
 
viewer - Variable in class org.jmol.minimize.Minimizer
 
viewer - Variable in class org.jmol.modelset.AtomCollection
 
viewer - Variable in class org.jmol.modelset.Measurement
 
viewer - Variable in class org.jmol.popup.JmolPopup
 
viewer - Variable in class org.jmol.shape.Object2d
 
viewer - Variable in class org.jmol.shape.Shape
 
viewer - Variable in class org.jmol.shape.ShapeRenderer
 
viewer - Variable in class org.jmol.viewer.ColorManager
 
viewer - Variable in class org.jmol.viewer.Compiler
 
viewer - Variable in class org.jmol.viewer.Eval
 
viewer - Variable in class org.jmol.viewer.FileManager
 
viewer - Variable in class org.jmol.viewer.FrameExportJmolAdapter
 
viewer - Variable in class org.jmol.viewer.FrameRenderer
 
viewer - Variable in class org.jmol.viewer.ModelManager
 
viewer - Variable in class org.jmol.viewer.MouseManager
 
viewer - Variable in class org.jmol.viewer.PickingManager
 
viewer - Variable in class org.jmol.viewer.RepaintManager
 
viewer - Variable in class org.jmol.viewer.ScriptManager
 
viewer - Variable in class org.jmol.viewer.SelectionManager
 
viewer - Variable in class org.jmol.viewer.StateManager
 
viewer - Variable in class org.jmol.viewer.StatusManager
 
viewer - Variable in class org.jmol.viewer.TransformManager
 
Viewer - Class in org.jmol.viewer
 
Viewer(Component, JmolAdapter) - Constructor for class org.jmol.viewer.Viewer
 
viewer - Variable in class org.openscience.jmol.app.AtomSetChooser
 
viewer - Variable in class org.openscience.jmol.app.ConsoleTextPane
 
viewer - Variable in class org.openscience.jmol.app.DisplayPanel
 
viewer - Variable in class org.openscience.jmol.app.Jmol
The data model.
viewer - Variable in class org.openscience.jmol.app.MeasurementTable
 
viewer - Variable in class org.openscience.jmol.app.PovrayDialog
 
viewer - Variable in class org.openscience.jmol.app.PreferencesDialog
 
viewer - Variable in class org.openscience.jmol.app.ScriptWindow
 
viewer - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
viewer - Variable in class org.openscience.jmol.app.webexport.Test
 
viewer - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
viewMeasurementTableAction - Variable in class org.openscience.jmol.app.Jmol
 
VISIBILITY_CLIPPED - Static variable in class org.jmol.g3d.Line3D
 
VISIBILITY_OFFSCREEN - Static variable in class org.jmol.g3d.Line3D
 
VISIBILITY_UNCLIPPED - Static variable in class org.jmol.g3d.Line3D
 
visibilityFlags - Variable in class org.jmol.shape.Mesh
 
visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
 
visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
visible - Variable in class org.jmol.shape.Mesh
 
visible - Variable in class org.jmol.shape.Object2d
 
visible - Variable in class org.jmol.shapespecial.Dipole
 
visible - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
 
visible - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
 
visible - Static variable in class org.jmol.viewer.Token
 
Visua - Class in org.jmol.jcamp
 
Visua() - Constructor for class org.jmol.jcamp.Visua
 
visualRange - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
visualRange - Variable in class org.jmol.viewer.TransformManager
 
vNorm - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
Vo - Variable in class org.jmol.util.Eigen
 
volume - Variable in class org.jmol.symmetry.UnitCell.Data
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
VolumeData - Class in org.jmol.jvxl.data
 
VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
 
volumeData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
volumeData - Variable in class org.jmol.jvxl.readers.VoxelReader
 
VolumeDataInterface - Interface in org.jmol.api
 
VolumeDataReader - Class in org.jmol.jvxl.readers
 
VolumeDataReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.VolumeDataReader
 
VolumeFileReader - Class in org.jmol.jvxl.readers
 
VolumeFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.VolumeFileReader
 
volumetricMatrix - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.readers.VoxelReader
 
volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.readers.VoxelReader
 
voxelCounts - Variable in class org.jmol.adapter.readers.more.CubeReader
 
voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelCounts - Variable in class org.jmol.jvxl.readers.VoxelReader
 
voxelData - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelData - Variable in class org.jmol.jvxl.readers.VoxelReader
 
voxelData - Variable in class org.jmol.quantum.QuantumCalculation
 
voxelIsInTrough(float, float, float, float, float, float) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
voxelLocation - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
voxelPtToXYZ(int, int, int, Point3f) - Method in interface org.jmol.api.VolumeDataInterface
 
voxelPtToXYZ(int, int, int, Point3f) - Method in class org.jmol.jvxl.data.VolumeData
 
voxelReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
voxelReader - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
voxelReader - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
VoxelReader - Class in org.jmol.jvxl.readers
 
VoxelReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.VoxelReader
 
voxelVectors - Variable in class org.jmol.adapter.readers.more.CubeReader
 
voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
vpt0 - Variable in class org.jmol.shapespecial.DrawRenderer
 
vpt1 - Variable in class org.jmol.shapespecial.DrawRenderer
 
vpt2 - Variable in class org.jmol.shapespecial.DrawRenderer
 
VsampFactor - Variable in class org.jmol.util.JpegInfo
 
vTemp - Variable in class org.jmol.shapespecial.DrawRenderer
 
vTemp - Variable in class org.jmol.symmetry.PointGroup
 
vTemp2 - Variable in class org.jmol.shapespecial.DrawRenderer
 
Vx - Variable in class org.jmol.util.Eigen
 

W

waitForClientFileOrErrorMessage() - Method in class org.jmol.viewer.FileManager
the real entry point
waitForClientRelease() - Method in class org.jmol.g3d.Platform3D.ClearingThread
 
waitForQueue() - Method in class org.jmol.viewer.ScriptManager
 
walkDOMTree(JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
warn(String) - Method in class org.jmol.util.DefaultLogger
 
warn(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
warn(String) - Static method in class org.jmol.util.Logger
Writes a log at WARN level.
warn(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at WARN level with detail on exception.
warn(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level.
warn(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level with detail on exception.
warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
warning(int, String, String) - Method in class org.jmol.viewer.Eval
 
wasClicked(int, int) - Method in class org.jmol.shape.Frank
 
wasClicked(int, int) - Method in class org.jmol.shape.Shape
 
wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
 
wasInMotion - Variable in class org.jmol.viewer.Viewer
 
wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
 
wasUnQuoted - Variable in class org.jmol.adapter.readers.cifpdb.CifReader.RidiculousFileFormatTokenizer
 
wasX - Variable in class org.jmol.viewer.Eval.Rpn
 
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.Jmol
 
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.webexport.WebMaker
 
webExport - Variable in class org.openscience.jmol.app.Jmol
 
WebExport - Class in org.openscience.jmol.app.webexport
 
WebExport(JmolViewer, HistoryFile) - Constructor for class org.openscience.jmol.app.webexport.WebExport
 
webExport - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webFrame - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
WebMaker - Class in org.openscience.jmol.app.webexport
 
WebMaker() - Constructor for class org.openscience.jmol.app.webexport.WebMaker
 
WebMOReader - Class in org.jmol.adapter.readers.more
A molecular orbital reader for WebMO files.
WebMOReader() - Constructor for class org.jmol.adapter.readers.more.WebMOReader
 
webmoRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
webPageTitle - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
webPanel - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
WebPanel - Class in org.openscience.jmol.app.webexport
 
WebPanel(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.WebPanel
 
WebPanel.InstanceCellRenderer - Class in org.openscience.jmol.app.webexport
 
WebPanel.InstanceCellRenderer() - Constructor for class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
 
webPanels - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webPanels - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
whatsnewAction - Static variable in class org.openscience.jmol.app.Jmol
 
WhatsNewDialog - Class in org.openscience.jmol.app
 
WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.WhatsNewDialog
 
WhatsNewDialog.PageLoader - Class in org.openscience.jmol.app
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
WhatsNewDialog.PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.WhatsNewDialog.PageLoader
 
wheelClickFractionDown - Static variable in class org.jmol.viewer.MouseManager
 
wheelClickFractionUp - Static variable in class org.jmol.viewer.MouseManager
 
whilecmd - Static variable in class org.jmol.viewer.Token
 
WHITE - Static variable in class org.jmol.g3d.Graphics3D
 
wideWidthMilliAngstroms - Static variable in class org.jmol.shape.SticksRenderer
 
width - Variable in class org.jmol.export.Export3D
 
width - Variable in class org.jmol.export.image.GifEncoder
 
Width - Variable in class org.jmol.export.image.GifEncoder
 
width - Variable in class org.jmol.export.image.ImageEncoder
 
width - Variable in class org.jmol.export.image.PngEncoder
 
width - Variable in class org.jmol.g3d.Graphics3D
 
width - Variable in class org.jmol.g3d.Sphere3D
 
width - Variable in class org.jmol.g3d.Text3D
 
width - Variable in class org.jmol.shape.Mesh
 
width - Variable in class org.jmol.shape.MeshRenderer
 
width - Variable in class org.jmol.shape.SticksRenderer
 
width - Variable in class org.jmol.shapespecial.Draw
 
width - Variable in class org.jmol.viewer.TransformManager
 
width - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
widthOffscreen - Variable in class org.jmol.g3d.Platform3D
 
widths - Variable in class org.jmol.shape.Text
 
widthUnitVector - Variable in class org.jmol.modelsetbio.Sheet
 
wildID - Variable in class org.jmol.shapespecial.Dipoles
 
windowActivated(WindowEvent) - Method in class org.jmol.applet.Console
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.Splash.WindowListener
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowCentered - Variable in class org.jmol.viewer.TransformManager
 
windowCenteredFlag - Variable in class org.jmol.viewer.StateManager.Orientation
 
windowClosed(WindowEvent) - Method in class org.jmol.applet.Console
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowClosing(WindowEvent) - Method in class org.jmol.applet.Console
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.Jmol.AppCloser
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.MeasurementTable.MeasurementListWindowListener
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.PovrayDialog.PovrayWindowListener
Closes the dialog when window closing event occurs.
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeactivated(WindowEvent) - Method in class org.jmol.applet.Console
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeiconified(WindowEvent) - Method in class org.jmol.applet.Console
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowHeight - Variable in class org.jmol.g3d.Graphics3D
 
windowHeight - Variable in class org.jmol.g3d.Platform3D
 
windowHeight - Variable in class org.jmol.shape.Object2d
 
windowIconified(WindowEvent) - Method in class org.jmol.applet.Console
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowName - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
windowOpened(WindowEvent) - Method in class org.jmol.applet.Console
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.RecentFilesDialog
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowSize - Variable in class org.jmol.g3d.Platform3D
 
windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowWidth - Variable in class org.jmol.g3d.Graphics3D
 
windowWidth - Variable in class org.jmol.g3d.Platform3D
 
windowWidth - Variable in class org.jmol.shape.Object2d
 
wing - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wing0 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wing1 - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wingHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wingT - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wingVectors - Variable in class org.jmol.modelset.Polymer
 
wingVectors - Variable in class org.jmol.shapebio.BioShape
 
wingVectors - Variable in class org.jmol.shapebio.BioShapeRenderer
 
wireframe() - Method in class org.jmol.viewer.Eval
 
wireframe - Static variable in class org.jmol.viewer.Token
 
Wireframe - Static variable in class org.openscience.jmol.app.webexport.Molecules
 
Wireframe - Static variable in class org.openscience.jmol.app.webexport.Orbitals
 
wireframeOnly - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
 
wireframeRotation - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
within - Static variable in class org.jmol.viewer.Token
 
withinAtomSetIterator - Variable in class org.jmol.modelset.ModelCollection
 
withinModelIterator - Variable in class org.jmol.modelset.ModelCollection
 
words - Variable in class org.jmol.popup.PopupResourceBundle
 
wrappedApplet - Variable in class org.jmol.appletwrapper.AppletWrapper
 
WrappedApplet - Interface in org.jmol.appletwrapper
 
wrappedAppletClassName - Variable in class org.jmol.appletwrapper.AppletWrapper
 
wrappedAppletClassName - Variable in class org.jmol.appletwrapper.WrappedAppletLoader
 
WrappedAppletLoader - Class in org.jmol.appletwrapper
 
WrappedAppletLoader(AppletWrapper, String) - Constructor for class org.jmol.appletwrapper.WrappedAppletLoader
 
write(Token[]) - Method in class org.jmol.viewer.Eval
 
write - Static variable in class org.jmol.viewer.Token
 
Write_JCamp() - Method in class org.jmol.jcamp.Visua
 
writeAction - Variable in class org.openscience.jmol.app.Jmol
 
writeActionProperty - Static variable in class org.openscience.jmol.app.Jmol
 
WriteArray(byte[], BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeByte(int, int) - Method in class org.jmol.export.image.PngEncoder
Write a single byte into the pngBytes array at a given position.
writeBytes(byte[], int) - Method in class org.jmol.export.image.PngEncoder
Write an array of bytes into the pngBytes array.
writeBytes(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
Write an array of bytes into the pngBytes array, specifying number of bytes to write.
WriteCompressedData(BufferedOutputStream, JpegInfo, DCT, Huffman) - Static method in class org.jmol.util.JpegEncoder
 
WriteDHTHeader(int[], int[], BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeEnd() - Method in class org.jmol.export.image.PngEncoder
Write a PNG "IEND" chunk into the pngBytes array.
WriteEOI(BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeFile(String, String) - Static method in class org.openscience.jvxl.Jvxl
 
writeFileBytes(String, byte[]) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
writeHeader() - Method in class org.jmol.export.image.PngEncoder
Write a PNG "IHDR" chunk into the pngBytes array.
WriteHeaders(BufferedOutputStream, JpegInfo, DCT) - Static method in class org.jmol.util.JpegEncoder
 
writeImageData() - Method in class org.jmol.export.image.PngEncoder
Write the image data into the pngBytes array.
writeInfo - Variable in class org.jmol.viewer.Viewer
 
writeInt2(int, int) - Method in class org.jmol.export.image.PngEncoder
Write a two-byte integer into the pngBytes array at a given position.
writeInt4(int, int) - Method in class org.jmol.export.image.PngEncoder
Write a four-byte integer into the pngBytes array at a given position.
writeMacros() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosAtom() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosBond() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosFinish() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosTextPixel() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosTriangle() - Method in class org.jmol.export._PovrayExporter
 
WriteMarker(byte[], BufferedOutputStream) - Static method in class org.jmol.util.JpegEncoder
 
writeString(OutputStream, String) - Static method in class org.jmol.export.image.GifEncoder
 
writeString(String, int) - Method in class org.jmol.export.image.PngEncoder
Write a string into the pngBytes array at a given position.
writeString(OutputStream, String) - Static method in class org.jmol.export.image.PpmEncoder
 
writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
 
writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
 

X

x - Variable in class org.jmol.g3d.Sphere3D
 
x - Variable in class org.jmol.jcamp.ZoneVisu
 
x(double) - Method in class org.jmol.jcamp.ZoneVisu
 
X - Variable in class org.jmol.quantum.QuantumCalculation
 
x1_zoom - Variable in class org.jmol.jcamp.ZoneVisu
 
x1t - Variable in class org.jmol.g3d.Line3D
 
X2 - Variable in class org.jmol.quantum.QuantumCalculation
 
x2_zoom - Variable in class org.jmol.jcamp.ZoneVisu
 
x2t - Variable in class org.jmol.g3d.Line3D
 
x_units - Variable in class org.jmol.jcamp.Visua
 
x_units - Variable in class org.jmol.jcamp.ZoneVisu
 
xA - Variable in class org.jmol.g3d.Cylinder3D
 
xA - Variable in class org.jmol.shape.SticksRenderer
 
xAf - Variable in class org.jmol.g3d.Cylinder3D
 
xAnchor - Variable in class org.jmol.viewer.MouseManager
 
xAxis1 - Variable in class org.jmol.shape.SticksRenderer
 
xAxis2 - Variable in class org.jmol.shape.SticksRenderer
 
xB - Variable in class org.jmol.shape.SticksRenderer
 
xCenter - Variable in class org.jmol.g3d.Circle3D
 
xCurrent - Variable in class org.jmol.viewer.MouseManager
 
xd - Variable in class org.jmol.jcamp.ZoneVisu
 
xEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
xf - Variable in class org.jmol.jcamp.ZoneVisu
 
xGT - Static variable in class org.jmol.g3d.Line3D
 
xLast - Variable in class org.jmol.g3d.Graphics3D
 
xlateAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
xLight - Static variable in class org.jmol.g3d.Shade3D
 
xLightsource - Static variable in class org.jmol.g3d.Shade3D
 
xLowerLimit - Variable in class org.jmol.jcamp.ZoneVisu
 
xLT - Static variable in class org.jmol.g3d.Line3D
 
xMax - Variable in class org.jmol.g3d.Cylinder3D
 
xMax - Variable in class org.jmol.quantum.QuantumCalculation
 
xMin - Variable in class org.jmol.g3d.Cylinder3D
 
xMin - Variable in class org.jmol.quantum.QuantumCalculation
 
XmlArgusReader - Class in org.jmol.adapter.readers.xml
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
 
XmlArgusReader(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
 
XmlArgusReader(XmlReader, AtomSetCollection, JSObject) - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
 
XmlArgusReader.ArgusHandler - Class in org.jmol.adapter.readers.xml
 
XmlArgusReader.ArgusHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader.ArgusHandler
 
XmlArgusReader.ArgusHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader.ArgusHandler
 
XmlChem3dReader - Class in org.jmol.adapter.readers.xml
An chem3d c3xml reader
XmlChem3dReader(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
 
XmlChem3dReader(XmlReader, AtomSetCollection, JSObject) - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
 
XmlChem3dReader.Chem3dHandler - Class in org.jmol.adapter.readers.xml
 
XmlChem3dReader.Chem3dHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader.Chem3dHandler
 
XmlChem3dReader.Chem3dHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader.Chem3dHandler
 
XmlCmlReader - Class in org.jmol.adapter.readers.xml
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
 
XmlCmlReader(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
 
XmlCmlReader(XmlReader, AtomSetCollection, JSObject) - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
 
XmlCmlReader.CmlHandler - Class in org.jmol.adapter.readers.xml
 
XmlCmlReader.CmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader.CmlHandler
 
XmlCmlReader.CmlHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader.CmlHandler
 
XmlMolproReader - Class in org.jmol.adapter.readers.xml
A Molpro 2005 reader
XmlMolproReader(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
 
XmlMolproReader(XmlReader, AtomSetCollection, JSObject) - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
 
XmlMolproReader.MolproHandler - Class in org.jmol.adapter.readers.xml
 
XmlMolproReader.MolproHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
XmlMolproReader.MolproHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader.MolproHandler
 
XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
An Odyssey xodydata reader
XmlOdysseyReader(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
XmlOdysseyReader(XmlReader, AtomSetCollection, JSObject) - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
XmlOdysseyReader.OdysseyHandler - Class in org.jmol.adapter.readers.xml
 
XmlOdysseyReader.OdysseyHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader.OdysseyHandler
 
XmlOdysseyReader.OdysseyHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader.OdysseyHandler
 
XmlReader - Class in org.jmol.adapter.readers.xml
A generic XML reader template -- by itself, does nothing.
XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
 
XmlReader.DummyResolver - Class in org.jmol.adapter.readers.xml
 
XmlReader.DummyResolver() - Constructor for class org.jmol.adapter.readers.xml.XmlReader.DummyResolver
 
XmlReader.JmolXmlHandler - Class in org.jmol.adapter.readers.xml
 
XmlReader.JmolXmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
XmlReader.JmolXmlHandler(XMLReader) - Constructor for class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
 
xmlRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
xNav - Variable in class org.jmol.viewer.StateManager.Orientation
 
XplorReader - Class in org.jmol.jvxl.readers
 
XplorReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.XplorReader
 
xPt - Variable in class org.jmol.viewer.Eval.Rpn
 
xRaster - Variable in class org.jmol.g3d.Cylinder3D
 
xStack - Variable in class org.jmol.viewer.Eval.Rpn
 
xTip - Variable in class org.jmol.g3d.Cylinder3D
 
xTrans - Variable in class org.jmol.viewer.StateManager.Orientation
 
xTranslationFraction - Variable in class org.jmol.viewer.TransformManager
 
xUpperLimit - Variable in class org.jmol.jcamp.ZoneVisu
 
xWhenPressed - Variable in class org.jmol.viewer.MouseManager10
 
xy - Variable in class org.jmol.shape.Hover
 
XY_ZTOP - Static variable in class org.jmol.viewer.JmolConstants
 
xyCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
xypParameter(int) - Method in class org.jmol.viewer.Eval
 
xyz - Variable in class org.jmol.shape.Object2d
 
xyz - Variable in class org.jmol.symmetry.SymmetryOperation
 
xyz - Static variable in class org.jmol.viewer.Token
 
xyz_coordinates - Static variable in class org.jmol.adapter.readers.more.CsfReader
 
xyzBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
xyzFraction(float, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
xyzList - Variable in class org.jmol.symmetry.SpaceGroup
 
xyzMax - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
xyzMin - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
xyzOriginal - Variable in class org.jmol.symmetry.SymmetryOperation
 
XyzReader - Class in org.jmol.adapter.readers.molxyz
Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) 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
XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
 
xyzToPixelVector(Vector3f) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
xyzToVoxelPt(float, float, float, Point3i) - Method in interface org.jmol.api.VolumeDataInterface
 
xyzToVoxelPt(float, float, float, Point3i) - Method in class org.jmol.jvxl.data.VolumeData
 

Y

y - Variable in class org.jmol.g3d.Sphere3D
 
y - Variable in class org.jmol.jcamp.ZoneVisu
 
Y - Variable in class org.jmol.quantum.QuantumCalculation
 
y1t - Variable in class org.jmol.g3d.Line3D
 
Y2 - Variable in class org.jmol.quantum.QuantumCalculation
 
y2t - Variable in class org.jmol.g3d.Line3D
 
y_units - Variable in class org.jmol.jcamp.Visua
 
y_units - Variable in class org.jmol.jcamp.ZoneVisu
 
Y_Values - Variable in class org.jmol.jcamp.ZoneVisu
 
yA - Variable in class org.jmol.g3d.Cylinder3D
 
yA - Variable in class org.jmol.shape.SticksRenderer
 
yAf - Variable in class org.jmol.g3d.Cylinder3D
 
yAnchor - Variable in class org.jmol.viewer.MouseManager
 
yAxis1 - Variable in class org.jmol.shape.SticksRenderer
 
yAxis2 - Variable in class org.jmol.shape.SticksRenderer
 
yB - Variable in class org.jmol.shape.SticksRenderer
 
yCenter - Variable in class org.jmol.g3d.Circle3D
 
yCurrent - Variable in class org.jmol.viewer.MouseManager
 
YELLOW - Static variable in class org.jmol.g3d.Graphics3D
 
yEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
YFactor - Variable in class org.jmol.jcamp.Visua
 
YFactor - Variable in class org.jmol.jcamp.ZoneVisu
 
yGT - Static variable in class org.jmol.g3d.Line3D
 
yLast - Variable in class org.jmol.g3d.Graphics3D
 
yLight - Static variable in class org.jmol.g3d.Shade3D
 
yLightsource - Static variable in class org.jmol.g3d.Shade3D
 
yLT - Static variable in class org.jmol.g3d.Line3D
 
yMax - Variable in class org.jmol.g3d.Cylinder3D
 
yMax - Variable in class org.jmol.quantum.QuantumCalculation
 
yMin - Variable in class org.jmol.g3d.Cylinder3D
 
yMin - Variable in class org.jmol.quantum.QuantumCalculation
 
yNav - Variable in class org.jmol.viewer.StateManager.Orientation
 
yRaster - Variable in class org.jmol.g3d.Cylinder3D
 
yTip - Variable in class org.jmol.g3d.Cylinder3D
 
yTrans - Variable in class org.jmol.viewer.StateManager.Orientation
 
yTranslationFraction - Variable in class org.jmol.viewer.TransformManager
 
yWhenPressed - Variable in class org.jmol.viewer.MouseManager10
 

Z

z - Variable in class org.jmol.g3d.Sphere3D
 
Z - Variable in class org.jmol.quantum.QuantumCalculation
 
z - Variable in class org.jmol.shape.Object2d
 
Z - Variable in class org.jmol.shapebio.BioShapeRenderer
 
z1t - Variable in class org.jmol.g3d.Line3D
 
Z2 - Variable in class org.jmol.quantum.QuantumCalculation
 
z2t - Variable in class org.jmol.g3d.Line3D
 
zA - Variable in class org.jmol.g3d.Cylinder3D
 
zA - Variable in class org.jmol.shape.SticksRenderer
 
zAf - Variable in class org.jmol.g3d.Cylinder3D
 
zap(boolean) - Method in class org.jmol.viewer.Eval
 
zap() - Method in class org.jmol.viewer.ModelManager
 
zap - Static variable in class org.jmol.viewer.Token
 
zap(boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
zap(String) - Method in class org.jmol.viewer.Viewer
 
zB - Variable in class org.jmol.shape.SticksRenderer
 
zbuf - Variable in class org.jmol.g3d.Graphics3D
 
zbuf - Variable in class org.jmol.g3d.Sphere3D
 
zBuffer - Variable in class org.jmol.g3d.Platform3D
 
zBufferT - Variable in class org.jmol.g3d.Platform3D
 
zbufT - Variable in class org.jmol.g3d.Graphics3D
 
zCenter - Variable in class org.jmol.g3d.Circle3D
 
zEndcap - Variable in class org.jmol.g3d.Cylinder3D
 
zerobase - Variable in class org.jmol.modelset.AtomIteratorWithinSet
 
zeroBasedXyzRasmol - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zeroFontId - Variable in class org.jmol.shape.Labels
 
zeroOffset - Variable in class org.jmol.shape.Labels
 
zGT - Static variable in class org.jmol.g3d.Line3D
 
ZipUtil - Class in org.jmol.util
 
ZipUtil() - Constructor for class org.jmol.util.ZipUtil
 
zLight - Static variable in class org.jmol.g3d.Shade3D
 
zLightsource - Static variable in class org.jmol.g3d.Shade3D
 
zLT - Static variable in class org.jmol.g3d.Line3D
 
zMargin - Variable in class org.jmol.g3d.Graphics3D
 
zMax - Variable in class org.jmol.quantum.QuantumCalculation
 
zMin - Variable in class org.jmol.quantum.QuantumCalculation
 
ZoneVisu - Class in org.jmol.jcamp
 
ZoneVisu() - Constructor for class org.jmol.jcamp.ZoneVisu
 
zoom(boolean) - Method in class org.jmol.viewer.Eval
 
zoom - Variable in class org.jmol.viewer.StateManager.Orientation
 
zoom - Static variable in class org.jmol.viewer.Token
 
Zoom_Back - Variable in class org.jmol.jcamp.Visua
 
Zoom_In - Variable in class org.jmol.jcamp.Visua
 
Zoom_Out - Variable in class org.jmol.jcamp.Visua
 
zoomAction - Variable in class org.openscience.jmol.app.DisplayPanel
 
Zoomback() - Method in class org.jmol.jcamp.ZoneVisu
 
ZoomBufGra - Variable in class org.jmol.jcamp.ZoneVisu
 
ZoomBufImg - Variable in class org.jmol.jcamp.ZoneVisu
 
zoomBy(int) - Method in class org.jmol.viewer.TransformManager
standard response to user mouse vertical shift-drag
zoomBy(int) - Method in class org.jmol.viewer.Viewer
 
zoomByFactor(float) - Method in class org.jmol.viewer.TransformManager
 
zoomByFactor(float) - Method in class org.jmol.viewer.Viewer
 
zoomByPercent(float) - Method in class org.jmol.viewer.TransformManager
 
zoomEnabled - Variable in class org.jmol.viewer.TransformManager
 
zoomFactor - Variable in class org.jmol.viewer.TransformManager11
 
Zoomin() - Method in class org.jmol.jcamp.ZoneVisu
 
zoomLarge - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
Zoomout() - Method in class org.jmol.jcamp.ZoneVisu
 
zoomPercent - Variable in class org.jmol.viewer.TransformManager
 
zoomPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zoomRatio - Variable in class org.jmol.viewer.TransformManager
 
zoomTo - Static variable in class org.jmol.viewer.Token
 
zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
 
ZPOS_FLAGS - Static variable in class org.jmol.shape.Labels
 
zRaster - Variable in class org.jmol.g3d.Cylinder3D
 
zroot - Variable in class org.jmol.g3d.Sphere3D
 
zShade - Variable in class org.jmol.g3d.Graphics3D
 
zShade - Variable in class org.jmol.viewer.StateManager.GlobalSettings
 
zShift - Variable in class org.jmol.g3d.Cylinder3D
 
zShift - Variable in class org.jmol.g3d.Sphere3D
 
zSlab - Variable in class org.jmol.shape.Object2d
 
zTip - Variable in class org.jmol.g3d.Cylinder3D
 
zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager
 
zValueFromPercent(int) - Method in class org.jmol.viewer.Viewer
 
zXMax - Variable in class org.jmol.g3d.Cylinder3D
 
zXMin - Variable in class org.jmol.g3d.Cylinder3D
 

_

_(String) - Static method in class org.jmol.i18n.GT
 
_(String, String) - Static method in class org.jmol.i18n.GT
 
_(String, int) - Static method in class org.jmol.i18n.GT
 
_(String, Object[]) - Static method in class org.jmol.i18n.GT
 
_(String, boolean) - Static method in class org.jmol.i18n.GT
 
_(String, String, boolean) - Static method in class org.jmol.i18n.GT
 
_(String, int, boolean) - Static method in class org.jmol.i18n.GT
 
_(String, Object[], boolean) - Static method in class org.jmol.i18n.GT
 
_activeLevels - Static variable in class org.jmol.util.Logger
 
_allIntegrationValues - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_axisColor - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_axisTextColor - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_decForm - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_Exporter - Class in org.jmol.export
 
_Exporter() - Constructor for class org.jmol.export._Exporter
 
_graphCurveColor - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_graphDataUtils - Variable in class org.jmol.jcamp.Visua
 
_graphDataUtils - Variable in class org.jmol.jcamp.ZoneVisu
 
_grid - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_integrate - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_integrateCurveColor - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_integrateTextColor - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_integrationValues - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_lastPoint - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_logger - Static variable in class org.jmol.util.Logger
 
_logLevel - Static variable in class org.jmol.util.Logger
 
_MayaExporter - Class in org.jmol.export
 
_MayaExporter() - Constructor for class org.jmol.export._MayaExporter
 
_PovrayExporter - Class in org.jmol.export
 
_PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
 
_reverse - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_textColor - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_unsortedIntegrationValues - Variable in class org.jmol.jcamp.GraphCharacteristics
 
_VrmlExporter - Class in org.jmol.export
 
_VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
 
_zoomIn - Variable in class org.jmol.jcamp.GraphCharacteristics
 
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