- a - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
-
- a - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- a - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- a - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- a - Variable in class org.jmol.jvxl.readers.MapFileReader
-
- a - Variable in class org.jmol.minimize.forcefield.Calculation
-
- a - Variable in class org.jmol.modelsetbio.AminoPolymer.Bridge
-
- a - Variable in class org.jmol.util.SimpleUnitCell
-
- 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.util.SimpleUnitCell
-
- 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
-
- AANscale(double[], int[], int) - Static method in class org.jmol.util.DCT
-
- AANscaleFactor - Static variable in class org.jmol.util.DCT
-
- aaPlus - Static variable in class org.jmol.viewer.JmolConstants
-
- aaRet - Variable in class org.jmol.modelset.AtomCollection
-
- aaSp2 - Static variable in class org.jmol.viewer.JmolConstants
-
- aaStep - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- aaStepCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- aaStepNavCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- aaT - Variable in class org.jmol.shape.MeasuresRenderer
-
- aaTest1 - Variable in class org.jmol.viewer.TransformManager
-
- aatoken - Variable in class org.jmol.script.ScriptContext
-
- aatoken - Variable in class org.jmol.script.ScriptEvaluator
-
- aatoken - Variable in class org.jmol.script.ScriptFunction
-
- aatokenCompiled - Variable in class org.jmol.script.ScriptCompiler
-
- aaTotal - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- abc - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- abNo - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- aboutComputedMenuBaseCount - Variable in class org.jmol.popup.JmolPopup
-
- AboutDialog - Class in org.openscience.jmol.app.jmolpanel
-
- AboutDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
-
- AboutDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
-
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.jmolpanel.AboutDialog.PageLoader
-
- abs - Static variable in class org.jmol.script.Token
-
- absolute - Static variable in class org.jmol.script.Token
-
- ABSOLUTE_MIN_MESH_SIZE - Static variable in class org.jmol.shapebio.BioShapeRenderer
-
- absoluteButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- abYes - Variable in class org.openscience.jmol.app.jmolpanel.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, String) - Method in class org.jmol.console.JmolConsole.FileChecker
-
- 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
-
- acos - Static variable in class org.jmol.script.Token
-
- ACtableNumber - Variable in class org.jmol.util.JpegInfo
-
- action - Variable in class org.jmol.viewer.ActionManager.Gesture
-
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
-
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
-
- ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_center - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_count - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_select - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
-
- ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
-
- actionInfo - Static variable in class org.jmol.viewer.ActionManager
-
- actionManager - Variable in class org.jmol.awt.Mouse
-
- actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- ActionManager - Class in org.jmol.viewer
-
- ActionManager() - Constructor for class org.jmol.viewer.ActionManager
-
- actionManager - Variable in class org.jmol.viewer.Viewer
-
- ActionManager.Gesture - Class in org.jmol.viewer
-
- ActionManager.Gesture(int) - Constructor for class org.jmol.viewer.ActionManager.Gesture
-
- ActionManager.HoverWatcher - Class in org.jmol.viewer
-
- ActionManager.HoverWatcher() - Constructor for class org.jmol.viewer.ActionManager.HoverWatcher
-
- ActionManager.MotionPoint - Class in org.jmol.viewer
-
- ActionManager.MotionPoint() - Constructor for class org.jmol.viewer.ActionManager.MotionPoint
-
- ActionManager.Mouse - Class in org.jmol.viewer
-
- ActionManager.Mouse(int) - Constructor for class org.jmol.viewer.ActionManager.Mouse
-
- ActionManager.TimeoutThread - Class in org.jmol.viewer
-
- ActionManager.TimeoutThread(String, int, String) - Constructor for class org.jmol.viewer.ActionManager.TimeoutThread
-
- ActionManagerMT - Class in org.jmol.multitouch
-
- ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
-
- actionNames - Static variable in class org.jmol.viewer.ActionManager
-
- actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
-
- actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
-
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
-
- actionPerformed(ActionEvent) - Method in class org.jmol.popup.SimplePopup.MenuItemListener
-
- actionPerformed(ActionEvent) - Method in class org.openscience.chimetojmol.ChimePanel
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- 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
-
- actionRotateBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
-
- actionStates - Variable in class org.jmol.viewer.Viewer
-
- actionStatesRedo - Variable in class org.jmol.viewer.Viewer
-
- activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- active - Variable in class org.jmol.export.dialog.FilePreview
-
- actualID - Variable in class org.jmol.shapesurface.Isosurface
-
- adapter - Variable in class org.jmol.multitouch.ActionManagerMT
-
- 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 - Static variable in class org.jmol.script.Token
-
- add(float) - Method in class org.jmol.util.Quaternion
-
- add(int, int, int, long) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JmolConstants
-
- addAllPixels - Variable in class org.jmol.g3d.Graphics3D
-
- addAllPixels - Variable in class org.jmol.g3d.Sphere3D
-
- addAllTriangles() - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- addAtom(Atom) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- addAtom() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addAtom(int, Group, short, String, int, int, float, float, float) - Method in class org.jmol.modelset.ModelCollection
-
- addAtom(int, Group, short, String, int, int, float, float, float, float, float, float, float, int, float, int, float, Object[], boolean, char, byte, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- addAtom(boolean, BitSet, int, Object, short, String, int, float, Object[], int, float, float, float, float, boolean, int, String, float, float, float, char, float) - Method in class org.jmol.modelset.ModelLoader
-
- addAtom() - Method in class org.jmol.smiles.SmilesSearch
-
- addAtomOr() - Method in class org.jmol.smiles.SmilesAtom
-
- addAtoms(BitSet) - Method in interface org.jmol.api.AtomIndexIterator
-
- addAtoms(BitSet) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
turns this into a SPHERICAL iterator
for "within Distance" measures
- addAtoms(int) - Method in class org.jmol.modelset.Group
-
- 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
-
- addAttrib(List<String[]>, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
- addAxis(int, Vector3f) - Method in class org.jmol.symmetry.PointGroup
-
- addBinding(String, Object) - Method in class org.jmol.viewer.binding.Binding
-
- 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.
- addBondOr() - Method in class org.jmol.smiles.SmilesBond
-
- addBonds(String, int) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- addBondToAtom(Atom, Bond) - Method in class org.jmol.modelset.BondCollection
-
- addBoundBoxPoint(Point3f) - Method in class org.jmol.util.BoxInfo
-
- addBracketedBioName(StringBuffer, JmolNode, String) - Method in class org.jmol.smiles.SmilesGenerator
-
- addBridge(AminoPolymer.Bridge, Map<int[][], Boolean>) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
-
- addBs(StringBuffer, String, BitSet) - Static method in class org.jmol.viewer.SelectionManager
-
- addBundle(String, String) - Method in class org.jmol.i18n.GT
-
- addBundles(String, String, String, String) - Method in class org.jmol.i18n.GT
-
- addBytes(byte[], int, int) - Method in class org.jmol.util.ZipUtil.GZipData
-
- addCheckboxMenuItem(Object, String, String, String, boolean) - Method in class org.jmol.popup.SimplePopup
-
- addCheckboxMenuItem(Object, String, String, String, boolean, boolean) - Method in class org.jmol.popup.SimplePopup
-
- addColix(short, boolean) - Method in class org.jmol.export._IdtfExporter
-
- addColorToMap(Map<String, BitSet>, String, BitSet) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
adds a set of specifically-colored vertices to the map,
ensuring that no vertex is in two maps.
- 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
-
- addContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
-
- addContextVariable(Map<String, ScriptVariable>, String) - Static method in class org.jmol.script.ScriptCompiler
-
- addContourPoints(List<Object>, BitSet, int, StringBuffer, Point3f[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
- addContourVertex(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.SimplePopup
-
- addData10F() - Method in class org.jmol.quantum.MOCalculation
-
- addData5D() - Method in class org.jmol.quantum.MOCalculation
-
- addData6D() - Method in class org.jmol.quantum.MOCalculation
-
- addData7F() - Method in class org.jmol.quantum.MOCalculation
-
- addDataP() - Method in class org.jmol.quantum.MOCalculation
-
- addDataS() - Method in class org.jmol.quantum.MOCalculation
-
- addDataSP() - Method in class org.jmol.quantum.MOCalculation
-
- addDirectory(String, String) - Static 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
-
- addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- addFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
-
- addFile(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
Adds this file to the history.
- addForce(Vector3d, int, double) - Method in class org.jmol.minimize.forcefield.Calculations
-
- addFunction(ScriptFunction) - Method in class org.jmol.viewer.StateManager
-
- addFunction(ScriptFunction) - Method in class org.jmol.viewer.Viewer
-
- addGroup(Chain, Group) - Method in class org.jmol.modelset.ModelLoader
-
- addGroup3Name(String) - Static method in class org.jmol.modelset.Group
-
- addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
-
- addHbond(List<Bond>, Monomer, Monomer, int, int, Map<String, Boolean>) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
- addHelpItems(JMenu, String, String) - Method in class org.jmol.console.AppletConsole
-
- addHelpMenuBar(JMenuBar) - Method in class org.jmol.console.AppletConsole
-
- addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- addHetero(String, String) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- addHydrogenBond(List<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
-
- addHydrogens - Variable in class org.jmol.jvxl.readers.Parameters
-
- addHydrogens(List<Atom>, Point3f[]) - Method in class org.jmol.modelset.ModelSet
-
these are hydrogens that are being added due to a load 2D command and are
therefore not to be flagged as NEW
- addhydrogens - Static variable in class org.jmol.script.Token
-
- addHydrogens(BitSet, boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
- addHydrogensInline(BitSet, List<Atom>, Point3f[]) - Method in class org.jmol.viewer.Viewer
-
- addImplicitHydrogenAtoms(JmolAdapter, int) - Method in interface org.jmol.api.JmolBioResolver
-
- addImplicitHydrogenAtoms(JmolAdapter, int) - Method in class org.jmol.modelsetbio.Resolver
-
- addIncompleteFaces(FastBitSet) - 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
-
- addIntersectionVertex(Point3f, float, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSurface
-
- addItems(String[][]) - Method in class org.jmol.popup.PopupResource
-
- addJmolFiles(String) - Method in class org.openscience.chimetojmol.ChimePanel
-
- addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- addJsonTuple(StringBuilder, Tuple3f) - Static method in class org.jmol.util.Escape
-
- addKeyBuffer(char) - Method in class org.jmol.awt.Mouse
-
- addLadder(Map<int[][], Boolean>) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
-
- addListener(JmolSelectionListener) - Method in class org.jmol.viewer.SelectionManager
-
- addMacrosMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- addMenuItem(Object, String) - Method in class org.jmol.popup.SimplePopup
-
- addMenuItem(Object, String, String, String) - Method in class org.jmol.popup.SimplePopup
-
- addMenuItems(String, String, Object, PopupResource) - Method in class org.jmol.popup.SimplePopup
-
- addMenuSeparator(Object) - Method in class org.jmol.popup.SimplePopup
-
- addMenuSubMenu(Object, Object) - Method in class org.jmol.popup.SimplePopup
-
- addMesh(String, MeshSurface, Matrix4f, Matrix4f, short, Point, BitSet) - Method in class org.jmol.export._ObjExporter
-
Adds a new mesh using the given data (faces, vertices, and normals) and
colix after transforming it via the given affine transform matrix.
- addMeshData(String, int, int, int, int, StringBuffer, StringBuffer, StringBuffer, StringBuffer, StringBuffer, StringBuffer) - Method in class org.jmol.export._IdtfExporter
-
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
-
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
-
- addMo(AdfReader.SymmetryData, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
- addMOData(int, List<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- addMolecule(JmolMolecule[], int, JmolNode[], int, BitSet, int, int, BitSet) - Static method in class org.jmol.util.JmolMolecule
-
- addMolFile(StringBuffer, BitSet, BitSet, boolean, Quaternion) - Method in class org.jmol.modelset.ModelCollection
-
- 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.
- addName(String) - Method in class org.jmol.script.ContextToken
-
- addNeighboringVertexes(short[], short, short) - Static method in class org.jmol.geodesic.Geodesic
-
- addNested(String) - Method in class org.jmol.smiles.SmilesSearch
-
- addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addNewBond(int, int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
add the bond and mark it for molecular processing
- addNewBond(String, String, int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- 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.script.ScriptCompilationTokenParser
-
- addNextTokenIf(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- addNormal(Vector3f, Vector3f, float) - Static method in class org.jmol.smiles.SmilesAromatic
-
- addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- addOp(Token) - Method in class org.jmol.script.ScriptMathProcessor
-
addOp The primary driver of the Reverse Polish Notation evaluation engine.
- addOp(Token, boolean) - Method in class org.jmol.script.ScriptMathProcessor
-
- addOperation(String, int) - Method in class org.jmol.symmetry.SpaceGroup
-
- addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D.Pixel
-
- addPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D.ShadePixel
-
- addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
-
- addPoint(Point3f, int) - Method in class org.jmol.shapespecial.Draw
-
- addPoint(int) - Method in class org.jmol.smiles.SmilesMeasure
-
- addPoint(Point3f, Point3f, Point3f, float) - Static method in class org.jmol.util.BoxInfo
-
- addPolygon(int, int, int, int, int, int, BitSet) - Method in class org.jmol.util.MeshSurface
-
- addPolygon(int[], int, BitSet) - Method in class org.jmol.util.MeshSurface
-
- addPolygon(int[], BitSet) - Method in class org.jmol.util.MeshSurface
-
- addPrimitive() - Method in class org.jmol.smiles.SmilesAtom
-
- addPrimitive() - Method in class org.jmol.smiles.SmilesBond
-
- addPrimitiveLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- addProcess(String, ScriptContext) - Method in class org.jmol.script.ParallelProcessor
-
- addProcess(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- addProperties(Properties) - Method in class org.jmol.export.history.HistoryFile
-
Adds the given properties to the history.
- addProperty(String, String) - Method in class org.jmol.export.history.HistoryFile
-
Adds the given property to the history.
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.export.JmolFileDropper
-
- addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
-
- addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
-
- addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
-
- addResidueHydrogenBond(Atom, Atom, int, int, float, List<Bond>) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- 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(EnumStructure, String, int, int, char, int, char, int) - Method in class org.jmol.modelset.Model
-
- addSecondaryStructure(EnumStructure, String, int, int, char, int, char, int) - Method in class org.jmol.modelset.Polymer
-
- addSecondaryStructure(EnumStructure, String, int, int, char, int, char, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- addSecondaryStructure(EnumStructure, String, int, int, 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
-
- addShader(String, short) - Method in class org.jmol.export._IdtfExporter
-
- addShapeProperty(List<Object[]>, String, Object) - Method in class org.jmol.script.ScriptEvaluator
-
- addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
-
- addSlater(int, int, int, int, int, double, float) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
We build two data structures for each slater:
int[] slaterInfo[] = {iatom, a, b, c, d}
float[] slaterData[] = {zeta, coef}
where
psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r)
Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r)
and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
- addSpaceGroupOperation(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
-
- addSpaceGroupOperation(Matrix4f) - Method in interface org.jmol.api.SymmetryInterface
-
- addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
-
- addSpaceGroupOperation(Matrix4f) - 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
-
- addStereoCheck(int, JmolNode[], int, String) - Method in class org.jmol.smiles.SmilesGenerator
-
checks a group and either adds a new group to the growing
check string or returns null
- addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addStructuresFromTags(EnumStructure[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- addSubstituteTokenIf(int, Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- addSymmetry(String, int) - Method in class org.jmol.symmetry.SpaceGroup
-
- addSymmetry(String, Matrix4f) - Method in class org.jmol.symmetry.SpaceGroup
-
- addTexture(short, String) - Method in class org.jmol.export._ObjExporter
-
Adds a texture to the .mtl file if it is a new texture.
- addTickInfo(StringBuffer, TickInfo, boolean) - Static method in class org.jmol.shape.FontLineShape
-
- addTo(StringBuffer) - Method in class org.jmol.util.ZipUtil.GZipData
-
- addToBonds(Bond, Bond[]) - Method in class org.jmol.modelset.BondCollection
-
- addToken(String, Token) - Static method in class org.jmol.script.Token
-
- addTokenToPostfix(int, Object) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- addTokenToPostfix(int, int, Object) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- addTokenToPostfix(Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- addTokenToPrefix(Token) - Method in class org.jmol.script.ScriptCompiler
-
- addToMeasurement(int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
-
- addToMenu(Object, JComponent) - Method in class org.jmol.popup.SimplePopup
-
- addTrajectoryStep() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
-
- addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
addTriangleCheck adds a triangle along with a 3-bit check indicating
which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.PmeshReader
-
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
-
- addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
-
- addTuple(int, 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
-
- addUnitCellOffset(Point3f) - Method in class org.jmol.viewer.Viewer
-
- addVariable(String, boolean) - Method in class org.jmol.script.ScriptFunction
-
- addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- 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, float, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- addVertexCopy(Point3f, float, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- 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) - Method in class org.jmol.util.MeshSurface
-
- addVertexCopy(Point3f, float) - Method in class org.jmol.util.MeshSurface
-
- addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- addVibrationVector(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- addWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
-
- addWindowBorder(String, Point) - Method in class org.jmol.export.history.HistoryFile
-
Adds the window border to the history.
- addWindowInfo(String, Component, Point) - Method in class org.jmol.export.history.HistoryFile
-
Adds the window informations to the history.
- addWindowListener() - Method in class org.jmol.console.JmolConsole
-
- addWindowPosition(String, Point) - Method in class org.jmol.export.history.HistoryFile
-
Adds the window position to the history.
- addWindowSize(String, Dimension) - Method in class org.jmol.export.history.HistoryFile
-
Adds the window size to the history.
- addWindowVisibility(String, boolean) - Method in class org.jmol.export.history.HistoryFile
-
Adds the window visibility to the history.
- addX(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
-
- addX(Object) - Method in class org.jmol.script.ScriptMathProcessor
-
- addX(BitSet) - Method in class org.jmol.script.ScriptMathProcessor
-
- addX(Point3f) - Method in class org.jmol.script.ScriptMathProcessor
-
- addX(boolean) - Method in class org.jmol.script.ScriptMathProcessor
-
- addX(int) - Method in class org.jmol.script.ScriptMathProcessor
-
- addX(float) - Method in class org.jmol.script.ScriptMathProcessor
-
- addXNum(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
-
- addZoomTranslationNavigationText(StringBuffer) - Method in class org.jmol.viewer.TransformManager
-
- adfContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- AdfReader - Class in org.jmol.adapter.readers.quantum
-
TODO: adf-2007.out causes failure reading basis functions
A reader for ADF output.
- AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
-
- AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
-
- AdfReader.SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
-
- adjust - Static variable in class org.jmol.script.Token
-
- adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelCollection
-
- adjustForWindow - Variable in class org.jmol.shape.Object2d
-
- adjustment - Variable in class org.jmol.jvxl.readers.MapFileReader
-
- 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.DOMReader
-
- ADP_TYPE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- adpmax - Static variable in class org.jmol.script.Token
-
- adpmin - Static variable in class org.jmol.script.Token
-
- adpMode - Variable in class org.jmol.atomdata.AtomData
-
- aEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- Ah - Variable in class org.jmol.util.JpegInfo
-
- AimsReader - Class in org.jmol.adapter.readers.xtal
-
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format
samples of relevant lines in geometry.in file are included as comments below
modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines
and to bring it into compliance with other load options (such as overriding
file-based symmetry or unit cell parameters).
- AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
-
- Al - Variable in class org.jmol.util.JpegInfo
-
- AlchemyReader - Class in org.jmol.adapter.readers.simple
-
TRIPOS simple Alchemy reader.
- AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
-
- align - Static variable in class org.jmol.script.Token
-
- 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
-
- alignLeft - Variable in class org.jmol.modelset.LabelToken
-
- 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.script.Token
-
- ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- allCarbohydrates - Static variable in class org.jmol.viewer.JmolConstants
-
- allconnected - Static variable in class org.jmol.script.Token
-
- allData - Variable in class org.jmol.util.CifDataReader
-
- allfloat - Static variable in class org.jmol.script.Token
-
- allFractionalRelative - Variable in class org.jmol.symmetry.UnitCell
-
- allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- allInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- allocateArray(JmolMolecule[], int) - Static method in class org.jmol.util.JmolMolecule
-
- allocateBioPolymer(Group[], int, boolean) - Static method in class org.jmol.modelsetbio.BioPolymer
-
- allocateBitmap(int) - Static method in class org.jmol.util.FastBitSet
-
- 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.Platform3D
-
- allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Platform3D
-
- allocateRenderer(int, Graphics3D) - Method in class org.jmol.viewer.RepaintManager
-
- allocateRgbImage(int, int, int[], int, boolean) - Method in interface org.jmol.api.ApiPlatform
-
- allocateRgbImage(int, int, int[], int, boolean) - Static method in class org.jmol.awt.Image
-
- allocateRgbImage(int, int, int[], int, boolean) - Method in class org.jmol.awt.Platform
-
- allocateShape(int) - Method in class org.jmol.viewer.ShapeManager
-
- allocateSimpleViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolSimpleViewer
-
This is the main access point for creating an application
or applet viewer.
- allocateTBuffers(boolean) - Method in class org.jmol.g3d.Platform3D
-
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
-
This is the main access point for creating an application
or applet viewer.
- allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
-
default null htmlName, URL bases, comandOptions, and statusListener.
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - 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
-
- allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
-
- allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
-
- allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
-
- allocRaster(boolean) - Method in class org.jmol.g3d.Cylinder3D
-
- allocTempEnum(int) - Method in class org.jmol.util.TempArray
-
- allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
-
- allocTempPoints(int) - Method in class org.jmol.util.TempArray
-
- allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
-
- allocTempScreens(int) - Method in class org.jmol.util.TempArray
-
- allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
-
- allocVertexColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
-
- allowedQuaternionFrames - Static variable in class org.jmol.viewer.JmolConstants
-
- allowembeddedscripts - Static variable in class org.jmol.script.Token
-
- allowEmbeddedScripts - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowgestures - Static variable in class org.jmol.script.Token
-
- allowGestures - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowkeystrokes - Static variable in class org.jmol.script.Token
-
- allowKeyStrokes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowMapData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
-
- allowMesh - Variable in class org.jmol.shapesurface.Isosurface
-
- allowmodelkit - Static variable in class org.jmol.script.Token
-
- allowModelkit - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowmoveatoms - Static variable in class org.jmol.script.Token
-
- allowMoveAtoms - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- allowmultitouch - Static variable in class org.jmol.script.Token
-
- allowMultiTouch - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowMultiTouch() - Method in class org.jmol.viewer.Viewer
-
- allowNegative - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- allowrotateselected - Static variable in class org.jmol.script.Token
-
- allowRotateSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- allowRotateSelected() - Method in class org.jmol.viewer.Viewer
-
- allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- allowSignedFeatures - Variable in class org.jmol.popup.SimplePopup
-
- allowSmilesUnbracketed(String) - Static method in class org.jmol.smiles.SmilesAtom
-
- allowSpecAtom() - Method in class org.jmol.modelset.ModelSet
-
- allowSpecAtom() - Method in class org.jmol.viewer.Viewer
-
- allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
-
- allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
-
- allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
-
- allPositive - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
-
- allSelectedWidgets() - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- almost180 - Static variable in class org.jmol.modelset.AtomCollection
-
- alpha - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
-
- alpha - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- alpha - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- alpha - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- alpha - Variable in class org.jmol.jvxl.readers.MapFileReader
-
- alpha - Variable in class org.jmol.util.SimpleUnitCell
-
- ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.shapebio.BioShape
-
- ALPHA_SHIFT - Static variable in class org.jmol.g3d.Graphics3D
-
- alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- 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
-
- AlphaPolymer.Code - Enum in org.jmol.modelsetbio
-
- AlphaPolymer.Code() - Constructor for enum org.jmol.modelsetbio.AlphaPolymer.Code
-
- alphas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
-
- ALT - Static variable in class org.jmol.util.ColorEncoder
-
- ALT - Static variable in class org.jmol.viewer.binding.Binding
-
- ALT_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- ALT_MASK - Static variable in class org.jmol.api.Event
-
- altArgbsCpk - Variable in class org.jmol.viewer.ColorManager
-
- altArgbsCpk - Static variable in class org.jmol.viewer.JmolConstants
-
- altElementCounts - Variable in class org.jmol.util.JmolMolecule
-
- altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
-
- altElementMax - Static variable in class org.jmol.util.Elements
-
length of the altElementSymbols, altElementNames, altElementNumbers arrays
- altElementMax - Variable in class org.jmol.util.JmolMolecule
-
- altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
-
- altElementNames - Static variable in class org.jmol.util.Elements
-
- altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
-
- altElementNumbers - Static variable in class org.jmol.util.Elements
-
- altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
-
- altElementSymbols - Static variable in class org.jmol.util.Elements
-
- 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.util.Elements
-
- altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
-
- altloc - Static variable in class org.jmol.script.Token
-
- altlocs - Variable in class org.jmol.popup.SimplePopup
-
- altNames - Variable in class org.jmol.adapter.readers.more.P2nReader
-
- altVertices - Variable in class org.jmol.util.MeshSurface
-
- ambientFraction - Static variable in class org.jmol.g3d.Shade3D
-
- ambientPercent - Static variable in class org.jmol.g3d.Shade3D
-
- ambientpercent - Static variable in class org.jmol.script.Token
-
- ambientPercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- ambiguityType - Variable in class org.jmol.symmetry.SpaceGroup
-
- ambiguousNames - Static variable in class org.jmol.symmetry.SpaceGroup
-
- amino - Static variable in class org.jmol.script.Token
-
- AMINO - Static variable in class org.jmol.util.ColorEncoder
-
- 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
-
- AminoPolymer.Bridge - Class in org.jmol.modelsetbio
-
- AminoPolymer.Bridge(Atom, Atom, Map<int[][], Boolean>) - Constructor for class org.jmol.modelsetbio.AminoPolymer.Bridge
-
- ampacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- AmpacReader - Class in org.jmol.adapter.readers.simple
-
A reader for AMPAC output.
- AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
-
- AMPLITUDE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for vibration scale.
- AMPLITUDE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Precision of the vibration scale slider
- AMPLITUDE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value of vibration scale.
- amplitudeSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- anaglyphChannelBytes - Variable in class org.jmol.g3d.Graphics3D
-
- anaglyphLength - Variable in class org.jmol.g3d.Graphics3D
-
- and(FastBitSet) - Method in class org.jmol.util.FastBitSet
-
- andBitSet(BitSet) - Method in class org.jmol.shapespecial.Polyhedra
-
- andequals - Static variable in class org.jmol.script.Token
-
- andNot(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
- andNot(FastBitSet) - Method in class org.jmol.util.FastBitSet
-
- angle - Static variable in class org.jmol.script.Token
-
- angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
-
- anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.Slice
-
- anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- angles - Variable in class org.jmol.minimize.forcefield.Calculations
-
- angles - Variable in class org.jmol.minimize.Minimizer
-
- angleUnits - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- angleUnitsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- angleXY - Variable in class org.openscience.jmol.app.surfacetool.Slice
-
- angleXY - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- angleXYSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- angleZSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- angMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- angstroms - Static variable in class org.jmol.script.Token
-
- 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.SurfaceReader
-
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JmolConstants
-
- angstromsToPixels(float) - Method in class org.jmol.viewer.TransformManager
-
- angularPart(double, double, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- animation() - Method in class org.jmol.script.ScriptEvaluator
-
- animation - Static variable in class org.jmol.script.Token
-
- animationDirection() - Method in class org.jmol.script.ScriptEvaluator
-
- animationDirection - Variable in class org.jmol.viewer.AnimationManager
-
- animationfps - Static variable in class org.jmol.script.Token
-
- animationFps - Variable in class org.jmol.viewer.AnimationManager
-
- animationFps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- AnimationManager - Class in org.jmol.viewer
-
- AnimationManager(Viewer) - Constructor for class org.jmol.viewer.AnimationManager
-
- animationManager - Variable in class org.jmol.viewer.Viewer
-
- AnimationManager.AnimationThread - Class in org.jmol.viewer
-
- AnimationManager.AnimationThread(int, int, int) - Constructor for class org.jmol.viewer.AnimationManager.AnimationThread
-
- animationMode() - Method in class org.jmol.script.ScriptEvaluator
-
- animationOn - Variable in class org.jmol.viewer.AnimationManager
-
- animationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
-
- animationPaused - Variable in class org.jmol.viewer.AnimationManager
-
- animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
-
- animationThread - Variable in class org.jmol.viewer.AnimationManager
-
- animThread - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- anionLookupTable - Static variable in class org.jmol.util.Elements
-
- 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_ID - 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.SurfaceReader
-
- anisotropy - Static variable in class org.jmol.script.Token
-
- anisou() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- 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.jmolpanel.PovrayDialog
-
- antialiasdisplay - Static variable in class org.jmol.script.Token
-
- 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 - Static variable in class org.jmol.script.Token
-
- antialiasImages - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- antialiasThisFrame - Variable in class org.jmol.g3d.Graphics3D
-
- antialiastranslucent - Static variable in class org.jmol.script.Token
-
- antialiasTranslucent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- anum - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- aoMax - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- aoMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- aPar - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
-
- ApbsReader - Class in org.jmol.jvxl.readers
-
- ApbsReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.ApbsReader
-
- aperatureAngle - Variable in class org.jmol.export.___Exporter
-
- aperatureAngle - Variable in class org.jmol.viewer.TransformManager
-
- ApiPlatform - Interface in org.jmol.api
-
- apiPlatform - Variable in class org.jmol.api.JmolSimpleViewer
-
- apiPlatform - Variable in class org.jmol.g3d.Font3D
-
- apiPlatform - Variable in class org.jmol.g3d.Graphics3D
-
- apiPlatform - Variable in class org.jmol.g3d.Platform3D
-
- apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- appConsole - Variable in class org.jmol.viewer.Viewer
-
- AppConsole - Class in org.openscience.jmol.app.jmolpanel
-
- AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole
-
general entry point
- AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole
-
- AppConsole.ConsoleDocument - Class in org.openscience.jmol.app.jmolpanel
-
- AppConsole.ConsoleDocument() - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- AppConsole.ConsoleTextPane - Class in org.openscience.jmol.app.jmolpanel
-
- AppConsole.ConsoleTextPane(AppConsole) - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- AppConsole.ExecuteCommandThread - Class in org.openscience.jmol.app.jmolpanel
-
- AppConsole.ExecuteCommandThread(String) - Constructor for class org.openscience.jmol.app.jmolpanel.AppConsole.ExecuteCommandThread
-
- append - Variable in class org.jmol.export.dialog.FilePreview
-
- append - Static variable in class org.jmol.script.Token
-
- append(String) - Method in class org.jmol.util.OutputStringBuffer
-
- append(char) - Method in class org.jmol.util.OutputStringBuffer
-
- appendAtomProperties(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- appendAtomSetCollection(List<?>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Appends an AtomSetCollection
- appendAtomTokenValue(Viewer, Atom, LabelToken, StringBuffer, int[]) - Static method in class org.jmol.modelset.LabelToken
-
- appendAttrib(StringBuffer, Object, Object) - Static method in class org.jmol.util.XmlUtil
-
- appendCdata(StringBuffer, String, Object[], String) - Static method in class org.jmol.util.XmlUtil
-
"
will convert ]]> to ]] >
- appendCmd(StringBuffer, String) - Static method in class org.jmol.shape.Shape
-
- appendCmd(StringBuffer, String) - Static method in class org.jmol.viewer.StateManager
-
- appendContourTriangleIntersection(int, float, float, StringBuffer) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
appends an integer (3, 5, or 6) representing two sides of a triangle ABC --
AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges
for the intersection point base-90-encoded.
- appendEncodedBitSetTag(StringBuffer, String, BitSet, int, Object[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
- appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- appendLoadStates(StringBuffer) - Method in class org.jmol.modelset.ModelCollection
-
- appendLoadStates(StringBuffer) - Method in class org.jmol.viewer.Viewer
-
- appendLogData(String) - Method in class org.jmol.minimize.forcefield.Calculations
-
- appendNew - Variable in class org.jmol.modelset.ModelLoader
-
- appendnew - Static variable in class org.jmol.script.Token
-
- appendNew - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- appendTag(StringBuffer, String, Object[], Object, boolean, boolean) - Static method in class org.jmol.util.XmlUtil
-
- appendTag(StringBuffer, String, Object[], Object) - Static method in class org.jmol.util.XmlUtil
-
standard data"
- appendTag(StringBuffer, String, Object) - Static method in class org.jmol.util.XmlUtil
-
standard data"
standard "
- appendTickInfo(StringBuffer, int) - Method in class org.jmol.shape.FontLineShape
-
- appendXmlColorData(StringBuffer, String, String, boolean, float, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
- appendXmlEdgeData(StringBuffer, JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
- appendXmlTriangleData(StringBuffer, int[][], int, BitSet, int[], boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ...
- appendXmlVertexData(StringBuffer, JvxlData, int[], Point3f[], float[], int, String, int, BitSet, boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
encode the vertex data.
- appendXmlVertexOnlyData(StringBuffer, JvxlData, MeshData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
- appletCodeBase - Variable in class org.jmol.viewer.FileManager
-
- appletCodeBase - Variable in class org.jmol.viewer.Viewer
-
- AppletConsole - Class in org.jmol.console
-
- AppletConsole(JmolViewer, Container) - Constructor for class org.jmol.console.AppletConsole
-
general entry point
- AppletConsole() - Constructor for class org.jmol.console.AppletConsole
-
- AppletConsole.ControlEnterTextArea - Class in org.jmol.console
-
- AppletConsole.ControlEnterTextArea() - Constructor for class org.jmol.console.AppletConsole.ControlEnterTextArea
-
- appletContext - Variable in class org.jmol.viewer.Viewer
-
- appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- 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.SimplePopup
-
- 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 - Static variable in class org.jmol.script.Token
-
- 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 - Class in org.jmol.applet
-
- AppletWrapper(String, String, int, String[]) - Constructor for class org.jmol.applet.AppletWrapper
-
- appletWrapper - Variable in class org.jmol.applet.ClassPreloader
-
- appletWrapper - Variable in class org.jmol.applet.Jmol
-
- appletWrapper - Variable in class org.jmol.applet.TickerThread
-
- appletWrapper - Variable in class org.jmol.applet.WrappedAppletLoader
-
- apply() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- applyAllSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- applyBlueAnaglyph() - Method in class org.jmol.g3d.Graphics3D
-
- applyButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- applyColorScale() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- 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) - Static method in class org.jmol.awt.Mouse
-
- applyRotation(Matrix3f, boolean, BitSet, Vector3f) - Method in class org.jmol.viewer.TransformManager
-
- applySelectStyle(String, int) - Method in class org.jmol.viewer.ActionManager
-
- applyStereochemistry() - Method in class org.jmol.modelset.ModelLoader
-
- applySymmetry - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- 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(List<Matrix4f>, float[], boolean, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
-
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- applySymmetryAndSetTrajectory() - 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 - Static variable in class org.jmol.script.Token
-
- applySymmetryToBonds - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- approx(Tuple3f) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- approx(float) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- approx(float, float) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- approx0(Tuple3f) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- arc - Static variable in class org.jmol.script.Token
-
- arcBall0 - Variable in class org.jmol.viewer.TransformManager
-
- arcBall0Rotation - Variable in class org.jmol.viewer.TransformManager
-
- arcBall1 - Variable in class org.jmol.viewer.TransformManager
-
- arcBallAxis - Variable in class org.jmol.viewer.TransformManager
-
- area - Static variable in class org.jmol.script.Token
-
- areAxesTainted() - Method in class org.jmol.viewer.Viewer
-
- areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- areEqual(ScriptVariable, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
-
- areEqual(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
-
for JUnit test, mainly
- areEqual(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
- 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 - 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 enum org.jmol.constant.EnumPalette
-
Default table of CPK atom colors.
- argbsCpk - Variable in class org.jmol.util.ColorEncoder
-
- argbsCpk - Variable in class org.jmol.viewer.ColorManager
-
- argbsCpkRasmol - Static variable in enum org.jmol.constant.EnumPalette
-
- 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.util.JmolEdge
-
- argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsRoygb - Variable in class org.jmol.util.ColorEncoder
-
- argbsRoygbScale - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsRwb - Variable in class org.jmol.util.ColorEncoder
-
- argbsRwbScale - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsShapely - Variable in class org.jmol.util.ColorEncoder
-
- argbsShapely - Static variable in class org.jmol.viewer.JmolConstants
-
- argusImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
-
- aromatic - Static variable in class org.jmol.script.Token
-
- aromaticAmbiguous - Variable in class org.jmol.smiles.SmilesAtom
-
- array - Static variable in class org.jmol.script.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(List<String>) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
-
- arrayPt - Variable in class org.jmol.script.ScriptVariable.Sort
-
- ArrayUtil - Class in org.jmol.util
-
- ArrayUtil() - Constructor for class org.jmol.util.ArrayUtil
-
- arrow - Static variable in class org.jmol.script.Token
-
- 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
-
- as - Static variable in class org.jmol.script.Token
-
- asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
-
- asBoolean() - Method in class org.jmol.script.ScriptVariable
-
- ascent - Variable in class org.jmol.g3d.Text3D
-
- ascent - Variable in class org.jmol.shape.LabelsRenderer
-
- ascent - Variable in class org.jmol.shape.Text
-
- asFloat() - Method in class org.jmol.script.ScriptVariable
-
- ashades - Static variable in class org.jmol.g3d.Colix3D
-
- ashadesGreyscale - Static variable in class org.jmol.g3d.Colix3D
-
- ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
-
- ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
-
- asInt() - Method in class org.jmol.script.ScriptVariable
-
- aspectRatio - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- asPopup - Variable in class org.jmol.popup.SimplePopup
-
- assign() - Method in class org.jmol.script.ScriptEvaluator
-
- assign - Static variable in class org.jmol.script.Token
-
- 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
-
- assignAtom(int, String, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- assignAtom(int, Point3f, String) - Method in class org.jmol.viewer.Viewer
-
- assignBond(int, char) - Method in class org.jmol.viewer.Viewer
-
- assignConnect(int, int) - Method in class org.jmol.viewer.Viewer
-
- assignPotentials(Atom[], float[], BitSet, BitSet, BitSet, String) - Method in interface org.jmol.api.MepCalculationInterface
-
- assignPotentials(Atom[], float[], BitSet, BitSet, BitSet, String) - Method in class org.jmol.quantum.MepCalculation
-
- assignPotentials(Atom[], float[], BitSet, BitSet, BitSet, String) - Method in class org.jmol.quantum.MlpCalculation
-
- assignValueFromGapColorForKin(String) - Method in class org.jmol.jvxl.readers.KinemageReader
-
C++ code gives these as " value > x.x ? "xxxxx", etc.
- assocCutoff - Variable in class org.jmol.jvxl.readers.Parameters
-
- assocCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- 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
-
- asString() - Method in class org.jmol.script.ScriptVariable
-
- assumeAtomRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- asThread - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- astrType - Static variable in class org.jmol.script.Token
-
- asVector - Variable in class org.jmol.script.ScriptMathProcessor
-
- asVector - Variable in class org.jmol.smiles.SmilesSearch
-
- ASYM_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- atokenInfix - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- atom(int) - 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(int, int, float, float, float, float, BitSet, int, short, int, boolean, char) - Constructor for class org.jmol.modelset.Atom
-
- atom - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
-
- 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_IN_FRAME - 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.FontLineShapeRenderer
-
- atomA - Variable in class org.jmol.shape.SticksRenderer
-
- atomA0 - Variable in class org.jmol.shape.SticksRenderer
-
- atomArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- atomB - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- atomB - Variable in class org.jmol.shape.SticksRenderer
-
- atomB0 - Variable in class org.jmol.shape.SticksRenderer
-
- atomC - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- atomCenterOrCoordinateParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- atomCharges - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- AtomCollection - Class in org.jmol.modelset
-
- AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
-
- AtomCollection.AtomSorter - Class in org.jmol.modelset
-
- AtomCollection.AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
-
- atomCoordAngstroms - Variable in class org.jmol.quantum.MepCalculation
-
- atomCount - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- atomCount - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- atomCount - Variable in class org.jmol.adapter.readers.more.MdTopReader
-
- atomCount - Variable in class org.jmol.adapter.readers.more.Mol2Reader
-
- atomCount - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- atomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- atomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- atomCount - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
-
- atomCount - Variable in class org.jmol.adapter.readers.simple.AmpacReader
-
- atomCount - Variable in class org.jmol.adapter.readers.simple.CubeReader
-
- atomCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- atomCount - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
-
- atomCount - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- atomCount - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- atomCount - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- atomCount - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- 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.SimplePopup
-
- atomCount - Variable in class org.jmol.shape.AtomShape
-
- atomCount - Variable in class org.jmol.shapesurface.Contact
-
- atomCount - Variable in class org.jmol.smiles.SmilesGenerator
-
- atomCount - Variable in class org.jmol.util.JmolMolecule
-
- atomD - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- 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.SurfaceGenerator
-
- atomDataServer - Variable in class org.jmol.jvxl.readers.VolumeDataReader
-
- atomExpression(int) - Method in class org.jmol.script.ScriptEvaluator
-
- atomExpression(Token[], int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- atomExpression - Static variable in class org.jmol.viewer.PropertyManager
-
- atomExpressionCommand - Static variable in class org.jmol.script.Token
-
- atomFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- atomFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- atomFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- atomFormats - Variable in class org.jmol.shape.Hover
-
- atomFrag - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- ATOMIC_ORBITAL_ZERO_CUT_OFF - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- atomicAndIsotopeNumber - Variable in class org.jmol.modelset.Atom
-
- atomicMass - Variable in class org.jmol.smiles.SmilesAtom
-
- atomicMass - Static variable in class org.jmol.util.Elements
-
- atomicNumber - Variable in class org.jmol.atomdata.AtomData
-
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
- atomicorbital - Static variable in class org.jmol.script.Token
-
- atomID - Variable in class org.jmol.modelset.Atom
-
- atomid - Static variable in class org.jmol.script.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_C1_PRIME - 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_C4_PRIME - 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_OD1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OE2 - 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_SG - 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.simple.HyperChemReader
-
- atomIndex - Variable in class org.jmol.adapter.smarter.Atom
-
- atomIndex - Variable in class org.jmol.atomdata.AtomData
-
- 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.AtomIteratorWithinModel
-
- atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
-
- atomindex - Static variable in class org.jmol.script.Token
-
- atomIndex - Variable in class org.jmol.shape.Hover
-
- atomIndex - Variable in class org.jmol.shape.Mesh
-
- atomIndex - Variable in class org.jmol.shapesurface.Isosurface
-
- 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.api
-
note: YOU MUST RELEASE THE ITERATOR
- atomIndexLast - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- AtomIteratorWithinModel - Class in org.jmol.modelset
-
- AtomIteratorWithinModel() - Constructor for class org.jmol.modelset.AtomIteratorWithinModel
-
- AtomIteratorWithinModelSet - Class in org.jmol.modelset
-
- AtomIteratorWithinModelSet(BitSet) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
-
- AtomIteratorWithinModelSet() - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
-
- atomLabels - Variable in class org.jmol.shape.Labels
-
- atomList - Variable in class org.jmol.util.JmolMolecule
-
- atomMap - Variable in class org.jmol.minimize.Minimizer
-
- atomMolecule - Variable in class org.jmol.atomdata.AtomData
-
- atomName - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- atomName - Variable in class org.jmol.adapter.smarter.Atom
-
- atomname - Static variable in class org.jmol.script.Token
-
- atomName - Variable in class org.jmol.smiles.SmilesAtom
-
- 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.quantum.GamessReader
-
- atomNames - Variable in class org.jmol.adapter.readers.quantum.PsiReader
-
- atomNames - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- atomNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- atomNames - Variable in class org.jmol.modelset.AtomCollection
-
- atomNo - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- atomno - Static variable in class org.jmol.script.Token
-
- atomOrPointPicked(int, Point3fi, int) - Method in class org.jmol.viewer.ActionManager
-
- atompicking - Static variable in class org.jmol.script.Token
-
- atomPicking - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- atomPickingMode - Variable in class org.jmol.viewer.ActionManager
-
- atomPositions - Variable in class org.jmol.adapter.readers.simple.AmpacReader
-
- atomProp - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- atomproperty - Static variable in class org.jmol.script.Token
-
- atomPropertyFloat(Viewer, Atom, int) - Static method in class org.jmol.modelset.Atom
-
called by isosurface and int comparator via atomProperty()
and also by getBitsetProperty()
- atomPropertyInt(Atom, int) - Static method in class org.jmol.modelset.Atom
-
called by isosurface and int comparator via atomProperty()
and also by getBitsetProperty()
- AtomPropertyMapper - Class in org.jmol.jvxl.readers
-
- AtomPropertyMapper(SurfaceGenerator, String) - Constructor for class org.jmol.jvxl.readers.AtomPropertyMapper
-
- atomPropertyString(Viewer, Atom, int) - Static method in class org.jmol.modelset.Atom
-
- atomPropertyTuple(Atom, int) - Static method in class org.jmol.modelset.Atom
-
- atomPts - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- atomRadius - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- atomRadius - Variable in class org.jmol.atomdata.AtomData
-
- atomRadius - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
-
- atoms - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- 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.modelset.AtomIteratorWithinModel
-
- atoms - Variable in class org.jmol.modelset.MeasurementData
-
- atoms - Static variable in class org.jmol.script.Token
-
- 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.shapesurface.Contact
-
- atoms - Variable in class org.jmol.smiles.SmilesGenerator
-
- atoms - Variable in class org.jmol.symmetry.PointGroup
-
- atomSerial - Variable in class org.jmol.adapter.smarter.Atom
-
- atomSerials - Variable in class org.jmol.modelset.AtomCollection
-
- 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.jmolpanel
-
A JFrame that allows for choosing an Atomset to view.
- AtomSetChooser(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- AtomSetChooser.AtomSet - Class in org.openscience.jmol.app.jmolpanel
-
Objects in the AtomSetChooser tree
- AtomSetChooser.AtomSet(int, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
-
- atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- AtomSetCollection - Class in org.jmol.adapter.smarter
-
- AtomSetCollection(String, AtomSetCollectionReader) - 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(List<?>) - 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.viewer.FileManager.DOMReader
-
- atomSetCollection - Variable in class org.jmol.viewer.FileManager.FileReader
-
- atomSetCollection - Variable in class org.jmol.viewer.FileManager.FilesReader
-
- atomSetCollectionAuxiliaryInfo - 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.jmolpanel.AtomSetChooser.AtomSet
-
The index of that AtomSet
- atomSetName - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
-
The name of the AtomSet
- atomSetNumbers - 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
-
- atomSite - Variable in class org.jmol.smiles.SmilesAtom
-
- atomsOr - Variable in class org.jmol.smiles.SmilesAtom
-
- atomSym - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- atomSymmetry - Variable in class org.jmol.modelset.Atom
-
- atomSyms - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- atomTest - Variable in class org.jmol.symmetry.SymmetryOperation
-
- atomtype - Static variable in class org.jmol.script.Token
-
- atomTypeFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- atomTypes - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- atomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
-
- atomTypes - Variable in class org.jmol.adapter.readers.more.MdTopReader
-
- atomTypes - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
- atomTypes - Static variable in class org.jmol.minimize.Minimizer
-
- atomTypes - Variable in class org.jmol.modelset.AtomCollection
-
- atomtypes - Static variable in class org.jmol.script.Token
-
- atomTypes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- atomx - Static variable in class org.jmol.script.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.script.Token
-
- atomz - Static variable in class org.jmol.script.Token
-
- attEcho - Variable in class org.jmol.console.ScriptEditor
-
- attEcho - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- attError - Variable in class org.jmol.console.ScriptEditor
-
- attError - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- attHighlight - Variable in class org.jmol.console.ScriptEditor
-
- attPrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- attributesCommand - Variable in class org.jmol.console.AppletConsole
-
- atts - Variable in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
-
- attStatus - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- attUserInput - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- augmentGroup3List(Object, String, boolean) - Method in class org.jmol.popup.JmolPopup
-
- AUTH_ATOM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- auto - Static variable in class org.jmol.script.Token
-
- autoBond(BitSet, BitSet, BitSet, BitSet, short, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- autoBond(BitSet, BitSet, BitSet, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- autobond - Static variable in class org.jmol.script.Token
-
- autoBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- autoBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- autoBond_Pre_11_9_24(BitSet, BitSet, BitSet, BitSet, short) - Method in class org.jmol.modelset.ModelCollection
-
- autoCalculate(int) - Method in class org.jmol.viewer.Viewer
-
- autoExit - Variable in class org.jmol.viewer.Viewer
-
- autofps - Static variable in class org.jmol.script.Token
-
- autoFps - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- autoHbond(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
a generalized formation of HBONDS, carried out in relation to calculate
HBONDS {atomsFrom} {atomsTo}.
- autoHbond(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
-
- average - Static variable in class org.jmol.script.Token
-
- averageAtomPoint - Variable in class org.jmol.modelset.ModelCollection
-
- averageBufferPixel(int[], int[], int, int) - Static method in class org.jmol.g3d.Graphics3D
-
- AviCreator - Class in org.jmol.export.image
-
- AviCreator() - Constructor for class org.jmol.export.image.AviCreator
-
- ax - Variable in class org.jmol.g3d.Triangle3D
-
- axE - Variable in class org.jmol.g3d.Triangle3D
-
- axes(int) - Method in class org.jmol.script.ScriptEvaluator
-
- axes - Static variable in class org.jmol.script.Token
-
- 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_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
-
- axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- axesAreTainted - Variable in class org.jmol.viewer.Viewer
-
- axescolor - Static variable in class org.jmol.script.Token
-
- axesMaxN - Static variable in class org.jmol.symmetry.PointGroup
-
- axesmode - Static variable in class org.jmol.script.Token
-
- axesMode - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- axesmolecular - Static variable in class org.jmol.script.Token
-
- axesorientationrasmol - Static variable in class org.jmol.script.Token
-
- axesOrientationRasmol - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- axesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- AxesRenderer - Class in org.jmol.shape
-
- AxesRenderer() - Constructor for class org.jmol.shape.AxesRenderer
-
- axesscale - Static variable in class org.jmol.script.Token
-
- axesScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- axesunitcell - Static variable in class org.jmol.script.Token
-
- axeswindow - Static variable in class org.jmol.script.Token
-
- axis - Static variable in class org.jmol.script.Token
-
- axis - Variable in class org.jmol.shapespecial.DrawMesh
-
- axis1color - Static variable in class org.jmol.script.Token
-
- axis2color - Static variable in class org.jmol.script.Token
-
- axis3color - Static variable in class org.jmol.script.Token
-
- axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- axisangle - Static variable in class org.jmol.script.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
-
- axisNX - Static variable in class org.jmol.viewer.JmolConstants
-
- axisNY - Static variable in class org.jmol.viewer.JmolConstants
-
- axisNZ - Static variable in class org.jmol.viewer.JmolConstants
-
- axisPoints - Variable in class org.jmol.shape.Axes
-
- axisPoints - Static variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- axisType - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
-
- axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- axisX - Static variable in class org.jmol.viewer.JmolConstants
-
- axisXY - Variable in class org.jmol.shape.Axes
-
- axisY - Static variable in class org.jmol.viewer.JmolConstants
-
- axisZ - Static variable in class org.jmol.viewer.JmolConstants
-
- axW - Variable in class org.jmol.g3d.Triangle3D
-
- ay - Variable in class org.jmol.g3d.Triangle3D
-
- az - Variable in class org.jmol.g3d.Triangle3D
-
- azE - Variable in class org.jmol.g3d.Triangle3D
-
- azW - Variable in class org.jmol.g3d.Triangle3D
-
- c - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
-
- c - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- c - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- c - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- c - Variable in class org.jmol.jvxl.readers.MapFileReader
-
- c - Variable in class org.jmol.minimize.forcefield.Calculation
-
- C - Static variable in class org.jmol.modelsetbio.AminoMonomer
-
- c - Variable in class org.jmol.quantum.MOCalculation
-
- c - Static variable in class org.jmol.quantum.NciCalculation
-
- c - Variable in class org.jmol.util.SimpleUnitCell
-
- c1 - Variable in class org.jmol.g3d.Hermite3D
-
- C1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
-
- 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
-
- C4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
-
- 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.util.SimpleUnitCell
-
- CA - Static variable in class org.jmol.modelsetbio.AminoMonomer
-
- cA_ - Variable in class org.jmol.util.SimpleUnitCell
-
- CageRenderer - Class in org.jmol.shape
-
- CageRenderer() - Constructor for class org.jmol.shape.CageRenderer
-
- calc(int, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
-
- calc - Variable in class org.jmol.minimize.forcefield.ForceField
-
- calc(double[][]) - Method in class org.jmol.util.Eigen
-
- 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.api.JmolViewer
-
- calcAtomsMinMax(BitSet, BoxInfo) - Method in class org.jmol.modelset.ModelCollection
-
- calcAtomsMinMax(BitSet, BoxInfo) - Method in class org.jmol.viewer.Viewer
-
- calcAveragePoint(Point3f, Point3f, Point3f) - Static method in class org.jmol.util.Measure
-
- calcAveragePointN(Point3f[], int, Point3f) - Static method in class org.jmol.util.Measure
-
- calcAxis() - Method in class org.jmol.modelsetbio.Helix
-
- calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
-
- calcAxis() - Method in class org.jmol.modelsetbio.Sheet
-
- calcBestAxisThroughPoints(Point3f[], Point3f, Vector3f, Vector3f, int) - Static method in class org.jmol.util.Measure
-
- calcBfactorRange(BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- calcBfactorRange() - Method in class org.jmol.shapebio.BioShape
-
- calcBioParameters() - Method in class org.jmol.modelset.Group
-
- calcBioParameters() - Method in class org.jmol.modelsetbio.Monomer
-
- calcBoundBoxDimensions(BitSet, float) - Method in class org.jmol.modelset.ModelCollection
-
- calcBoundBoxDimensions(BitSet, float) - Method in class org.jmol.viewer.Viewer
-
- calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
-
sets all camera and scale factors needed by
the specific perspective model instantiated
- 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
-
- calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
-
- calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
-
- calcFactors(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- calcGreyscaleRgbFromRgb(int) - Static method in class org.jmol.g3d.Graphics3D
-
Return a greyscale rgb value 0-FF using NTSC color luminance algorithm
- calcHbondEnergy(Point3f, Point3f, AminoMonomer, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
-
based on RasMol 2.7.2.1.1 model
checkDistances:
When we are seriously looking for H bonds, we want to
also check that distCN > distCH and that the OH distance
is less than 3 Angstroms.
- calcLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
-
- calcMeanPositionalDisplacement(int) - Method in class org.jmol.shapebio.BioShape
-
Calculates the mean positional displacement in milliAngstroms.
- calcMetrics() - Method in class org.jmol.shape.Frank
-
- calcNavigationDepthPercent() - Method in class org.jmol.viewer.TransformManager11
-
- 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.
- calcNavSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager11
-
- calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- calcOptions - Variable in class org.jmol.adapter.readers.quantum.GamessReader
-
- calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
-
- 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
-
- calcPlane(int, float[]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
-
Fill this plane with data based on the current set of raw data planes.
- calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
-
For reduced density only; coloring is done point by point.
- calcRasmolHydrogenBonds(BitSet, BitSet, List<Bond>, boolean, int, boolean) - Method in class org.jmol.modelset.ModelCollection
-
These are not actual hydrogen bonds.
- calcRasmolHydrogenBonds(Polymer, BitSet, BitSet, List<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelset.Polymer
-
- calcRasmolHydrogenBonds(Polymer, BitSet, BitSet, List<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- calcRasmolHydrogenBonds(Polymer, BitSet, BitSet, List<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
-
- calcRectRubberBand() - Method in class org.jmol.viewer.ActionManager
-
- 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(FastBitSet, float, int, int, int) - Method in class org.jmol.shapespecial.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(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
-
- calcSphereShading() - Static method in class org.jmol.g3d.Shade3D
-
- calcSurfaceDistances() - Method in class org.jmol.modelset.AtomCollection
-
- calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
-
- calcType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- calculate(VolumeDataInterface, BitSet, Point3f[], float[], int) - Method in interface org.jmol.api.MepCalculationInterface
-
- calculate(RadiusData, float, BitSet, BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
- calculate(VolumeDataInterface, BitSet, Point3f[], float[], int) - Method in class org.jmol.quantum.MepCalculation
-
- calculate() - Method in class org.jmol.script.ScriptEvaluator
-
- calculate - Static variable in class org.jmol.script.Token
-
- calculateAnglesInDegrees() - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- calculateCodes(float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- calculatedArea - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- calculatedArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- calculatedDipole - Variable in class org.jmol.shapespecial.Dipoles
-
- calculatedVolume - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- calculatedVolume - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
-
- calculateFractionalPoint(float, Point3f, Point3f, float, float, Point3f) - Method in class org.jmol.jvxl.data.VolumeData
-
- calculateGeodesicSurface(BitSet, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
-
- calculateGeodesicSurface(BitSet, float) - Method in class org.jmol.shapesurface.Isosurface
-
- calculateHydrogens(BitSet, int[], boolean, boolean, List<Atom>) - Method in class org.jmol.modelset.AtomCollection
-
get a list of potential H atom positions based on
elemental valence and formal charge
- calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
-
- 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(Group[], int, int, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- calculateQuaternionRotation(Point3f[][], float[], boolean) - Static method in class org.jmol.util.Measure
-
- calculateR0(double, double, double, double, double) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
-
- calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
-
- calculateRunsFourOrMore(AlphaPolymer.Code[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- calculateStraightness() - Method in class org.jmol.modelset.ModelCollection
-
- calculateStraightness() - Method in class org.jmol.viewer.Viewer
-
- calculateStructures(boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.Model
-
- calculateStructures(BitSet, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
-
- calculateStructures(Polymer[], int, List<Bond>, boolean, boolean, boolean) - Method in class org.jmol.modelset.Polymer
-
- calculateStructures(boolean) - Method in class org.jmol.modelset.Polymer
-
- calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
Uses Levitt & Greer algorithm to calculate protein secondary
structures using only alpha-carbon atoms.
- calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- calculateStructures(Polymer[], int, List<Bond>, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
-
- calculateStructures(BitSet, boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
- calculateStructuresAllExcept(BitSet, boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
-
allows rebuilding of PDB structures;
also accessed by ModelManager from Eval
- calculateStructuresDssp(Polymer[], int, List<Bond>, boolean, boolean, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
- calculateStruts(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
see comments in org.jmol.modelsetbio.AlphaPolymer.java
Struts are calculated for atoms in bs1 connecting to atoms in bs2.
- calculateStruts(BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
-
see comments in org.jmol.modelsetbio.AlphaPolymer.java
Struts are calculated for atoms in bs1 connecting to atoms in bs2.
- calculateStruts(ModelSet, BitSet, BitSet, List<Atom>, float, int, boolean) - Method in class org.jmol.modelset.Polymer
-
- calculateStruts(ModelSet, BitSet, BitSet, List<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
Algorithm of George Phillips phillips@biochem.wisc.edu
originally a contribution to pyMol as struts.py; adapted here by Bob Hanson
for Jmol 1/2010
Return a vector of support posts for rapid prototyping models along the
lines of George Phillips for Pymol except on actual molecular segments
(biopolymers), not PDB chains (which may or may not be continuous).
- calculateStruts(BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
-
- calculateStrutsStatic(ModelSet, BitSet, BitSet, List<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- calculateSurface(BitSet, float) - Method in class org.jmol.modelset.AtomCollection
-
- calculateSurface(BitSet, float) - Method in class org.jmol.viewer.Viewer
-
- calculateVolume(BitSet, EnumVdw) - Method in class org.jmol.modelset.AtomCollection
-
- calculateVolumeOrArea(int, boolean, boolean) - Method in class org.jmol.jvxl.data.MeshData
-
- calculateVolumeOrArea(boolean) - Method in class org.jmol.shapesurface.Isosurface
-
- calculateVolumes() - Method in class org.jmol.jvxl.data.MeshData
-
- Calculation - Class in org.jmol.minimize.forcefield
-
- Calculation() - Constructor for class org.jmol.minimize.forcefield.Calculation
-
- calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
The number of the calculation being interpreted.
- calculationNumber - Variable in class org.jmol.adapter.readers.quantum.QchemReader
-
The number of the calculation being interpreted.
- Calculations - Class in org.jmol.minimize.forcefield
-
- Calculations(ForceField, MinAtom[], MinBond[], int[][], int[][], double[], List<Object[]>) - 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[], List<Object[]>) - 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.smarter.AtomSetCollectionReader
-
- 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
-
- 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
-
- callbacks - Variable in class org.jmol.applet.Jmol
-
- cameradepth - Static variable in class org.jmol.script.Token
-
- 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.export.___Exporter
-
- cameraDistance - Variable in class org.jmol.viewer.TransformManager
-
- cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
-
- cameraPosition - Variable in class org.jmol.export.___Exporter
-
- cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
-
- canAdd(AminoPolymer.Bridge) - Method in class org.jmol.modelsetbio.AminoPolymer.Bridge
-
- canBeNormalized(Vector3d) - Static method in class org.jmol.minimize.Util
-
- canBeSquared(double) - Static method in class org.jmol.minimize.Util
-
- cancel - Static variable in class org.jmol.script.Token
-
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- cancelPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Responds to cancel being press- or equivalent eg window closed.
- canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
-
- canDownsample - Variable in class org.jmol.jvxl.readers.VolumeFileReader
-
- canImport(JComponent, DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
-
- canIncrement() - Method in class org.jmol.script.ScriptVariable
-
- canNavigate() - Method in class org.jmol.viewer.TransformManager
-
- canNavigate() - Method in class org.jmol.viewer.TransformManager11
-
- CANONICAL_DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- CANONICAL_DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- CANONICAL_FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- CANONICAL_FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- 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
-
- cap - Static variable in class org.jmol.script.Token
-
- capCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- capData(Point4f, float) - Method in interface org.jmol.api.VolumeDataInterface
-
- capData(Point4f, float) - Method in class org.jmol.jvxl.data.VolumeData
-
- capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- cappingObject - Variable in class org.jmol.shape.Mesh
-
- cappingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
-
- capPlanesPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- carbohydrate - Static variable in class org.jmol.script.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
-
- cardinality() - Method in class org.jmol.util.FastBitSet
-
- cardinality(int) - Method in class org.jmol.util.FastBitSet
-
- 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 - Static variable in class org.jmol.script.Token
-
- Cartoon - Class in org.jmol.shapebio
-
- Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
-
- CARTOON_VISIBILITY_FLAG - Static variable in class org.jmol.modelsetbio.NucleicMonomer
-
- cartoonbaseedges - Static variable in class org.jmol.script.Token
-
- cartoonBaseEdges - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- CartoonRenderer - Class in org.jmol.shapebio
-
- CartoonRenderer() - Constructor for class org.jmol.shapebio.CartoonRenderer
-
- cartoonrockets - Static variable in class org.jmol.script.Token
-
- cartoonRockets - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- casecmd - Static variable in class org.jmol.script.Token
-
- CastepDensityReader - Class in org.jmol.jvxl.readers
-
- CastepDensityReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.CastepDensityReader
-
- CastepReader - Class in org.jmol.adapter.readers.xtal
-
CASTEP (http://www.castep.org) .cell file format relevant section of .cell
file are included as comments below
preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many
thanks to Keith Refson for his assistance with this implementation -- atom's
mass is encoded as bfactor -- FILTER options include "q=n" where n is an
integer or "q={1/4 1/4 0}" -- for non-simple fractions, you must use the
exact form of the wavevector description: -- load "xxx.phonon" FILTER
"q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just
specify SUPERCELL {a b c} where -- the number of cells matches a given
wavevector -- SUPERCELL {4 4 1}, for example -- following this with ".1" ".2"
etc.
- CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
-
- catchcmd - Static variable in class org.jmol.script.Token
-
- cationLookupTable - Static variable in class org.jmol.util.Elements
-
- cavity - Static variable in class org.jmol.script.Token
-
- 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.util.SimpleUnitCell
-
- cbAxesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cbClearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cbOpenFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cbPerspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cbShowAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cbShowBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cc1 - Variable in class org.jmol.g3d.Line3D
-
- cc2 - Variable in class org.jmol.g3d.Line3D
-
- cch - Variable in class org.jmol.util.CifDataReader
-
- cchBuf - Variable in class org.jmol.adapter.smarter.LimitedLineReader
-
- cchBuf - Variable in class org.jmol.util.LimitedLineReader
-
- cchScript - Variable in class org.jmol.script.ScriptCompiler
-
- cchToken - Variable in class org.jmol.script.ScriptCompiler
-
- cd() - Method in class org.jmol.script.ScriptEvaluator
-
- cd - Static variable in class org.jmol.script.Token
-
- cd(String) - Method in class org.jmol.viewer.Viewer
-
- cell() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- cell - Static variable in class org.jmol.script.Token
-
- cell0 - Variable in class org.jmol.shape.UccageRenderer
-
- cell1 - Variable in class org.jmol.shape.UccageRenderer
-
- cellParameterType - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- cellParamNames - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- cellParams - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
-
- 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.SurfaceReader
-
- center - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
-
- center(int) - Method in class org.jmol.script.ScriptEvaluator
-
- center - Static variable in class org.jmol.script.Token
-
- 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.shapespecial.EllipsoidsRenderer
-
- center - Variable in class org.jmol.shapesurface.Isosurface
-
- center - Variable in class org.jmol.symmetry.PointGroup
-
- center - Static variable in class org.jmol.viewer.JmolConstants
-
- center - Variable in class org.jmol.viewer.StateManager.Orientation
-
- center - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- center - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- centerAt() - Method in class org.jmol.script.ScriptEvaluator
-
- centerAt - Static variable in class org.jmol.script.Token
-
- centerAt(int, int, Point3f) - Method in class org.jmol.viewer.TransformManager
-
- centerAt(int, int, Point3f) - Method in class org.jmol.viewer.Viewer
-
- centerAtomIndex - Variable in class org.jmol.symmetry.PointGroup
-
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
-
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
-
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Centers the dialog on the screen.
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
-
- centerDipole() - Method in class org.jmol.shapespecial.Dipole
-
- centerI - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- centerParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- centerParameter(int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- centers - Variable in class org.jmol.shapespecial.Polyhedra
-
- centers - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- 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.jmolpanel.PreferencesDialog
-
- ch1 - Variable in class org.jmol.modelset.LabelToken
-
- 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.script.Token
-
- chainAtomCounts - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- chaincasesensitive - Static variable in class org.jmol.script.Token
-
- 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.script.ScriptEvaluator
-
- 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
-
- charge - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- chargesFound - Variable in class org.jmol.adapter.readers.simple.MopacReader
-
- ChargesOnly - Variable in class org.jmol.popup.SimplePopup
-
- chargeSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
-
- charToken() - Method in class org.jmol.script.ScriptCompiler
-
- check - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
-
- check - Static variable in class org.jmol.script.Token
-
- check() - Method in class org.jmol.smiles.SmilesMeasure
-
- check(int, int, int, long, long) - Method in class org.jmol.viewer.ActionManager.Mouse
-
- check - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- checkAction(ActionEvent) - Method in class org.jmol.console.ScriptEditor
-
- checkAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
-
- checkAims(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkAlchemy(String) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkAtomArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- checkAtomLine(boolean, boolean, String, String, StringBuffer) - Static method in class org.jmol.jvxl.readers.VolumeFileReader
-
checks an atom line for "ANGSTROMS", possibly overriding the data's natural
units, BOHR (similar to Gaussian CUBE files).
- checkAutoBondLegacy() - Method in class org.jmol.viewer.Viewer
-
- checkAxisOrder(int, Vector3f, Point3f) - Method in class org.jmol.symmetry.PointGroup
-
- checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[], float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- checkBinary(String) - Method in class org.jmol.jvxl.readers.PmeshReader
-
- checkBioType(String, int) - Method in class org.jmol.smiles.SmilesParser
-
- checkBondArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- checkBoolean(Map<String, Object>, String) - Method in class org.jmol.popup.SimplePopup
-
- checkBoundsMinMax(Point3f, Point3f) - Method in class org.jmol.shape.Shape
-
- checkBoxListener - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- checkBrace(SmilesSearch, char, char) - Method in class org.jmol.smiles.SmilesParser
-
- checkBridge(AminoPolymer.Bridge, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, boolean, int, int) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge
- checkBulge(AminoPolymer.Bridge, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, boolean, int) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
- checkButton - Variable in class org.jmol.console.ScriptEditor
-
- checkButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- checkByteCount - Variable in class org.jmol.shape.Mesh
-
- checkCalculationType() - Method in class org.jmol.quantum.MOCalculation
-
- checkCarbohydrate(String) - Static method in class org.jmol.viewer.JmolConstants
-
- checkCastep(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkCharge(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
-
- checkChirality(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
-
- checkClick(TouchPoint, List<Event>, boolean) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
-
- checkCommand() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- checkContinue() - Method in class org.jmol.script.ScriptEvaluator
-
checks to see if there is a pause condition, during which commands can
still be issued, but with the ! first.
- checkContour(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares.Triangle
-
- checkCoordinatesChanged() - Method in class org.jmol.viewer.Viewer
-
- checkCount - Variable in class org.jmol.util.MeshSurface
-
- checkCp(ContactPair, ContactPair, int, int) - Static method in class org.jmol.shapesurface.Contact
-
- checkCrystal(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- 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
-
- checkDistance(Point3f, Point3f, float, float, int, int, int, Point3f) - Method in interface org.jmol.api.SymmetryInterface
-
- checkDistance(Point3f, Point3f, float, float, int, int, int, Point3f) - Method in class org.jmol.symmetry.Symmetry
-
- checkDistance(Point3f, Point3f, float, float, int, int, int, Point3f) - Method in class org.jmol.symmetry.UnitCell
-
- checkedSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
-
- checkField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- checkFilenames - Variable in class org.openscience.chimetojmol.ChimePanel
-
- checkFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkFilter(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkFloatRange(float, float, float) - Static method in class org.jmol.viewer.Viewer
-
- checkFlowCommand(String) - Method in class org.jmol.script.ScriptCompiler
-
- checkFlowEnd(int, String, int) - Method in class org.jmol.script.ScriptCompiler
-
- checkFlowEndBrace() - Method in class org.jmol.script.ScriptCompiler
-
- checkFlowStartBrace(boolean) - Method in class org.jmol.script.ScriptCompiler
-
- checkFoldingXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkForceEndIf() - Method in class org.jmol.script.ScriptFlowContext
-
- checkForCoordinate(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- checkForItemSelector(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- checkformat(int) - Method in class org.openscience.jmol.app.webexport.Molecules
-
- checkformat(int) - Method in class org.openscience.jmol.app.webexport.Orbitals
-
- checkGenNBO(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkGreater - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- checkGromacs(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
-
- checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- checkHeaderContains(String) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkImpliedScriptCmd - Variable in class org.jmol.script.ScriptCompiler
-
- checkIn(String, Applet) - Static method in class org.jmol.applet.JmolAppletRegistry
-
- checking - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
-
- checking - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- checkInternalSlab(Point3f) - Method in class org.jmol.viewer.TransformManager
-
- checkIntRange(int, int, int) - Static method in class org.jmol.viewer.Viewer
-
- checkLast(int) - Method in class org.jmol.script.ScriptEvaluator
-
- checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
sets continuing and doProcessLines
- checkLength(int) - Method in class org.jmol.script.ScriptEvaluator
-
- checkLength(int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- checkLength23() - Method in class org.jmol.script.ScriptEvaluator
-
- checkLength34() - Method in class org.jmol.script.ScriptEvaluator
-
- checkLine() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
-
- checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
-
- checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Reads a Collection of AtomSets from a BufferedReader.
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
- checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
-
- checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
-
- checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
-
- checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
-
- checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkLineContinuation() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkLineStarts(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkLogic(SmilesSearch, String, SmilesAtom, SmilesBond, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
-
- checkMatch(SmilesAtom, int, int, boolean) - Method in class org.jmol.smiles.SmilesSearch
-
Check for a specific match of a model set atom with a pattern position
- checkMatchBond(SmilesAtom, SmilesAtom, SmilesBond, int, int, JmolEdge) - Method in class org.jmol.smiles.SmilesSearch
-
- checkMemory() - Static method in class org.jmol.util.Logger
-
- checkMenuClick(Object, String) - Method in class org.jmol.modelkit.ModelKitPopup
-
- checkMenuClick(Object, String) - Method in class org.jmol.popup.SimplePopup
-
- checkMesh(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- checkMeshBB(Shape[], int, BoxInfo) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- checkMinAttachedAngle(Atom, float, Vector3f, Vector3f, boolean) - Static method in class org.jmol.modelset.ModelCollection
-
- checkMinimization() - Method in class org.jmol.viewer.Viewer
-
- checkMinZ(Atom, int[]) - Method in class org.jmol.modelset.Group
-
- checkMol(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkMopacGraphf(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkMotion(int) - Method in class org.jmol.viewer.ActionManager
-
- checkMotionRotateZoom(int, int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
-
- checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- checkNested(SmilesSearch, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
-
- checkNewGroup(JmolAdapter, char, String, int, char, boolean) - Method in class org.jmol.modelset.ModelLoader
-
- checkNewSetCommand() - Method in class org.jmol.script.ScriptCompiler
-
- checkNormals(short, short, short) - Method in class org.jmol.shape.MeshRenderer
-
- checkNotPDB() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- 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, BitSet) - Method in class org.jmol.shapesurface.Isosurface
-
- checkObjectClicked(int, int, int, BitSet) - Method in class org.jmol.viewer.ShapeManager
-
- checkObjectClicked(int, int, int) - Method in class org.jmol.viewer.Viewer
-
- checkObjectDragged(int, int, int, int, int, BitSet) - Method in class org.jmol.shape.Labels
-
- 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, BitSet, int) - Method in class org.jmol.viewer.ShapeManager
-
- checkObjectDragged(int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
-
- checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shape.Frank
-
- 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.shape.Sticks
-
- checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shapespecial.Draw
-
- checkObjectHovered(int, int, BitSet) - Method in class org.jmol.shapesurface.Isosurface
-
- checkObjectHovered(int, int, BitSet, boolean) - Method in class org.jmol.viewer.ShapeManager
-
- 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
-
- checkOptions(CommandLine, Options) - Method in class org.openscience.jmol.app.JmolApp
-
- checkOrbitalType(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- checkOut(String) - Static method in class org.jmol.applet.JmolAppletRegistry
-
- checkPhiPsi(float[], float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
- checkPoint(Tuple3f) - Method in class org.jmol.export._IdtfExporter
-
- checkPoint(Point3fi) - Method in class org.jmol.modelset.MeasurementPending
-
- checkPointOrAtomClicked(int, int, int, int, long, boolean, int) - Method in class org.jmol.viewer.ActionManager
-
- checkPrimitiveAtom(SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
-
- checkPrimitiveBond(SmilesBond, int, int, JmolEdge) - Method in class org.jmol.smiles.SmilesSearch
-
- checkPrivateKey(double) - Method in class org.jmol.api.JmolViewer
-
- checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
-
Simple method to ensure that the image creator (which writes files) was in
fact opened by this viewer and not by some manipulation of the applet.
- checkPt(float[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
two values -- v1, and v2, which need not be ordered v1 < v2.
- checkRasmolHydrogenBond(AminoMonomer, Polymer, int, Point3f, BitSet, List<Bond>, int[][], boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- checkResume(String) - Method in class org.jmol.viewer.Viewer
-
- checkScript() - Method in class org.jmol.console.ScriptEditor
-
- checkScriptAndOpenFiles - Variable in class org.openscience.jmol.app.JmolApp
-
- checkScriptExecution(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- checkScriptNoFiles - Variable in class org.openscience.jmol.app.JmolApp
-
- checkScriptSilent(String) - Method in class org.jmol.script.ScriptEvaluator
-
a method for just checking a script
- checkSigned - Variable in class org.openscience.chimetojmol.ChimePanel
-
- checkSlab(int, Point3f, float, float, Point4f, Point3f[]) - Static method in class org.jmol.util.MeshSurface
-
- checkSlideZoom(int) - Method in class org.jmol.viewer.ActionManager
-
- checkSpecial - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- checkSpecial(int, String[], boolean) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkSpecialData(InputStream, String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
called by SmarterJmolAdapter to see if we have a Spartan directory and, if so,
open it and get all the data into the correct order.
- checkSpecialInZip(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
called by SmarterJmolAdapter to see if we can automatically assign a file
from the zip file.
- checkSpecialMenu(String, Object, String) - Method in class org.jmol.popup.JmolPopup
-
- checkSpecialMenu(String, Object, String) - Method in class org.jmol.popup.SimplePopup
-
- checkSpecialParameterSyntax() - Method in class org.jmol.script.ScriptCompiler
-
- checkSpecialVoxel(Point3f, float, Point3f, float, float, Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- checkStandardDeviation(Vector3f[], Vector3f, int, float) - Static method in class org.jmol.smiles.SmilesAromatic
-
- checkStepping(String) - Method in class org.jmol.viewer.Viewer
-
- checkStereochemistry() - Method in class org.jmol.smiles.SmilesSearch
-
- checkStereochemistry(boolean, JmolNode, int, int, JmolNode, JmolNode, JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesSearch
-
- checkStereoPairs(JmolNode, int, JmolNode[], int) - Method in class org.jmol.smiles.SmilesGenerator
-
- checkSubs - Variable in class org.openscience.chimetojmol.ChimePanel
-
- checkTicks(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- checkTimer(String) - Static method in class org.jmol.util.Logger
-
- checkToken(int) - Method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- checkTwoAtomAction(int, Point3fi, int) - Method in class org.jmol.viewer.ActionManager
-
- checkType(String[][], String) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- checkUnitCell(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkUnitCellItem(String[], String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- checkUnitCellOffset() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- checkUnquotedFileName() - Method in class org.jmol.script.ScriptCompiler
-
- checkUserAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
-
- checkValencesAndBond(Atom, Atom, int, short, BitSet) - Method in class org.jmol.modelset.BondCollection
-
- checkWien2k(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- checkWithin(Point3f, List<Point3f>, float, boolean) - Static method in class org.jmol.shape.Mesh
-
- checkXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
- chem3dImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
-
- CHEM_COMP_AC_CHARGE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_NAME - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_SYM - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_X - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_X_IDEAL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_Y - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_Y_IDEAL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_Z - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_AC_Z_IDEAL - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_BOND_AROMATIC_FLAG - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_BOND_ATOM_ID_1 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_BOND_ATOM_ID_2 - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- CHEM_COMP_BOND_VALUE_ORDER - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- 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
-
- chemCompBondFields - 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.jmolpanel.JmolPanel
-
- chemical - Static variable in class org.jmol.script.Token
-
- chemicalName - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- chFirst - Variable in class org.jmol.script.ScriptCompiler
-
- ChimePanel - Class in org.openscience.chimetojmol
-
- ChimePanel() - Constructor for class org.openscience.chimetojmol.ChimePanel
-
- chimePath - Variable in class org.openscience.chimetojmol.ChimePanel
-
- ChimeToJmol - Class in org.openscience.chimetojmol
-
- ChimeToJmol() - Constructor for class org.openscience.chimetojmol.ChimeToJmol
-
- ChimeToJmol.ApplicationCloser - Class in org.openscience.chimetojmol
-
- ChimeToJmol.ApplicationCloser() - Constructor for class org.openscience.chimetojmol.ChimeToJmol.ApplicationCloser
-
- chiralClass - Variable in class org.jmol.smiles.SmilesAtom
-
- chiralOrder - Variable in class org.jmol.smiles.SmilesAtom
-
- choice - Variable in class org.jmol.export.dialog.Dialog
-
- chooseBestBoundBox() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- chooser - Variable in class org.jmol.export.dialog.FilePreview
-
- chooser - Variable in class org.openscience.chimetojmol.ChimePanel
-
- chop(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- chord - Variable in class org.jmol.util.ContactPair
-
- chpt0 - Variable in class org.jmol.script.ScriptFunction
-
- chrg - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- CifDataReader - Class in org.jmol.util
-
- CifDataReader(JmolLineReader) - Constructor for class org.jmol.util.CifDataReader
-
- CifDataReader(BufferedReader) - Constructor for class org.jmol.util.CifDataReader
-
- cifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- 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
-
- circle - Static variable in class org.jmol.script.Token
-
- 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
-
- CIRCLE_FRACTION - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- circleNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- cl_block(OutputStream) - Method in class org.jmol.export.image.GifEncoder
-
- cl_hash(int) - Method in class org.jmol.export.image.GifEncoder
-
- clash - Static variable in class org.jmol.script.Token
-
- classBase - Static variable in class org.jmol.adapter.smarter.Resolver
-
- CLASSBASE_OPTIONS - Static variable in class org.jmol.viewer.JmolConstants
-
- classifyName(String, boolean) - Method in class org.jmol.viewer.FileManager
-
- ClassPreloader - Class in org.jmol.applet
-
- ClassPreloader(AppletWrapper) - Constructor for class org.jmol.applet.ClassPreloader
-
- clauseAlternateSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseAnd() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseAtomSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseCell() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseChainSpec(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseComparator(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseConnected() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseDefine(boolean, boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseItemSelector() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseModelSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseNot() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseOr(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clausePrimitive() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseResidueSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseResNameSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseSequenceSpec() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseSubstructure() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clauseWithin(boolean) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- clean() - Method in class org.jmol.shape.MeshCollection
-
- clean() - Method in class org.jmol.shapespecial.Draw
-
- cleanPattern(String, boolean) - Static method in class org.jmol.smiles.SmilesParser
-
- cleanRegistry() - Static method in class org.jmol.applet.JmolAppletRegistry
-
- cleanScriptComments(String) - Method in class org.jmol.script.ScriptCompiler
-
allows for three kinds of comments.
- cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- clear() - Method in class org.jmol.awt.Mouse
-
- clear() - Method in class org.jmol.export.history.HistoryFile
-
- clear() - Method in class org.jmol.jvxl.data.JvxlData
-
- clear() - Method in class org.jmol.minimize.Minimizer
-
- clear() - Method in class org.jmol.multitouch.ActionManagerMT
-
- clear - Static variable in class org.jmol.script.Token
-
- 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() - Method in class org.jmol.util.CommandHistory
-
clears the history.
- clear() - Method in class org.jmol.util.FastBitSet
-
- clear(int) - Method in class org.jmol.util.FastBitSet
-
- clear(int, int) - Method in class org.jmol.util.FastBitSet
-
- clear() - Method in class org.jmol.util.TempArray
-
- clear() - Method in class org.jmol.viewer.ActionManager
-
- clear() - Method in class org.jmol.viewer.AnimationManager
-
- 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.RepaintManager
-
- clear(int) - Method in class org.jmol.viewer.RepaintManager
-
- clear() - Method in class org.jmol.viewer.ScriptManager
-
- clear() - Method in class org.jmol.viewer.SelectionManager
-
- clear(StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager
-
- clear() - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- clear() - Method in class org.jmol.viewer.TransformManager
-
- clear() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- clear_flg - Variable in class org.jmol.export.image.GifEncoder
-
- clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
-
- clearAtomSets() - Method in class org.jmol.viewer.Viewer
-
- clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
-
- clearBfactorRange() - Method in class org.jmol.viewer.Viewer
-
- clearBindings() - Method in class org.jmol.viewer.ActionManager
-
- clearBioPolymers(Group[], int, BitSet) - Method in interface org.jmol.api.JmolBioResolver
-
- clearBioPolymers(Group[], int, BitSet) - Method in class org.jmol.modelsetbio.Resolver
-
- clearBonds() - Method in class org.jmol.modelset.Atom
-
- clearButton - Variable in class org.jmol.console.ScriptEditor
-
- clearButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- 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
-
- clearContent(String) - Method in class org.jmol.console.AppletConsole
-
- clearContent(String) - Method in class org.jmol.console.JmolConsole
-
- clearContent() - Method in class org.jmol.console.ScriptEditor.EditorDocument
-
Removes all content of the script window, and add a new prompt.
- clearContent() - Method in class org.jmol.console.ScriptEditor.EditorTextPane
-
- clearContent(String) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
-
- clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- clearContent() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
Removes all content of the script window, and add a new prompt.
- clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelCollection
-
- clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEvaluator
-
- clearFontCache() - Static method in class org.jmol.g3d.Text3D
-
- clearForces() - Method in class org.jmol.minimize.forcefield.ForceField
-
- clearFunctions() - Method in class org.jmol.viewer.StateManager
-
- clearFunctions() - Method in class org.jmol.viewer.Viewer
-
- clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- clearHighlight() - Method in class org.jmol.console.ScriptEditor.EditorDocument
-
- clearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- clearInButton - Variable in class org.jmol.console.AppletConsole
-
- clearingThread - Variable in class org.jmol.g3d.Platform3D
-
- clearKeyBuffer() - Method in class org.jmol.awt.Mouse
-
- clearMeasurements() - Method in class org.jmol.api.JmolViewer
-
- clearMeasurements() - Method in class org.jmol.viewer.Viewer
-
- clearMinimization() - Method in class org.jmol.viewer.Viewer
-
- clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
-
- clearMouse() - Method in interface org.jmol.api.ApiPlatform
-
- clearMouse() - Method in class org.jmol.awt.Platform
-
- clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
-
- clearOutButton - Variable in class org.jmol.console.AppletConsole
-
- clearQueue() - Method in class org.jmol.viewer.ScriptManager
-
- clearRasmolHydrogenBonds(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- 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
-
- clearShapeManager(Error) - Method in class org.jmol.script.ParallelProcessor
-
- clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
-
- clearSpin() - Method in class org.jmol.viewer.TransformManager
-
- clearState(boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- clearTimeout(String) - Method in class org.jmol.viewer.Viewer
-
- clearTimeouts() - Method in class org.jmol.viewer.ActionManager
-
- clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- clearVibration() - Method in class org.jmol.viewer.TransformManager
-
- CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- clickabilityFlags - Variable in class org.jmol.modelset.Atom
-
- clickable - Static variable in class org.jmol.script.Token
-
- clickableMax - Static variable in class org.jmol.viewer.ShapeManager
-
- clicked - Variable in class org.jmol.viewer.ActionManager
-
- CLICKED - Static variable in class org.jmol.viewer.binding.Binding
-
- clickedCount - Variable in class org.jmol.viewer.ActionManager
-
- client - Variable in class org.jmol.modelset.MeasurementData
-
- client - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- clientHasBuffer - Variable in class org.jmol.g3d.Platform3D.ClearingThread
-
- clipboard - Static variable in class org.jmol.script.Token
-
- clipCode(int, int, int) - Method in class org.jmol.export.Export3D
-
- clipCode(int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- clipCode(int) - Method in class org.jmol.g3d.Graphics3D
-
- clipImage(String) - Method in interface org.jmol.api.JmolImageCreatorInterface
-
- clipImage(String) - Method in class org.jmol.api.JmolViewer
-
- clipImage(String) - Method in class org.jmol.export.image.ImageCreator
-
- clipImage(String) - Method in class org.jmol.viewer.Viewer
-
- clipped - Variable in class org.jmol.g3d.Cylinder3D
-
- clockBaseline - Variable in class org.jmol.applet.AppletWrapper
-
- clockWidth - Variable in class org.jmol.applet.AppletWrapper
-
- clockX - Variable in class org.jmol.applet.AppletWrapper
-
- clone() - Method in class org.jmol.util.FastBitSet
-
- 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(int) - 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
-
- cloneLastAtomSet(int, Point3f[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- cloneLastAtomSet(int, Point3f[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- 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.SimplePopup
-
- close() - Method in class org.jmol.util.BinaryDocument
-
- close() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- close() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- closeButton - Variable in class org.jmol.console.ScriptEditor
-
- closeButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- closePreview() - Method in class org.jmol.export.dialog.Dialog
-
- closeReader() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- closeReader() - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- closeReader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- closest - Variable in class org.jmol.modelset.ModelSet
-
- closeTag(StringBuffer, String) - Static method in class org.jmol.util.XmlUtil
-
- cM - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- cmdpt0 - Variable in class org.jmol.script.ScriptFunction
-
- cmil - Variable in class org.jmol.popup.SimplePopup
-
- 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 enum org.jmol.constant.EnumAxesMode
-
Code of axes mode.
- code - Variable in class org.jmol.i18n.GT.Language
-
- code - Variable in enum org.jmol.util.JmolEdge.EnumBondOrder
-
- code - Variable in enum org.jmol.viewer.FileManager.EnumFileStatus
-
- codetab - Variable in class org.jmol.export.image.GifEncoder
-
- coef - Variable in class org.jmol.g3d.Sphere3D
-
- coef - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- coef - Variable in class org.jmol.quantum.SlaterData
-
- coef - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
-
- coef - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- coef1 - Static variable in class org.jmol.quantum.NciCalculation
-
- coef2 - Static variable in class org.jmol.quantum.NciCalculation
-
- coef3 - Static variable in class org.jmol.quantum.NciCalculation
-
- coef_indices - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- coefCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- coeffs - Variable in class org.jmol.quantum.MOCalculation
-
- coefs - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
-
- coefs - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- coefs - Variable in class org.jmol.quantum.MOCalculation
-
- col - Static variable in class org.jmol.script.Token
-
- 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.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.util.MeshSurface
-
- 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
-
- colixHighlight - Variable in class org.jmol.shape.Halos
-
- colixHoogsteenEdge - Variable in class org.jmol.shapebio.CartoonRenderer
-
- 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
-
- colixSugarEdge - Variable in class org.jmol.shapebio.CartoonRenderer
-
- colixWatsonCrickEdge - Variable in class org.jmol.shapebio.CartoonRenderer
-
- collapsed - Static variable in class org.jmol.script.Token
-
- collapsed - Variable in class org.jmol.shapespecial.Polyhedra.Polyhedron
-
- COLLECTION - Static variable in class org.openscience.jmol.app.jmolpanel.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.script.Token
-
- color - Variable in enum org.jmol.constant.EnumStructure
-
- color - Variable in class org.jmol.jvxl.data.JvxlData
-
- color() - Method in class org.jmol.script.ScriptEvaluator
-
- color - Static variable in class org.jmol.script.Token
-
- COLOR - Static variable in class org.jmol.shape.Echo
-
- color - Variable in class org.jmol.shape.Mesh
-
- color - Variable in class org.jmol.shape.MeshCollection
-
- color - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- color4(short) - Method in class org.jmol.export._PovrayExporter
-
- colorArgbs - Static variable in class org.jmol.g3d.Graphics3D
-
- colorAtoms(short, BitSet) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
color a specific set of vertices based on a set of atoms
- 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.jmolpanel.AppConsole.ConsoleDocument
-
- colorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- colorData - Variable in class org.jmol.viewer.ColorManager
-
- colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
-
- colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
-
- colorDensity - Variable in class org.jmol.shape.Mesh
-
- colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
-
- colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- ColorEncoder - Class in org.jmol.util
-
- ColorEncoder(ColorEncoder) - Constructor for class org.jmol.util.ColorEncoder
-
- colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
-
- colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
-
- colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- colorHash - Variable in class org.jmol.export.image.GifEncoder
-
- colorIndex(int, int) - Static method in class org.jmol.util.ColorEncoder
-
- colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- ColorManager - Class in org.jmol.viewer
-
- ColorManager(Viewer, Graphics3D) - Constructor for class org.jmol.viewer.ColorManager
-
- colorManager - Variable in class org.jmol.viewer.Viewer
-
- colorNames - Static variable in class org.jmol.applet.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
-
- colorPhase - Variable in class org.jmol.jvxl.readers.Parameters
-
- colorPhases - Static variable in class org.jmol.jvxl.readers.SurfaceReader
-
- colorPointFromInt(int, Point3f) - Static method in class org.jmol.g3d.Graphics3D
-
- colorPointFromInt2(int) - 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.JvxlXmlReader
-
- colorPtr - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- colorPtToInt(Point3f) - Static method in class org.jmol.g3d.Graphics3D
-
- colorrasmol - Static variable in class org.jmol.script.Token
-
- colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
-
- colors - Static variable in class org.jmol.applet.AppletWrapper
-
- colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
-
- colorscheme - Static variable in class org.jmol.script.Token
-
- colorSchemes - Static variable in class org.jmol.util.ColorEncoder
-
- colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
-
- colorShape(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- colorShape(int, int, int, String, float, BitSet) - Method in class org.jmol.script.ScriptEvaluator
-
- colorTriadToInt(float, float, float) - Static method in class org.jmol.g3d.Graphics3D
-
- colorVertices(short, BitSet) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
color a specific set of vertices
- colorVertices(short, BitSet, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
color a specific set of vertices a specific color
- combineSurfaces(List<ContactPair>, int, int, float[], Object, boolean, boolean) - Method in class org.jmol.shapesurface.Contact
-
- comma - Static variable in class org.jmol.script.Token
-
- command - Static variable in class org.jmol.script.Token
-
- commandExpected() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- 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.script.ScriptEvaluator
-
- commandLineOptions - Variable in class org.jmol.export.___Exporter
-
- commandList - Variable in class org.jmol.util.CommandHistory
-
Array of commands.
- commandOptions - Variable in class org.openscience.jmol.app.JmolApp
-
- commands - Static variable in class org.jmol.script.Token
-
- commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- commands - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- commandStart - Variable in class org.jmol.script.ScriptFlowContext
-
- commandWatcherThread - Variable in class org.jmol.viewer.ScriptManager
-
- comment - Variable in class org.jmol.script.ScriptCompiler
-
- Comment - Variable in class org.jmol.util.JpegInfo
-
- commentChar - Variable in class org.jmol.export.___Exporter
-
- COMP_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- comparator - Static variable in class org.jmol.script.Token
-
- compare(Map<String, Object>, Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
-
- compare(SlaterData, SlaterData) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
-
- compare(GifEncoder.ColorItem, GifEncoder.ColorItem) - Method in class org.jmol.export.image.GifEncoder.ColorVector.CountComparator
-
- compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
-
- compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
-
- compare(String[], String[]) - Method in class org.jmol.modelsetbio.Resolver.BondSorter
-
- compare() - Method in class org.jmol.script.ScriptEvaluator
-
- compare(ScriptVariable, ScriptVariable) - Method in class org.jmol.script.ScriptVariable.Sort
-
- compare - Static variable in class org.jmol.script.Token
-
- compare(Object[], Object[]) - Method in class org.jmol.symmetry.UnitCell.Esort
-
- compareFloat(int, float[], int, float) - Method in class org.jmol.script.ScriptEvaluator
-
- compareFloat(int, float, float) - Static method in class org.jmol.script.ScriptEvaluator
-
- compareInt(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- compareString(int, int, String) - Method in class org.jmol.script.ScriptEvaluator
-
- compareString(int, String, String) - Method in class org.jmol.script.ScriptEvaluator
-
- compHeight - Variable in class org.jmol.util.JpegInfo
-
- CompID - Variable in class org.jmol.util.JpegInfo
-
- compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
-
Compiles a set of tokens for each primitive element of a
label.
- compile(String, String, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
-
- compile0(boolean) - Method in class org.jmol.script.ScriptCompiler
-
- compileCommand() - Method in class org.jmol.script.ScriptCompiler
-
- compileExpression() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- compileExpressions() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- compiler - Variable in class org.jmol.script.ScriptEvaluator
-
- compiler - Variable in class org.jmol.script.ScriptFlowContext
-
- compiler - Variable in class org.jmol.viewer.Viewer
-
- compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- compileScriptFileInternal(String, String, String, String) - Method in class org.jmol.script.ScriptEvaluator
-
- compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- completeCommand(String) - Method in class org.jmol.console.AppletConsole
-
- completeCommand(String) - Method in class org.jmol.console.JmolConsole
-
- completeCommand(Map<String, Token>, boolean, boolean, String, int) - Static method in class org.jmol.script.Token
-
- completeCommand(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- completeInitialization(Graphics, Dimension) - Method in class org.jmol.applet.AppletWrapper
-
- compnd - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- compndOld() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- compndSource(boolean) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- component - Variable in class org.jmol.smiles.SmilesAtom
-
- componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- Components - Variable in class org.jmol.util.JpegInfo
-
- componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.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(Tuple3f, Tuple3f, Tuple3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
-
- computeAngle(Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
-
- computeHelicalAxis(String, int, Point3f, Point3f, Quaternion) - Static method in class org.jmol.util.Measure
-
- computeTorsion(Tuple3f, Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
-
- compWidth - Variable in class org.jmol.util.JpegInfo
-
- concatList(ScriptVariable, ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- concatTokens(String[], int, int) - Static method in class org.jmol.util.Parser
-
- conect() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- coneNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- CONF_TYPE_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- configuration() - Method in class org.jmol.script.ScriptEvaluator
-
- configuration - Static variable in class org.jmol.script.Token
-
- configurationPtr - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- configurationPtr - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- configurationSelected - Variable in class org.jmol.popup.JmolPopup
-
- conformationIndex - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- conformationIndex - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- connect(float[][]) - Method in class org.jmol.modelset.ModelSet
-
- connect(int) - Method in class org.jmol.script.ScriptEvaluator
-
- connect - Static variable in class org.jmol.script.Token
-
- connect(float[][]) - Method in class org.jmol.viewer.Viewer
-
- connectAll(int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- connectAllBad(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- connected - Static variable in class org.jmol.script.Token
-
- connections - Variable in class org.jmol.shape.Mesh
-
- connections - Variable in class org.jmol.shape.MeshCollection
-
- connections - Variable in class org.jmol.viewer.StateManager.Connections
-
- connectivity - Variable in class org.jmol.smiles.SmilesAtom
-
- 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
-
- connectorFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- connectorFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- connectors - Variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- console() - Method in class org.jmol.script.ScriptEvaluator
-
- console - Static variable in class org.jmol.script.Token
-
- console - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- consoleButton - Variable in class org.jmol.console.ScriptEditor
-
- consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- consoleMessage(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel
-
- ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.ConsoleTextArea
-
- ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.ConsoleTextArea
-
- consoleTextPane - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- constrainQuadratic(double, double, double, int) - Method in class org.jmol.minimize.forcefield.Calculations
-
- constraint - Static variable in class org.jmol.script.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.adapter.readers.quantum.SpartanInputReader
-
- 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.jmolpanel.MeasurementTable
-
- constructMeasurementButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- constructMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- constructRadiusPolyhedron(int, AtomIndexIterator) - Method in class org.jmol.shapespecial.Polyhedra
-
- contact() - Method in class org.jmol.script.ScriptEvaluator
-
- contact - Static variable in class org.jmol.script.Token
-
- Contact - Class in org.jmol.shapesurface
-
- Contact() - Constructor for class org.jmol.shapesurface.Contact
-
- contactPair - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- contactPair - Variable in class org.jmol.jvxl.readers.Parameters
-
- ContactPair - Class in org.jmol.util
-
- ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
-
- ContactRenderer - Class in org.jmol.shapesurface
-
- ContactRenderer() - Constructor for class org.jmol.shapesurface.ContactRenderer
-
- contactType - Variable in class org.jmol.util.ContactPair
-
- container - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- contains(int, int) - Method in class org.jmol.util.Rectangle
-
- contentPath - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- context - Variable in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
-
- context - Variable in class org.jmol.script.ParallelProcessor.Process
-
- contextPath - Variable in class org.jmol.script.ScriptContext
-
- contextPath - Variable in class org.jmol.script.ScriptEvaluator
-
- ContextToken - Class in org.jmol.script
-
- ContextToken(int, int, Object) - Constructor for class org.jmol.script.ContextToken
-
- ContextToken(int, Object) - Constructor for class org.jmol.script.ContextToken
-
- contextVariables - Variable in class org.jmol.script.ContextToken
-
- contextVariables - Variable in class org.jmol.script.ScriptCompiler
-
- contextVariables - Variable in class org.jmol.script.ScriptContext
-
- contextVariables - Variable in class org.jmol.script.ScriptEvaluator
-
- CONTINUE - Static variable in class org.jmol.script.ScriptCompiler
-
- CONTINUE_MAX - Static variable in class org.jmol.util.JpegEncoder
-
- CONTINUE_MAX_BUFFER - Static variable in class org.jmol.util.JpegEncoder
-
- CONTINUE_STRING - Static variable in class org.jmol.util.JpegEncoder
-
- continuecmd - Static variable in class org.jmol.script.Token
-
- continueMatch(int, int, boolean) - Method in class org.jmol.smiles.SmilesSearch
-
- continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- contour - Static variable in class org.jmol.script.Token
-
- CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
-
- CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
-
- contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
-
- contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
-
- contourColixes - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- contourColors - Variable in class org.jmol.jvxl.data.JvxlData
-
- contourFromZero - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contourFromZero - Variable in class org.jmol.jvxl.readers.Parameters
-
- contourIncrements - Variable in class org.jmol.jvxl.readers.Parameters
-
- contourIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
-
- contourlines - Static variable in class org.jmol.script.Token
-
- contourPlaneMaximumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contourPlaneMinimumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contours - Static variable in class org.jmol.script.Token
-
- contoursDiscrete - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
-
- contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contourType - Variable in class org.jmol.jvxl.readers.Parameters
-
- contourValues - Variable in class org.jmol.jvxl.data.JvxlData
-
- contourValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
-
- contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- contourVertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- contractions - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- controlHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- controlHermites - Variable in class org.jmol.shapespecial.DrawRenderer
-
- controlPoints - Variable in class org.jmol.modelset.Polymer
-
- controlPoints - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- controlPointScreens - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- converged - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
- convertToMegabytes(long) - Method in class org.jmol.popup.JmolPopup
-
- coord - Variable in class org.jmol.minimize.MinAtom
-
- coord - Static variable in class org.jmol.script.Token
-
- coordinateInRange(int, int, Point3f, int, Point3i) - Method in class org.jmol.shape.Shape
-
- 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.script.ScriptEvaluator
-
- coordinatesAreFractional - Variable in class org.jmol.symmetry.SymmetryInfo
-
- coordinatesArePrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- 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) - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- copyColixTranslucency(short, short) - Static method in class org.jmol.g3d.Graphics3D
-
- copyDirectory(String, File, File, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
-
- copyFile(String, File, File, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
-
- copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- 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.jmolpanel.JmolPanel
-
- copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- cordMidPoints - Variable in class org.jmol.shapebio.RocketsRenderer
-
- corner - Variable in class org.jmol.shape.Axes
-
- corners - Static variable in class org.jmol.script.Token
-
- corners - Variable in class org.jmol.shapebio.RocketsRenderer
-
- cos - Static variable in class org.jmol.script.Token
-
- cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
-
- cosBeta - Variable in class org.jmol.util.SimpleUnitCell
-
- cosGamma - Variable in class org.jmol.util.SimpleUnitCell
-
- 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
-
- count - Static variable in class org.jmol.script.Token
-
- countBitsInWord(int) - Static method in class org.jmol.util.FastBitSet
-
- 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
-
- counter - Variable in class org.jmol.script.ParallelProcessor
-
- countGroup(int, String, String) - Method in class org.jmol.modelset.ModelLoader
-
- countPlusIndices - Variable in class org.jmol.modelset.Measurement
-
- countStereo(String) - Method in class org.jmol.smiles.SmilesMatcher
-
- countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
-
- countTokens(String, int) - Static method in class org.jmol.util.Parser
-
- covalent - Static variable in class org.jmol.script.Token
-
- covalentHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
-
- covalentMars - Static variable in class org.jmol.util.Elements
-
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
-
- create - Static variable in class org.jmol.script.Token
-
- createAndShowGUI(JmolViewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- createArrayOfArrayList(int) - Static method in class org.jmol.util.ArrayUtil
-
Helper method for creating a List[] without warnings.
- createArrayOfHashtable(int) - Static method in class org.jmol.util.ArrayUtil
-
Helper method for creating a Map[] without warnings.
- createAtomDataSet(int, Object, BitSet) - Method in class org.jmol.modelset.ModelSet
-
- createAtomSeCollectionFromArrayData(List<Object>, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
-
- createAtomSeCollectionFromStrings(String[], StringBuffer, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
-
- createAtomSerialMap() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- createAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
-
- createAtomSetCollectionFromFile(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
-
- createAtomSetCollectionFromFiles(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
-
- createAtomSetCollectionFromReader(String, String, Reader, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
-
not used in Jmol project -- will close reader
- createAtomSetCollectionFromString(String, StringBuffer, Map<String, Object>, boolean, boolean) - Method in class org.jmol.viewer.FileManager
-
- createBonds(boolean) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
Use the site bitset to check for atoms that are within
+/-dx Angstroms of the specified distances in GEOM_BOND
where dx is determined by the uncertainty (dx) in the record.
- createContours(float, float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- createCube() - Method in interface org.jmol.api.QuantumCalculationInterface
-
- createCube() - Method in class org.jmol.quantum.MOCalculation
-
- createCube() - Method in class org.jmol.quantum.NciCalculation
-
- 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
-
- createFunction(String, String, String) - Method in class org.jmol.script.ScriptEvaluator
-
for the ISOSURFACE command
- createGeodesic() - Static method in class org.jmol.geodesic.Geodesic
-
- createImage(Object) - Method in interface org.jmol.api.ApiPlatform
-
can be ignored (return null) if platform cannot save images
- createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolImageCreatorInterface
-
- createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
-
Starting with Jmol 11.8.RC5, for a context where the Jmol application
is embedded in another application simply to send the returned message
to the application.
- createImage(String, String, Object, int, int, int) - Method in class org.jmol.api.JmolViewer
-
- createImage(String, String, Object, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- createImage(Object) - Static method in class org.jmol.awt.Image
-
- createImage(Object) - Method in class org.jmol.awt.Platform
-
- createImage(String, String, Object, int, int) - Method in class org.jmol.export._ObjExporter
-
- 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
-
offer to let application do the image creation.
- createImage(String, String, Object, int, int, int, BitSet, String[]) - Method in class org.jmol.viewer.Viewer
-
from eval write command only includes option to write set of files
- createImage(String, String, Object, int, int, int) - Method in class org.jmol.viewer.Viewer
-
- createImage(String, String, Object, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
-
general routine for creating an image or writing data to a file
passes request to statusManager to pass along to app or applet
jmolStatusListener interface
- createImage(String, String, Object, int, int, int, String[], boolean) - Method in class org.jmol.viewer.Viewer
-
- createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- createImageStatus(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Starting with Jmol 11.8.RC5, this is just informational
if type == null and null is returned, then it means "Jmol, you handle it"
- createInstance(ApiPlatform) - Static method in class org.jmol.g3d.Platform3D
-
- createIsosurface(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- createLadders(List<AminoPolymer.Bridge>, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
"ladder =: one or more consecutive bridges of identical type" (p.
- 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, int) - Method in class org.jmol.shapesurface.Isosurface
-
- createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create a menu for the app.
- createMenubar() - Method in class org.jmol.console.AppletConsole
-
- createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create the menubar for the app.
- createMenuItem(String) - Method in class org.jmol.console.AppletConsole
-
- createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
This is the hook through which all menu items are
created.
- createMeshCylinder(int, int, int, int, int) - Method in class org.jmol.shapebio.BioShapeRenderer
-
- createModelSet(JmolAdapter, Object, BitSet) - Method in class org.jmol.modelset.ModelLoader
-
- createModelSet(String, String, StringBuffer, Object, BitSet, boolean) - Method in class org.jmol.viewer.ModelManager
-
- createModelSetAndReturnError(Object, boolean, StringBuffer) - Method in class org.jmol.viewer.Viewer
-
finally(!) we are ready to create the
"model set" from the "atom set collection"
- createMonteCarloOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
-
create a movie from a set of image files
- createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.export.image.AviCreator
-
- createNewAtomSet(Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- createOrbital() - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- createPdfDocument(String, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
-
- createPdfDocument(String, Object) - Method in class org.openscience.jmol.app.jmolpanel.PdfCreator
-
- createSet(int, int, int) - Method in class org.jmol.jvxl.data.MeshData
-
- createSlaterData(int, String, String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
- createSpaceGroup(int, String, float[]) - Method in interface org.jmol.api.SymmetryInterface
-
- createSpaceGroup(int, String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
-
- createSpaceGroup(String) - Static method in class org.jmol.symmetry.SpaceGroup
-
- createSpaceGroup(int, String, float[]) - Method in class org.jmol.symmetry.Symmetry
-
- createSphereShape(int) - Static method in class org.jmol.g3d.Sphere3D
-
- createSphericalSlaterByType(int, int, String, float, float) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
We have the type as a string and need to translate that
to exponents for x, y, z, and r.
- createSurfaceTool() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- createTextureFile(String, MeshSurface, Point) - Method in class org.jmol.export._ObjExporter
-
Writes a texture file with the colors in the colixes array in a way that it
can be mapped by the texture coordinates vt.
- createTool(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Hook through which every toolbar item is created.
- createToolbar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create the toolbar.
- createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create a button to go inside of the toolbar.
- createTopoMap(BitSet) - Method in class org.jmol.smiles.SmilesSearch
-
- createTransferable(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
-
- createTreeModel() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Creates the treeModel of the AtomSets available in the JmolViewer
- createVCRController(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Creates a VCR type set of controller inside a JPanel.
- createVoxelData() - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
-
Developer must customize this method
- createWebExport() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- createZipSet(String, String, boolean) - Method in class org.jmol.viewer.FileManager
-
- 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
-
- criterion - Static variable in class org.jmol.script.Token
-
- cross - Static variable in class org.jmol.script.Token
-
- cross - Static variable in class org.jmol.shapespecial.DipolesRenderer
-
- cross0 - Variable in class org.jmol.shapespecial.DipolesRenderer
-
- cross1 - Variable in class org.jmol.shapespecial.DipolesRenderer
-
- crossed - Static variable in class org.jmol.script.Token
-
- 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
- crystalContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- CrystalReader - Class in org.jmol.adapter.readers.xtal
-
A reader of OUT and OUTP files for CRYSTAL
http://www.crystal.unito.it/
- CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
-
- csfLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- CsfReader - Class in org.jmol.adapter.readers.quantum
-
CSF file reader based on CIF idea -- fluid property fields.
- CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
-
- CTRL - Static variable in class org.jmol.viewer.binding.Binding
-
- CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
-
- CTRL_MASK - Static variable in class org.jmol.api.Event
-
- CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
-
- cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- cubeCountX - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- cubeCountY - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- cubeCountZ - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- cubeFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- 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
-
- cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- cubeIterators - Variable in class org.jmol.bspt.Bspf
-
- CubeReader - Class in org.jmol.adapter.readers.simple
-
Gaussian cube file format
http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html
this is good because it is source code
http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c
http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
distances are in Bohrs because we are reading Gaussian cube OUTPUT files
not Gaussian cube INPUT files.
- CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
-
- CubeReader - Class in org.jmol.jvxl.readers
-
- CubeReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.CubeReader
-
- cubeVertexOffsets - Static variable in class org.jmol.util.BoxInfo
-
- cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
-
- cubeVertexOffsets - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- 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 - Variable in class org.jmol.viewer.ActionManager
-
- 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
-
- currentCompnd - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- currentCursor - Variable in class org.jmol.viewer.Viewer
-
- currentDipole - Variable in class org.jmol.shapespecial.Dipoles
-
- currentDirection - Variable in class org.jmol.viewer.AnimationManager
-
- 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.jmolpanel.AtomSetChooser
-
- currentKey - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- currentlocalpath - Static variable in class org.jmol.script.Token
-
- currentlyRendering - Variable in class org.jmol.g3d.Graphics3D
-
- currentlyRendering() - Method in class org.jmol.g3d.Graphics3D
-
- currentMenuItemId - Variable in class org.jmol.popup.SimplePopup
-
- 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.AnimationManager
-
- currentNormalOrigin - Variable in class org.jmol.export._ObjExporter
-
Wavefront OBJ refers to vertices and normals and textures by their location
in the file.
- currentObject - Variable in class org.jmol.shape.Object2dShape
-
- currentPalette - Variable in class org.jmol.util.ColorEncoder
-
- currentPoints - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- currentProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- currentResno - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
-
- currentShadeIndex - Variable in class org.jmol.g3d.Graphics3D
-
- currentShapeID - Variable in class org.jmol.viewer.Viewer
-
- currentShapeState - Variable in class org.jmol.viewer.Viewer
-
- currentSize - Variable in class org.jmol.export.dialog.FilePreview.FPPanel
-
- currentSize - Variable in class org.openscience.molecularplayground.MPJmolApp.KioskPanel
-
- currentStep - Variable in class org.jmol.minimize.forcefield.ForceField
-
- currentTextureOrigin - Variable in class org.jmol.export._ObjExporter
-
Wavefront OBJ refers to vertices and normals and textures by their location
in the file.
- currentThread - Variable in class org.jmol.script.ScriptEvaluator
-
- currentTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
-
- currentVertexOrigin - Variable in class org.jmol.export._ObjExporter
-
Wavefront OBJ refers to vertices and normals and textures by their location
in the file.
- cursor - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog.PageLoader
-
- cursor - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
-
- cursor - Variable in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog.PageLoader
-
- CURSOR_CROSSHAIR - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_DEFAULT - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_HAND - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_MOVE - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_WAIT - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_ZOOM - Static variable in class org.jmol.viewer.JmolConstants
-
- cursorPos - Variable in class org.jmol.util.CommandHistory
-
Current position of the cursor;
- curve - Static variable in class org.jmol.script.Token
-
- curx - Variable in class org.jmol.export.image.GifEncoder
-
- cury - Variable in class org.jmol.export.image.GifEncoder
-
- CUSTOM - Static variable in class org.jmol.util.ColorEncoder
-
- CUT - Static variable in class org.jmol.quantum.MOCalculation
-
- cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- cutoff - Variable in class org.jmol.jvxl.data.JvxlData
-
- cutoff - Variable in class org.jmol.jvxl.readers.Parameters
-
- cutoff - Static variable in class org.jmol.script.Token
-
- cutoff - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- cutoffAutomatic - Variable in class org.jmol.jvxl.readers.Parameters
-
- cutoffRange - Variable in class org.jmol.shapesurface.Isosurface
-
- cx - Variable in class org.jmol.bspt.CubeIterator
-
- CX - Variable in class org.jmol.quantum.MOCalculation
-
- cxyz - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- 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
-
- cylinder - Static variable in class org.jmol.script.Token
-
- 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
-
- cylinderMatrix - Variable in class org.jmol.export._IdtfExporter
-
- cylinderNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- cz - Variable in class org.jmol.bspt.CubeIterator
-
- CZ - Variable in class org.jmol.quantum.MOCalculation
-
- F_ADDRESS_BITS_PER_WORD - Static variable in class org.jmol.util.FastBitSet
-
miguel 8 Feb 2010
Below are implementations of bitmap functionality on top of arrays.
- F_BIT_INDEX_MASK - Static variable in class org.jmol.util.FastBitSet
-
- F_BITS_PER_WORD - Static variable in class org.jmol.util.FastBitSet
-
- F_INT_ALL_BITS_SET - Static variable in class org.jmol.util.FastBitSet
-
- FACE_COUNT_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
-
- facecenteroffset - Static variable in class org.jmol.script.Token
-
- 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.shapespecial.DotsRenderer
-
- facePoints - Static variable in class org.jmol.util.BoxInfo
-
- facePt1 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
-
- facePt2 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
-
- facePt3 - Variable in class org.jmol.shapespecial.GeoSurfaceRenderer
-
- faces - Variable in class org.jmol.export.MeshData.Data
-
- faceVertexesArrays - Static variable in class org.jmol.geodesic.Geodesic
-
- faceVertexesIcosahedron - Static variable in class org.jmol.geodesic.Geodesic
-
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right
-- Bob Hanson, 1/5/2010
slater scaling based on zeta, n, l, and x y z exponents.
- fact - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- fact1 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
-
- factoredLengths - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- factorType - Variable in class org.jmol.atomdata.RadiusData
-
- FALSE - Static variable in class org.jmol.viewer.SelectionManager
-
- falsifyMesh() - Method in class org.jmol.shapebio.BioShape
-
- falsifyNearbyMesh(int) - Method in class org.jmol.shapebio.BioShape
-
- FastBitSet - Class in org.jmol.util
-
- FastBitSet() - Constructor for class org.jmol.util.FastBitSet
-
- FastBitSet(int) - Constructor for class org.jmol.util.FastBitSet
-
- FastBitSet(FastBitSet) - Constructor for class org.jmol.util.FastBitSet
-
- 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(float) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- 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
-
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
-
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
-
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
-
- fcoord(Tuple3f) - Method in interface org.jmol.api.SymmetryInterface
-
- fcoord(Tuple3f) - Method in class org.jmol.symmetry.Symmetry
-
- fcoord(Tuple3f) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- fd_oldFileName - Variable in class org.jmol.export.JmolFileDropper
-
- FD_PROPERTY_INLINE - Static variable in class org.jmol.export.JmolFileDropper
-
- fd_propSupport - Variable in class org.jmol.export.JmolFileDropper
-
- fdup(String, int, int) - Static method in class org.jmol.util.TextFormat
-
fdup duplicates p or q formats for formatCheck
and the format() function.
- 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.jmolpanel.AtomSetChooser
-
- fFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
-
- 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
-
- ffTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
-
- 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.quantum.CsfReader
-
- fieldCount - Variable in class org.jmol.util.CifDataReader
-
- 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.quantum.CsfReader
-
- file - Variable in class org.jmol.export.history.HistoryFile
-
The location of the history file.
- file() - Method in class org.jmol.script.ScriptEvaluator
-
- file - Static variable in class org.jmol.script.Token
-
- file - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- fileButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- FileButton - Variable in class org.openscience.jmol.app.webexport.Test
-
- filecachedirectory - Static variable in class org.jmol.script.Token
-
- filecaching - Static variable in class org.jmol.script.Token
-
- FileChooser - Class in org.jmol.export.dialog
-
JFileChooser with possibility to fix size and location
- FileChooser() - Constructor for class org.jmol.export.dialog.FileChooser
-
- fileChooser - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- fileCoordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- fileDotModel - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- fileField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- fileHasUnitCell - Variable in class org.jmol.popup.SimplePopup
-
- fileHeader - Variable in class org.jmol.modelset.ModelLoader
-
- fileHeader - Variable in class org.jmol.util.CifDataReader
-
- 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.jmolpanel.RecentFilesDialog
-
- FileManager - Class in org.jmol.viewer
-
- FileManager(Viewer) - Constructor for class org.jmol.viewer.FileManager
-
- fileManager - Variable in class org.jmol.viewer.Viewer
-
- FileManager.ArrayDataReader - Class in org.jmol.viewer
-
ArrayDataReader subclasses BufferedReader and overrides its
read, readLine, mark, and reset methods so that JmolAdapter
works with String[] arrays without any further adaptation.
- FileManager.ArrayDataReader(String[]) - Constructor for class org.jmol.viewer.FileManager.ArrayDataReader
-
- FileManager.DataReader - Class in org.jmol.viewer
-
Just a simple abstract class to join a String reader and a String[]
reader under the same BufferedReader umbrella.
- FileManager.DataReader(Reader) - Constructor for class org.jmol.viewer.FileManager.DataReader
-
- FileManager.DOMReader - Class in org.jmol.viewer
-
- FileManager.DOMReader(Object, Map<String, Object>) - Constructor for class org.jmol.viewer.FileManager.DOMReader
-
- FileManager.Encoding - Enum in org.jmol.viewer
-
- FileManager.Encoding() - Constructor for enum org.jmol.viewer.FileManager.Encoding
-
- FileManager.EnumFileStatus - Enum in org.jmol.viewer
-
- FileManager.EnumFileStatus(int) - Constructor for enum org.jmol.viewer.FileManager.EnumFileStatus
-
- FileManager.FileReader - Class in org.jmol.viewer
-
- FileManager.FileReader(String, String, String, String, BufferedReader, Map<String, Object>, boolean) - Constructor for class org.jmol.viewer.FileManager.FileReader
-
- FileManager.FilesReader - Class in org.jmol.viewer
-
open a set of models residing in different files
- FileManager.FilesReader(String[], String[], String[], FileManager.DataReader[], Map<String, Object>, boolean) - Constructor for class org.jmol.viewer.FileManager.FilesReader
-
- FileManager.StringDataReader - Class in org.jmol.viewer
-
- FileManager.StringDataReader(String) - Constructor for class org.jmol.viewer.FileManager.StringDataReader
-
- FileManager.VectorDataReader - Class in org.jmol.viewer
-
VectorDataReader subclasses BufferedReader and overrides its
read, readLine, mark, and reset methods so that JmolAdapter
works with Vector arrays without any further adaptation.
- FileManager.VectorDataReader(List<String>) - Constructor for class org.jmol.viewer.FileManager.VectorDataReader
-
- FileMolOnly - Variable in class org.jmol.popup.SimplePopup
-
- fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- fileName - Variable in class org.jmol.atomdata.AtomData
-
- filename - Variable in class org.jmol.console.ScriptEditor
-
- 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.MsmsReader
-
- fileName - Variable in class org.jmol.jvxl.readers.Parameters
-
- filename - Variable in class org.jmol.script.ScriptCompiler
-
- filename - Variable in class org.jmol.script.ScriptContext
-
- filename - Variable in class org.jmol.script.ScriptEvaluator
-
- fileName - Variable in class org.jmol.viewer.FileManager
-
- fileName - Variable in class org.jmol.viewer.ModelManager
-
- fileNameIn - Variable in class org.jmol.viewer.FileManager.FileReader
-
- fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- fileOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- 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.FPPanel - Class in org.jmol.export.dialog
-
- FilePreview.FPPanel(JmolAdapter, String) - Constructor for class org.jmol.export.dialog.FilePreview.FPPanel
-
- FileReader - Class in org.openscience.jvxl
-
- FileReader() - Constructor for class org.openscience.jvxl.FileReader
-
- files - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- fileStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- fileTypeIn - Variable in class org.jmol.viewer.FileManager.FileReader
-
- fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- FileTyper - Class in org.openscience.jmol.app.jmolpanel
-
- FileTyper() - Constructor for class org.openscience.jmol.app.jmolpanel.FileTyper
-
- fileTypesIn - Variable in class org.jmol.viewer.FileManager.FilesReader
-
- FileUnitOnly - Variable in class org.jmol.popup.SimplePopup
-
- fileWriter(File, JList) - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- fill - Static variable in class org.jmol.script.Token
-
- fillArc - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
-
- fillAtomData(AtomData, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- fillAtomData(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
-
- fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelCollection
-
- fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
-
- fillConeSceen(byte, int, Point3f, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillConeSceen(byte, int, Point3f, Point3f) - Method in class org.jmol.export.Export3D
-
- fillConeSceen(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
-
- fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillConeScreen(short, byte, int, Point3f, Point3f, boolean) - Method in class org.jmol.export.___Exporter
-
- fillConeScreen(short, byte, int, Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
-
- fillConeScreen(short, byte, int, Point3f, Point3f, boolean) - Method in class org.jmol.export.__RayTracerExporter
-
- fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in class org.jmol.export.Export3D
-
- fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in class org.jmol.g3d.Graphics3D
-
- fillConicalCylinder(Point3f, Point3f, int, short, byte) - Method in class org.jmol.export.__RayTracerExporter
-
- fillConicalCylinder(Point3f, Point3f, int, short, byte) - Method in class org.jmol.export._TachyonExporter
-
- fillCsfArray(String, String[], int, Object) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- fillCylinder(short, short, 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(short, short, 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.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
-
- fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillCylinderScreen(byte, int, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillCylinderScreen(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.___Exporter
-
- fillCylinderScreen(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__CartesianExporter
-
- fillCylinderScreen(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__RayTracerExporter
-
- fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
-
- fillCylinderScreen(byte, int, Point3i, Point3i) - Method in class org.jmol.export.Export3D
-
- fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- fillCylinderScreen(byte, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- fillCylinderScreenMad(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.___Exporter
-
- fillCylinderScreenMad(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__CartesianExporter
-
- fillCylinderScreenMad(short, byte, int, Point3f, Point3f) - Method in class org.jmol.export.__RayTracerExporter
-
- fillDataBlock(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills an array with a predefined number of lines of data that is
arranged in fixed FORTRAN-like column format
- fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills an array with a pre-defined number of lines of token data,
skipping blank lines in the process
- fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillEllipsoid(Point3f, Point3f[], short, int, int, int, int, Matrix3f, double[], Matrix4f, Point3i[]) - Method in class org.jmol.export.___Exporter
-
- fillEllipsoid(Point3f, Point3f[], short, int, int, int, int, Matrix3f, double[], Matrix4f, Point3i[]) - Method in class org.jmol.export.__CartesianExporter
-
- fillEllipsoid(Point3f, Point3f[], short, int, int, int, int, Matrix3f, double[], Matrix4f, Point3i[]) - Method in class org.jmol.export.__RayTracerExporter
-
- fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.export.Export3D
-
- fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.g3d.Graphics3D
-
- fillFace(short, Point3i, Point3i, Point3i) - Method in class org.jmol.shapespecial.PolyhedraRenderer
-
- fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills a float array with string data from a file
- fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Extracts a block of frequency data from a file.
- fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
-
- 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, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
-
- fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
-
- fillOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- 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
- fillSphere(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphere(int, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphere(int, Point3f) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphere(short, int, Point3f) - Method in class org.jmol.export.___Exporter
-
- fillSphere(short, int, Point3f) - Method in class org.jmol.export.__CartesianExporter
-
- fillSphere(short, int, Point3f) - Method in class org.jmol.export.__RayTracerExporter
-
- fillSphere(int, int, int, int) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphere(int, Point3i) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphere(int, Point3f) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphere(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillSphere(int, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillSphere(int, Point3f) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - 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, short, short, Point3i, short, short, Point3i, short, short, float) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillTriangle(short, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.export.___Exporter
-
- fillTriangle(short, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
-
- fillTriangle(short, Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.export.__RayTracerExporter
-
- fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short) - 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(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(Point3i, short, short, Point3i, short, short, Point3i, short, short) - 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
-
- fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
- fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
-
- fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filter - Variable in class org.jmol.export.image.PngEncoder
-
- filter - Static variable in class org.jmol.script.Token
-
- filter1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filter2 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- 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
-
- filterAltLoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterAtom(Atom, int) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- filterAtom(Atom, int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterAtomType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterChain - Variable 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
-
- filterElement - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterEveryNth - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterGroup3 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterIsNot - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- filterN - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- filterSub(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
-
Perform "sub" filtering on the given row.
- filterTokens - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- filterUp(byte[], int, int) - Method in class org.jmol.export.image.PngEncoder
-
Perform "up" filtering on the given row.
- fin() - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- 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
-
- finalizeHydrogens() - Method in interface org.jmol.api.JmolBioResolver
-
- finalizeHydrogens() - Method in class org.jmol.modelsetbio.Resolver
-
- finalizeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- 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.JmolRendererInterface
-
- finalizeOutput() - Method in class org.jmol.export.___Exporter
-
- finalizeOutput() - Method in class org.jmol.export._IdtfExporter
-
- finalizeOutput() - Method in class org.jmol.export._ObjExporter
-
- finalizeOutput() - Method in class org.jmol.export._PovrayExporter
-
- finalizeOutput() - Method in class org.jmol.export.Export3D
-
- finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
-
- finalizePdbCharges() - Method in class org.jmol.modelsetbio.Resolver
-
- finalizePdbMultipleBonds() - Method in class org.jmol.modelsetbio.Resolver
-
- finalizeReader() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.more.P2nReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- finalizeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- finalizeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- finalizeShapes() - Method in class org.jmol.modelset.ModelLoader
-
- finalizeTrajectory(List<Point3f[]>, List<Vector3f[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- finalizeTrajectory() - 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(String, String, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- find(List<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
-
- find - Static variable in class org.jmol.script.Token
-
- find(Measurement) - Method in class org.jmol.shape.Measures
-
- find(String, String, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
-
Searches for all matches of a pattern within a SMILES string.
- find(String, SmilesSearch, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
-
- findAdditionalAxes(int) - Method in class org.jmol.symmetry.PointGroup
-
- findApplets(String, String, String, List<String>) - Static method in class org.jmol.applet.JmolAppletRegistry
-
- findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
-
- findAtomsInRectangle(Rectangle, BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- findAtomsInRectangle(Rectangle) - Method in class org.jmol.viewer.Viewer
-
- findAxis(Point3f[], int, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- 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
-
- 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
-
- findEdge(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- findElementsPresent() - Method in class org.jmol.modelset.ModelLoader
-
- findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Have the viewer show a particular frame with frequencies
if it can be found.
- findHelixes(int[][][], int, BitSet, char[], boolean, boolean, List<Bond>, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
-
(p.
- findHelixes(int, int[][][], int, EnumStructure, int, BitSet, BitSet, char[], boolean, boolean, List<Bond>, BitSet) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- 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
-
- findMinMaxX(int) - Method in class org.jmol.g3d.Cylinder3D
-
- findMinMaxY() - Method in class org.jmol.g3d.Cylinder3D
-
- findNearestAtom(int, int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
-
- findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
-
- findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- findNearestAtomIndex(int, int, BitSet) - 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, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
-
- findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
-
- 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[], BitSet) - Method in class org.jmol.shape.Shape
-
- findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.shapebio.BioShape
-
- findNearestAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
-
- findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
-
- findNearestAtomIndex(int, int, boolean) - Method in class org.jmol.viewer.Viewer
-
- findNearestLabel(int, int) - Method in class org.jmol.shape.Labels
-
- findNearestShapeAtomIndex(int, int, Atom[], BitSet) - Method in class org.jmol.viewer.ShapeManager
-
- findNearestThreePoints(float, float, float[][], int[]) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- findNotAttached(int, int[][], int[], int) - Method in class org.jmol.modelset.AtomCollection
-
- 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
-
- findString - Variable in class org.jmol.jvxl.readers.KinemageReader
-
- findValue(int, int, boolean, BitSet) - Method in class org.jmol.shapesurface.Isosurface
-
- finish() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- finish() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
- finish(Object) - Method in class org.jmol.api.JmolAdapter
-
- first - Variable in class org.jmol.modelset.TickInfo
-
- first - Static variable in class org.jmol.script.Token
-
- firstAtom - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
-
- firstAtomIndex - Variable in class org.jmol.modelset.Group
-
- firstAtomIndex - Variable in class org.jmol.modelset.Model
-
- firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
-
- firstAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
-
- firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
-
- firstChar - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- firstFrameDelay - Variable in class org.jmol.viewer.AnimationManager
-
- firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
-
- firstIsotope - Static variable in class org.jmol.util.Elements
-
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
- firstLastStep - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- firstMatchOnly - Variable in class org.jmol.smiles.SmilesSearch
-
- firstModelIndex - Variable in class org.jmol.atomdata.AtomData
-
- firstModelIndex - Variable in class org.jmol.viewer.AnimationManager
-
Animation support
- firstMoleculeIndex - 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
-
- fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
-
- fixChime(String, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
-
- fixChirality(SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
-
- fixDataString(String) - Static method in class org.jmol.util.Parser
-
- fixed() - Method in class org.jmol.script.ScriptEvaluator
-
- fixed - Static variable in class org.jmol.script.Token
-
- fixedCount - Variable in class org.jmol.jvxl.readers.PmeshReader
-
- fixedOrigin - Variable in class org.jmol.shape.Axes
-
- fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
-
- fixedRotationCenter - Variable in class org.jmol.export.___Exporter
-
- fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
-
- fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
-
- fixedtemp - Static variable in class org.jmol.script.Token
-
- fixedTranslation - Variable in class org.jmol.viewer.TransformManager
-
- fixFileName(File) - Method in class org.openscience.chimetojmol.ChimePanel
-
- fixFileNames(String, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
-
- fixFileNames(String, String, char) - Method in class org.openscience.chimetojmol.ChimePanel
-
- fixFileNameVariables(String, String) - Static method in class org.jmol.viewer.FileManager
-
- 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, BitSet) - Method in class org.jmol.modelset.Chain
-
- fixIndices(int, BitSet) - Method in class org.jmol.modelset.Group
-
- fixIndices(int, int, BitSet) - Method in class org.jmol.modelset.Model
-
- fixInlineString(String, char) - Method in class org.jmol.viewer.Viewer
-
- fixLabel(Atom, String) - Method in class org.jmol.shape.HoverRenderer
-
- fixModelSpec(Token) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- fixName(String) - Static method in class org.jmol.util.ColorEncoder
-
- fixOrbitalType() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- fixPath(String) - Static method in class org.jmol.viewer.FileManager
-
- fixPeriodic(Point3f, Point3f) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
-
- fixPoint(float, float) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
-
- fixQ(Quaternion) - Method in class org.jmol.util.Quaternion
-
- fixScript(String, String) - Method in class org.jmol.popup.SimplePopup
-
- fixScriptPath(String, String) - Method in class org.jmol.script.ScriptEvaluator
-
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- fixString(String) - Static method in class org.jmol.util.Escape
-
- fixTag(String) - Method in class org.jmol.adapter.readers.quantum.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, Map<String, Object>) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- fixUnicode(String[], int) - Static method in class org.jmol.viewer.FileManager
-
- fixUnits(String) - Static method in class org.jmol.modelset.Measurement
-
- fixValue(float, String, boolean) - Method in class org.jmol.modelset.Measurement
-
- fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- FLAG_CANINCREMENT - Static variable in class org.jmol.script.ScriptVariable
-
- FLAG_LOCALVAR - Static variable in class org.jmol.script.ScriptVariable
-
- FLAG_MASK - Static variable in class org.jmol.modelset.Atom
-
- FLAG_OFFSET - Static variable in class org.jmol.shape.Labels
-
- flags - Variable in class org.jmol.script.ScriptVariable
-
- FLAGS - Static variable in class org.jmol.shape.Labels
-
- flat - Static variable in class org.jmol.script.Token
-
- FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- flip(int) - Method in class org.jmol.util.FastBitSet
-
- flip(int, int) - Method in class org.jmol.util.FastBitSet
-
- flipLighting(int) - Method in class org.jmol.shape.Mesh
-
- fList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
-
- flistValue(Token, int) - Static method in class org.jmol.script.ScriptVariable
-
- floatArraySet(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- floatArraySet(int, int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- floatparam - Static variable in class org.jmol.script.Token
-
- floatParameter(int, float, float) - Method in class org.jmol.script.ScriptEvaluator
-
- floatParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
process a general string or set of parameters as an array of floats,
allowing for relatively free form input
- floatproperty - Static variable in class org.jmol.script.Token
-
- floatRange - Variable in class org.jmol.shapebio.BioShape
-
- floatSetting(int) - Method in class org.jmol.script.ScriptEvaluator
-
- floatValue() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- flowCommand - Static variable in class org.jmol.script.Token
-
- flowContext - Variable in class org.jmol.script.ScriptCompiler
-
- flowControl(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- flush(Object) - Static method in class org.jmol.awt.Image
-
- 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.g3d.Graphics3D
-
- flushImage(Object) - Method in interface org.jmol.api.ApiPlatform
-
- flushImage(Object) - Method in class org.jmol.awt.Platform
-
- flushQueue(String) - Method in class org.jmol.viewer.ScriptManager
-
- flushShades() - Static method in class org.jmol.g3d.Colix3D
-
- flushSphereCache() - Static method in class org.jmol.g3d.Sphere3D
-
- fmatSuperCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- fmt(int) - Method in class org.jmol.applet.Jmol
-
- fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- FoldingXyzReader - Class in org.jmol.adapter.readers.simple
-
This reader is for current.xyz files generated by Folding@Home project
(see
http://folding.stanford.edu)
I have not found a precise description of the file format.
- FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
-
- font - Variable in class org.jmol.applet.AppletWrapper
-
- Font - Class in org.jmol.awt
-
methods required by Jmol that access java.awt.Font
private to org.jmol.awt
- Font() - Constructor for class org.jmol.awt.Font
-
- font - Variable in class org.jmol.g3d.Font3D
-
- font(int, float) - Method in class org.jmol.script.ScriptEvaluator
-
- font - Static variable in class org.jmol.script.Token
-
- font - Variable in class org.jmol.shape.Text
-
- Font3D - Class in org.jmol.g3d
-
Provides font support using a byte fid
(Font ID) as an index into font table.
- Font3D(ApiPlatform, byte, int, int, float, float, Object) - Constructor for class org.jmol.g3d.Font3D
-
- font3d - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- font3d - Variable in class org.jmol.shape.FontShape
-
- font3d - Variable in class org.jmol.shape.LabelsRenderer
-
- font3d - Variable in class org.jmol.shape.Measures
-
- 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.applet.AppletWrapper
-
- fontcaching - Static variable in class org.jmol.script.Token
-
- fontCaching - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- fontFace - Static variable in class org.jmol.applet.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.applet.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.applet.AppletWrapper
-
- fontMetrics - Variable in class org.jmol.g3d.Font3D
-
- fontScale - Variable in class org.jmol.shape.Text
-
- fontscaling - Static variable in class org.jmol.script.Token
-
- fontScaling - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- FontShape - Class in org.jmol.shape
-
- FontShape() - Constructor for class org.jmol.shape.FontShape
-
- fontSize - Variable in class org.jmol.applet.AppletWrapper
-
- fontSize - Variable in class org.jmol.g3d.Font3D
-
- fontsize - Static variable in class org.jmol.script.Token
-
- FONTSIZE - Static variable in class org.jmol.shape.Echo
-
- FONTSIZE - Static variable in class org.jmol.shape.Hover
-
- fontSizeDivisor - Static variable in class org.jmol.applet.AppletWrapper
-
- fontSizeNominal - Variable in class org.jmol.g3d.Font3D
-
- fontStringWidth(Object, String) - Method in interface org.jmol.api.ApiPlatform
-
- fontStringWidth(Object, String) - Method in class org.jmol.awt.Platform
-
- 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 - Static variable in class org.jmol.script.Token
-
- forceAutoBond - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- forceDisplay() - Method in class org.jmol.i18n.GT.Language
-
- forceEndIf - Variable in class org.jmol.script.ScriptFlowContext
-
- ForceField - Class in org.jmol.minimize.forcefield
-
- ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
-
- ForceFieldReader - Class in org.jmol.adapter.readers.more
-
- ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
-
- ForceFieldUFF - Class in org.jmol.minimize.forcefield
-
- ForceFieldUFF() - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
-
- forceFlowEnd(Token) - Method in class org.jmol.script.ScriptCompiler
-
- forceNoAddHydrogens - Variable in class org.jmol.script.ScriptEvaluator
-
- forcePlatformAWT - Static variable in class org.jmol.g3d.Platform3D
-
- forcmd - Static variable in class org.jmol.script.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.util.Elements
-
- FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
-
ionic radii are looked up using an array of shorts (16 bits each)
that contains the atomic number, the charge, and the radius in two
consecutive values, encoded as follows:
(atomicNumber << 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.script.Token
-
- formalChargeAndFlags - Variable in class org.jmol.modelset.Atom
-
- format(float, String, Tuple3f) - Method in class org.jmol.modelset.LabelToken
-
- format - Static variable in class org.jmol.script.Token
-
- format(float, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
-
- format(double, int, int, boolean, 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
-
- formatCheck(String) - Static method in class org.jmol.util.TextFormat
-
formatCheck checks p and q formats and duplicates if necessary
"%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
- formatDecimal(float, int) - Static method in class org.jmol.util.TextFormat
-
- formatDistance(String) - Method in class org.jmol.modelset.Measurement
-
- formatLabel(Viewer, Atom, String) - Static method in class org.jmol.modelset.LabelToken
-
- formatLabel(Viewer, Atom, LabelToken[], char, int[]) - Static method in class org.jmol.modelset.LabelToken
-
returns a formatted string based on the precompiled label tokens
- formatLabel(Viewer, Bond, LabelToken[], Map<String, Object>, int[]) - Static method in class org.jmol.modelset.LabelToken
-
- formatLabel(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
-
- formatMeasurement(String, String, boolean) - Method in class org.jmol.modelset.Measurement
-
- formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
-
- formats - Variable in class org.jmol.shape.Labels
-
- formatString(float, String, 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, double, 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
-
- forPoint3 - Variable in class org.jmol.script.ScriptCompiler
-
- forwardDCT(float[][]) - Static method in class org.jmol.util.DCT
-
- foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
-
- foundDistance2() - Method in class org.jmol.bspt.CubeIterator
-
After calling nextElement(), allows one to find out
the value of the distance squared.
- foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
- foundDuringLastSync - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- fourdots - Static variable in class org.jmol.shape.SticksRenderer
-
- fp8ShadeIndexUp - Variable in class org.jmol.g3d.Cylinder3D
-
- fps - Static variable in class org.jmol.script.Token
-
- fps - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- FPS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for the fps slider.
- fpsSlider - Variable in class org.openscience.jmol.app.jmolpanel.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
-
- fraction(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- fractionalOffset - Variable in class org.jmol.symmetry.UnitCell
-
- fractionalPoint - Variable in class org.jmol.script.ScriptEvaluator
-
- fractionalrelative - Static variable in class org.jmol.script.Token
-
- fractionalRelative - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- fractionData - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- fractionPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- fracx - Static variable in class org.jmol.script.Token
-
- fracxyz - Static variable in class org.jmol.script.Token
-
- fracy - Static variable in class org.jmol.script.Token
-
- fracz - Static variable in class org.jmol.script.Token
-
- frame(int) - Method in class org.jmol.script.ScriptEvaluator
-
- frame - Static variable in class org.jmol.script.Token
-
- frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- frameControl(int) - Method in class org.jmol.script.ScriptEvaluator
-
- frameOffset - Variable in class org.jmol.viewer.TransformManager
-
- frameOffsets - Variable in class org.jmol.viewer.TransformManager
-
- frameOffsets - Variable in class org.jmol.viewer.Viewer
-
- framePointer - Variable in class org.jmol.viewer.AnimationManager.AnimationThread
-
- framePointer2 - Variable in class org.jmol.viewer.AnimationManager.AnimationThread
-
- FramesOnly - Variable in class org.jmol.popup.SimplePopup
-
- frameStep - Variable in class org.jmol.viewer.AnimationManager
-
- frameTimeMillis - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- frameTitles - Variable in class org.jmol.modelset.ModelCollection
-
- frank(int) - Method in class org.jmol.script.ScriptEvaluator
-
- frank - Static variable in class org.jmol.script.Token
-
- Frank - Class in org.jmol.shape
-
- Frank() - Constructor for class org.jmol.shape.Frank
-
- frankAscent - Variable in class org.jmol.shape.Frank
-
- frankClicked(int, int) - Method in class org.jmol.viewer.ShapeManager
-
- frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
-
- frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
-
- frankDescent - Variable in class org.jmol.shape.Frank
-
- 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.SimplePopup
-
- 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
-
- freeEnum - Variable in class org.jmol.util.TempArray
-
- freeEnumSize - 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
-
- freeTempEnum(EnumStructure[]) - Method in class org.jmol.util.TempArray
-
- freeTempEnum(EnumStructure[]) - 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
-
- freezeModels() - Method in class org.jmol.modelset.ModelCollection
-
- freqAtom0 - Variable in class org.jmol.adapter.readers.simple.AmpacReader
-
- fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- from - Static variable in class org.jmol.script.Token
-
- 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.script.Token
-
- FRONT_FLAG - Static variable in class org.jmol.shape.Labels
-
- frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- frontedges - Static variable in class org.jmol.script.Token
-
- frontlit - Static variable in class org.jmol.script.Token
-
- frontonly - Static variable in class org.jmol.script.Token
-
- frontOnly - Variable in class org.jmol.shape.Mesh
-
- frontOnly - Variable in class org.jmol.shape.MeshRenderer
-
- frontOnly - Variable in class org.jmol.shapespecial.PolyhedraRenderer
-
- frontonly - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
-
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
-
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
-
- fset0 - Variable in class org.jmol.shape.UccageRenderer
-
- fSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
-
- full - Static variable in class org.jmol.script.Token
-
- fullCommand - Variable in class org.jmol.script.ScriptEvaluator
-
- fullCommand - Variable in class org.jmol.shapesurface.LcaoCartoon
-
- fullCubePolygon - Static variable in class org.jmol.util.TriangleData
-
- fullName - Variable in class org.jmol.applet.Jmol
-
- fullName - Variable in class org.jmol.viewer.Viewer
-
- fullpath - Variable in class org.jmol.script.ScriptContext
-
- fullPathName - Variable in class org.jmol.viewer.FileManager
-
- fullPathName - Variable in class org.jmol.viewer.ModelManager
-
- fullPathNameIn - Variable in class org.jmol.viewer.FileManager.FileReader
-
- fullPathNamesIn - Variable in class org.jmol.viewer.FileManager.FilesReader
-
- fullplane - Static variable in class org.jmol.script.Token
-
- fullTrim(String) - Method in class org.jmol.util.CifDataReader
-
specially for names that might be multiline
- fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
-
- fullylit - Static variable in class org.jmol.script.Token
-
- func - Variable in class org.jmol.jvxl.readers.IsoFxyReader
-
- func - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
-
- func - Variable in class org.jmol.jvxl.readers.Parameters
-
- function() - Method in class org.jmol.script.ScriptEvaluator
-
- function - Variable in class org.jmol.script.ScriptFlowContext
-
- function - Static variable in class org.jmol.script.Token
-
- functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
-
- functionName - Variable in class org.jmol.script.ScriptContext
-
- functionName - Variable in class org.jmol.script.ScriptEvaluator
-
- functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
-
for isosurface FUNCTIONXY
- functionXY(String, int, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- functionxy - Static variable in class org.jmol.script.Token
-
- 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.jmolpanel.StatusListener
-
this is just a test method for isosurface FUNCTIONXY
- functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
-
for isosurface FUNCTIONXYZ
- functionXYZ(String, int, int, int) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- functionxyz - Static variable in class org.jmol.script.Token
-
- functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.StatusManager
-
- functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
-
- functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
-
- fux - Static variable in class org.jmol.script.Token
-
- fuxyz - Static variable in class org.jmol.script.Token
-
- fuy - Static variable in class org.jmol.script.Token
-
- fuz - Static variable in class org.jmol.script.Token
-
- fValue(Token) - Static method in class org.jmol.script.ScriptVariable
-
- 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.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.ShapeManager
-
- 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.quantum
-
- GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
-
- gamessUKContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- GamessUKReader - Class in org.jmol.adapter.readers.quantum
-
- GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
-
- gamessUSContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- GamessUSReader - Class in org.jmol.adapter.readers.quantum
-
- GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
-
- gamma - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
-
- gamma - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- gamma - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- gamma - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- gamma - Variable in class org.jmol.jvxl.readers.MapFileReader
-
- gamma - Variable in class org.jmol.util.SimpleUnitCell
-
- gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- gaussianContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
-
- gaussianCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
-
- GaussianDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
-
- GaussianReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian 94/98/03/09 output files.
- GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
-
- gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
-
- gaussians - Variable in class org.jmol.quantum.MOCalculation
-
- GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian Wfn files -- not implemented yet
- GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
-
- generalResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- generateAllOperators(HallInfo) - Method in class org.jmol.symmetry.SpaceGroup
-
- generateBaseEllipse() - Method in class org.jmol.g3d.Cylinder3D
-
- generateBaseEllipsePrecisely(boolean) - Method in class org.jmol.g3d.Cylinder3D
-
- generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- generateCube() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- 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.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.script.ScriptCompilationTokenParser
-
- generateSolventCavity() - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- generateSolventCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- generateSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- generateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- GenNBOReader - Class in org.jmol.adapter.readers.quantum
-
NBO file nn reader will pull in other files as necessary
acknowledgments: Grange Hermitage, Frank Weinhold
- GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
-
- 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_DISTANCE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- geomBondFields - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- geomOpt - Variable in class org.jmol.adapter.readers.xtal.DmolReader
-
- geosurface - Static variable in class org.jmol.script.Token
-
- GeoSurface - Class in org.jmol.shapespecial
-
- GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
-
- GeoSurfaceRenderer - Class in org.jmol.shapespecial
-
- GeoSurfaceRenderer() - Constructor for class org.jmol.shapespecial.GeoSurfaceRenderer
-
- gestureServer - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
- gestureswipefactor - Static variable in class org.jmol.script.Token
-
- gestureSwipeFactor - Variable in class org.jmol.viewer.ActionManager
-
- get(int) - Method in class org.jmol.util.FastBitSet
-
- get(int) - Method in class org.jmol.util.Int2IntHash
-
- get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
-
- get2SidedNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Graphics3D
-
- get2SidedNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Normix3D
-
- get3dContour(List<Object>, float, short) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- get3dProjection(Vector3f) - Method in class org.jmol.util.Quaternion
-
- get3DStraightness(String, Quaternion, Quaternion) - Static method in class org.jmol.modelsetbio.BioPolymer
-
- getAction() - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Fetch the action that was created for the given
command.
- getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
-
- getActionName(int) - Static method in class org.jmol.viewer.ActionManager
-
- getActions() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- getActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- getActions() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- getAdapterName() - Method in class org.jmol.api.JmolAdapter
-
- getAdditionalHydrogens(BitSet, boolean, boolean, List<Atom>) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getAllCifData() - Method in class org.jmol.util.CifDataReader
-
reads all Cif Data for a reader defined in the constructor
- getAllData() - Method in class org.jmol.util.CompoundDocument
-
- getAllData(String, String, Map<String, String>) - Method in class org.jmol.util.CompoundDocument
-
reads a compound document directory and saves all data in a Hashtable
so that the files may be organized later in a different order.
- getAllData(String, String) - Method in class org.jmol.util.CompoundDocument
-
- getAllData(InputStream, String[], String, String, Map<String, String>) - Static method in class org.jmol.util.ZipUtil
-
reads a ZIP file and saves all data in a Hashtable
so that the files may be organized later in a different order.
- getAllInfo() - Method in class org.jmol.shape.Measures
-
- getAllInfoAsString() - Method in class org.jmol.shape.Measures
-
- getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
-
- getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
-
- getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
- getAllowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
-
- getAllowGestures() - 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
-
- getAllProperties(ScriptVariable, String) - Method in class org.jmol.script.ScriptMathProcessor
-
- 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
-
- getAmbientPercent() - Static method in class org.jmol.g3d.Graphics3D
-
- getAminoAcidValenceAndCharge(String, String, int[]) - Static method in class org.jmol.viewer.JmolConstants
-
returns an array if we have special hybridization or charge
- getAnglefromZ() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
-
- getAngles() - Method in class org.jmol.minimize.Minimizer
-
- getAngleUnits() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getAngleUnitsList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- 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.AnimationManager
-
- getAnimationInfo() - Method in class org.jmol.viewer.Viewer
-
- getAnimationReplayMode() - Method in class org.jmol.viewer.Viewer
-
- getAnisoBorU(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getApiPlatform() - Method in class org.jmol.viewer.Viewer
-
- getAppConsole(JmolViewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
-
- getAppConsole(JmolViewer) - Method in class org.jmol.console.AppletConsole
-
don't delete! used by Viewer after it gets the class by name
- getAppConsole(JmolViewer) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
don't delete! used by Viewer after it gets the class by name
- getAppendNew() - Method in class org.jmol.viewer.Viewer
-
- getAppletContext() - 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.AppletWrapper
-
- getAppletInfo() - Method in class org.jmol.applet.Jmol
-
- getAppletInfo() - Method in interface org.jmol.applet.WrappedApplet
-
- getAppletInfo() - Method in class org.jmol.viewer.Viewer
-
- getAppletPath(boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getApplicationInterface(String) - Static method in class org.jmol.api.Interface
-
- 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(short) - Static method in class org.jmol.g3d.Graphics3D
-
- getArgb() - Method in class org.jmol.g3d.Rgb16
-
- getArgb(float) - Method in class org.jmol.util.ColorEncoder
-
- getArgbFromPalette(float, float, float, int) - 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
[red,green,blue] or a valid JavaScript color
- getArgbGreyscale(short) - Static method in class org.jmol.g3d.Colix3D
-
- getArgbHbondType(int) - Static method in class org.jmol.util.JmolEdge
-
- getArgbParam(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getArgbParam(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getAromaticDottedBondMask() - Method in class org.jmol.shape.SticksRenderer
-
- getAscent(Object) - Static method in class org.jmol.awt.Font
-
- getAscent() - Method in class org.jmol.g3d.Font3D
-
- 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
-
- 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
-
- 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.script.ScriptEvaluator
-
- getAtomBits(int, Object) - Method in class org.jmol.viewer.Viewer
-
- getAtomBitSet(ScriptEvaluator, Object) - Static method in class org.jmol.script.ScriptEvaluator
-
a general method to evaluate a string representing an atom set.
- getAtomBitSet(ScriptEvaluator, Object) - Method in class org.jmol.viewer.Viewer
-
- getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
-
- getAtomBitSetVector(ScriptEvaluator, int, Object) - Static method in class org.jmol.script.ScriptEvaluator
-
just provides a vector list of atoms in a string-based expression
- getAtomBitSetVector(Object) - Method in class org.jmol.viewer.Viewer
-
- getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.AtomCollection
-
general unqualified lookup of atom set type
- getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.BondCollection
-
- getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelCollection
-
- 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
-
- getAtomCollectionReader(String, String, BufferedReader, Map<String, Object>, int) - Static method in class org.jmol.adapter.smarter.Resolver
-
the main method for reading files.
- getAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
- getAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the estimated number of atoms contained in the file.
- getAtomCount() - Method in class org.jmol.api.JmolViewer
-
- getAtomCount() - Method in class org.jmol.modelset.AtomCollection
-
- getAtomCount() - Method in class org.jmol.modelset.ModelLoader
-
- 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.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
-
- getAtomGroupQuaternions(BitSet, int, char) - Method in class org.jmol.modelset.ModelCollection
-
- getAtomGroupQuaternions(BitSet, int) - Method in class org.jmol.viewer.Viewer
-
- getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
-
- getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
-
- getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
-
- getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.JmolNode
-
- getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
-
- getAtomicCharges() - Method in class org.jmol.viewer.Viewer
-
- getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atomic mass of the atom.
- getAtomicMass(int) - Static method in class org.jmol.util.Elements
-
- getAtomicNumber(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
-
- getAtomicPotentials(boolean, BitSet, BitSet, String) - Method in class org.jmol.viewer.Viewer
-
- getAtomicPropertyState(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- getAtomicPropertyState(StringBuffer, byte, BitSet, String, float[]) - Method in class org.jmol.modelset.AtomCollection
-
- getAtomicPropertyState(StringBuffer, byte, BitSet, String, float[]) - Method in class org.jmol.viewer.Viewer
-
- getAtomID() - Method in class org.jmol.modelset.Atom
-
- getAtomIdentityInfo(int, Map<String, Object>) - Method in class org.jmol.modelset.ModelCollection
-
- getAtomIdentityInfo(int, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
- getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
-
- getAtomIndex1() - Method in class org.jmol.modelset.Bond
-
- getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
-
- getAtomIndex1() - Method in class org.jmol.util.JmolEdge
-
- getAtomIndex2() - Method in class org.jmol.modelset.Bond
-
- getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
-
- getAtomIndex2() - Method in class org.jmol.util.JmolEdge
-
- getAtomIndexFromAtomNumber(int, BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- getAtomIndexFromAtomNumber(int) - Method in class org.jmol.viewer.Viewer
-
- getAtomIndexFromPrimitiveIndex(int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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.
- getAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
-
- getAtomLabel(int, int, int, int, int, boolean, String) - Static method in class org.jmol.smiles.SmilesAtom
-
- 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
-
- getAtomMinMax(BitSet, BitSet[]) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- 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(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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() - Method in class org.jmol.smiles.SmilesAtom
-
- getAtomName() - Method in interface org.jmol.util.JmolNode
-
- 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.adapter.readers.more.MdTopReader
-
- 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
-
- getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
-
- 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
-
- getAtomPointVector(BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- getAtomPointVector(BitSet) - Method in class org.jmol.viewer.Viewer
-
- getAtomPropertiesLike(String) - Static method in class org.jmol.script.Token
-
- getAtomQuaternion(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, Atom, Quaternion, Point3f, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getAtomResidueInfo(StringBuffer, Atom) - Static method in class org.jmol.modelset.ModelCollection
-
- getAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getAtoms(BitSet, boolean, boolean, boolean, boolean, boolean, boolean, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- 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
-
- 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
-
- getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Create the AtomSetCollection and return it
- getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
-
- getAtomSetCollection(String, boolean, Map<String, Object>, StringBuffer) - Method in class org.jmol.viewer.Viewer
-
- getAtomSetCollectionAuxiliaryInfo() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- 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.
- getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Direct DOM HTML4 page reading; Egon was interested in this at one point.
- getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
- getAtomSetCollectionFromReader(String, String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
all in one -- for TestSmarterJmolAdapter
- getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
needed to consolidate a set of models into one model; could start
with AtomSetCollectionReader[] or with AtomSetCollection[]
- getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
- 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.
- getAtomSetCollectionOrBufferedReaderFromZip(InputStream, String, String[], Map<String, Object>, boolean, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
A rather complicated means of reading a ZIP file, which could be a
single file, or it could be a manifest-organized file, or it could be
a Spartan directory.
- getAtomSetCollectionOrBufferedReaderFromZip(InputStream, String, String[], Map<String, Object>, boolean, boolean) - Method in class org.jmol.api.JmolAdapter
-
- getAtomSetCollectionReader(String, String, BufferedReader, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
The primary file or string reader -- returns just the reader now
- getAtomSetCollectionReader(String, String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
Read an atomSetCollection object from a bufferedReader and close the reader.
- getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
primary for String[] or File[] reading -- two options
are implemented --- return a set of simultaneously open readers,
or return one single collection using a single reader
- getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
-
Associate a atomSetCollection object with an array of BufferedReader.
- 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.jmolpanel.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.
- getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
-
- getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
-
- getAtomSite() - Method in interface org.jmol.util.JmolNode
-
- getAtomsNearSurface(float, String) - Method in class org.jmol.script.ScriptEvaluator
-
- getAtomsWithin(float, Point4f) - Method in class org.jmol.modelset.AtomCollection
-
- getAtomsWithin(float, Point3f[], BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- getAtomsWithin(float, BitSet, boolean, RadiusData) - 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, BitSet, int) - Method in class org.jmol.modelset.ModelCollection
-
- getAtomsWithin(float, Point3f) - Method in class org.jmol.viewer.Viewer
-
- getAtomsWithin(float, Point3f[], BitSet) - Method in class org.jmol.viewer.Viewer
-
- getAtomsWithin(float, Point4f) - Method in class org.jmol.viewer.Viewer
-
- getAtomsWithin(float, BitSet, boolean, RadiusData) - 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
-
- getAtomType() - Method in class org.jmol.modelset.Atom
-
- getAtomTypes() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- 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
-
- getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
-
- getAtomUniqueID1() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
-
- getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapter.BondIterator
-
- getAtomUniqueID2() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
-
- getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapter.BondIterator
-
- getAtomVdwRadius(int, EnumVdw) - Method in class org.jmol.modelset.AtomCollection
-
- getAttached(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
-
- 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._IdtfExporter
-
- 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
-
- getAxesForEllipsoid(double[], Vector3f[], float[]) - Static method in class org.jmol.util.Quadric
-
- getAxesMode(int) - Static method in enum org.jmol.constant.EnumAxesMode
-
- 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() - 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
-
- 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
-
- getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
-
- getBackgroundArgb() - 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
-
- getBasePairBits(String) - Method in class org.jmol.modelset.ModelCollection
-
- getBasePairInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- getBaseRing6Points(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getBboxVertices() - Method in class org.jmol.modelset.ModelCollection
-
- getBboxVertices() - Method in class org.jmol.util.BoxInfo
-
- 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
-
- getBfactor100Hi() - Method in class org.jmol.viewer.Viewer
-
- getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
-
- getBFactors() - Method in class org.jmol.modelset.AtomCollection
-
- getBgColixes(short[]) - Method in interface org.jmol.api.JmolRendererInterface
-
- getBgColixes(short[]) - Method in class org.jmol.export.Export3D
-
- getBgColixes(short[]) - Method in class org.jmol.g3d.Graphics3D
-
- getBinaryStringForBytes(byte[]) - Static method in class org.jmol.util.ZipUtil
-
- getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
-
- getBindingInfo(String[], String) - Method in class org.jmol.viewer.binding.Binding
-
- getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
-
- getBindings() - Method in class org.jmol.viewer.binding.Binding
-
- 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
-
- getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
-
- getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
-
- getBioPolymerLength() - Method in class org.jmol.modelset.Group
-
- getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
-
- getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
-
- getBioSmiles(JmolNode[], int, BitSet, boolean, boolean, String) - Method in class org.jmol.smiles.SmilesGenerator
-
- getBioStructureTypeName(boolean) - Method in enum org.jmol.constant.EnumStructure
-
- getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
-
- getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
-
- getBioStructureTypeName() - Method in interface org.jmol.util.JmolNode
-
- getBitSet(ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- getBitsetIdent(BitSet, String, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getBitsetProperty(BitSet, int, Point3f, Point4f, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getBitsetPropertyFloat(BitSet, int, float, float) - Method in class org.jmol.script.ScriptEvaluator
-
- getBitsetPropertySelector(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getBitSets(SmilesSearch, boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
-
- 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.
- 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.modelset.Model
-
- getBondCount() - Method in class org.jmol.smiles.SmilesAtom
-
- 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
-
- getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
-
- getBondedAtomIndex(int) - Method in interface org.jmol.util.JmolNode
-
- getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
-
- getBondInfo(int) - Method in class org.jmol.modelset.ModelCollection
-
- getBondInfo(JmolAdapter, String, Object) - Method in class org.jmol.modelsetbio.Resolver
-
- getBondingRadiusFloat(short, int) - Static method in class org.jmol.api.JmolAdapter
-
- getBondingRadiusFloat() - Method in class org.jmol.modelset.Atom
-
- getBondingRadiusFloat(short, int) - Static method in class org.jmol.util.Elements
-
- getBondingRadiusFloat(int, int, short[]) - Static method in class org.jmol.util.Elements
-
- 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(int, BitSet) - Method in class org.jmol.modelset.BondCollection
-
- getBondIterator(BitSet) - Method in class org.jmol.modelset.BondCollection
-
- getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
-
- getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
- getBondList(Object) - Method in class org.jmol.api.JmolAdapter
-
- 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
-
- getBondNotTo(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
-
- getBondOrder(int) - Method in class org.jmol.api.JmolViewer
-
- getBondOrder(int) - Method in class org.jmol.modelset.BondCollection
-
- getBondOrder(float, float, float, float, float) - Static method in class org.jmol.modelset.BondCollection
-
- getBondOrder(int) - Method in class org.jmol.viewer.Viewer
-
- getBondOrderFromFloat(float) - Static method in class org.jmol.util.JmolEdge
-
- getBondOrderFromString(String) - Static method in class org.jmol.script.ScriptEvaluator
-
- getBondOrderFromString(String) - Static method in class org.jmol.util.JmolEdge
-
- getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.JmolEdge
-
- getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.JmolEdge
-
used for formatting labels and in the connect PARTIAL command
- getBondOrderString(int) - Static method in class org.jmol.smiles.SmilesBond
-
- 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(int, StringBuffer, int, int[], boolean) - 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
-
- getBondSelectionModeOr() - Method in class org.jmol.viewer.Viewer
-
- getBondsForSelectedAtoms(BitSet, boolean) - Method in class org.jmol.modelset.BondCollection
-
- getBondsForSelectedAtoms(BitSet) - Method in class org.jmol.viewer.Viewer
-
- getBondStereochemistry(JmolEdge, JmolNode) - Method in class org.jmol.smiles.SmilesGenerator
-
Retrieves the saved character based on the index of the bond.
- getBondTo(int) - Method in class org.jmol.minimize.MinAtom
-
- getBondTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesAtom
-
if atom is null, return bond TO this atom (bond.getAtom2() == this)
otherwise, return bond connecting this atom with
that atom
- 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
-
- getBoolean(boolean) - Static method in class org.jmol.script.ScriptVariable
-
- 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
-
- getBooleanValue(String, boolean) - Method in class org.jmol.applet.Jmol
-
- getBoundBox(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
-
- getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
-
- getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelCollection
-
- getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
-
- 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.api.JmolViewer
-
- getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelCollection
-
- getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
-
- getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
-
- getBoundBoxInfo() - Method in class org.jmol.modelset.ModelCollection
-
- getBoundBoxInfo() - Method in class org.jmol.util.BoxInfo
-
- 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.util.BoxInfo
-
- getBoundBoxVertices() - Method in class org.jmol.viewer.Viewer
-
- getBoundingBox() - Method in class org.jmol.shape.Mesh
-
- getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- getBox(int) - Method in class org.jmol.shape.Labels
-
- getBoxInfo(BitSet, float) - Method in class org.jmol.modelset.ModelCollection
-
- getBoxInfo(BitSet, float) - Method in class org.jmol.viewer.Viewer
-
- getBoxVec() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getBranch2dZ(int, int, BitSet, BitSet, Vector3f, Vector3f, Vector3f) - Method in class org.jmol.modelset.ModelLoader
-
- getBranchBitSet(JmolNode[], int, BitSet, List<BitSet>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
-
given a set of atoms, a subset of atoms to test, two atoms that start the
branch, and whether or not to allow the branch to cycle back on itself,
deliver the set of atoms constituting this branch.
- getBranchBitSet(int, int) - Method in class org.jmol.viewer.Viewer
-
- getBreakableContext(int) - Method in class org.jmol.script.ScriptFlowContext
-
- getBrickValue(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
-
- getBridge(int[][][][], int, int, int, int, List<AminoPolymer.Bridge>, Atom, Atom, AminoPolymer, AminoPolymer, List<Bond>, Map<String, Boolean>, boolean, Map<int[][], Boolean>) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
- getBridges(Polymer[], int[][][][], List<AminoPolymer.Bridge>, List<AminoPolymer.Bridge>, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, BitSet, List<Bond>, BitSet[]) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
(p.
- getBsIgnore() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getBsOK() - Method in class org.jmol.quantum.NciCalculation
-
grid-based discrete SCF calculation needs to know which
atoms to consider inter and which intramolecular
- 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
-
- getBsVoxels() - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- getBsVoxels() - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
-
- getBufferedInputStream(String) - Method in class org.jmol.viewer.FileManager
-
- getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
-
- getBufferedReader() - Method in class org.jmol.viewer.FileManager.DataReader
-
- getBufferedReaderForString(String) - Static method in class org.jmol.viewer.FileManager
-
- getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
-
- getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.viewer.FileManager.FilesReader
-
called by SmartJmolAdapter to request another buffered reader or binary document,
rather than opening all the readers at once.
- getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
-
- getBufferedReaderOrErrorMessageFromName(String, String[], boolean) - Method in class org.jmol.viewer.Viewer
-
- getBufferedReaderOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
-
- getBytes(Image) - Static method in class org.jmol.export.image.GifEncoder
-
- getBytes(Image, int) - Static method in class org.jmol.export.image.PngEncoder
-
- getBytes(Image, int, int) - Static method in class org.jmol.export.image.PngEncoder
-
- getBytes(Image) - Static method in class org.jmol.export.image.PpmEncoder
-
- getBytes(ApiPlatform, Object, int, String) - Static method in class org.jmol.util.JpegEncoder
-
- getBytes64(byte[]) - Static method in class org.jmol.util.Base64
-
- getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getC2() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getC4P() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getCachedLine() - Method in class org.jmol.g3d.Line3D
-
- getCallback(String) - Static method in enum org.jmol.constant.EnumCallback
-
- getCameraFactors() - Method in class org.jmol.viewer.TransformManager
-
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters
It also should serve as a valuable resource for anyone adapting Jmol and
wanting to know how the Jmol 11+ camera business works.
- getCameraFactors() - Method in class org.jmol.viewer.Viewer
-
- getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
-
- getCanonicalCopy(float) - Method in interface org.jmol.api.SymmetryInterface
-
- getCanonicalCopy(float) - Method in class org.jmol.symmetry.Symmetry
-
- getCanonicalCopy(float) - Method in class org.jmol.symmetry.UnitCell
-
- getCanonicalCopy(float) - Method in class org.jmol.util.BoxInfo
-
- getCanonicalCopy(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
-
- getCapOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
-
- getCapSlabObject(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getCapSlabObject(String, boolean) - Static method in class org.jmol.util.MeshSurface
-
legacy -- for some scripts with early isosurface slabbing
- getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
-
- getCarbonylOxygenAtom() - 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
-
- getCartoonBaseEdgesFlag() - Method in class org.jmol.viewer.Viewer
-
- 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
- getCenter() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getCenterAndPoints(List<BitSet[]>, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getCenterAndPoints(List<Point3f>) - Static method in class org.jmol.util.Measure
-
- getCenterAndPoints(List<BitSet[]>, boolean) - Method in class org.jmol.viewer.Viewer
-
- getCenters() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- 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
-
- getChainID() - Method in class org.jmol.smiles.SmilesAtom
-
- getChainID() - Method in interface org.jmol.util.JmolNode
-
- 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
-
- getChar(String, int) - Static method in class org.jmol.smiles.SmilesParser
-
- getCharge() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the charge of the atom.
- getCharges() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- getChemicalInfo(String, char) - Method in class org.jmol.viewer.Viewer
-
- 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.
- getChiralityClass(String) - Static method in class org.jmol.smiles.SmilesAtom
-
- getChiralOrder() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the chiral order of the atom.
- getCifData(int) - Method in class org.jmol.viewer.Viewer
-
- getCifLoopData() - Method in class org.jmol.util.CifDataReader
-
- getCircleData() - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a circle.
- getCircleResource() - Method in class org.jmol.export._IdtfExporter
-
- getClickabilityFlags() - Method in class org.jmol.modelset.Atom
-
- getClickableSet() - Method in class org.jmol.modelset.AtomCollection
-
- getClickableSet() - Method in class org.jmol.viewer.Viewer
-
- getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
-
- getClipboardText() - Method in interface org.jmol.api.JmolImageCreatorInterface
-
- 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
-
- getClosestNormal(IsosurfaceMesh, Point3f, Point3f, Vector3f) - Method in class org.jmol.shapesurface.Isosurface
-
- getClosestPoint(IsosurfaceMesh, int, Point3f, Point3f, Vector3f) - Method in class org.jmol.shapesurface.Isosurface
-
- getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
-
- getCmlBondOrder(int) - Static method in class org.jmol.util.JmolEdge
-
- getCode() - Method in enum org.jmol.constant.EnumAxesMode
-
- getCode() - Method in enum org.jmol.viewer.FileManager.EnumFileStatus
-
- getCodeFromName(String) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
-
- 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
-
- getColixArray(String) - Static method in class org.jmol.g3d.Graphics3D
-
- 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
-
- getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
-
- getColixBondPalette(Bond, int) - 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
-
- getColixTranslucencyFractional(short) - Static method in class org.jmol.g3d.Graphics3D
-
- getColixTranslucencyLevel(short) - Static method in class org.jmol.g3d.Graphics3D
-
- getColixTranslucent(int) - Static method in class org.jmol.g3d.Graphics3D
-
- getColixTranslucent(short, boolean, float) - Static method in class org.jmol.g3d.Graphics3D
-
- getCollectionName() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getColor() - Method in enum org.jmol.constant.EnumStructure
-
- getColor(String) - Method in class org.jmol.jvxl.readers.KinemageReader
-
- getColor(int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getColorArgbOrGray(short) - Method in interface org.jmol.api.JmolRendererInterface
-
- getColorArgbOrGray(short) - Method in class org.jmol.export.Export3D
-
- getColorArgbOrGray(short) - Method in class org.jmol.g3d.Graphics3D
-
- getColorArgbOrGray(short) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
-
- getColorEncoder(String) - Method in class org.jmol.viewer.Viewer
-
- getColorFromName(String) - Method in class org.jmol.applet.AppletWrapper
-
- getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
-
- getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
-
- getColorKey() - Method in class org.jmol.util.ColorEncoder
-
- getColorList(int, short[], int, BitSet, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
-
input an array of colixes; returns a Vector for the color list and a
HashTable for correlating the colix with a specific color index
- getColorPhaseIndex(String) - Static method in class org.jmol.jvxl.readers.SurfaceReader
-
- getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
-
- getColorRange(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
-
- getColorScheme() - Method in class org.jmol.util.ColorEncoder
-
- getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
-
- getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
-
- getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
-
- getColorSchemeList(String) - Method in class org.jmol.viewer.Viewer
-
- getColorSchemeName() - Method in class org.jmol.util.ColorEncoder
-
- getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
-
- getColorTriad(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getColumnClass(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
-
- getColumnCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
-
- getColumnName(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
-
- getCommand(int, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
used for recall of commands in the application console
- getCommand() - Method in class org.jmol.util.CommandHistory
-
Calculates the command to return.
- getCommand() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- getCommandDown() - Method in class org.jmol.util.CommandHistory
-
Retrieves the following command from the top of the list, updates list position.
- getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Generates a commandline from the options set for povray path
etc and sets in the textField.
- getCommands(Map<String, BitSet>) - Static method in class org.jmol.viewer.StateManager
-
- getCommands(Map<String, BitSet>, Map<String, BitSet>) - Static method in class org.jmol.viewer.StateManager
-
- getCommands(Map<String, BitSet>, Map<String, BitSet>, String) - Static method in class org.jmol.viewer.StateManager
-
- getCommands(Map<String, BitSet>, StringBuffer, String, String) - Static method in class org.jmol.viewer.StateManager
-
- getCommandSet(String) - Static method in class org.jmol.script.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.jmolpanel.AppConsole.ConsoleDocument
-
- getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
- getCommandUp() - Method in class org.jmol.util.CommandHistory
-
Retrieves the following command from the bottom of the list, updates list position.
- getCompressionLevel() - Method in class org.jmol.export.image.PngEncoder
-
Retrieve compression level
- getConeData() - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a cone.
- getConeMesh(Point3f, Matrix3f, short) - Static method in class org.jmol.export.___Exporter
-
- getConeResource() - Method in class org.jmol.export._IdtfExporter
-
- getConformation(int, int, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getConformation(BitSet, int) - Method in class org.jmol.modelset.Polymer
-
- getConformation(BitSet, int) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getConformation(Atom[], BitSet, int) - Method in class org.jmol.modelsetbio.Monomer
-
clear out bits that are not associated with the nth conformation
counting for each residue from the beginning of the file listing
- getConformation(int, int, boolean) - Method in class org.jmol.viewer.Viewer
-
- getConnectionPoints() - Method in class org.jmol.shapespecial.DrawRenderer
-
- getConstraintList() - Method in class org.jmol.minimize.forcefield.Calculations
-
- getContext(boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getContextTrace(StringBuffer, boolean) - Method in class org.jmol.script.ScriptContext
-
- getContextVariableAsVariable(String) - Method in class org.jmol.script.ScriptEvaluator
-
- getContextVariables() - Method in class org.jmol.script.ScriptEvaluator
-
- getContextVariables() - Method in class org.jmol.viewer.Viewer
-
- getContourList(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- getContourPoint(Point3f[], int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
- getContourPoint(Point3f[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
- getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
create a set of contour data.
- getContourType() - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- getContourValues() - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
-
- getContrastingBlackOrWhite(Color) - Method in class org.jmol.applet.AppletWrapper
-
- getControlPoint(int, Vector3f) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- getControlPoint(int, Vector3f) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getControlPoints(float) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getCoordinateMap(Tuple3f[], int[], BitSet) - Method in class org.jmol.export.__CartesianExporter
-
- 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
-
- getCorrelationMaps(String, JmolNode[], int, BitSet, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getCorrelationMaps(String, JmolNode[], int, BitSet, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
-
Rather than returning bitsets, this method returns the
sets of matching atoms in array form so that a direct
atom-atom correlation can be made.
- getCount() - Method in class org.jmol.modelset.Measurement
-
- getCountPlusIndices() - Method in class org.jmol.modelset.Measurement
-
- getCovalentBondCount() - Method in class org.jmol.modelset.Atom
-
- getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the number of bonds of this atom.
- getCovalentBondCount() - Method in interface org.jmol.util.JmolNode
-
- getCovalentBondOrder(int) - Static method in class org.jmol.util.JmolEdge
-
- getCovalentBondsForAtoms(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
-
- getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
-
- getCovalentHydrogenCount() - Method in interface org.jmol.util.JmolNode
-
- getCovalentlyConnectedBitSet(JmolNode[], JmolNode, BitSet, boolean, boolean, List<BitSet>, BitSet) - Static method in class org.jmol.util.JmolMolecule
-
- getCovalentOrder() - Method in class org.jmol.modelset.Bond
-
- getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
-
- getCovalentOrder() - Method in class org.jmol.util.JmolEdge
-
- getCovalentRadiusFloat() - Method in class org.jmol.modelset.Atom
-
- getCreatingImage() - Method in class org.jmol.viewer.Viewer
-
- getCriticalPoints(Point3f[], Point3f) - Static method in class org.jmol.util.BoxInfo
-
- getCrossHairMinMax() - Method in class org.jmol.viewer.ShapeManager
-
- getCrossHairMinMax() - Method in class org.jmol.viewer.Viewer
-
- getCrossLink(int, List<Integer>) - Method in class org.jmol.modelsetbio.Monomer
-
- getCrossLink(int, List<Integer>, Group) - Method in class org.jmol.modelsetbio.Monomer
-
- getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelset.Atom
-
- getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelset.Group
-
- getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelsetbio.Monomer
-
- getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getCrossLinkLeadAtomIndexes(List<Integer>) - Method in class org.jmol.smiles.SmilesAtom
-
- getCrossLinkLeadAtomIndexes(List<Integer>) - Method in interface org.jmol.util.JmolNode
-
- 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.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
-
- getCurrentX() - Method in class org.jmol.viewer.ActionManager
-
- getCurrentY() - Method in class org.jmol.viewer.ActionManager
-
- getCursor() - 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
-
- getCylinderData(boolean) - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a cylinder.
- getCylinderResource(boolean) - Method in class org.jmol.export._IdtfExporter
-
- getData() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- getData(String, String) - Method in class org.jmol.api.JmolViewer
-
- getData(Viewer, int, int, BioPolymer, char, char, int, BitSet, BitSet, boolean, boolean, boolean, boolean, boolean, boolean, float, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Static method in class org.jmol.modelsetbio.BioPolymer
-
- getData(String) - Method in class org.jmol.script.ScriptCompiler
-
- getData() - Method in class org.jmol.util.CifDataReader
-
general reader for loop data
fills loopData with fieldCount fields
- 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
-
- getDataBlock() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- 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
-
- getDataFloat3D(String) - Method in class org.jmol.viewer.DataManager
-
- getDataFloat3D(String) - Method in class org.jmol.viewer.Viewer
-
- getDataSeparator() - Method in class org.jmol.viewer.Viewer
-
- getDataState(StringBuffer, StringBuffer, String) - Method in class org.jmol.viewer.DataManager
-
- getDE(MinAtom, int, int, double) - Method in class org.jmol.minimize.forcefield.ForceField
-
- getDE(float[], int, int, int, int, boolean) - Method in class org.jmol.util.MeshSurface
-
- 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
-
- getDef(String) - Method in class org.jmol.export.UseTable
-
Hashtable htDefs contains references to _n where n is a number.
- getDefaultColix() - Method in class org.jmol.shapesurface.Isosurface
-
- getDefaultColorRasmol() - Method in class org.jmol.viewer.ColorManager
-
- getDefaultCount(int, boolean) - Static method in class org.jmol.smiles.SmilesAtom
-
- getDefaultDirectory(String) - Method in class org.jmol.viewer.FileManager
-
- getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
-
- getDefaultDrawArrowScale() - Method in class org.jmol.viewer.Viewer
-
- getDefaultLargePDBRendering(StringBuffer, int) - Method in class org.jmol.modelset.Model
-
- getDefaultLattice() - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getDefaultLattice() - Method in class org.jmol.viewer.Viewer
-
- getDefaultLoadFilter() - Method in class org.jmol.viewer.Viewer
-
- getDefaultLoadScript() - Method in class org.jmol.viewer.Viewer
-
- getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
-
When creating a new bond, determine bond diameter from order
- getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
-
- getDefaultParam(int) - Static method in class org.jmol.viewer.PropertyManager
-
- getDefaultRadiusData() - Method in class org.jmol.viewer.Viewer
-
- getDefaultState() - Method in class org.jmol.shape.Labels
-
- getDefaultStructure(BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
-
- getDefaultStructure(BitSet, BitSet) - Method in class org.jmol.viewer.Viewer
-
- getDefaultStructureDSSP() - Method in class org.jmol.viewer.Viewer
-
- getDefaultTranslucent() - Method in class org.jmol.viewer.Viewer
-
- getDefaultVdwNameOrData(int, EnumVdw, BitSet) - Method in class org.jmol.viewer.DataManager
-
- getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelCollection
-
- getDefaultVdwTypeNameOrData(int, EnumVdw) - Method in class org.jmol.viewer.Viewer
-
- getDefinedState(StringBuffer, boolean) - Method in class org.jmol.modelset.ModelSet
-
- getDegrees(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
-
- getDegrees(int, int) - Method in class org.jmol.viewer.ActionManager
-
- 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
- getDescent(Object) - Static method in class org.jmol.awt.Font
-
- getDescent() - Method in class org.jmol.g3d.Font3D
-
- getDescription() - Method in class org.jmol.export.dialog.Dialog.TypeFilter
-
- getDescription(SymmetryInterface, Point3f, Point3f, String) - Method in class org.jmol.symmetry.SymmetryOperation
-
- getDescription(SymmetryOperation, String, SymmetryInterface, Point3f, Point3f, String) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- getDFMap(String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
finds the position in the Jmol-required list of function types.
- getDialog() - Method in class org.jmol.export.dialog.FileChooser
-
- getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- getDiameter(int, int) - Method in class org.jmol.shape.FontLineShapeRenderer
-
- getDictRefValue(Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- getDiffusePercent() - Static method in class org.jmol.g3d.Graphics3D
-
- getDigits(String, int, int[]) - Static method in class org.jmol.smiles.SmilesParser
-
- 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.util.Measure
-
- 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
-
- getDisplay() - Method in class org.jmol.api.JmolViewer
-
- getDisplay() - 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
-
- getDitheredNoisyShadeIndex(float, float, float, float) - Static method in class org.jmol.g3d.Shade3D
-
- getDotDensity() - Method in class org.jmol.viewer.Viewer
-
- getDoTranslate() - Static method in class org.jmol.i18n.GT
-
- getDotScale() - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getDouble(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
-
- getDragSelected() - 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.Viewer
-
- getDrawObjectAxis(String, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getDrawPicking() - Method in class org.jmol.viewer.Viewer
-
- getDualHydrogenBondArray(Polymer[], int, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
(p.
- getDX(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getDY(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getDynamicMeasurements() - Method in class org.jmol.viewer.Viewer
-
- getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
-
- getEchoStateActive() - Method in class org.jmol.viewer.Viewer
-
- getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- getEdgeData() - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- getEdgePoints(Point3f[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- getEdges() - Method in class org.jmol.modelset.Atom
-
- getEdges() - Method in class org.jmol.smiles.SmilesAtom
-
- getEdges() - Method in interface org.jmol.util.JmolNode
-
- getEigenvalues() - Method in class org.jmol.util.Eigen
-
- getEigenvectors() - Method in class org.jmol.util.Eigen
-
- getEigenvectorsFloatTransposed() - Method in class org.jmol.util.Eigen
-
transpose V and turn into floats
- getElectronDensityLoadInfo() - Method in class org.jmol.viewer.Viewer
-
- getElementAndAtomCount(boolean) - Method in class org.jmol.util.JmolMolecule
-
- 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.smiles.SmilesAtom
-
Returns the atomic number of the element or 0
- getElementNumber(short) - Static method in class org.jmol.util.Elements
-
- getElementNumber() - Method in interface org.jmol.util.JmolNode
-
- 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(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
-
- getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
-
- getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
-
- getElementSymbol(boolean) - Method in class org.jmol.modelset.Atom
-
- getElementSymbol() - Method in class org.jmol.modelset.Atom
-
- getElementSymbol(int) - Method in class org.jmol.modelset.AtomCollection
-
- 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(Vector3f[], float, float, 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(Vector3f[], float, float, float) - Method in class org.jmol.symmetry.Symmetry
-
- getEllipsoid(float[]) - Method in class org.jmol.symmetry.UnitCell
-
- getEllipsoid(Vector3f[], float, float, float) - Method in class org.jmol.symmetry.UnitCell
-
- getEllipsoidShade(float, float, float, int, Matrix4f) - Static method in class org.jmol.g3d.Sphere3D
-
- getEmbeddedScript(String) - Static method in class org.jmol.script.ScriptCompiler
-
- getEmptySet() - Static method in class org.jmol.util.FastBitSet
-
- 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
-
- getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
within element
- 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
-
- getEnergy() - Method in class org.jmol.modelset.Bond
-
- getEnergy() - Method in class org.jmol.modelset.HBond
-
- getEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
-
- 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.api.JmolViewer
-
- getErrorMessage() - Method in class org.jmol.script.ScriptEvaluator
-
- getErrorMessage() - Method in class org.jmol.viewer.Viewer
-
- getErrorMessageUntranslated() - Method in class org.jmol.api.JmolViewer
-
- getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptEvaluator
-
- getErrorMessageUntranslated() - Method in exception org.jmol.script.ScriptEvaluator.ScriptException
-
- getErrorMessageUntranslated() - Method in class org.jmol.viewer.Viewer
-
- getEventName(int) - Static method in class org.jmol.multitouch.ActionManagerMT
-
- getExecutionWalltime() - Method in class org.jmol.script.ScriptEvaluator
-
- getExecutor() - Static method in class org.jmol.script.ParallelProcessor
-
- getExecutor() - Method in class org.jmol.viewer.Viewer
-
- getExitRate() - Method in class org.jmol.multitouch.ActionManagerMT
-
- getExitRate() - Method in class org.jmol.viewer.ActionManager
-
- getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
-
- getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getExportDate() - Static method in class org.jmol.export.___Exporter
-
- getExportDriverList() - Method in class org.jmol.viewer.Viewer
-
- getExportName() - Method in interface org.jmol.api.JmolRendererInterface
-
- getExportName() - Method in class org.jmol.export.Export3D
-
- getExportName() - Method in class org.jmol.g3d.Graphics3D
-
- getExportType() - Method in interface org.jmol.api.JmolRendererInterface
-
- getExportType() - Method in class org.jmol.export.Export3D
-
- getExportType() - Method in class org.jmol.g3d.Graphics3D
-
- getFacePlane(int, Vector3f) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- getFaces() - Method in class org.jmol.export.MeshData.Data
-
- getFaces() - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- getFaces() - Method in class org.jmol.util.MeshSurface
-
- getFacesFromCriticalPoints(Point3f[]) - Static method in class org.jmol.util.BoxInfo
-
- getFaceVertexes(int) - Static method in class org.jmol.geodesic.Geodesic
-
- getFaceVertexesArrays() - Static method in class org.jmol.geodesic.Geodesic
-
- getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceField
-
- getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
-
- getFile(int) - Method in class org.jmol.console.JmolConsole.FileChecker
-
- getFile() - Method in class org.jmol.export.history.HistoryFile
-
- getFile() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- getFileAsBytes(String, OutputStream) - Method in class org.jmol.api.JmolViewer
-
- getFileAsBytes(String, OutputStream) - Method in class org.jmol.viewer.FileManager
-
- getFileAsBytes(String, OutputStream) - Method in class org.jmol.viewer.Viewer
-
- getFileAsImage(String, String[]) - Method in class org.jmol.viewer.FileManager
-
- getFileAsImage(String, String[]) - Method in class org.jmol.viewer.Viewer
-
- getFileAsString(String) - Method in class org.jmol.api.JmolViewer
-
- getFileAsString(String[], int, boolean) - Method in class org.jmol.api.JmolViewer
-
- getFileAsString(String) - Method in class org.jmol.util.CompoundDocument
-
- getFileAsString(CompoundDocument.CmpDocDirectoryEntry, boolean) - Method in class org.jmol.util.CompoundDocument
-
- getFileAsString(String) - Method in class org.jmol.viewer.Viewer
-
- getFileAsString(String, int, boolean) - Method in class org.jmol.viewer.Viewer
-
- getFileAsString(String[], int, boolean) - Method in class org.jmol.viewer.Viewer
-
- getFileContents(File) - Method in class org.openscience.chimetojmol.ChimePanel
-
- getFileData(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- getFileData(int) - Method in class org.jmol.modelset.ModelSet
-
- getFileData() - Method in class org.jmol.viewer.Viewer
-
- getFileDataOrErrorAsString(String[], int, boolean) - Method in class org.jmol.viewer.FileManager
-
- getFileHeader(int) - Method in class org.jmol.modelset.ModelCollection
-
- getFileHeader() - Method in class org.jmol.util.CifDataReader
-
- getFileHeader() - Method in class org.jmol.viewer.Viewer
-
- getFileInfo() - Method in class org.jmol.viewer.FileManager
-
- getFileInfo(Object, String) - Static method in class org.jmol.viewer.PropertyManager
-
- getFileInfo() - Method in class org.jmol.viewer.Viewer
-
- getFileList() - Method in class org.openscience.chimetojmol.ChimePanel
-
- getFileName() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getFileName() - Method in class org.jmol.viewer.FileManager
-
- getFileName() - Method in class org.jmol.viewer.Viewer
-
- getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
-
- getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.export.dialog.Dialog
-
- getFileNameFromDialog(String, int) - Method in class org.jmol.viewer.Viewer
-
- getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
-
- getFilePath(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- getFileReferences(String, List<String>) - Static method in class org.jmol.viewer.FileManager
-
- getFiles() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
-
From SmarterJmolAdapter.getFileTypeName(Object atomSetCollectionOrReader)
just return the file type with no exception issues
- getFileType() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getFileTypeName() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Just get the resolved file type; if a file, does NOT close the reader
- getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the type of this file or molecular model, if known.
- getFileTypeName(String) - Method in class org.jmol.viewer.FileManager
-
- getFilter() - Method in class org.jmol.export.image.PngEncoder
-
Retrieve filtering scheme
- getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
-
- getFirstAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getFloat(int, int) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- getFloat() - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- getFloat() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- getFloatEncodedInt(String) - Static method in class org.jmol.script.ScriptEvaluator
-
Encodes a string such as "2.10" as an integer instead of a float
so as to distinguish "2.1" from "2.10"
used for model numbers and partial bond orders.
- getFloatShadeIndexNormalized(float, float, float) - Static method in class org.jmol.g3d.Shade3D
-
- 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
-
- getFontAscent(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getFontAscent(Object) - Method in class org.jmol.awt.Platform
-
- getFontCaching() - Method in class org.jmol.viewer.Viewer
-
- getFontCommand(String, Font3D) - Static method in class org.jmol.shape.Shape
-
- getFontDescent(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getFontDescent(Object) - Method in class org.jmol.awt.Platform
-
- 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
-
- getFontMetrics(Object, Object) - Method in interface org.jmol.api.ApiPlatform
-
- getFontMetrics(Object, Object) - Static method in class org.jmol.awt.Font
-
- getFontMetrics(Object, Object) - Method in class org.jmol.awt.Platform
-
- 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
-
- getFontStyleID(String) - Static method in class org.jmol.g3d.Graphics3D
-
- 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.smiles.SmilesAtom
-
- getFormalCharge() - Method in interface org.jmol.util.JmolNode
-
- getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
get all integers after letters
negative entries are spaces (1Xn)
- getFp8ShadeIndex(float, float, float) - Static method in class org.jmol.g3d.Shade3D
-
- getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
-
- getFractionalCoord(Vector3f) - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- getFractionalCoord(char, boolean) - Method in class org.jmol.modelset.Atom
-
- getFractionalCoord(boolean) - 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
-
- getFractionalRelative() - Method in class org.jmol.viewer.Viewer
-
- getFractionalUnitCoord(char) - Method in class org.jmol.modelset.Atom
-
- getFractionalUnitCoord(boolean) - Method in class org.jmol.modelset.Atom
-
- getFractionalUnitDistance(Point3f, Point3f, Point3f) - Method in class org.jmol.modelset.Atom
-
- getFrame() - Method in interface org.jmol.console.JmolFrame
-
- getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- getFrame() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- getFrame() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getFrameOffsets(BitSet) - Method in class org.jmol.modelset.ModelSet
-
- getFrameOffsets() - Method in class org.jmol.viewer.Viewer
-
- getFrameTitle(int) - Method in class org.jmol.modelset.ModelCollection
-
- getFrameTitle() - Method in class org.jmol.viewer.Viewer
-
- getFrontPlane() - Method in class org.jmol.viewer.TransformManager
-
- getFrontPlane() - Method in class org.jmol.viewer.Viewer
-
- getFullPathName() - Method in class org.jmol.script.ScriptEvaluator
-
- getFullPathName() - Method in class org.jmol.viewer.FileManager
-
- getFullPathName() - Method in class org.jmol.viewer.Viewer
-
- getFullPathNameOrError(String) - Method in class org.jmol.viewer.FileManager
-
just check for a file as being readable.
- getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
-
- getFullPDBHeader(int) - Method in class org.jmol.modelset.ModelCollection
-
- getFunction(String) - Method in class org.jmol.viewer.StateManager
-
- getFunction(String) - Method in class org.jmol.viewer.Viewer
-
- getFunctionCalls(String) - Method in class org.jmol.viewer.StateManager
-
- getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
-
- getFunctions(boolean) - Method in class org.jmol.viewer.StateManager
-
- getFunctionZfromXY() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
-
- getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- getGhostOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getGlobalSettings(StateManager.GlobalSettings, boolean) - Method in class org.jmol.viewer.StateManager
-
- getGlobalSettings() - Method in class org.jmol.viewer.Viewer
-
- getGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getGraphics(Object) - Static method in class org.jmol.awt.Image
-
- getGraphics(Object) - Method in class org.jmol.awt.Platform
-
- getGraphics(Object) - Method in class org.jmol.g3d.Platform3D
-
- getGraphics3D() - Method in class org.jmol.viewer.Viewer
-
- getGreyscaleRendering() - Method in class org.jmol.viewer.Viewer
-
- getGroup() - Method in class org.jmol.modelset.Atom
-
- getGroup(int) - Method in class org.jmol.modelset.Chain
-
- getGroup1(char) - Method in class org.jmol.modelset.Atom
-
- getGroup1() - Method in class org.jmol.modelset.Group
-
- getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
-
- getGroup1(char) - Method in interface org.jmol.util.JmolNode
-
- getGroup3() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
-
- getGroup3() - Method in class org.jmol.api.JmolAdapter.AtomIterator
-
- getGroup3(boolean) - 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
-
- getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
-
- getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
-
- getGroup3(boolean) - Method in interface org.jmol.util.JmolNode
-
- getGroup3List() - Static method in class org.jmol.viewer.JmolConstants
-
- getGroup3Pt(String) - Static method in class org.jmol.viewer.JmolConstants
-
- getGroupAtom(Atom, int, String) - Method in class org.jmol.modelset.ModelCollection
-
- getGroupBits(BitSet) - Method in class org.jmol.modelset.Atom
-
- getGroupBits(BitSet) - Method in class org.jmol.smiles.SmilesAtom
-
- getGroupBits(BitSet) - Method in interface org.jmol.util.JmolNode
-
- 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
-
- getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
-
- getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
-
- getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
- getGroupIndex() - Method in class org.jmol.modelset.Atom
-
- getGroupIndex() - Method in class org.jmol.modelset.Group
-
- getGroupInfo(int) - Method in class org.jmol.modelset.Group
-
- getGroupParameter(int) - Method in class org.jmol.modelset.Atom
-
- getGroupParameter(int) - Method in class org.jmol.modelset.Group
-
- getGroups() - Method in class org.jmol.modelset.ModelCollection
-
In versions earlier than 12.1.51, groups[] was a
field of ModelCollection.
- getGroups() - Method in class org.jmol.modelset.Polymer
-
- getGroups() - Method in class org.jmol.modelsetbio.BioPolymer
-
- getGroupsWithin(int, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- getGroupsWithin(int, BitSet) - Method in class org.jmol.viewer.Viewer
-
- getGzippedBytesAsString(byte[]) - Static method in class org.jmol.util.ZipUtil
-
- getGzippedInputStream(byte[]) - Static method in class org.jmol.util.ZipUtil
-
- getHallLatticeEquivalent(int) - Static method in class org.jmol.symmetry.Translation
-
- getHandedness(JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesSearch
-
compares the
- getHash(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getHaveStraightness() - Method in class org.jmol.modelset.AtomCollection
-
- getHbondsAngleMin() - Method in class org.jmol.viewer.Viewer
-
- getHbondsBackbone() - Method in class org.jmol.viewer.Viewer
-
- getHbondsDistanceMax() - Method in class org.jmol.viewer.Viewer
-
- getHbondsRasmol() - 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 class org.jmol.jvxl.readers.EfvetReader
-
- getHeight(Object) - Static method in class org.jmol.awt.Image
-
- getHeight() - Method in class org.jmol.g3d.Font3D
-
- getHeightUnitVector() - Method in class org.jmol.modelsetbio.Sheet
-
- getHelixData(BitSet, int) - Method in class org.jmol.modelset.AtomCollection
-
- getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
-
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- getHelixData(BitSet, int) - Method in class org.jmol.viewer.Viewer
-
- getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
-
- getHelixStep() - Method in class org.jmol.viewer.Viewer
-
- getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
-
- getHelp(String) - Method in class org.jmol.viewer.Viewer
-
- getHermiteLevel() - Method in class org.jmol.viewer.Viewer
-
- getHermiteList(int, 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
-
- getHexCode(short) - Static method in class org.jmol.g3d.Graphics3D
-
- getHexCodes(short[]) - Static method in class org.jmol.g3d.Graphics3D
-
- getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
-
- getHexitValue(char) - Static method in class org.jmol.util.Escape
-
- 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
-
- getHklPlane(Point3f) - Method in class org.jmol.script.ScriptEvaluator
-
- 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, int, Vector3f, Vector3f, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
-
- getHybridizationAndAxes(int, Vector3f, Vector3f, String) - Method in class org.jmol.viewer.Viewer
-
- getHybridizationAndAxesD(int, Vector3f, Vector3f, String) - Method in class org.jmol.modelset.AtomCollection
-
dsp3 (trigonal bipyramidal, see-saw, T-shaped)
or d2sp3 (square planar, square pyramidal, octahedral)
- getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
- getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the hydrogen atom count -- for ligand files
- getHydrogens(JmolNode, BitSet) - Method in class org.jmol.smiles.SmilesSearch
-
- getHydrophobicity() - Method in class org.jmol.modelset.Atom
-
- getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
-
- getHydrophobicity(int) - Static method in class org.jmol.util.Elements
-
- getIAddGridPoints() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getIcon(String) - Method in class org.jmol.modelkit.ModelKitPopup
-
- getIcon(String) - Method in class org.jmol.popup.SimplePopup
-
- getIcon(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- getId() - Method in enum org.jmol.constant.EnumStructure
-
- getId(Object) - Method in class org.jmol.popup.SimplePopup
-
- 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(boolean) - Method in class org.jmol.modelset.Atom
-
- getImage(boolean) - Method in class org.jmol.viewer.Viewer
-
- getImageAs(String, int, int, int, String, OutputStream) - Method in class org.jmol.api.JmolViewer
-
- getImageAs(String, int, int, int, String, OutputStream) - Method in class org.jmol.viewer.Viewer
-
- getImageAs(String, int, int, int, String, OutputStream, String) - Method in class org.jmol.viewer.Viewer
-
- getImageBytes(String, int, String, Object, OutputStream) - Method in interface org.jmol.api.JmolImageCreatorInterface
-
- getImageBytes(String, int, String, Object, OutputStream) - Method in class org.jmol.export.image.ImageCreator
-
- 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
-
- getImageHeight(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getImageHeight(Object) - Method in class org.jmol.awt.Platform
-
- getImageWidth(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getImageWidth(Object) - Method in class org.jmol.awt.Platform
-
- getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
-
- getImplicitHydrogenCount(Atom) - Method in class org.jmol.modelset.AtomCollection
-
- getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
-
- getImplicitHydrogenCount() - Method in interface org.jmol.util.JmolNode
-
- getIndex() - Method in class org.jmol.modelset.Atom
-
- 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
-
- getIndex() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atom index of the atom.
- getIndex() - Method in interface org.jmol.util.JmolNode
-
- 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(Map<String, Object>) - Method in class org.jmol.modelsetbio.ProteinStructure
-
- getInfo(int) - Method in class org.jmol.shape.Measures
-
- getInfo() - Method in class org.jmol.shape.Mesh
-
- getInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.PointGroup
-
- getInfo(String, SymmetryInterface) - Static method in class org.jmol.symmetry.SpaceGroup
-
- getInfo() - Method in class org.jmol.util.Quaternion
-
- getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
-
- getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
-
- 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.jmolpanel.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.modelset.ModelCollection
-
- getInlineData(StringBuffer, String, boolean, String) - Static method in class org.jmol.viewer.DataManager
-
- getInlineData(StringBuffer, String, boolean) - Static method in class org.jmol.viewer.Viewer
-
- getInMotion() - Method in class org.jmol.viewer.Viewer
-
- getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
-
- getInputStreamOrErrorMessageFromName(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
-
- getInputStreamOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
-
- getInputStreamOrPost(String, boolean, byte[], boolean, URL, String) - Static method in class org.jmol.viewer.FileManager
-
- 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
-
- getInstance() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- getInstance(JmolViewer, String, int, int, int) - Static method in class org.openscience.jmol.app.webexport.JmolInstance
-
- getInstanceList() - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- getInstanceName(int) - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- getInt() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- getInt(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
-
- getInterface(String) - Static method in class org.jmol.api.Interface
-
- getInterruptScript() - Method in class org.jmol.viewer.Viewer
-
- getIntersection(Point4f, Point4f) - Static method in class org.jmol.util.Measure
-
- getIntersection(Point3f, Vector3f, Point4f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getIntersection(float, Point4f, Point3f[], List<Point3f[]>, float[], MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSurface
-
- getInverseNormix(short) - Static method in class org.jmol.g3d.Graphics3D
-
- getInverseNormix(short) - Static method in class org.jmol.g3d.Normix3D
-
- getIonicRadii() - Method in class org.jmol.modelset.AtomCollection
-
- getIsHetero() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
-
- getIsHetero() - Method in class org.jmol.api.JmolAdapter.AtomIterator
-
- getIsosurfaceDataRange(int, String) - Method in class org.jmol.script.ScriptEvaluator
-
- getIsosurfaceJvxl(boolean, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getIsosurfaceKey() - Method in class org.jmol.viewer.Viewer
-
- getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
-
- getIsotopeNumber() - Method in class org.jmol.modelset.Atom
-
- getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
-
- getIsotopeNumber(short) - Static method in class org.jmol.util.Elements
-
- getIsotopeNumber() - Method in interface org.jmol.util.JmolNode
-
- getIsPositiveOnly() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getItem(int) - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelCollection
-
only some models can be iterated through.
- getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
-
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
-
Each Widget must implement this function and make sure to use
the appletID number to specify the target applet i.e.
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
-
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
-
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
-
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
-
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
-
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
-
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
-
A COPY OF THIS .JS FILE MUST BE STORED IN THE html PART OF WEBEXPORT
- 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
-
- getJbr() - Method in class org.jmol.modelset.ModelCollection
-
- getJMenu() - Method in interface org.jmol.api.JmolPopupInterface
-
- getJMenu() - Method in class org.jmol.popup.JmolPopup
-
- getJmol(JFrame, int, int, String) - Static method in class org.openscience.jmol.app.Jmol
-
- getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
-
- getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- getJmolAtom(int) - Method in class org.jmol.smiles.SmilesSearch
-
- 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) - Method in class org.jmol.viewer.ColorManager
-
- getJmolPerspective() - Method in class org.jmol.export.___Exporter
-
- getJmolValue(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- 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.StateManager
-
- getJones() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- getJpgImage(Viewer, int, String) - Method in interface org.jmol.api.ApiPlatform
-
used for JPG writing only; can be ignored
- getJpgImage(ApiPlatform, Viewer, int, String) - Static method in class org.jmol.awt.Image
-
- getJpgImage(Viewer, int, String) - Method in class org.jmol.awt.Platform
-
- getJSliderLabelTable(JSlider) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- getJSONArray(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
-
- getJustifyMeasurements() - Method in class org.jmol.viewer.Viewer
-
- getJvxlData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- GetKey - Interface in org.jmol.console
-
- getKey() - Method in interface org.jmol.console.GetKey
-
- getKey() - Method in class org.jmol.console.KeyJCheckBox
-
- getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
-
- getKey() - Method in class org.jmol.console.KeyJMenu
-
- getKey() - Method in class org.jmol.console.KeyJMenuItem
-
- getKey(Object) - Static method in class org.jmol.console.KeyJMenuItem
-
- getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
-
- getKey(int) - Static method in class org.jmol.export.image.GifEncoder
-
- getLabel(String) - Method in class org.jmol.console.JmolConsole
-
- getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
-
- getLabel(int, boolean, 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.jmolpanel.GuiMap
-
- getLabelString() - Method in class org.jmol.modelset.Measurement
-
- getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.KeyJMenuItem
-
- getLanguage() - Static method in class org.jmol.i18n.GT
-
- getLanguage() - Method in class org.jmol.viewer.Viewer
-
- getLanguageList() - Static method in class org.jmol.i18n.GT
-
- getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getLastConventional - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- getLastError() - Static method in exception org.jmol.smiles.InvalidSmilesException
-
- getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getLastException() - Method in class org.jmol.smiles.SmilesMatcher
-
- 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
-
- getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
-
- 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.openscience.jvxl.MonitorInputStream
-
- getLevel(int) - Static method in class org.jmol.util.Logger
-
Returns the text corresponding to a level.
- getLigandBondInfo(JmolAdapter, Object, String) - Method in class org.jmol.modelsetbio.Resolver
-
reads PDB ligand CIF info and creates a bondInfo object.
- getLigandInfo(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- getLigandInfo(Object) - Method in class org.jmol.viewer.Viewer
-
- getLigandModel(String) - Method in class org.jmol.viewer.Viewer
-
obtain CIF data for a ligand for purposes of adding hydrogens
- getLightingInfo() - Method in class org.jmol.export._TachyonExporter
-
- getLightSource() - Static method in class org.jmol.g3d.Graphics3D
-
- getLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- getLine() - Method in class org.jmol.jvxl.readers.XplorReader
-
- getLine() - Method in class org.jmol.util.XmlReader
-
- getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- getLinearOffset(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEvaluator
-
- getList(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getList() - Method in class org.jmol.script.ScriptVariable
-
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
-
- getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
-
- getLoadAtomDataTolerance() - Method in class org.jmol.viewer.Viewer
-
- getLoadState(Map<String, Object>) - 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(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
- getLocalDirectory(JmolViewer, boolean) - Static method in class org.jmol.viewer.FileManager
-
- getLocalPathForWritingFile(JmolViewer, String) - Static method in class org.jmol.viewer.FileManager
-
- getLocalUrl(File) - Static method in class org.jmol.viewer.FileManager
-
- getLogData() - Method in class org.jmol.minimize.forcefield.Calculations
-
- getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
-
- getLogFile() - Method in class org.jmol.viewer.Viewer
-
- getLogGestures() - Method in class org.jmol.viewer.Viewer
-
- getLogLevel() - Static method in class org.jmol.util.Logger
-
- getLong(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
-
- getMad() - Method in class org.jmol.modelset.Bond
-
- getMadBond() - Method in class org.jmol.api.JmolViewer
-
- getMadBond() - Method in class org.jmol.viewer.Viewer
-
- getMadParameter() - Method in class org.jmol.script.ScriptEvaluator
-
- getMappedAtoms(JmolNode, JmolNode, JmolNode[]) - Method in class org.jmol.smiles.SmilesSearch
-
- getMaps - Variable in class org.jmol.smiles.SmilesSearch
-
- getMarBond() - Method in class org.jmol.viewer.Viewer
-
- getMarchingSquares() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getMass() - Method in class org.jmol.modelset.Atom
-
- getMasses() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the number of a matching atom in a molecule.
- getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
-
- getMatrix() - Method in class org.jmol.util.Quaternion
-
- getMatrix4f(Matrix3f, Tuple3f) - Static method in class org.jmol.script.ScriptMathProcessor
-
- getMatrixFromString(String, float[], boolean) - Method in interface org.jmol.api.SymmetryInterface
-
- getMatrixFromString(String, float[], boolean) - Method in class org.jmol.symmetry.Symmetry
-
- getMatrixFromString(String, float[], boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
-
- 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
-
- getMaxMathParams(int) - Static method in class org.jmol.script.Token
-
- getMaxRadius() - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- 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
-
- getMeasurements(Viewer) - Method in class org.jmol.modelset.MeasurementData
-
if this is the client, then this method
can be called to get the result vector
- getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
-
Used by MouseManager and Picking Manager to build the script
- getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
-
- getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
-
- getMenu(String) - Method in interface org.jmol.api.JmolPopupInterface
-
- getMenu(String) - Method in class org.jmol.popup.JmolPopup
-
- getMenu(String) - Method in class org.jmol.popup.MainPopupResourceBundle
-
- getMenu(String) - Method in class org.jmol.popup.PopupResource
-
- getMenu(String) - Method in class org.jmol.viewer.Viewer
-
- getMenuCurrent() - Method in class org.jmol.popup.JmolPopup
-
- getMenuCurrent(StringBuffer, int, Object, String) - Method in class org.jmol.popup.JmolPopup
-
- getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Fetch the menu item that was created for the given
command.
- getMenuItemCount(Object) - Method in class org.jmol.popup.SimplePopup
-
- getMenuListener() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- getMenuName(int) - Method in class org.jmol.viewer.Viewer
-
- getMenus(boolean) - Method in interface org.jmol.api.JmolModelKitInterface
-
- getMenus(boolean) - Method in class org.jmol.modelkit.ModelKit
-
- getMenuText(String) - Method in class org.jmol.popup.SimplePopup
-
- getMesh(String) - Method in class org.jmol.shape.MeshCollection
-
- getMeshCommand(StringBuffer, int) - Method in class org.jmol.shapesurface.Isosurface
-
- getMeshData(String, int[][], Tuple3f[], Tuple3f[]) - Method in class org.jmol.export._IdtfExporter
-
- getMeshData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getMeshDataServer() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getMeshHeader(String, int, int, int, int, StringBuffer) - Method in class org.jmol.export._IdtfExporter
-
- getMessageQueue() - Method in class org.jmol.viewer.StatusManager
-
- getMessageQueue() - Method in class org.jmol.viewer.Viewer
-
- getMessageStyleChime() - Method in class org.jmol.viewer.Viewer
-
- getMiddle() - Method in class org.openscience.jmol.app.surfacetool.Slice
-
- 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(boolean) - Method in class org.jmol.viewer.Viewer
-
- getMiniPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
-
- getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- getMinMax(float[], boolean, int) - Static method in class org.jmol.script.ScriptEvaluator
-
- getMinMax(Object, int) - Static method in class org.jmol.script.ScriptMathProcessor
-
- getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getMinMaxPoint(Object, int) - Static method in class org.jmol.script.ScriptMathProcessor
-
calculates the statistical value for x, y, and z independently
- getMinMaxQuaternion(Object, int) - Static method in class org.jmol.script.ScriptMathProcessor
-
- getMinPixelSelRadius() - Method in class org.jmol.viewer.Viewer
-
- getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
-
- getMissingHydrogenCount() - Method in class org.jmol.smiles.SmilesSearch
-
- getMnemonic(String) - Static method in class org.jmol.console.KeyJMenuItem
-
- 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.
- getModelAdapter() - Method in class org.jmol.api.JmolViewer
-
- getModelAdapter() - Method in class org.jmol.viewer.Viewer
-
- getModelAtomBitSetIncludingDeleted(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
note -- this method returns ALL atoms, including deleted.
- getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelCollection
-
Note that this method returns all atoms, included deleted ones.
- getModelAtomProperty(Atom, String) - Method in class org.jmol.modelset.ModelCollection
-
- getModelAtomProperty(Atom, String) - 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, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getModelBitSet(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
-
- getModelCellRange(int) - Method in class org.jmol.modelset.ModelCollection
-
- getModelCenter() - Method in class org.jmol.export.__CartesianExporter
-
- getModelCml(BitSet, int, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getModelCml(BitSet, int, boolean) - Method in class org.jmol.viewer.Viewer
-
- 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, boolean, boolean, String) - Method in class org.jmol.modelset.ModelCollection
-
- getModelExtract(Object, boolean, String) - 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.api.JmolViewer
-
- 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 class org.jmol.modelset.Atom
-
- getModelIndex() - Method in class org.jmol.modelset.Group
-
- getModelIndex() - Method in class org.jmol.modelset.Model
-
- getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
-
- getModelIndex() - Method in interface org.jmol.util.JmolNode
-
- 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
-
- getModelKit(Viewer, Object) - Method in interface org.jmol.api.JmolModelKitInterface
-
- getModelKit(Viewer, Object) - Method in class org.jmol.modelkit.ModelKit
-
- getModelkitMode() - Method in class org.jmol.viewer.Viewer
-
- getModelKitStateBitset(BitSet, BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- getModelKitStateBitSet(BitSet, BitSet) - 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() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- 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() - Method in class org.jmol.modelset.Model
-
- 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(Viewer, String, Object) - Static method in class org.jmol.viewer.PropertyManager
-
- 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.Group
-
- 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.modelset.ModelLoader
-
- 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
-
- 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
-
- getModelTitle() - Method in class org.jmol.modelset.Model
-
- getModelTitle(int) - Method in class org.jmol.modelset.ModelCollection
-
- getModelTitle(int) - Method in class org.jmol.viewer.Viewer
-
- getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
-
- getModelUndeletedAtomsBitSet(BitSet) - Method in class org.jmol.viewer.Viewer
-
- getModelUnitCell(int) - Method in class org.jmol.viewer.Viewer
-
- getModeMultipleBond() - Method in class org.jmol.viewer.Viewer
-
- getModifiers(int) - Static method in class org.jmol.viewer.binding.Binding
-
- getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- getMoInfo(int) - Method in class org.jmol.modelset.ModelCollection
-
- getMoInfo(int) - Method in class org.jmol.viewer.Viewer
-
- getMoJvxl(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getMolecularFormula(String, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getMolecularFormula(String, boolean) - Method in class org.jmol.smiles.SmilesMatcher
-
- getMolecularFormula(JmolNode[], BitSet, boolean) - Static method in class org.jmol.util.JmolMolecule
-
- getMolecularFormula(boolean) - Method in class org.jmol.util.JmolMolecule
-
- getMolecule(String, boolean) - Static method in class org.jmol.smiles.SmilesParser
-
- getMoleculeBitSet(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- getMoleculeBitSet(int) - Method in class org.jmol.modelset.ModelCollection
-
- getMoleculeBitSet(int) - Method in class org.jmol.viewer.Viewer
-
- getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelCollection
-
- getMoleculeIndex(int, boolean) - 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(boolean) - Method in class org.jmol.modelset.Atom
-
- getMolecules() - Method in class org.jmol.modelset.ModelCollection
-
- getMolecules(JmolNode[], BitSet[], List<BitSet>, BitSet) - Static method in class org.jmol.util.JmolMolecule
-
Creates an array of JmolMolecules from a set of atoms in the form of simple
JmolNodes.
- getMolName() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
-
- getMonomerCount() - Method in class org.jmol.modelsetbio.ProteinStructure
-
- getMonomerIndex() - Method in class org.jmol.modelset.Atom
-
- getMonomerIndex() - Method in class org.jmol.modelset.Group
-
- getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
-
- getMonomerIndex() - Method in class org.jmol.modelsetbio.ProteinStructure
-
- getMonomerSequenceAtoms(BitSet, BitSet) - Method in class org.jmol.modelsetbio.Monomer
-
- getMoState(int) - Method in class org.jmol.shapesurface.MolecularOrbital
-
- getMOString(float[]) - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
-
- getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
-
- getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
-
- getMotionFixedAtoms() - Method in class org.jmol.viewer.Viewer
-
- getMoTokens(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- getMouseAction(int, int) - Static method in class org.jmol.viewer.binding.Binding
-
- getMouseAction(String) - Static method in class org.jmol.viewer.binding.Binding
-
create an action code from a string such as "CTRL-LEFT-double click"
- getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
-
- getMouseEnabled() - Method in class org.jmol.viewer.Viewer
-
- getMouseInfo() - Method in class org.jmol.viewer.ActionManager
-
- getMouseInfo() - Method in class org.jmol.viewer.Viewer
-
- getMouseManager(Viewer, ActionManager) - Method in interface org.jmol.api.ApiPlatform
-
- getMouseManager(Viewer, ActionManager) - Method in class org.jmol.awt.Platform
-
- getMoveToText(boolean) - 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
-
- getMultipleBondRadiusFactor() - Method in class org.jmol.viewer.Viewer
-
- getMultipleBondSpacing() - Method in class org.jmol.viewer.Viewer
-
- getMyInfo() - Method in class org.jmol.modelsetbio.Monomer
-
- getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- 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 enum org.jmol.constant.EnumAnimationMode
-
- getName() - Method in enum org.jmol.constant.EnumCallback
-
- getName() - Method in enum org.jmol.constant.EnumStereoMode
-
- getName() - Method in enum org.jmol.constant.EnumStructure
-
- getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
-
- getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- getName() - Method in class org.jmol.symmetry.PointGroup
-
- getName() - Method in class org.jmol.symmetry.SpaceGroup
-
- getName() - Method in class org.jmol.viewer.binding.Binding
-
- getNameFromCode(int) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
-
- getNameList() - Static method in enum org.jmol.constant.EnumCallback
-
- getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
-
- getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
-
- getNavigateSurface() - 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
-
- 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
-
- getNavOn() - Method in class org.jmol.viewer.TransformManager
-
- getNavOn() - Method in class org.jmol.viewer.Viewer
-
- getNavPtHeight() - Method in class org.jmol.viewer.TransformManager11
-
- getNBackbonesDisplayed() - Method in class org.jmol.modelset.Atom
-
- getNBOCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
-
- getNboCharges() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- getNBOs - Variable in class org.jmol.adapter.readers.quantum.MOReader
-
- getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- getNegCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getNeighbors(AtomIndexIterator) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
- getNeighborVertexesArrays() - Static method in class org.jmol.geodesic.Geodesic
-
- getNested(int) - Method in class org.jmol.smiles.SmilesSearch
-
- getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
-
- getNewDfCoefMap() - Static method in class org.jmol.api.JmolAdapter
-
- getNewDfCoefMap() - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getNewFixedRotationCenter() - Method in class org.jmol.viewer.TransformManager
-
- getNextComment() - Method in class org.jmol.script.ScriptEvaluator
-
- getNextDataToken() - Method in class org.jmol.util.CifDataReader
-
first checks to see if the next token is an unquoted
control code, and if so, returns null
- getNextPreloadClassName() - Method in class org.jmol.applet.AppletWrapper
-
- getNextQuotedString() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- getNextQuotedString(String, int) - Static method in class org.jmol.util.Parser
-
- getNextQuotedString(String, int[]) - Static method in class org.jmol.util.Parser
-
- getNextStatement() - Method in class org.jmol.script.ScriptEvaluator
-
when paused, indicates what statement will be next
- getNextToken() - Method in class org.jmol.util.CifDataReader
-
- getNextValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- getNextVoxelValue() - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- getNHPoint(Point3f, Vector3f, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getNitrogenAtom() - Method in class org.jmol.modelset.Group
-
- getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getNitrogenHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getNode(int) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getNoneSelected() - Method in class org.jmol.viewer.Viewer
-
- getNormal() - Method in class org.jmol.util.Quaternion
-
- getNormalCount() - Method in class org.jmol.export.MeshData.Data
-
- getNormalDirected(Vector3f) - Method in class org.jmol.util.Quaternion
-
- getNormalFromCenter(Point3f, Point3f, Point3f, Point3f, boolean, Vector3f) - Static method in class org.jmol.util.Measure
-
- getNormalizedDE() - Method in class org.jmol.minimize.forcefield.ForceField
-
- getNormalMap(Tuple3f[], int, BitSet, List<String>) - Method in class org.jmol.export.__CartesianExporter
-
- getNormals() - Method in class org.jmol.export.MeshData.Data
-
- getNormals(Point3f[], Point4f) - Method in class org.jmol.shape.Mesh
-
- getNormalThroughPoints(JmolNode, JmolNode, JmolNode, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.smiles.SmilesAromatic
-
- getNormalThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getNormalToLine(Point3f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Graphics3D
-
- getNormix(Vector3f, BitSet) - Static method in class org.jmol.g3d.Normix3D
-
- getNormix(double, double, double, int, BitSet) - Static method in class org.jmol.g3d.Normix3D
-
- getNormixVector(short) - Static 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.util.SimpleUnitCell
-
- getNoValue() - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
-
Get that value that represents "no value" so that it can be
disregarded in terms of recording and reporting the min/max/mean.
- getNoValue() - Method in class org.jmol.quantum.NciCalculation
-
- getNPQ(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
- getNPQd(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
for D orbitals, MOPAC adds 1 to n for noble gases
but subtracts 1 from n for transition metals
- getNPQp(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
for P orbitals, MOPAC adds 1 to n for helium only
- getNPQs(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
for S orbitals, MOPAC adds 1 to n for noble gases other than helium
- getNucleicPhosphorusAtom(int) - Method in class org.jmol.modelsetbio.NucleicPolymer
-
- getNumberFromCode(int) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
-
- getNumericalToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- getNumericParameter(String) - Method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- getObjectAsSections(String, String, Map<String, String>) - Method in class org.jmol.viewer.FileManager
-
delivers file contents and directory listing for a ZIP/JAR file into sb
- getObjectBoundingBox(String) - Method in class org.jmol.script.ScriptEvaluator
-
- getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- getObjectMap(Map<String, Token>, boolean) - Method in class org.jmol.api.JmolViewer
-
retrieves list of draw/isosurface objects
- getObjectMap(Map<String, Token>, boolean) - Method in class org.jmol.viewer.ShapeManager
-
- getObjectMap(Map<String, Token>, boolean) - 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
-
- getOccupancy100() - Method in class org.jmol.modelset.Atom
-
- getOctant(Point3f) - Static method in class org.jmol.util.Quadric
-
- getOffset(int, int) - Static method in class org.jmol.shape.Object2d
-
- getOffset(int) - Method in class org.jmol.util.CompoundDocument
-
- getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
-
- getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
-
- getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.JmolNode
-
- getOffsetVertices(Point4f) - Method in class org.jmol.shape.Mesh
-
- getOpenFileNameFromDialog(String, JmolViewer, String, Object, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
-
- getOpenFileNameFromDialog(String, JmolViewer, String, Object, String, boolean) - Method in class org.jmol.export.dialog.Dialog
-
- getOpenFileNameFromDialog(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- 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
-
- getOptions() - Method in class org.openscience.jmol.app.JmolApp
-
- getOrAddBond(Atom, Atom, int, short, BitSet, float, boolean) - Method in class org.jmol.modelset.BondCollection
-
- getOrAllocateChain(Model, char) - Method in class org.jmol.modelset.ModelLoader
-
- getOrderName() - Method in class org.jmol.modelset.Bond
-
- getOrderNumberAsString() - Method in class org.jmol.modelset.Bond
-
- getOrientation() - Method in class org.jmol.viewer.StateManager
-
- getOrientation(String) - Method in class org.jmol.viewer.StateManager
-
- getOrientation() - Method in class org.jmol.viewer.Viewer
-
- 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, String) - 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
-
- getOrSetNewVariable(String, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getOrSetNewVariable(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
-
- getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
-
- getOtherAtom(JmolNode) - Method in class org.jmol.modelset.Bond
-
- getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
-
- getOtherAtom(JmolNode) - Method in class org.jmol.smiles.SmilesBond
-
- getOtherAtom(JmolNode) - Method in class org.jmol.util.JmolEdge
-
- getOutputStream(String, String[]) - Method in class org.jmol.viewer.Viewer
-
- getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
-
- getP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- getPageAuthorName() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getPairs(BitSet, BitSet, RadiusData, int) - Method in class org.jmol.shapesurface.Contact
-
- getPalette(String) - Static method in enum org.jmol.constant.EnumPalette
-
- getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
-
- getPaletteBW() - Method in class org.jmol.util.ColorEncoder
-
- getPaletteColorCount(int) - Method in class org.jmol.util.ColorEncoder
-
- getPaletteID(String) - Static method in enum org.jmol.constant.EnumPalette
-
- getPaletteID() - Method in class org.jmol.modelset.Atom
-
- getPaletteId() - Method in class org.jmol.modelset.HBond
-
- getPaletteName(byte) - Static method in enum org.jmol.constant.EnumPalette
-
- getPaletteWB() - Method in class org.jmol.util.ColorEncoder
-
- getPane() - Method in class org.jmol.console.JmolConsole
-
- 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, Map<String, FFParam>) - Static method in class org.jmol.minimize.forcefield.Calculations
-
- getParameter(float[], int, double, String) - Static method in class org.jmol.quantum.NciCalculation
-
- getParameter(String, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
strictly a getter -- returns "" if not found
- getParameter(String, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getParameter(String) - Method in class org.jmol.viewer.Viewer
-
- getParameterEscaped(String) - Method in class org.jmol.script.ScriptEvaluator
-
- 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.script.Token
-
- getParamType(int) - Static method in class org.jmol.viewer.PropertyManager
-
- getParent(Object) - Method in class org.jmol.popup.JmolPopup
-
- getParent() - Method in class org.jmol.script.ScriptFlowContext
-
- getParent() - Method in class org.jmol.smiles.SmilesSearch
-
- getParentItem(String, Matrix4f) - Method in class org.jmol.export._IdtfExporter
-
- getPartialBondDotted(int) - Static method in class org.jmol.util.JmolEdge
-
- getPartialBondOrder(int) - Static method in class org.jmol.util.JmolEdge
-
- getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.script.ScriptEvaluator
-
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5
+ (m % 0x1F)
- getPartialBondOrderFromString(String) - Static method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
-
- getPartialCharges() - Method in class org.jmol.viewer.Viewer
-
- getPartialDots() - Method in class org.jmol.viewer.Viewer
-
- getPathHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Just recovers the path settings from last session.
- getPdbAtomData(BitSet, OutputStringBuffer) - Method in class org.jmol.modelset.ModelCollection
-
- getPdbBondInfo(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getPdbBondInfo(String) - Method in class org.jmol.viewer.Viewer
-
- getPdbCharge(String, String) - Method in class org.jmol.modelset.ModelLoader
-
- getPdbConformation(BitSet, int) - Method in class org.jmol.modelset.Model
-
- getPdbData(int, String, BitSet, Object[], OutputStringBuffer) - Method in class org.jmol.modelset.ModelCollection
-
- getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelset.Polymer
-
- getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- getPdbData(Viewer, BioPolymer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Static method in class org.jmol.modelsetbio.BioPolymer
-
- getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelsetbio.NucleicPolymer
-
- getPdbData(Viewer, char, char, int, int, BitSet, BitSet, boolean, boolean, boolean, LabelToken[], OutputStringBuffer, StringBuffer, BitSet) - Method in class org.jmol.modelsetbio.PhosphorusPolymer
-
- getPdbData(BitSet, OutputStringBuffer) - Method in class org.jmol.viewer.Viewer
-
- getPdbData(int, String, Object[]) - Method in class org.jmol.viewer.Viewer
-
- getPDBHeader(int) - Method in class org.jmol.modelset.ModelCollection
-
- getPDBHeader() - 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.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.SurfaceReader
-
- getPhongExponent() - Static method in class org.jmol.g3d.Graphics3D
-
- getPickedPoint(Point3f, int) - Method in class org.jmol.shape.MeshCollection
-
- getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
-
- getPickingMode() - Method in class org.jmol.viewer.Viewer
-
- getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
-
- getPickingSpinRate() - Method in class org.jmol.viewer.Viewer
-
- getPickingState() - Method in class org.jmol.viewer.ActionManager
-
- getPickingStyle(String) - Static method in class org.jmol.viewer.ActionManager
-
- getPickingStyle() - Method in class org.jmol.viewer.ActionManager
-
- getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
-
- GetPixel(int, int) - Method in class org.jmol.export.image.GifEncoder
-
- getPlane(int, float[]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
-
- getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
- getPlane(int, boolean) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- getPlane(int, float[]) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- getPlane() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getPlane(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- getPlane(float[], boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
-
- getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
-
- getPlane(Vector3f) - Method in class org.jmol.symmetry.PointGroup
-
- getPlane(String) - Static method in class org.openscience.jvxl.Jvxl
-
- getPlaneIntersection(int, Point4f, float, int, int) - Method in class org.jmol.modelset.ModelCollection
-
- getPlaneIntersection(int, Point4f, float, int) - Method in class org.jmol.viewer.Viewer
-
- getPlaneNormals(JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesSearch
-
- getPlaneProcessed(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
Retrieve raw file planes and pass them to the calculation object for
processing into new data.
- getPlaneProjection(Point3f, Point4f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getPlaneShade(int, int, double[]) - Method in class org.jmol.g3d.Sphere3D
-
- getPlaneThroughPoint(Point3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
-
- getPlaneThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
-
- getPlaneValue(int) - Method in class org.jmol.quantum.NciCalculation
-
We always have four raw planes in hand; we just need to know which
three to use in any particular case.
- getPoint() - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- getPoint(int, Point3f) - Method in class org.jmol.jvxl.data.VolumeData
-
- getPoint(String, int, int[], boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
-
- getPoint(Map<String, Object>) - Method in class org.jmol.viewer.ActionManager
-
- getPoint3f(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getPoint4f(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getPointArc() - Method in class org.jmol.modelset.Measurement
-
- getPointArray(int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getPointCount() - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getPointCount(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getPointer(int) - Static method in class org.jmol.shape.Object2d
-
- getPointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- 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
-
- getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
-
- getPointOrBitsetOperation(Token, ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
-
- getPointOrPlane(int, boolean, boolean, boolean, boolean, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getPointP(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
-
- getPoints() - Method in class org.jmol.modelset.Measurement
-
- getPointVector(Token, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getPolygonColorData(int, short[], BitSet) - Static method in class org.jmol.shapesurface.Isosurface
-
- 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
-
- getPolymerIndexInModel() - 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, List<Point3f[]>) - Method in class org.jmol.modelset.ModelCollection
-
- getPolymerPointsAndVectors(int, BitSet, List<Point3f[]>, boolean, float) - Method in class org.jmol.modelset.Polymer
-
- getPolymerPointsAndVectors(int, BitSet, List<Point3f[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getPolymerPointsAndVectors(BitSet, List<Point3f[]>) - Method in class org.jmol.viewer.Viewer
-
- getPolymerSequenceAtoms(int, int, BitSet, BitSet) - Method in class org.jmol.modelset.Polymer
-
- getPolymerSequenceAtoms(int, int, BitSet, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getPopInHeight() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getPopInWidth() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getPopupMenu() - Method in class org.jmol.viewer.Viewer
-
- getPort() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- getPosCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getPosition(Object) - Method in class org.jmol.popup.JmolPopup
-
- getPosition() - Method in class org.jmol.util.BinaryDocument
-
- getPosition() - Method in class org.openscience.jvxl.MonitorInputStream
-
- getPositionMin() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getPrecedence(int) - Static method in class org.jmol.script.Token
-
- getPrefixToken() - Method in class org.jmol.script.ScriptCompiler
-
- getPreserveState() - Method in class org.jmol.viewer.Viewer
-
This flag if set FALSE:
1) turns UNDO off for the application 2) turns history off 3) prevents
saving of inlinedata for later LOAD "" commands 4) turns off the saving of
changed atom properties 5) does not guarantee accurate state representation
6) disallows generation of the state
It is useful in situations such as web sites where memory is an issue and
there is no need for such.
- getPrivateKey() - Method in class org.jmol.export.Export3D
-
- getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
-
- getProperties() - Method in class org.jmol.export.history.HistoryFile
-
- getProperty(String, String, Object) - Method in class org.jmol.api.JmolSimpleViewer
-
- 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) - Method in interface org.jmol.applet.JmolAppletInterface
-
- getProperty(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- getProperty(String, String) - Method in class org.jmol.export.history.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() - Method in class org.jmol.script.ScriptEvaluator
-
- getproperty - Static variable in class org.jmol.script.Token
-
- getProperty(String, int) - Method in class org.jmol.shape.Axes
-
- getProperty(String, Object[]) - 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, Object[]) - Method in class org.jmol.shape.MeshCollection
-
- getProperty(String, int) - Method in class org.jmol.shape.MeshCollection
-
- getProperty(String, Object[]) - Method in class org.jmol.shape.Shape
-
- getProperty(String, int) - Method in class org.jmol.shape.Shape
-
- getProperty(String, int) - Method in class org.jmol.shape.Sticks
-
- getProperty(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
-
- getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
-
- getProperty(String, Object[]) - Method in class org.jmol.shapespecial.Draw
-
- getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
-
- getProperty(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
-
- getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
-
- getProperty(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
-
- getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
-
- getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
-
- getProperty(String, boolean) - Static method in class org.jmol.util.Logger
-
- getProperty(Viewer, String, String, Object) - Static method in class org.jmol.viewer.PropertyManager
-
- getProperty(Object) - Method in class org.jmol.viewer.ShapeManager
-
- 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 class org.jmol.applet.Jmol
-
- getPropertyAsJSON(String, String) - Method in class org.jmol.applet.Jmol
-
- getPropertyAsJSON(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- getPropertyAsJSON(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- getPropertyAsObject(Viewer, String, Object, String) - Static method in class org.jmol.viewer.PropertyManager
-
- getPropertyAsString(String) - Method in class org.jmol.applet.Jmol
-
- getPropertyAsString(String, String) - Method in class org.jmol.applet.Jmol
-
- getPropertyAsString(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- getPropertyAsString(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- getPropertyColorRange() - Method in class org.jmol.viewer.ColorManager
-
- getPropertyColorScheme() - Method in class org.jmol.viewer.Viewer
-
- getPropertyCount(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- getPropertyName(int) - Static method in class org.jmol.viewer.PropertyManager
-
- getPropertyNumber(String) - Static method in class org.jmol.viewer.PropertyManager
-
- getPropertyTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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
-
- getProteinStructureState(BitSet, boolean, boolean, int) - Method in class org.jmol.modelset.ModelCollection
-
- getProteinStructureState() - Method in class org.jmol.viewer.Viewer
-
- getProteinStructureSubType() - Method in class org.jmol.modelset.Atom
-
- getProteinStructureSubType() - Method in class org.jmol.modelset.Group
-
- getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- getProteinStructureTag() - Method in class org.jmol.modelset.Atom
-
- getProteinStructureTag() - Method in class org.jmol.modelset.Group
-
- getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getProteinStructureType(String) - Static method in enum org.jmol.constant.EnumStructure
-
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.
- 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.CarbohydrateMonomer
-
- getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
-
- getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
-
- getQuality(String) - Method in class org.jmol.export.dialog.Dialog
-
- getQuantumShell(String) - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getQuantumShellTag(int) - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getQuantumShellTagID(String) - Static method in class org.jmol.api.JmolAdapter
-
- getQuantumShellTagID(String) - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.api.JmolAdapter
-
- getQuantumShellTagIDSpherical(String) - Static method in enum org.jmol.constant.EnumQuantumShell
-
- getQuardricZ(double, double, double[], double[]) - Static method in class org.jmol.util.Quadric
-
- 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.AlphaMonomer
-
- getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- getQuaternionArray(Object) - Static method in class org.jmol.script.ScriptMathProcessor
-
- getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
-
- getQuaternionFrame(Point3f, Tuple3f, Tuple3f) - Static method in class org.jmol.util.Quaternion
-
- getQuaternionFrame(Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Quaternion
-
- getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
-
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- 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
-
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- getQuaternionParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getQuaternionStraightness(String, Quaternion, Quaternion) - Static method in class org.jmol.modelsetbio.BioPolymer
-
- getQuotedString(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- getRadius() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
-
- getRadius() - Method in class org.jmol.api.JmolAdapter.AtomIterator
-
- getRadius(int) - 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
-
- getRange(BitSet) - Method in class org.jmol.modelset.Polymer
-
- getRange(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getRangeGroups(int, BitSet, BitSet) - Method in class org.jmol.modelset.Polymer
-
- getRangeGroups(int, BitSet, BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
-
- getRasmolHydrogenBonds(Model, BitSet, BitSet, List<Bond>, boolean, int, boolean) - Method in class org.jmol.modelset.BondCollection
-
- getRasMolRadius() - Method in class org.jmol.modelset.Atom
-
- getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
-
- getRasmolSetting(int) - Method in class org.jmol.viewer.Viewer
-
- getRawNormal(Quaternion) - Static method in class org.jmol.util.Quaternion
-
- 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.jmolpanel.StatusListener
-
- getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
-
- getRenderableBitSet() - Method in class org.jmol.viewer.ShapeManager
-
- getRenderableBitSet() - Method in class org.jmol.viewer.Viewer
-
- getRenderer(int, Graphics3D) - Method in class org.jmol.viewer.RepaintManager
-
- 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
- getRendering() - Method in class org.jmol.shape.Mesh
-
- 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
- getRepaintWait() - Method in class org.jmol.viewer.Viewer
-
- getResidueLabels() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- getResiduePointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- getResno() - Method in class org.jmol.modelset.Atom
-
- getResno() - Method in class org.jmol.modelset.Group
-
- getResno() - Method in class org.jmol.smiles.SmilesAtom
-
- getResno() - Method in interface org.jmol.util.JmolNode
-
- 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
-
- getResourceStream(String) - Static method in class org.openscience.chimetojmol.ChimePanel
-
- getResourceString(Object, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getResult(boolean) - Method in class org.jmol.script.ScriptMathProcessor
-
- getRibbonAspectRatio() - Method in class org.jmol.viewer.Viewer
-
- getRibbonBorder() - Method in class org.jmol.viewer.Viewer
-
- getRingCache(int, int, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
-
- getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
-
- getRingPointer(int) - Static method in class org.jmol.smiles.SmilesParser
-
- getRmsd(Point3f[][], Quaternion) - Static method in class org.jmol.util.Measure
-
- getRnd(float) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- getRocketBarrelFlag() - Method in class org.jmol.viewer.Viewer
-
- getRotateBondIndex() - 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(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
-
- getRotationMatrix(Point3f, Point3f, float) - Method in class org.jmol.export.___Exporter
-
- getRotationMatrix(Point3f, Point3f, float, Point3f, Point3f) - Method in class org.jmol.export.___Exporter
-
- getRotationQuaternion() - Method in class org.jmol.viewer.TransformManager
-
- getRotationQuaternion() - Method in class org.jmol.viewer.Viewer
-
- 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() - Method in class org.jmol.viewer.TransformManager
-
- getRowCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
-
- getRubberBand() - Method in class org.jmol.viewer.ActionManager
-
- 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
-
- getSavedOrienationText(String) - Method in class org.jmol.viewer.Viewer
-
- getSavedOrientationText(String) - Method in class org.jmol.viewer.StateManager
-
- 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(boolean) - Method in class org.jmol.viewer.Viewer
-
- getScalePixelsPerMicron() - Method in class org.jmol.shape.Object2d
-
- getSchemeIndex(String) - Static method in class org.jmol.util.ColorEncoder
-
- 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(Object) - Method in class org.jmol.api.JmolViewer
-
- getScreenImage() - Method in class org.jmol.g3d.Graphics3D
-
- getScreenImage(Object) - Method in class org.jmol.viewer.Viewer
-
- getScreenNormal(Point3f, Vector3f, float) - Method in class org.jmol.export.__RayTracerExporter
-
- 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.script.ScriptEvaluator
-
- getScript() - Method in class org.jmol.shape.Object2d
-
- getScriptBitSets(String, BitSet[]) - Method in class org.jmol.shapesurface.Isosurface
-
- getScriptButtonPercent() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- getScriptContext() - Method in class org.jmol.script.ScriptEvaluator
-
- getScriptCount() - Method in class org.jmol.viewer.ScriptManager
-
- getScriptDelay() - Method in class org.jmol.viewer.Viewer
-
- getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
-
- getScriptEditor() - Method in class org.jmol.console.JmolConsole
-
- getScriptID(ScriptContext) - Method in class org.jmol.script.ScriptEvaluator
-
- getScriptItem(boolean, boolean) - Method in class org.jmol.viewer.ScriptManager
-
- getScriptParams() - Method in class org.jmol.jvxl.readers.Parameters
-
- getSearch(String, int, BitSet) - Method in class org.jmol.minimize.Minimizer
-
- getSearch(SmilesSearch, String, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
-
- getSectorAllocationTable() - Method in class org.jmol.util.CompoundDocument
-
- getSectorData(StringBuffer, byte[], int, int, boolean, ZipUtil.GZipData) - Method in class org.jmol.util.CompoundDocument
-
- getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
-
- getSelectAllModels() - Method in class org.jmol.viewer.Viewer
-
- getSelectedAtomIterator(BitSet, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
-
- getSelectedAtomIterator(BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getSelectedAtomIterator(BitSet, boolean, boolean, boolean) - 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(boolean) - Method in class org.jmol.viewer.Viewer
-
- getSelectionSet(String) - Method in class org.jmol.viewer.ActionManager
-
- getSelectionSet(boolean) - Method in class org.jmol.viewer.SelectionManager
-
- getSelectionSet(boolean) - Method in class org.jmol.viewer.Viewer
-
- getSelectionSubset() - Method in class org.jmol.viewer.SelectionManager
-
- 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.script.ScriptEvaluator
-
- 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
-
- getSequence() - Method in class org.jmol.viewer.ActionManager
-
- 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.script.ScriptCompilationTokenParser
-
- 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
-
- getSerialID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- getSerialID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
-
- getSetAxesTypeMad(int) - Method in class org.jmol.script.ScriptEvaluator
-
- 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.script.Token
-
- getSettings(String) - Method in class org.jmol.shapesurface.MolecularOrbital
-
- getShadeIndex(Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
-
- getShadeIndex(short) - Method in class org.jmol.g3d.Normix3D
-
- getShadeIndex(float, float, float) - Static method in class org.jmol.g3d.Shade3D
-
- getShadeIndexNormalized(float, float, float) - Static method in class org.jmol.g3d.Shade3D
-
- getShades(int, boolean) - Static method in class org.jmol.g3d.Colix3D
-
- 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.viewer.ShapeManager
-
- getShapeClassName(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getShapeCommands(Map<String, BitSet>, Map<String, BitSet>) - Static method in class org.jmol.shape.Shape
-
- getShapeCommands(Map<String, BitSet>, Map<String, BitSet>, 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
-
- getShapeErrorState() - Method in class org.jmol.viewer.Viewer
-
- getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
-
Returns the shape type index for a shape object given the object name.
- getShapeInfo() - Method in class org.jmol.viewer.ShapeManager
-
- getShapeInfo() - Method in class org.jmol.viewer.Viewer
-
- getShapeManager() - Method in class org.jmol.viewer.Viewer
-
- getShapeNameParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEvaluator
-
- getShapeProperty(int, String, Object[]) - Method in class org.jmol.script.ScriptEvaluator
-
- getShapeProperty(int, String, int) - Method in class org.jmol.script.ScriptEvaluator
-
- getShapeProperty(int, String, int) - Method in class org.jmol.viewer.ShapeManager
-
- getShapeProperty(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
-
- getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
-
- getShapeProperty(int, String, Object[]) - 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
-
- getShapes() - Method in class org.jmol.viewer.ShapeManager
-
- 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.Echo
-
- getShapeState() - Method in class org.jmol.shape.FontLineShape
-
- getShapeState() - Method in class org.jmol.shape.FontShape
-
- 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.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.Dots
-
- getShapeState() - Method in class org.jmol.shapespecial.Draw
-
- getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
-
- getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
-
- getShapeState() - Method in class org.jmol.shapespecial.Vectors
-
- getShapeState() - Method in class org.jmol.shapesurface.Isosurface
-
- getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
-
- getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
-
- getShapeState(StringBuffer, boolean) - Method in class org.jmol.viewer.ShapeManager
-
- getShapeState(StringBuffer, boolean) - Method in class org.jmol.viewer.Viewer
-
- getShapeType(int) - Method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- getSheetSmoothing() - Method in class org.jmol.viewer.Viewer
-
- getSheetStructures(Polymer[], List<AminoPolymer.Bridge>, List<AminoPolymer.Bridge>, Map<String, AminoPolymer.Bridge>, Map<int[][], Boolean>, char[][], BitSet[], boolean, boolean) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
"sheet =: a set of one or more ladders connected by shared residues" (p.
- getShellEnumeration(int) - Static method in class org.jmol.api.JmolAdapter
-
- getShellOrder(int) - Static method in class org.jmol.quantum.MOCalculation
-
- getShortSectorAllocationTable() - Method in class org.jmol.util.CompoundDocument
-
- getShortStringData(int, int, boolean) - 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
-
- getSignature() - Method in class org.jmol.script.ScriptFunction
-
- getSize(int) - Method in class org.jmol.shape.AtomShape
-
- getSize(int) - Method in class org.jmol.shape.Shape
-
- getSize(Group) - Method in class org.jmol.shape.Shape
-
- getSize(Group) - Method in class org.jmol.shapebio.BioShapeCollection
-
- getSize(int) - Method in class org.jmol.shapespecial.Dots
-
- 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
- getSlabByAtom() - Method in class org.jmol.viewer.Viewer
-
- getSlabByMolecule() - Method in class org.jmol.viewer.Viewer
-
- getSlabColor() - Method in class org.jmol.util.MeshSurface
-
- getSlabDepthPlane(boolean) - Method in class org.jmol.viewer.TransformManager
-
- getSlabEnabled() - Method in class org.jmol.viewer.Viewer
-
- getSlabInfo() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getSlabObject(int, Object, boolean, Object) - Static method in class org.jmol.util.MeshSurface
-
- getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
-
- getSlabTranslucency() - Method in class org.jmol.util.MeshSurface
-
- getSlabType() - Method in class org.jmol.util.MeshSurface
-
- getSlabWithinRange(float, float) - Static method in class org.jmol.util.MeshSurface
-
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
-
scales slater using double factorials involving
quantum number n, l, and xyz exponents.
- getSlaterConstDSpherical(int, double, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
-
spherical scaling factors specifically for x2-y2 and z2 orbitals
see http://openmopac.net/Manual/real_spherical_harmonics.html
dz2 sqrt((1/2p)(5/8))(2cos2(q) -sin2(q)) sqrt(5/16p)(3z2-r2)/r2
dxz sqrt((1/2p)(15/4))(cos(q)sin(q))cos(f) sqrt(15/4p)(xz)/r2
dyz sqrt((1/2p)(15/4))(cos(q)sin(q))sin(f) sqrt(15/4p)(yz)/r2
dx2-y2 sqrt((1/2p)(15/16))sin2(q)cos2(f) sqrt(15/16p)(x2-y2)/r2
dxy sqrt((1/2p)(15/16))sin2(q)sin2(f) sqrt(15/4p)(xy)/r2
The fact() method returns sqrt(15/4p) for both z2 and x2-y2.
- getSlice() - Method in class org.openscience.jmol.app.surfacetool.Slice
-
- getSliceAngleXY() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getSliceMiddle() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getSlicePosition() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getSliceThickness() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getSmallMoleculeMaxAtoms() - Method in class org.jmol.viewer.Viewer
-
- getSmartAromatic() - Method in class org.jmol.viewer.Viewer
-
- getSmartsMatch(String, BitSet) - Method in class org.jmol.api.JmolViewer
-
- getSmartsMatch(String, BitSet) - Method in class org.jmol.viewer.Viewer
-
- getSmiles(JmolNode[], int, BitSet, boolean, boolean, boolean, String) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getSmiles(JmolNode[], int, BitSet) - Method in class org.jmol.smiles.SmilesGenerator
-
- getSmiles(StringBuffer, JmolNode, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
-
- getSmiles(JmolNode[], int, BitSet, boolean, boolean, boolean, String) - Method in class org.jmol.smiles.SmilesMatcher
-
- getSmiles(int, int, BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
returns the SMILES string for a sequence or atom set
does not include attached protons on groups
- getSmilesComponent(JmolNode, BitSet, boolean) - Method in class org.jmol.smiles.SmilesGenerator
-
creates a valid SMILES string from a model.
- getSmilesCorrelation(BitSet, BitSet, String, List<Point3f>, List<Point3f>, Matrix4f, List<BitSet>, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
-
- getSmilesMatches(String, String, BitSet, BitSet, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getSolventOn() - Method in class org.jmol.viewer.Viewer
-
- getSolventPoints(int, int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- 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, SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
-
- getSpaceGroupInfo(int, String, int, Point3f, Point3f, String) - Method in class org.jmol.modelset.ModelCollection
-
- getSpaceGroupInfo(String, SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
-
- getSpaceGroupInfo(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
-
- getSpartanDirs(String) - Static method in class org.jmol.adapter.smarter.Resolver
-
read the output file from the Spartan directory and decide from that what
files need to be read and in what order - usually M0001 or a set of Profiles.
- getSpartanFileList(String, String[]) - Static method in class org.jmol.adapter.smarter.Resolver
-
returns the list of files to read for every Spartan spardir.
- getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
-
- getSpecialAtomName(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
-
- 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
-
- getSpecularExponent() - Static method in class org.jmol.g3d.Graphics3D
-
- getSpecularPercent() - Static method in class org.jmol.g3d.Graphics3D
-
- 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
-
- getSpeedPixelsPerMillisecond(int, int) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getSphereData() - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a sphere.
- getSphereResource() - Method in class org.jmol.export._IdtfExporter
-
- getSphereShape(int) - Static method in class org.jmol.g3d.Sphere3D
-
- getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
-
- getSpinAxis(String, int) - Method in class org.jmol.shapespecial.Draw
-
- getSpinCenter(String, int, int) - Method in class org.jmol.shapespecial.Draw
-
- 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
-
- getSsbondsBackbone() - Method in class org.jmol.viewer.Viewer
-
- getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
-
- getStandardPdbHydrogenCount(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getStandardStringData(int, int, boolean) - 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() - Method in interface org.jmol.api.JmolGestureServerInterface
-
- getState(StringBuffer, boolean, 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() - Method in class org.jmol.shapespecial.Polyhedra.Polyhedron
-
- getState(StringBuffer) - Method in class org.jmol.util.ColorEncoder
-
- getState(StringBuffer) - Method in class org.jmol.viewer.AnimationManager
-
- getState(StringBuffer) - Method in class org.jmol.viewer.ColorManager
-
- getState(StringBuffer) - Method in class org.jmol.viewer.FileManager
-
- 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, int, int) - Method in class org.jmol.viewer.Viewer
-
- getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.ApiPlatform
-
- getStaticGraphics(Object, boolean) - Static method in class org.jmol.awt.Image
-
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
-
- 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
-
- getStatusManager() - Method in class org.jmol.viewer.Viewer
-
- getStereoFlag(JmolNode, JmolNode[], int, SmilesSearch.VTemp) - Static method in class org.jmol.smiles.SmilesGenerator
-
- getStereoImage(EnumStereoMode) - Method in class org.jmol.viewer.Viewer
-
- getStereoMode(String) - Static method in enum org.jmol.constant.EnumStereoMode
-
- getStereoRotationMatrix(boolean) - Method in class org.jmol.viewer.TransformManager
-
- getStraightness(float) - Static method in class org.jmol.modelsetbio.BioPolymer
-
- getStrandCount() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- getStrandCount() - Method in class org.jmol.api.JmolAdapter.StructureIterator
-
- getStrandCount(int) - Method in class org.jmol.viewer.Viewer
-
- getStream(InputStream) - Static method in class org.jmol.util.ZipUtil
-
- getStreamAsBytes(BufferedInputStream, OutputStream) - Static method in class org.jmol.viewer.FileManager
-
- 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(Viewer, String, String) - Method in class org.jmol.modelset.Measurement
-
- getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JSONObject
-
- getStringDetail() - Method in class org.jmol.modelset.Measurement
-
- getStringObjectAsVariable(String, String) - Method in class org.jmol.script.ScriptEvaluator
-
- getStringParameter(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- getStrucNo() - Method in class org.jmol.modelset.Atom
-
- getStrucNo() - Method in class org.jmol.modelset.Group
-
- getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- getStructure() - Method in class org.jmol.modelset.Group
-
- getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- getStructure(String) - Method in class org.jmol.popup.PopupResource
-
- getStructureCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getStructureID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- getStructureID() - Method in class org.jmol.api.JmolAdapter.StructureIterator
-
- getStructureId() - Method in class org.jmol.modelset.Atom
-
- getStructureId() - Method in class org.jmol.modelset.Group
-
- getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- getStructureId() - Method in class org.jmol.modelsetbio.Monomer
-
- getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
- getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get a StructureIterator.
- getStructureList() - Method in class org.jmol.modelset.ModelCollection
-
- getStructureList() - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getStructureList() - Method in class org.jmol.viewer.Viewer
-
- getStructureMidPoint(int) - Method in class org.jmol.modelsetbio.ProteinStructure
-
- getStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- 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
-
- getStrutDefaultRadius() - Method in class org.jmol.viewer.Viewer
-
- getStrutLengthMaximum() - Method in class org.jmol.viewer.Viewer
-
- getStrutsMultiple() - Method in class org.jmol.viewer.Viewer
-
- getStrutSpacingMinimum() - Method in class org.jmol.viewer.Viewer
-
- getSubPattern(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
-
- getSubstructureSet(String, JmolNode[], int, BitSet, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getSubstructureSet(String, JmolNode[], int, BitSet, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
-
Returns a bitset matching the pattern within atoms.
- getSubstructureSetArray(String, JmolNode[], int, BitSet, BitSet, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- getSubstructureSetArray(String, JmolNode[], int, BitSet, BitSet, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
-
Returns a vector of bitsets indicating which atoms match the pattern.
- getSubstructureType() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- getSubstructureType() - Method in class org.jmol.api.JmolAdapter.StructureIterator
-
- getSupported(String, boolean) - Method in class org.jmol.i18n.GT
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
-
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
-
The list of files returned by this function should contain the full path to
each file.
- getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getSurfaceData() - Method in class org.jmol.jvxl.readers.EfvetReader
-
- getSurfaceData() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- getSurfaceData() - Method in class org.jmol.jvxl.readers.PolygonFileReader
-
- 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
-
- getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
TEST: alternative EXACT position of fraction for spherical MarchingCubes
FOR: ttest.xyz:
2
isosurface molecular test showing discontinuities
C -2.70 0 0
C 2.75 0 0
RESULT:
LINEAR (points slightly within R):
$ isosurface resolution 5 volume area solvent 1.5 full
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
isosurfaceArea = [75.06620391572324]
isosurfaceVolume = [41.639681683494324]
NONLINEAR:
$ isosurface resolution 5 volume area solvent 1.5 full
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
isosurfaceArea = [75.11873783245028]
isosurfaceVolume = [41.727027252180655]
MSMS:
msms -if ttest.xyzrn -of ttest -density 5
MSMS 2.6.1 started on Local PC
Copyright M.F.
- getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getSurfacePointAndFraction(float, boolean, float, float, Point3f, Vector3f, int, int, int, int, int, float[], Point3f) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
getSurfacePointIndex is used by the Marching Cubes algorithm and
must return a unique integer identifier for
a vertex created by the Marching Cube algorithm when it finds an
edge.
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, Point3i, int, int, float, float, Point3f, Vector3f, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
-
- getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
-
- getSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
-
- getSurfaceSets() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getSymbol(String) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- getSymmetry() - Method in class org.jmol.viewer.Viewer
-
- getSymmetryInfo(BitSet, String, int, Point3f, Point3f, String, int) - Method in class org.jmol.modelset.ModelCollection
-
- getSymmetryInfo(BitSet, String, int, Point3f, Point3f, String, int) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getSymmetryOperation(int, String, int, Point3f, Point3f, String, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getSymmetryOperation(String, int, Point3f, Point3f, boolean) - Method in class org.jmol.viewer.Viewer
-
- getSymmetryOperationDescription(int, SymmetryInterface, Point3f, Point3f, String) - Method in interface org.jmol.api.SymmetryInterface
-
- getSymmetryOperationDescription(int, SymmetryInterface, Point3f, Point3f, String) - 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(boolean) - Method in class org.jmol.modelset.ModelCollection
-
- getSyncMode() - Method in class org.jmol.viewer.StatusManager
-
- getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
-
- getTaintedAtoms(byte) - Method in class org.jmol.modelset.AtomCollection
-
- getTaintedAtoms(byte) - Method in class org.jmol.viewer.Viewer
-
- getTargetValence() - Method in class org.jmol.modelset.Atom
-
- 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
-
- getTestFlag(int) - Method in class org.jmol.viewer.Viewer
-
- getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
-
- getText() - Method in interface org.jmol.api.JmolScriptEditorInterface
-
- getText() - Method in class org.jmol.console.AppletConsole
-
- getText() - Method in class org.jmol.console.JmolConsole
-
- getText() - Method in class org.jmol.console.ScriptEditor
-
- getText() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- getText() - Static method in class org.openscience.jmol.app.webexport.LogPanel
-
- getText3D(int, int, Graphics3D, String, Font3D, boolean) - Static method in class org.jmol.g3d.Text3D
-
- getTextureName(short) - Method in class org.jmol.export._ObjExporter
-
Returns the name to be used for the texture associated with the given
colix.
- 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
-
- getThetaDirected(Vector3f) - Method in class org.jmol.util.Quaternion
-
- getThetaRadians() - Method in class org.jmol.util.Quaternion
-
- getThicknessMax() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getTickInfo() - Method in class org.jmol.modelset.Measurement
-
- getTimeDifference(int) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- getTitle() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
gets the next token and sets global theToken and theValue
- getToken(int) - Method in class org.jmol.script.ScriptEvaluator
-
- getTokenFromName(String) - Static method in class org.jmol.script.Token
-
- getTokenPeeked() - Method in class org.jmol.util.CifDataReader
-
- getTokens(String) - Method in class org.jmol.adapter.readers.quantum.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.SurfaceFileReader
-
- 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.script.Token
-
- getTokFromName(String) - Static method in class org.jmol.script.Token
-
- getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
-
- 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
-
- getTrajectoryStep(Point3f[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
-
- getTrajectoryStep(Point3f[], boolean) - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- 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
-
- getTransformMatrix4(List<Point3f>, List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
-
- 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.script.ScriptEvaluator
-
- getTriangleData(Point3f, Point3f, Point3f) - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a triangle.
- getTriangleResource(String, Point3f, Point3f, Point3f) - Method in class org.jmol.export._IdtfExporter
-
- getTriangles() - Method in class org.jmol.jvxl.readers.EfvetReader
-
- getTrimmedLine() - Method in class org.jmol.g3d.Line3D
-
Cohen-Sutherland line clipping used to check visibility.
- getTrueAtomCount() - Method in class org.jmol.modelset.Model
-
- getType() - Method in interface org.jmol.api.JmolDialogInterface
-
- getType(Atom) - Static method in enum org.jmol.constant.EnumHBondType
-
- getType() - Method in class org.jmol.export.dialog.Dialog
-
- getType() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
-
- getType() - Method in class org.jmol.modelset.Polymer
-
- getType(int) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
-
- getUndeletedGroupAtomBits(BitSet) - Method in class org.jmol.viewer.Viewer
-
- getUnescapedStringLiteral() - Method in class org.jmol.script.ScriptCompiler
-
- 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.modelsetbio.Monomer
-
- 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
-
- getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
-
- getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
-
- getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
-
- 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
-
- getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
-
- getUnitCellInfoText() - Method in class org.jmol.modelset.ModelCollection
-
- getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
-
- getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
-
- getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
-
- getUnitCellMultiplier() - Method in class org.jmol.symmetry.UnitCell
-
- 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, boolean) - Method in class org.jmol.viewer.FileManager
-
- getUseMolecular() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- getUseNumberLocalization() - Method in class org.jmol.viewer.Viewer
-
- getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Returns a new File referenced by the property 'user.dir', or null
if the property is not defined.
- getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
-
- getUserVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getValAsObj() - Method in class org.jmol.script.ScriptVariable
-
- getValence() - Method in class org.jmol.modelset.Atom
-
- getValence() - Method in class org.jmol.modelset.Bond
-
- getValence() - Method in class org.jmol.smiles.SmilesAtom
-
- getValence() - Method in class org.jmol.smiles.SmilesBond
-
- getValence() - Method in interface org.jmol.util.JmolNode
-
- getValue(String, String) - Method in class org.jmol.applet.Jmol
-
- getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
for readers only
- getValue(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- getValue(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
-
- getValue(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- getValue() - Method in class org.jmol.modelset.Measurement
-
- getValue(double, boolean) - Method in class org.jmol.quantum.NciCalculation
-
- getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
-
- getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
-
- getValueAt(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- getValueAtPoint(Point3f, BitSet) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- getValueAtPoint(Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- getValueAtPoint(Point3f) - Method in class org.jmol.quantum.MepCalculation
-
- getValueLowerCase(String, String) - Method in class org.jmol.applet.Jmol
-
- getValues() - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- getVanderwaalsMar(int, EnumVdw) - Static method in class org.jmol.util.Elements
-
- getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
-
- getVanderwaalsMar(int, EnumVdw) - Method in class org.jmol.viewer.Viewer
-
- getVanderwaalsRadiusFloat(Viewer, EnumVdw) - Method in class org.jmol.modelset.Atom
-
- getVariable(Object) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableList(Map<String, ScriptVariable>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
-
- getVariableList() - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getVariableList() - Method in class org.jmol.viewer.Viewer
-
- getVdwClashRadius(ContactPair, double, double, double, double) - Static method in class org.jmol.shapesurface.Contact
-
well, heh, heh...
- getVdwLabel() - Method in enum org.jmol.constant.EnumVdw
-
- getVdwType(String) - Static method in enum org.jmol.constant.EnumVdw
-
- getVdwType(EnumVdw) - Method in class org.jmol.modelset.Atom
-
- getVdwType2(String) - Static method in enum org.jmol.constant.EnumVdw
-
- getVector(short) - Static method in class org.jmol.g3d.Normix3D
-
- getVector(int) - Method in class org.jmol.util.Quaternion
-
- getVector(int, float) - Method in class org.jmol.util.Quaternion
-
- getVectorsAndOrigin() - Method in class org.jmol.jvxl.readers.MapFileReader
-
- 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() - Method in class org.jmol.export.MeshData.Data
-
- getVertexCount(int) - Static method in class org.jmol.geodesic.Geodesic
-
- getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
-
- getVertexList(DrawMesh, int, int) - Static method in class org.jmol.shapespecial.Draw
-
- getVertexSource() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- getVertexValues(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- 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.jvxl.readers.EfvetReader
-
- getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
-
- getVertices() - Method in class org.jmol.symmetry.UnitCell
-
- getVertices() - Method in class org.jmol.util.MeshSurface
-
- getVibrationCoord(char) - Method in class org.jmol.modelset.Atom
-
- getVibrationCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
-
- 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, boolean) - Method in class org.jmol.modelset.AtomCollection
-
- getVibrationVector(int) - Method in class org.jmol.viewer.Viewer
-
- getViewer() - Method in class org.jmol.export.dialog.FilePreview.FPPanel
-
- getViewer() - Method in class org.jmol.shape.Shape
-
- getViewerData() - Method in class org.jmol.popup.SimplePopup
-
- getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
-
- getVisibleFramesBitSet() - Method in class org.jmol.viewer.AnimationManager
-
- getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
-
- getVisibleGhostBitSet() - Method in class org.jmol.shape.Mesh
-
- getVisibleSet() - Method in class org.jmol.modelset.AtomCollection
-
- getVisibleSet() - Method in class org.jmol.viewer.Viewer
-
- getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
-
- getVolume(Viewer, EnumVdw) - Method in class org.jmol.modelset.Atom
-
- getVolume() - Method in class org.jmol.util.ContactPair
-
- getVolume(BitSet, String) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getVoxel(int, int, int, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- 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
-
- getVoxelData(int) - Method in class org.jmol.jvxl.data.VolumeData
-
- getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
-
- getWidth(Object) - Static method in class org.jmol.awt.Image
-
- getWidth() - Method in class org.jmol.g3d.Text3D
-
- getWidthUnitVector() - Method in class org.jmol.modelsetbio.Sheet
-
- getWindow(Container) - Static method in class org.jmol.console.JmolConsole
-
- getWindowBorder(String) - Method in class org.jmol.export.history.HistoryFile
-
- getWindowPosition(String) - Method in class org.jmol.export.history.HistoryFile
-
- getWindowSize(String) - Method in class org.jmol.export.history.HistoryFile
-
- getWindowState(StringBuffer, int, int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- getWindowVisibility(String) - Method in class org.jmol.export.history.HistoryFile
-
- getWingAtom() - 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
-
- getWithinDistanceVector(List<Object[]>, float, Point3f, BitSet, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- getWord(String) - Method in class org.jmol.popup.PopupResource
-
- getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
-
- getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
-
- getWordContents() - Method in class org.jmol.popup.PopupResource
-
- getWordCountFromBitCount(int) - Static method in class org.jmol.util.FastBitSet
-
- getWorkingRadius(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- getWorkingRadius(Atom, AtomData) - Method in class org.jmol.modelset.AtomCollection
-
- getWrappedState(boolean, int, int) - Method in class org.jmol.viewer.Viewer
-
- 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.script.ScriptMathProcessor
-
- getX(SmilesAtom, JmolNode[], int, boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
-
- getXmlAttrib(String, String) - Static method in class org.jmol.util.XmlReader
-
- getXmlData(String, String, boolean, boolean) - Method in class org.jmol.util.XmlReader
-
- getXmlPoint(String, String) - Method in class org.jmol.util.XmlReader
-
- getXMLReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- 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() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
-
- getXYZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
-
- 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, boolean, 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
-
- getYCCArray(ApiPlatform) - Method in class org.jmol.util.JpegInfo
-
- getYOffset(int) - Static method in class org.jmol.shape.Object2d
-
- getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
-
- getZ() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
-
- getZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator
-
- getZapName() - Method in class org.jmol.viewer.Viewer
-
- 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(InputStream) - 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
-
- getZoom(int, BitSet, float) - Method in class org.jmol.script.ScriptEvaluator
-
- getZoomEnabled() - Method in class org.jmol.viewer.Viewer
-
- 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
-
- getZShadePower() - Static method in class org.jmol.g3d.Graphics3D
-
- geVdwBitSet() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- ghemicalMMLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- GhemicalMMReader - Class in org.jmol.adapter.readers.simple
-
- GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
-
- ghostCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- ghostPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- gibbsEnergy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- gibbsEnergy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- gibbsEntropy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- 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_CONECT - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- GLOBAL_FRACTCOORD - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- GLOBAL_ISPDB - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- GLOBAL_SYMMETRY - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- GLOBAL_UNITCELLS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- globalBooleans - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- globalDoApplySymmetry - Variable in class org.jmol.adapter.readers.xtal.AimsReader
-
- globalSerialID - Static variable in class org.jmol.modelsetbio.ProteinStructure
-
- goButton - Variable in class org.openscience.chimetojmol.ChimePanel
-
- goButton - Variable in class org.openscience.jmol.app.jmolpanel.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.jmolpanel.PovrayDialog
-
Save or else launch povray- ie do our thang!
- gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- gotoCmd(String) - Method in class org.jmol.script.ScriptEvaluator
-
- gotocmd - Static variable in class org.jmol.script.Token
-
- gotoCommand(int, boolean, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor
-
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
-
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
-
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- gotoParsedLine() - Method in class org.jmol.console.ScriptEditor
-
- gotoPosition(int, int) - Method in class org.jmol.console.ScriptEditor
-
- gotoSector(int) - Method in class org.jmol.util.CompoundDocument
-
- gotoTop() - Method in class org.jmol.console.ScriptEditor
-
- grabPixels(Object, int, int, int, int) - Method in interface org.jmol.api.ApiPlatform
-
- grabPixels(Object, int, int, int[]) - Method in interface org.jmol.api.ApiPlatform
-
used for JPG writing only; can be ignored
- grabPixels(Object, int, int, int[]) - Static method in class org.jmol.awt.Image
-
- grabPixels(Object, int, int, int, int) - Static method in class org.jmol.awt.Image
-
- grabPixels(Object, int, int, int[]) - Method in class org.jmol.awt.Platform
-
- grabPixels(Object, int, int, int, int) - Method in class org.jmol.awt.Platform
-
- grad - Variable in class org.jmol.quantum.NciCalculation
-
- GRADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- gradients - Variable in class org.jmol.minimize.forcefield.Calculations
-
- Graphics3D - Class in org.jmol.g3d
-
Provides high-level graphics primitives for 3D visualization.
- Graphics3D(ApiPlatform, boolean) - Constructor for class org.jmol.g3d.Graphics3D
-
Allocates a g3d object
- Graphics3D.Pixel - Class in org.jmol.g3d
-
- Graphics3D.Pixel() - Constructor for class org.jmol.g3d.Graphics3D.Pixel
-
- Graphics3D.ShadePixel - Class in org.jmol.g3d
-
- Graphics3D.ShadePixel() - Constructor for class org.jmol.g3d.Graphics3D.ShadePixel
-
- graphicsOffscreen - Variable in class org.jmol.g3d.Platform3D
-
- 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 - Static variable in class org.jmol.script.Token
-
- greyscaleRendering - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- gridpoints - Static variable in class org.jmol.script.Token
-
- gRight - Variable in class org.jmol.applet.Jmol
-
- GromacsReader - Class in org.jmol.adapter.readers.more
-
- GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
-
- 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 - Variable in class org.jmol.popup.SimplePopup
-
- group - Static variable in class org.jmol.script.Token
-
- group1 - Static variable in class org.jmol.script.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
-
- group3s - Variable in class org.jmol.adapter.readers.more.MdTopReader
-
- 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.ModelLoader
-
- groupID - Variable in class org.jmol.modelset.Group
-
- groupID - Variable in class org.jmol.multitouch.ActionManagerMT
-
- groupid - Static variable in class org.jmol.script.Token
-
- GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ARGININE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ION_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ION_MIN - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_LYSINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_PROLINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_WATER - Static variable in class org.jmol.viewer.JmolConstants
-
- groupIndex - Variable in class org.jmol.modelset.Group
-
- groupindex - Static variable in class org.jmol.script.Token
-
- groups - Variable in class org.jmol.modelset.Chain
-
- groups - Variable in class org.jmol.modelset.ModelLoader
-
- growAtomArrays(int) - Method in class org.jmol.modelset.ModelCollection
-
- 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, String, boolean) - Constructor for class org.jmol.i18n.GT.Language
-
- gto_exp - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- gui - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- guimap - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- GuiMap - Class in org.openscience.jmol.app.jmolpanel
-
- GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
-
- guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- guimap - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- gulpContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- GulpReader - Class in org.jmol.adapter.readers.xtal
-
Problems identified (Bob Hanson) --
-- Coordinates for the asymmetric unit are conventional.
- GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
-
- gxTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gxxTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gxyTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gxzTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gyTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gyyTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gyzTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gzTemp - Variable in class org.jmol.quantum.NciCalculation
-
- gzzTemp - Variable in class org.jmol.quantum.NciCalculation
-
- ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
-
- ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- ia - Variable in class org.jmol.minimize.forcefield.Calculation
-
- ia - Variable in class org.jmol.minimize.forcefield.Calculations
-
- iA - Variable in class org.jmol.util.MeshSurface
-
- iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
-
- iAtom - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- iAtom - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- iAtom - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- iatom - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.AtomIterator
-
- iAtom - Variable in class org.jmol.quantum.SlaterData
-
- iAtomSurface - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- iAtomSurface - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
-
- ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- ib - Variable in class org.jmol.minimize.forcefield.Calculation
-
- ib - Variable in class org.jmol.minimize.forcefield.Calculations
-
- iB - Variable in class org.jmol.util.MeshSurface
-
- ibond - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.BondIterator
-
- iBond - Variable in class org.jmol.modelset.BondIteratorSelected
-
- iBrace - Variable in class org.jmol.script.ScriptCompiler
-
- ic - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- ic - Variable in class org.jmol.minimize.forcefield.Calculation
-
- ic - Variable in class org.jmol.minimize.forcefield.Calculations
-
- iC - Variable in class org.jmol.util.MeshSurface
-
- ich - Variable in class org.jmol.util.CifDataReader
-
- iChain - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- ichBrace - Variable in class org.jmol.script.ScriptCompiler
-
- ichComment - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- ichCurrent - Variable in class org.jmol.adapter.smarter.LimitedLineReader
-
- ichCurrent - Variable in class org.jmol.util.LimitedLineReader
-
- ichCurrentCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- ichEnd - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- ichMathTerminator(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
-
For @{....}
- ichPeeked - Variable in class org.jmol.util.CifDataReader
-
- ichToken - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- iCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- iCommandError - Variable in class org.jmol.script.ScriptContext
-
- iCommandError - Variable in class org.jmol.script.ScriptEvaluator
-
- iCutout - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- ID - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- id - Variable in enum org.jmol.constant.EnumPalette
-
- id - Variable in enum org.jmol.constant.EnumQuantumShell
-
- id - Variable in enum org.jmol.constant.EnumStructure
-
- 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.modelset.TickInfo
-
- id - Static variable in class org.jmol.script.Token
-
- id - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
-
- id - Variable in class org.jmol.shapespecial.Ellipsoids.Ellipsoid
-
- iD - Variable in class org.jmol.util.MeshSurface
-
- id - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- iData - Variable in class org.jmol.minimize.forcefield.Calculation
-
- ident - Variable in class org.jmol.script.ScriptFlowContext
-
- identifier - Static variable in class org.jmol.script.Token
-
- identify - Static variable in class org.jmol.script.Token
-
- idFontFace - Variable in class org.jmol.g3d.Font3D
-
- idFontStyle - Variable in class org.jmol.g3d.Font3D
-
- idSpherical - Variable in enum org.jmol.constant.EnumQuantumShell
-
- iE - Variable in class org.jmol.util.MeshSurface
-
- ifCmd() - Method in class org.jmol.script.ScriptEvaluator
-
- ifcmd - Static variable in class org.jmol.script.Token
-
- ifPt - Variable in class org.jmol.script.ScriptMathProcessor
-
- ifStack - Variable in class org.jmol.script.ScriptMathProcessor
-
- ignore - Static variable in class org.jmol.script.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.script.ScriptEvaluator
-
- ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
-
- ignoreSymmetry - Variable in class org.jmol.adapter.smarter.Atom
-
- iGroup - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- ihalf - Variable in class org.jmol.util.ColorEncoder
-
- iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
-
- iHaveCenterBitSet - Variable in class org.jmol.shapespecial.Polyhedra
-
- iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- iHaveModelIndex - Variable in class org.jmol.shapesurface.Isosurface
-
- iHaveModelStatement - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- iHaveQuotedString - Variable in class org.jmol.script.ScriptCompiler
-
- 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.util.SimpleUnitCell
-
- ijkToPoint3f(int, Point3f, int) - Static method in class org.jmol.util.SimpleUnitCell
-
- Image - Class in org.jmol.awt
-
methods required by Jmol that access java.awt.Image
private to org.jmol.awt
- Image() - Constructor for class org.jmol.awt.Image
-
- 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 - Static variable in class org.jmol.script.Token
-
- image - Variable in class org.jmol.shape.Text
-
- imageChoices - Variable in class org.jmol.export.dialog.Dialog
-
- imageChoices - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- 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 - Variable in class org.jmol.export.dialog.Dialog
-
- imageExtensions - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- 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
-
- 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.jmolpanel.PovrayDialog
-
Called when the ImageSize check box is modified
- imageSizeHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- imageSizeRatioBox - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- imageSizeRatioCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- imageSizeTextHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- imageSizeTextWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- imageSizeWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- imagestate - Static variable in class org.jmol.script.Token
-
- imageState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- imageType - Variable in class org.jmol.export.dialog.Dialog
-
- imageType - Variable in class org.jmol.viewer.StatusManager
-
- imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- 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.jmolpanel.Splash
-
- imgWidth - Variable in class org.openscience.jmol.app.jmolpanel.Splash
-
- iMo0 - Variable in class org.jmol.adapter.readers.quantum.MOReader
-
- iMolecule - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
-
- implementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlReader
-
- implicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
-
- implicitStringCommand - Static variable in class org.jmol.script.Token
-
- importData(JComponent, Transferable) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
-
- in - Static variable in class org.jmol.script.Token
-
- IN_JMOL - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- inchi - Static variable in class org.jmol.script.Token
-
- inchikey - Static variable in class org.jmol.script.Token
-
- includeAllRelatedFrames(BitSet) - Method in class org.jmol.modelset.ModelSet
-
- includes(int, int) - Static method in class org.jmol.viewer.binding.Binding
-
- includeValueNaN - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- incompleteCmd - Variable in class org.jmol.console.JmolConsole
-
- increment(int) - Method in class org.jmol.script.ScriptVariable
-
- increment - Static variable in class org.jmol.script.Token
-
- incrementLineCount(String) - Method in class org.jmol.script.ScriptCompiler
-
- incrementX - Variable in class org.jmol.script.ScriptMathProcessor
-
- inDefinedStateBlock - Variable in class org.jmol.modelset.ModelCollection.StateScript
-
- index - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
-
- index - Variable in class org.jmol.bspt.Bspt
-
- 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.Measurement
-
- index - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
-
- index - Variable in class org.jmol.quantum.SlaterData
-
- index - Variable in class org.jmol.script.ScriptVariable
-
- index - Variable in class org.jmol.shape.Mesh
-
- index - Variable in class org.jmol.smiles.SmilesAtom
-
- index - Variable in class org.jmol.smiles.SmilesMeasure
-
- index - Variable in class org.jmol.symmetry.PointGroup.Operation
-
- index - Variable in class org.jmol.symmetry.SpaceGroup
-
- index - Variable in class org.jmol.util.JmolEdge
-
- index - Variable in class org.jmol.util.Point3fi
-
- index - Variable in class org.jmol.viewer.ActionManager.MotionPoint
-
- indexDown(float, int) - Static method in class org.jmol.jvxl.data.VolumeData
-
- indexes - Variable in class org.openscience.jmol.app.jmolpanel.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.util.JmolMolecule
-
- indicatedModelIndex - Variable in class org.jmol.shapespecial.Draw
-
- indices - Variable in class org.jmol.smiles.SmilesMeasure
-
- iNested - Variable in class org.jmol.smiles.SmilesAtom
-
- iNext - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- 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 - Variable in class org.jmol.atomdata.RadiusData
-
- info - Static variable in class org.jmol.script.Token
-
- info - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- info - Variable in class org.jmol.symmetry.PointGroup
-
- info(String) - Method in class org.jmol.util.DefaultLogger
-
- info() - Method in class org.jmol.util.LimitedLineReader
-
- info(String) - Static method in class org.jmol.util.Logger
-
og* Writes a log at INFO level.
- info(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at INFO level.
- INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
-
- INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
-
- INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
-
- INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
-
- INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
-
- INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
-
- INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
-
- infoLabel - Variable in class org.openscience.jmol.app.jmolpanel.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.quantum.NWChemReader
-
- init() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- init(XmlReader, AtomSetCollection) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- init() - Method in class org.jmol.applet.AppletWrapper
-
- init() - Method in class org.jmol.applet.Jmol
-
- init() - Method in interface org.jmol.applet.WrappedApplet
-
- initApplication() - Method in class org.jmol.applet.Jmol
-
- initHuf() - Method in class org.jmol.util.Huffman
-
- INITIAL_ATOMS - Static variable in class org.jmol.smiles.SmilesSearch
-
- initialFile - Variable in class org.jmol.export.dialog.Dialog
-
- initialize(BasisFunctionReader, String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- initialize() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- initialize(ModelSet) - Method in interface org.jmol.api.JmolBioResolver
-
- initialize(JmolViewer, boolean, String, boolean) - Method in interface org.jmol.api.JmolPopupInterface
-
- initialize(int, Point3f[], BitSet) - Method in class org.jmol.bspt.Bspf
-
- initialize(Point3f, float, boolean) - Method in class org.jmol.bspt.CubeIterator
-
initialize to return all points within the sphere defined
by center and radius
- initialize(boolean) - Method in class org.jmol.g3d.Platform3D
-
- initialize() - Method in class org.jmol.jvxl.readers.Parameters
-
- initialize(Bspf, BitSet, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
############## ITERATOR SHOULD BE RELEASED #################
- initialize(ModelSet) - Method in class org.jmol.modelsetbio.Resolver
-
- initialize(JmolViewer, boolean, String, boolean) - Method in class org.jmol.popup.JmolPopup
-
- initialize(int, int, int, Point3f[]) - Method in class org.jmol.quantum.MOCalculation
-
- initialize(int, int, int, Point3f[]) - Method in class org.jmol.quantum.QuantumCalculation
-
- initialize - Static variable in class org.jmol.script.Token
-
- initialize(int, Point3f[], Point4f) - Method in class org.jmol.shape.Mesh
-
- initialize() - Method in class org.jmol.shapebio.BioShapeCollection
-
- initialize() - Method in class org.jmol.shapespecial.Dots
-
- initialize(boolean) - Method in class org.jmol.viewer.Viewer
-
- initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- initializeAtomBondModelCounts(int) - 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
-
- initializeCartesianToFractional() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- initializeEigen() - Method in class org.jmol.quantum.NciCalculation
-
- initializeExporter(String, Viewer, double, Graphics3D, Object) - Method in interface org.jmol.api.JmolRendererInterface
-
- initializeExporter(String, Viewer, double, Graphics3D, Object) - Method in class org.jmol.export.Export3D
-
- initializeExporter(String, Viewer, double, Graphics3D, Object) - Method in class org.jmol.g3d.Graphics3D
-
- initializeExporter(JmolRendererInterface, String, Object) - Method in class org.jmol.viewer.Viewer
-
- initializeHydrogenAddition(ModelLoader, int) - Method in interface org.jmol.api.JmolBioResolver
-
- initializeHydrogenAddition(ModelLoader, int) - Method in class org.jmol.modelsetbio.Resolver
-
- initializeInfo(String, Map<String, Object>) - Method in class org.jmol.modelset.ModelLoader
-
- initializeIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- initializeIsosurface() - Method in class org.jmol.shapesurface.Isosurface
-
- initializeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- initializeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- initializeModel(boolean) - Method in class org.jmol.viewer.Viewer
-
- initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
-
- initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
-
- initializeOutput(Viewer, double, Graphics3D, Object) - Method in class org.jmol.export.___Exporter
-
- initializeOutput(Viewer, double, Graphics3D, Object) - Method in class org.jmol.export._ObjExporter
-
- initializeOutput(Viewer, double, Graphics3D, Object) - Method in class org.jmol.export._TachyonExporter
-
- initializePointers(int) - Method in class org.jmol.viewer.AnimationManager
-
- initializePolymer(BioShape) - Method in class org.jmol.shapebio.BioShapeRenderer
-
- initializeProperties() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- initializeReader() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.OdysseyReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- initializeShape(Viewer, Graphics3D, ModelSet, int) - Method in class org.jmol.shape.Shape
-
- initializeSurfaceData() - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- 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.SurfaceReader
-
- initIsosurface(int) - Method in class org.jmol.script.ScriptEvaluator
-
- 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
-
- initPlanes() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- initRenderer() - Method in class org.jmol.shape.AxesRenderer
-
- initRenderer() - Method in class org.jmol.shape.CageRenderer
-
- initRenderer() - Method in class org.jmol.shape.ShapeRenderer
-
- initRenderer() - Method in class org.jmol.shape.UccageRenderer
-
- initRenderer() - Method in class org.jmol.shapespecial.DotsRenderer
-
- initRenderer() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- initShape() - Method in class org.jmol.shape.Axes
-
- initShape() - Method in class org.jmol.shape.Bbcage
-
- initShape() - Method in class org.jmol.shape.Echo
-
- initShape() - Method in class org.jmol.shape.FontShape
-
- 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.Dots
-
- initShape() - Method in class org.jmol.shapespecial.Draw
-
- initShape() - Method in class org.jmol.shapespecial.GeoSurface
-
- initShape() - Method in class org.jmol.shapesurface.Contact
-
- initShape() - Method in class org.jmol.shapesurface.Isosurface
-
- initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
-
- initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
-
- initShape() - Method in class org.jmol.shapesurface.Plot3D
-
- initShape() - Method in class org.jmol.shapesurface.Pmesh
-
- initSlice() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- 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.jmolpanel.PreferencesDialog
-
- initWindows() - Method in class org.jmol.applet.Jmol
-
- inline - Static variable in class org.jmol.script.Token
-
- inlineNewlineChar - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- inMotion - Variable in class org.jmol.viewer.AnimationManager
-
- input - Variable in class org.jmol.console.AppletConsole
-
- inputCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
-
- inputFileName - Variable in class org.jmol.export.dialog.Dialog
-
- inputOnly - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- inputOnly - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- inputOnly - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- inputTabs - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- inRange(int, int) - Method in class org.jmol.viewer.ActionManager.Mouse
-
- INS_CODE - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- insertion - Static variable in class org.jmol.script.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
-
- insertString(int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
-
- insideMaskTable - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- insideOut - Variable in class org.jmol.jvxl.data.JvxlData
-
- insideOut - Variable in class org.jmol.jvxl.readers.Parameters
-
- insideout - Static variable in class org.jmol.script.Token
-
- insideOut - Variable in class org.jmol.shape.Mesh
-
- inSocket - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- installMainMenu(Object) - Method in class org.jmol.popup.JmolPopup
-
- instance - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- instanceList - Variable in class org.openscience.jmol.app.webexport.WebPanel
-
- instructionDispatchLoop(boolean) - Method in class org.jmol.script.ScriptEvaluator
-
here we go -- everything else in this class is called by this method or one
of its subsidiary methods.
- 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.AnimationManager
-
- intAsFloat - Variable in class org.jmol.modelset.LabelToken
-
- integer - Static variable in class org.jmol.script.Token
-
- integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- integration - Variable in class org.jmol.quantum.MOCalculation
-
- intenseFraction - Static variable in class org.jmol.g3d.Shade3D
-
- intercept(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares.Triangle
-
- 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
-
- interior - Static variable in class org.jmol.script.Token
-
- interlace - Variable in class org.jmol.export.image.GifEncoder
-
- Interlace - Variable in class org.jmol.export.image.GifEncoder
-
- intermolecular - Static variable in class org.jmol.script.Token
-
- internal - Static variable in class org.jmol.script.Token
-
- 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
-
- internalTranslation - Variable in class org.jmol.viewer.TransformManager
-
- interpolate(int, int) - Method in class org.jmol.g3d.Cylinder3D
-
- interpolateFraction(Point3f, Point3f, float, float, float, float[], float[], int) - Static method in class org.jmol.util.MeshSurface
-
- interpolatePoint(Point3f, Point3f, float, float, float, float, float[], float[], int) - Static method in class org.jmol.util.MeshSurface
-
- interpolatePrecisely(int, int) - Method in class org.jmol.g3d.Cylinder3D
-
- interpolateSphere(Point3f, Point3f, float, float, double, float, float, float[], float[], int) - Method in class org.jmol.util.MeshSurface
-
- interruptExecution - Variable in class org.jmol.script.ScriptEvaluator
-
- interruptQueueThreads() - Method in class org.jmol.viewer.ScriptManager
-
- interruptScript - Variable in class org.jmol.viewer.Viewer
-
- intersectID - Variable in class org.jmol.shapespecial.Draw
-
- intersection - Variable in class org.jmol.jvxl.readers.Parameters
-
- intersection - Static variable in class org.jmol.script.Token
-
- intersectPlane(Point4f, float, int) - Method in class org.jmol.util.BoxInfo
-
returns a set of points defining the geometric object within the given
plane that spans the unit cell within the given margins
- intersectPlane(Point4f, List<Object>, int) - Static method in class org.jmol.util.TriangleData
-
a generic cell - plane intersector -- used for finding the plane through a
unit cell
- intlTableNumber - Variable in class org.jmol.symmetry.SpaceGroup
-
- intlTableNumberExt - Variable in class org.jmol.symmetry.SpaceGroup
-
- intlTableNumberFull - Variable in class org.jmol.symmetry.SpaceGroup
-
- intparam - Static variable in class org.jmol.script.Token
-
- intParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- intParameter(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- intPeek() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- intproperty - Static variable in class org.jmol.script.Token
-
- intramolecular - Variable in class org.jmol.modelset.MeasurementData
-
- intramolecular - Static variable in class org.jmol.script.Token
-
- intramolecular - Variable in class org.jmol.shape.Measures
-
- intSetting(int) - Method in class org.jmol.script.ScriptEvaluator
-
- intThread - Variable in class org.jmol.viewer.AnimationManager.AnimationThread
-
- intToken(int) - Static method in class org.jmol.script.Token
-
- intValue - Variable in class org.jmol.script.Token
-
- intVariable(int) - Static method in class org.jmol.script.ScriptVariable
-
- inv() - Method in class org.jmol.util.Quaternion
-
- INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- invalidatedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- invalidateMesh - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- invalidatePolygons() - Method in class org.jmol.util.MeshSurface
-
- 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.shapesurface.Isosurface
-
- invalidateVertices(BitSet) - Method in class org.jmol.jvxl.data.MeshData
-
- invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
-
- invalidLead - Variable in class org.jmol.modelsetbio.BioPolymer
-
- 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.
- inverseMatrix - Variable in class org.jmol.jvxl.data.VolumeData
-
- inverseNormixes - Static variable in class org.jmol.g3d.Normix3D
-
- invertAtomCoord(Point3f, BitSet) - Method in class org.jmol.viewer.Viewer
-
- invertAtomCoord(Point4f, BitSet) - Method in class org.jmol.viewer.Viewer
-
- 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, int, BitSet, BitSet) - Method in class org.jmol.modelset.ModelSet
-
- invertSelected() - Method in class org.jmol.script.ScriptEvaluator
-
- invertSelected - Static variable in class org.jmol.script.Token
-
- invertSelected(Point3f, Point4f, int, BitSet) - 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.quantum.MopacGraphfReader
-
- iObj - Variable in class org.jmol.export._IdtfExporter
-
- iObj - Variable in class org.jmol.export.UseTable
-
- ionic - Static variable in class org.jmol.script.Token
-
- ionicRadii - Variable in class org.jmol.modelset.AtomCollection
-
- ioRead(byte[], int, int) - Method in class org.jmol.util.BinaryDocument
-
- ioReadByte() - Method in class org.jmol.util.BinaryDocument
-
- ioReadDouble() - Method in class org.jmol.util.BinaryDocument
-
- ioReadFloat() - Method in class org.jmol.util.BinaryDocument
-
- ioReadInt() - Method in class org.jmol.util.BinaryDocument
-
- ioReadLong() - Method in class org.jmol.util.BinaryDocument
-
- ioReadShort() - Method in class org.jmol.util.BinaryDocument
-
- iox - Variable in class org.jmol.export.image.ImageEncoder
-
- iPlaneRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
-
- iPrev - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- iProcess - Static variable in class org.jmol.script.ScriptEvaluator
-
- is(int) - Method in class org.jmol.modelset.Bond
-
- is2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
-
- is2D - Variable in class org.jmol.modelset.ModelLoader
-
- IS_HETERO_FLAG - Static variable in class org.jmol.modelset.Atom
-
- IS_POINTMAPPABLE - Static variable in class org.jmol.jvxl.readers.Parameters
-
- IS_SILENT - Static variable in class org.jmol.jvxl.readers.Parameters
-
- IS_SLABBABLE - 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.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.
- isAdded(int) - Method in class org.jmol.modelset.Group
-
- isAdjacentSp2(Atom) - Method in class org.jmol.modelset.AtomCollection
-
- isAligned(Point3f, Point3f, Point3f) - Method in class org.jmol.shapespecial.Polyhedra
-
- isAll - Variable in class org.jmol.modelset.MeasurementData
-
- isAll - Variable in class org.jmol.shape.Object2dShape
-
- isAll - Variable in class org.jmol.shapespecial.PolyhedraRenderer
-
- isAlphaMonomer() - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- isAlternateLocationMatch(String) - Method in class org.jmol.modelset.Atom
-
- isAltKeyReleased - Variable in class org.jmol.viewer.ActionManager
-
- isAmide - Variable in class org.jmol.minimize.MinBond
-
- isAminoMonomer() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- isAngstroms - Variable in class org.jmol.adapter.readers.simple.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.SurfaceReader
-
- 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
-
- isAntialiased() - Method in class org.jmol.viewer.Viewer
-
- isAntiparallel - Variable in class org.jmol.modelsetbio.AminoPolymer.Bridge
-
- isAppend - Variable in class org.jmol.viewer.FileManager.FileReader
-
- isAppend - Variable in class org.jmol.viewer.FileManager.FilesReader
-
- isAppendSelected() - Method in class org.jmol.export.dialog.FilePreview
-
- isApplet() - Method in class org.jmol.api.JmolViewer
-
- isApplet - Variable in class org.jmol.popup.SimplePopup
-
- 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.script.Token
-
- isAromatic - Variable in class org.jmol.smiles.SmilesAtom
-
- isAromatic() - Method in class org.jmol.smiles.SmilesAtom
-
- isArrayItem - Variable in class org.jmol.script.ScriptMathProcessor
-
- isArrayParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- isArrow - Variable in class org.jmol.shapespecial.Draw
-
- isAtEnd() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- isAtomAssignable(int) - Method in class org.jmol.modelset.ModelCollection
-
- isAtomAssignable(int) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- isAtomPDB(int) - Method in class org.jmol.modelset.ModelCollection
-
- isAtomPDB(int) - Method in class org.jmol.viewer.Viewer
-
- isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
-
- isAtomSelected(int) - Method in class org.jmol.viewer.Viewer
-
- isBarb - Variable in class org.jmol.shapespecial.Draw
-
- isBarb - Variable in class org.jmol.shapespecial.DrawMesh
-
- isBbcageDefault - Variable in class org.jmol.modelset.ModelCollection
-
- isBiColor - Variable in enum org.jmol.constant.EnumStereoMode
-
- isBiColor() - Method in enum org.jmol.constant.EnumStereoMode
-
- 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.adapter.smarter.AtomSetCollectionReader
-
- isBinary - Variable in class org.jmol.jvxl.readers.PmeshReader
-
- isBioAtom - Variable in class org.jmol.smiles.SmilesAtom
-
- isBioSequence - Variable in class org.jmol.smiles.SmilesParser
-
- 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.script.ScriptEvaluator
-
- isBondType() - Method in class org.jmol.shapespecial.Dipole
-
- isBondType(char, boolean, boolean) - Static method in class org.jmol.smiles.SmilesBond
-
- isBound(int, int) - Method in class org.jmol.viewer.ActionManager
-
- isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
-
- isBound(int, int) - Method in class org.jmol.viewer.Viewer
-
- isBreakableContext(int) - Static method in class org.jmol.script.ScriptCompiler
-
- 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
-
- isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
-
- isCavity - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- isCavity - Variable in class org.jmol.jvxl.readers.Parameters
-
- isCell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- isCellEditable(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
-
- isCenterParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- isCentrosymmetric - Variable in class org.jmol.symmetry.HallInfo
-
- isCheckOnly - Variable in class org.jmol.script.ScriptCompiler
-
- 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.export.Export3D
-
- isClipped(int, int) - Method in class org.jmol.export.Export3D
-
- 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
-
- isClosedFace - Variable in class org.jmol.jvxl.readers.PmeshReader
-
- isCmdf - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
-
- isCmdLine_C_Option - Variable in class org.jmol.script.ScriptEvaluator
-
- isCmdLine_C_Option - Variable in class org.jmol.viewer.Viewer
-
- isCmdLine_c_or_C_Option - Variable in class org.jmol.script.ScriptEvaluator
-
- isCmdLine_c_or_C_Option - Variable in class org.jmol.viewer.Viewer
-
- isColixColorInherited(short) - Static method in class org.jmol.g3d.Graphics3D
-
- isColixLastAvailable(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
-
- isColorExplicit - Variable in class org.jmol.shapesurface.Isosurface
-
- isColorIndex - Variable in class org.jmol.util.ColorEncoder
-
- isColorParam(int) - Method in class org.jmol.script.ScriptEvaluator
-
- isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
-
- isColorReversed - Variable in class org.jmol.jvxl.readers.Parameters
-
- isColorSolid - Variable in class org.jmol.util.MeshSurface
-
- isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- isCommandDisplayable(int) - Method in class org.jmol.script.ScriptEvaluator
-
provides support for the script editor
- isComment - Variable in class org.jmol.script.ScriptCompiler
-
- isCompoundDocument - Variable in class org.jmol.adapter.readers.quantum.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(Atom[], int) - Method in class org.jmol.modelset.Measurement
-
- 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
-
- isConnectedPrevious() - Method in class org.jmol.modelset.Group
-
- isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
-
- isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
-
- isConnectStateBug - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- isContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
-
- isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- isContoured - Variable in class org.jmol.jvxl.data.JvxlData
-
- isContoured - Variable in class org.jmol.jvxl.readers.Parameters
-
- isCore - Variable in class org.jmol.quantum.SlaterData
-
- isCovalent() - Method in class org.jmol.modelset.Bond
-
- isCovalent() - Method in class org.jmol.smiles.SmilesBond
-
- isCovalent() - Method in class org.jmol.util.JmolEdge
-
- isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
-
- isCrossed - Variable in class org.jmol.shapespecial.Draw
-
- isCrossLinked(JmolNode) - Method in class org.jmol.modelset.Atom
-
- isCrossLinked(Group) - Method in class org.jmol.modelset.Group
-
- isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
-
- isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- isCrossLinked(JmolNode) - Method in class org.jmol.smiles.SmilesAtom
-
- isCrossLinked(JmolNode) - Method in interface org.jmol.util.JmolNode
-
- 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.data.JvxlData
-
- isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
-
- isCutoffAbsolute - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- 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
-
- isDataOnly - Variable in class org.jmol.viewer.Viewer
-
- isDataOnly() - Method in class org.jmol.viewer.Viewer
-
- isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
-
- isDefaultColorRasmol - Variable in class org.jmol.viewer.ColorManager
-
- isDeleted() - Method in class org.jmol.modelset.Atom
-
- isDeleted() - Method in class org.jmol.smiles.SmilesAtom
-
- isDeleted() - Method in interface org.jmol.util.JmolNode
-
- isDiaxial(JmolNode, JmolNode, JmolNode, JmolNode, SmilesSearch.VTemp, float) - Static method in class org.jmol.smiles.SmilesSearch
-
- 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
-
- isDisplayAntialiased() - Method in class org.jmol.g3d.Graphics3D
-
is full scene / oversampling antialiasing GENERALLY in effect
- isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
-
- 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.modelset.Polymer
-
- isDna() - Method in class org.jmol.modelsetbio.BioPolymer
-
- isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- isDna() - Method in class org.jmol.smiles.SmilesAtom
-
- isDna() - Method in interface org.jmol.util.JmolNode
-
- isDrawType(String, int, float) - Method in class org.jmol.symmetry.PointGroup
-
- isDynamic - Variable in class org.jmol.modelset.Measurement
-
- isDynamic() - Method in class org.jmol.modelset.Measurement
-
- isE_fr_energy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- isE_wo_entrp - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- isEccentric - Variable in class org.jmol.jvxl.readers.Parameters
-
- isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- isElectronDensity - Variable in class org.jmol.quantum.MOCalculation
-
- isElectronDensityCalc - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- isEmbeddedExpression - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- isEmpty - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
-
- isEmpty() - Method in class org.jmol.util.FastBitSet
-
- isEnabled - Variable in class org.jmol.util.ZipUtil.GZipData
-
- isEndOfCommand - Variable in class org.jmol.script.ScriptCompiler
-
- isEqual(PointGroup) - Method in class org.jmol.symmetry.PointGroup
-
- isError() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- isError - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- isExcluded - Variable in class org.jmol.quantum.QuantumCalculation.QMAtom
-
- isExecuting - Variable in class org.jmol.script.ScriptEvaluator
-
- isExecutionPaused() - Method in class org.jmol.script.ScriptEvaluator
-
- isExecutionStepping() - Method in class org.jmol.script.ScriptEvaluator
-
- isExport - Variable in class org.jmol.shape.ShapeRenderer
-
- isExpressionNext() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- isFinalized - Variable in class org.jmol.symmetry.SymmetryOperation
-
- isFinite(double) - Static method in class org.jmol.minimize.Util
-
- isFirst - Variable in class org.jmol.smiles.SmilesAtom
-
- isFixed - Variable in class org.jmol.shape.MeshCollection
-
- isFixed - Variable in class org.jmol.shapespecial.DrawMesh
-
- isFlatSp2Ring(JmolNode[], BitSet, BitSet, float) - Static method in class org.jmol.smiles.SmilesAromatic
-
3D-SEARCH aromaticity test.
- isFloatParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- isFractional - Variable in class org.jmol.adapter.readers.xtal.AimsReader
-
- isFreqCalc - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- isFullSceneAntialiasingEnabled - Variable in class org.jmol.g3d.Graphics3D
-
- isFullyLit() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- isFunction - Variable in class org.jmol.script.ScriptContext
-
- isFunction(String) - Method in class org.jmol.viewer.StateManager
-
- isFunction(String) - Method in class org.jmol.viewer.Viewer
-
- isGesture - Variable in class org.jmol.viewer.TransformManager.SpinThread
-
- isGreaterOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- 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(byte[]) - Static method in class org.jmol.util.ZipUtil
-
- isGzip(InputStream) - Static method in class org.jmol.util.ZipUtil
-
- isHbonded(int, int, int, int, int[][][][]) - Static method in class org.jmol.modelsetbio.AminoPolymer
-
- isHeader - Variable in class org.jmol.util.CifDataReader
-
- isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- isHelix(float, float) - 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
-
- isHorizontal - Variable in class org.jmol.popup.SimplePopup
-
- isHover - Variable in class org.jmol.shape.Object2dShape
-
- isHoverEnabled() - Method in class org.jmol.viewer.Viewer
-
- iShowNormals - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
-
- iShowSolid - Variable in class org.jmol.shapespecial.DotsRenderer
-
- isHydrogen() - Method in class org.jmol.modelset.Bond
-
- isHydrogen(int) - Static method in class org.jmol.modelset.Bond
-
- isHydrogen() - Method in class org.jmol.smiles.SmilesBond
-
- isHydrogen() - Method in class org.jmol.util.JmolEdge
-
- 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
-
- isInFrame() - Method in class org.jmol.modelset.Atom
-
- isInitialized() - Method in class org.jmol.bspt.Bspf
-
- isInitialized(int) - Method in class org.jmol.bspt.Bspf
-
- isInLatticeCell(int, Point3f, Point3f, boolean) - Method in class org.jmol.modelset.ModelCollection
-
- isInPosition(Vector3f, float) - Method in class org.jmol.viewer.TransformManager
-
- isInPosition(Vector3f, float) - Method in class org.jmol.viewer.Viewer
-
- isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
-
- isInSelectionSubset(int) - Method in class org.jmol.viewer.SelectionManager
-
- isInSelectionSubset(int) - Method in class org.jmol.viewer.Viewer
-
- isInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
-
- isInside(float, float, boolean) - Static method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- isInsideOut() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- isInSymmetryRange(Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- isInt(float) - Static method in class org.jmol.adapter.readers.xtal.CastepReader
-
- isInTetrahedron(Point3f, Point3f, Point3f, Point3f, Point3f, Point4f, Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
-
- isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
-
- isInvalid - Variable in class org.jmol.g3d.Text3D
-
- isInvertible(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
-
- isJmolDataFrame - Variable in class org.jmol.modelset.Model
-
- 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
-
- isJmolManifest(String) - Static method in class org.jmol.util.ZipUtil
-
- isJmolVariable(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- isJmolVariable(String) - Method in class org.jmol.viewer.Viewer
-
- isJPEG - Variable in class org.jmol.export.dialog.Dialog.QualityListener
-
- isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
-
- iskiosk - Static variable in class org.jmol.script.Token
-
- isKiosk - Variable in class org.jmol.viewer.Viewer
-
- isKiosk() - Method in class org.jmol.viewer.Viewer
-
- isKiosk - Variable in class org.openscience.jmol.app.JmolApp
-
- isLabelOrHover - Variable in class org.jmol.shape.Object2d
-
- isLabelPropertyTok(int) - Static method in class org.jmol.modelset.LabelToken
-
- isLastFrame - Variable in class org.jmol.popup.SimplePopup
-
- isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
after reading a model, Q: Is this the last model?
- isLeadAtom() - Method in class org.jmol.modelset.Atom
-
- isLeadAtom(int) - Method in class org.jmol.modelset.Group
-
- isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
-
- isLeadAtom - Variable in class org.jmol.smiles.SmilesAtom
-
- isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
-
- isLeadAtom() - Method in interface org.jmol.util.JmolNode
-
- isLine - Variable in class org.jmol.shapespecial.Draw
-
- isLinear(Point3f[]) - Method in class org.jmol.symmetry.PointGroup
-
- isLineContinuation(int, boolean) - Method in class org.jmol.script.ScriptCompiler
-
- isLonePair - Variable in class org.jmol.shapesurface.LcaoCartoon
-
- isLongMode - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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
-
- isMathExpressionCommand - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- isMerged - Variable in class org.jmol.util.MeshSurface
-
- isMesh - Variable in class org.jmol.shapebio.Strands
-
- isModelKit - Variable in class org.jmol.modelset.Model
-
- isModelkit() - Method in class org.jmol.modelset.Model
-
- isModelKitMode() - Method in class org.jmol.viewer.Viewer
-
- isModelPDB(int) - Method in class org.jmol.viewer.Viewer
-
- isMolecular - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- isMolecular - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- isMolecular - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- isMolecular - Variable in class org.jmol.shapesurface.LcaoCartoon
-
- isMonomerSelected(int) - Method in class org.jmol.modelsetbio.BioPolymer
-
- isMouseDown - Variable in class org.jmol.awt.Mouse
-
- isMTClient() - Method in class org.jmol.viewer.ActionManager
-
- isMTServer() - Method in class org.jmol.viewer.ActionManager
-
- isMultiCell - Variable in class org.jmol.symmetry.SymmetryInfo
-
- isMultiConfiguration - Variable in class org.jmol.popup.SimplePopup
-
- isMultiFrame - Variable in class org.jmol.popup.SimplePopup
-
- isMultiModel - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
-
- isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
-
- isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
-
- isNav - Variable in class org.jmol.viewer.TransformManager.SpinThread
-
- isNavigating() - Method in class org.jmol.viewer.TransformManager
-
- isNavigating() - Method in class org.jmol.viewer.Viewer
-
- isNavigationMode - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
-
- isNci - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- isNear(double, double) - Static method in class org.jmol.minimize.Util
-
- isNear(double, double, double) - Static method in class org.jmol.minimize.Util
-
- isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
-
- isNearZero(double) - Static method in class org.jmol.minimize.Util
-
- 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
-
- isNewFormat - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- isNewSet - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- isNext(String) - Method in class org.jmol.util.XmlReader
-
- isNot - Variable in class org.jmol.smiles.SmilesBond
-
- isNot - Variable in class org.jmol.smiles.SmilesMeasure
-
- isNucleic() - Method in class org.jmol.modelset.Atom
-
- isNucleic() - Method in class org.jmol.modelset.Group
-
- isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- isNucleic - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- isNucleic() - Method in class org.jmol.smiles.SmilesAtom
-
- isNucleic() - Method in interface org.jmol.util.JmolNode
-
- 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
-
- IsoFxyzReader - Class in org.jmol.jvxl.readers
-
- IsoFxyzReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoFxyzReader
-
- IsoIntersectReader - Class in org.jmol.jvxl.readers
-
- IsoIntersectReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoIntersectReader
-
- 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
-
- IsoMlpReader - Class in org.jmol.jvxl.readers
-
- IsoMlpReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoMlpReader
-
- 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
-
- isOpFunc(Token) - Static method in class org.jmol.script.ScriptMathProcessor
-
- IsoPlaneReader - Class in org.jmol.jvxl.readers
-
- IsoPlaneReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.IsoPlaneReader
-
- isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- IsoShapeReader - Class in org.jmol.jvxl.readers
-
- IsoShapeReader(SurfaceGenerator, float) - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
-
- IsoShapeReader(SurfaceGenerator, int, int, int, float, int) - 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
-
- IsoSolventReader.Edge - Class in org.jmol.jvxl.readers
-
- IsoSolventReader.Edge(int, int) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Edge
-
- IsoSolventReader.Face - Class in org.jmol.jvxl.readers
-
- IsoSolventReader.Face(int, int, int, IsoSolventReader.Edge, Point3f) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- isosurface(int) - Method in class org.jmol.script.ScriptEvaluator
-
- isosurface - Static variable in class org.jmol.script.Token
-
- Isosurface - Class in org.jmol.shapesurface
-
- Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
-
- isosurface - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
-
- isosurfacekey - Static variable in class org.jmol.script.Token
-
- isosurfaceKey - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- IsosurfaceMesh - Class in org.jmol.shapesurface
-
- IsosurfaceMesh(String, Graphics3D, short, int) - Constructor for class org.jmol.shapesurface.IsosurfaceMesh
-
- isosurfacepropertysmoothing - Static variable in class org.jmol.script.Token
-
- isosurfacePropertySmoothing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.Token
-
- isosurfacePropertySmoothingPower - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- IsosurfaceRenderer - Class in org.jmol.shapesurface
-
- IsosurfaceRenderer() - Constructor for class org.jmol.shapesurface.IsosurfaceRenderer
-
- isOutput - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- isOutputFile - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- isPaletteVariable(byte) - Static method in enum org.jmol.constant.EnumPalette
-
- isParallel(Vector3f, Vector3f) - Method in class org.jmol.symmetry.PointGroup
-
- isParallel - Variable in class org.jmol.viewer.Viewer
-
- isParallel() - Method in class org.jmol.viewer.Viewer
-
- isPartial() - Method in class org.jmol.modelset.Bond
-
- isPass2() - Method in interface org.jmol.api.JmolRendererInterface
-
- isPass2() - Method in class org.jmol.export.Export3D
-
- isPass2 - Variable in class org.jmol.g3d.Graphics3D
-
- isPass2() - Method in class org.jmol.g3d.Graphics3D
-
- isPaused - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- isPDB - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- 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.modelset.ModelLoader
-
- isPDB - Variable in class org.jmol.popup.SimplePopup
-
- isPdbSequential() - Method in class org.jmol.viewer.Viewer
-
- isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
-
- isPeriodic() - Method in interface org.jmol.api.SymmetryInterface
-
- isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
-
- isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
-
- 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
-
- isPhonon - Variable in class org.jmol.adapter.readers.xtal.CastepReader
-
- isPhosphorusMonomer() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- isPickable(IsosurfaceMesh, BitSet) - Method in class org.jmol.shapesurface.Isosurface
-
- isPickAtomAssignCharge - Variable in class org.jmol.viewer.ActionManager
-
- 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.script.ScriptEvaluator
-
- 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
-
- isPolymer - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- isPolymer - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- isPolymer() - Method in interface org.jmol.api.SymmetryInterface
-
- isPolymer - Variable in class org.jmol.shape.CageRenderer
-
- isPolymer() - Method in class org.jmol.symmetry.Symmetry
-
- isPolymer() - Method in class org.jmol.util.SimpleUnitCell
-
- isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
-
- isPossibleHBond(EnumHBondType, EnumHBondType) - Static method in enum org.jmol.constant.EnumHBondType
-
- 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.adapter.readers.xtal.CrystalReader
-
- isPrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- isPrintOnly - Variable in class org.jmol.viewer.Viewer
-
- isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
-
- isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- isPromolecular - Variable in class org.jmol.quantum.NciCalculation
-
- isProperties - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- isProtein() - Method in enum org.jmol.constant.EnumStructure
-
- isProtein() - Method in class org.jmol.modelset.Atom
-
- isProtein - Variable in class org.jmol.modelset.Group
-
- isProtein() - Method in class org.jmol.modelset.Group
-
- isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- isProtein() - Method in class org.jmol.smiles.SmilesAtom
-
- isProtein() - Method in interface org.jmol.util.JmolNode
-
- 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
-
- isPurine() - Method in class org.jmol.smiles.SmilesAtom
-
- isPurine() - Method in interface org.jmol.util.JmolNode
-
- 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
-
- isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
-
- isPyrimidine() - Method in interface org.jmol.util.JmolNode
-
- isQuantumBasisSupported(char) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- isRadical - Variable in class org.jmol.shapesurface.LcaoCartoon
-
- 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
-
- isReducedDensity - Variable in class org.jmol.quantum.NciCalculation
-
- isRepaintPending() - Method in class org.jmol.viewer.Viewer
-
- isReset - Variable in class org.jmol.viewer.TransformManager.SpinThread
-
- isReversed - Variable in class org.jmol.shapespecial.Draw
-
- isReversed - Variable in class org.jmol.util.ColorEncoder
-
- isrhombohedral - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- isRingBond(StringBuffer, int, int) - Static method in class org.jmol.smiles.SmilesSearch
-
- isRingCheck - Variable in class org.jmol.smiles.SmilesSearch
-
- 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.modelset.Polymer
-
- isRna() - Method in class org.jmol.modelsetbio.BioPolymer
-
- isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
-
- isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- isRna() - Method in class org.jmol.smiles.SmilesAtom
-
- isRna() - Method in interface org.jmol.util.JmolNode
-
- isRotated45 - Variable in class org.jmol.shapespecial.Draw
-
- isRubberBandSelect(int) - Method in class org.jmol.viewer.ActionManager
-
- isSameAtoms(Dipole, String) - Method in class org.jmol.shapespecial.Dipoles
-
- isScaled - Variable in class org.jmol.shape.Labels
-
- isScaleSet - Variable in class org.jmol.util.BoxInfo
-
- isScreened - Variable in class org.jmol.g3d.Graphics3D
-
- isScreenedA - Variable in class org.jmol.g3d.Cylinder3D
-
- isScreenedB - Variable in class org.jmol.g3d.Cylinder3D
-
- isScriptEditorVisible() - Method in class org.jmol.viewer.Viewer
-
- isScriptExecuting() - Method in class org.jmol.api.JmolViewer
-
- isScriptExecuting() - Method in class org.jmol.script.ScriptEvaluator
-
- isScriptExecuting() - Method in class org.jmol.viewer.Viewer
-
- isScriptQueued - Variable in class org.jmol.viewer.Viewer
-
- isSelectAction(int) - Method in class org.jmol.viewer.ActionManager
-
- 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
-
- isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- isSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
-
- isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- isSetBrace - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- isSetOrDefine - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- 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) - 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.script.ScriptCompiler
-
- isShowScriptOutput - Variable in class org.jmol.script.ScriptCompiler
-
- isSigned - Variable in class org.jmol.applet.AppletWrapper
-
- isSigned() - Method in class org.jmol.applet.AppletWrapper
-
- isSigned - Variable in class org.jmol.applet.Jmol
-
- isSigned - Variable in class org.jmol.popup.SimplePopup
-
- isSignedApplet - Variable in class org.jmol.viewer.Viewer
-
- isSignedApplet() - Method in class org.jmol.viewer.Viewer
-
- isSignedAppletLocal - Variable in class org.jmol.viewer.Viewer
-
- isSilent - Variable in class org.jmol.jvxl.readers.Parameters
-
- isSilent - Variable in class org.jmol.minimize.Minimizer
-
- isSilent - Variable in class org.jmol.script.ScriptCompiler
-
- isSilent - Variable in class org.jmol.smiles.SmilesSearch
-
- isSilent - Variable in class org.jmol.viewer.Viewer
-
- isSilent - Variable in class org.openscience.jmol.app.JmolApp
-
- isSlab - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- isSlab - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- isSlab() - Method in interface org.jmol.api.SymmetryInterface
-
- isSlab - Variable in class org.jmol.shape.CageRenderer
-
- isSlab() - Method in class org.jmol.symmetry.Symmetry
-
- isSlab() - Method in class org.jmol.util.SimpleUnitCell
-
- isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
-
- isSlabEnabled - Variable in class org.jmol.export.__RayTracerExporter
-
- isSmarts - Variable in class org.jmol.smiles.SmilesParser
-
- isSmarts - Variable in class org.jmol.smiles.SmilesSearch
-
- isSmilesFind - Variable in class org.jmol.smiles.SmilesSearch
-
- isSpaceOrTab(char) - Static method in class org.jmol.script.ScriptCompiler
-
- isSpartanArchive(String) - Method in class org.jmol.adapter.readers.quantum.SpartanReader
-
- isSpecTerminator(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- 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.calc.MarchingCubes
-
- isSquared - Variable in class org.jmol.jvxl.data.VolumeData
-
- 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.script.ScriptCompilationTokenParser
-
- isStateScript - Variable in class org.jmol.script.ScriptContext
-
- isStateScript - Variable in class org.jmol.script.ScriptEvaluator
-
- isStaticFunction(String) - Static method in class org.jmol.viewer.StateManager
-
- isStereo() - Method in class org.jmol.modelset.Bond
-
- isStereoDouble() - Method in class org.jmol.viewer.Viewer
-
- isStereoSlave - Variable in class org.jmol.applet.Jmol
-
- isStringArray(String) - Static method in class org.jmol.util.Escape
-
- isStructureTainted() - Method in class org.jmol.modelset.Model
-
- isSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- isSurface - Variable in class org.jmol.shapespecial.Dots
-
- isSurfacePoint - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- isSymmetry - Variable in class org.jmol.popup.SimplePopup
-
- isSynced - Variable in class org.jmol.viewer.StatusManager
-
- isSyntaxCheck - Variable in class org.jmol.script.ScriptContext
-
- isSyntaxCheck - Variable in class org.jmol.script.ScriptEvaluator
-
- isSyntaxCheck - Variable in class org.jmol.script.ScriptMathProcessor
-
Reverse Polish Notation Engine for IF, SET, and %{...} -- Bob Hanson
2/16/2007 Just a (not so simple?) RPN processor that can handle boolean,
int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f
hansonr@stolaf.edu
- isTainted(int, byte) - Method in class org.jmol.modelset.AtomCollection
-
- isTainted - Variable in class org.jmol.viewer.Viewer
-
- iStep - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- isToFile - Variable in class org.jmol.export.___Exporter
-
- isToken(int) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- 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
-
- isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelCollection
-
- 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
-
- isTranslucent - Variable in class org.jmol.util.ColorEncoder
-
- isTransparent - Variable in class org.jmol.export.image.GifEncoder.ColorItem
-
- isTriangleSet - Variable in class org.jmol.shape.Mesh
-
- istructure - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
-
- isTurn(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- isTwoSided - Variable in class org.jmol.shape.Mesh
-
- isTypeSet - Variable in class org.jmol.adapter.readers.quantum.GamessReader
-
- isUnitCell - Variable in class org.jmol.popup.SimplePopup
-
- isUpdating - Variable in class org.jmol.applet.Jmol
-
- isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
-
- isUserFunction(String) - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- isUserToken - Variable in class org.jmol.script.ScriptCompiler
-
- isUserValue - Variable in class org.jmol.shapespecial.Dipole
-
- isUserValue - Variable in class org.jmol.shapespecial.Dipoles
-
- isV3000 - Variable in class org.jmol.adapter.readers.molxyz.MolReader
-
- isValid - Variable in class org.jmol.bspt.Bspf
-
- isValid - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
-
- isValid - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- isValid() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- isValid() - Method in class org.jmol.modelset.Measurement
-
- 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
-
- isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
-
- 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
-
- isVariable(String) - Method in class org.jmol.script.ScriptFunction
-
- isVariableType(Object) - Static method in class org.jmol.script.ScriptVariable
-
- isVdw - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- isVector - Variable in class org.jmol.shapespecial.Draw
-
- isVector - Variable in class org.jmol.shapespecial.DrawMesh
-
- isVersion3 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- isVersion5 - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- isVertices - Variable in class org.jmol.shapespecial.Draw
-
- isVibration - Variable in class org.jmol.popup.SimplePopup
-
- isVibrationOn() - Method in class org.jmol.viewer.TransformManager
-
- isVibrationOn() - Method in class org.jmol.viewer.Viewer
-
- isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
-
- isVisible(int) - 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(int) - Method in class org.jmol.modelsetbio.ProteinStructure
-
- isWithin(Point3f) - Method in class org.jmol.util.BoxInfo
-
- isWithinCell(int, Point3f, int, int, int, int, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
-
- isWithinFourBonds(Atom) - Method in class org.jmol.modelset.Atom
-
- isWithinNot - Variable in class org.jmol.shapesurface.Isosurface
-
- isWithinRadius(Point3f) - Method in class org.jmol.bspt.CubeIterator
-
checks one Point3f for distance
- isWithinStructure(EnumStructure) - Method in class org.jmol.modelset.Atom
-
- isWithinStructure(EnumStructure) - Method in class org.jmol.modelset.Group
-
- isWithinStructure(EnumStructure) - Method in class org.jmol.modelsetbio.AminoMonomer
-
- isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
-
- isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
-
- isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- isXLowToHigh - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- isXYZ - Variable in class org.jmol.modelset.ModelCollection
-
- isZapped - Variable in class org.jmol.popup.SimplePopup
-
- isZeroBased - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- isZipFile(String) - Static method in class org.jmol.util.ZipUtil
-
- isZipFile(InputStream) - Static method in class org.jmol.util.ZipUtil
-
- isZipFile(byte[]) - Static method in class org.jmol.util.ZipUtil
-
- isZoomArea(int) - Method in class org.jmol.viewer.ActionManager
-
- itemStateChanged(ItemEvent) - Method in class org.jmol.export.dialog.Dialog.ExportChoiceListener
-
- itemStateChanged(ItemEvent) - Method in class org.jmol.popup.SimplePopup.CheckboxMenuItemListener
-
- itemStateChanged(ItemEvent) - Method in class org.openscience.chimetojmol.ChimePanel
-
- itemStateChanged(ItemEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- iter - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- iter - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- 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.jvxl.readers.PmeshReader
-
- iToken - Variable in class org.jmol.script.ScriptContext
-
- iToken - Variable in class org.jmol.script.ScriptEvaluator
-
- itokenInfix - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- iVal - Variable in class org.jmol.minimize.forcefield.FFParam
-
- iValue(Token) - Static method in class org.jmol.script.ScriptVariable
-
- p - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
-
- p0 - Variable in class org.jmol.quantum.NciCalculation
-
- p1 - Variable in class org.jmol.quantum.NciCalculation
-
- p1 - Variable in class org.jmol.shape.SticksRenderer
-
- p2 - Variable in class org.jmol.quantum.NciCalculation
-
- p2 - Variable in class org.jmol.shape.SticksRenderer
-
- p2nLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- P2nReader - Class in org.jmol.adapter.readers.more
-
P2N file reader.
- P2nReader() - Constructor for class org.jmol.adapter.readers.more.P2nReader
-
- P_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- P_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
-
- packageJSON(String, StringBuilder) - Static method in class org.jmol.util.Escape
-
- packageJSON(String, String) - Static method in class org.jmol.util.Escape
-
- packageReadable(String, String, StringBuilder) - Static method in class org.jmol.util.Escape
-
- packageReadable(String, String, String) - Static method in class org.jmol.util.Escape
-
- packed - Static variable in class org.jmol.script.Token
-
- pageAuthorName - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- pageAuthorName - Variable in class org.openscience.jmol.app.webexport.WebPanel
-
- pages - Variable in class org.openscience.chimetojmol.ChimePanel
-
- paint(Graphics) - Method in class org.jmol.applet.AppletWrapper
-
- paint(Graphics) - Method in class org.jmol.applet.Jmol
-
- paint(Graphics) - Method in interface org.jmol.applet.WrappedApplet
-
- paint(Graphics) - Method in class org.jmol.export.dialog.FilePreview.FPPanel
-
- paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
-
- paint(Graphics) - Method in class org.openscience.molecularplayground.MPJmolApp.KioskPanel
-
- paintCounter - Variable in class org.jmol.applet.Jmol
-
- pairSearch(List<Object[]>, CalculationsUFF.PairCalc) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
-
- PALETTE_ALTLOC - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_AMINO - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_CHAIN - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_CPK - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_ENERGY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_FIXEDTEMP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_FORMAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_GROUP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_INSERTION - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_JMOL - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_MOLECULE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_MONOMER - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_NONE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_PARTIAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_POLYMER - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_PROPERTY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_RASMOL - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_SHAPELY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_STRAIGHTNESS - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_STRUCTURE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_SURFACE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_TEMP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_TYPE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_VARIABLE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_VOLATILE - Static variable in class org.jmol.constant.StaticConstants
-
- paletteBW - Variable in class org.jmol.util.ColorEncoder
-
- paletteID - Variable in class org.jmol.modelset.Atom
-
- paletteID - Variable in class org.jmol.modelset.HBond
-
- paletteIDs - Variable in class org.jmol.shape.AtomShape
-
- paletteIDs - Variable in class org.jmol.shapebio.BioShape
-
- paletteWB - Variable in class org.jmol.util.ColorEncoder
-
- palindrome - Static variable in class org.jmol.script.Token
-
- 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
-
- parallel - Static variable in class org.jmol.script.Token
-
- ParallelProcessor - Class in org.jmol.script
-
- ParallelProcessor(String, int) - Constructor for class org.jmol.script.ParallelProcessor
-
- parallelProcessor - Variable in class org.jmol.script.ScriptContext
-
- parallelProcessor - Variable in class org.jmol.script.ScriptEvaluator
-
- ParallelProcessor.Process - Class in org.jmol.script
-
the idea here is that the process { ...
- ParallelProcessor.Process(String, ScriptContext) - Constructor for class org.jmol.script.ParallelProcessor.Process
-
- ParallelProcessor.RunProcess - Class in org.jmol.script
-
- ParallelProcessor.RunProcess(ParallelProcessor.Process, Object, ShapeManager) - Constructor for class org.jmol.script.ParallelProcessor.RunProcess
-
- parameterAsString(int) - Method in class org.jmol.script.ScriptEvaluator
-
- parameterExpression(int, int, String, boolean, boolean, int, boolean, Map, String) - Method in class org.jmol.script.ScriptEvaluator
-
This is the primary driver of the RPN (reverse Polish notation) expression
processor.
- parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- parameterExpressionToken(int) - Method in class org.jmol.script.ScriptEvaluator
-
- parameterIndex(String) - Static method in class org.jmol.adapter.readers.xtal.GulpReader
-
- Parameters - Class in org.jmol.jvxl.readers
-
- Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
-
- parameters - Variable in class org.jmol.jvxl.readers.Parameters
-
- parameters - Static variable in class org.jmol.script.Token
-
- params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- params - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- paramTypes - Static variable in class org.jmol.script.Token
-
- parB - Variable in class org.jmol.minimize.forcefield.Calculation
-
- parC - Variable in class org.jmol.minimize.forcefield.Calculation
-
- parenCount - Variable in class org.jmol.script.ScriptCompiler
-
- parenCount - Variable in class org.jmol.script.ScriptMathProcessor
-
- parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
-
- parent - Variable in class org.jmol.script.ScriptFlowContext
-
- parent - Variable in class org.jmol.smiles.SmilesAtom
-
- parent - Variable in class org.jmol.smiles.SmilesSearch
-
- parentContext - Variable in class org.jmol.script.ScriptContext
-
- parse(String) - Method in class org.jmol.smiles.SmilesParser
-
Parses a SMILES String
- parseAtom(SmilesSearch, SmilesAtom, String, SmilesAtom, SmilesBond, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
-
Parses an atom definition
- parseBond(SmilesSearch, SmilesBond, String, SmilesBond, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
-
- 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
-
- parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
-
- parseCommandParameter(String) - Method in class org.jmol.script.ScriptCompiler
-
- parsedContext - Variable in class org.jmol.console.ScriptEditor
-
- parsedData - Variable in class org.jmol.console.ScriptEditor
-
- parseFloat(String) - Method in class org.jmol.adapter.readers.quantum.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.SurfaceFileReader
-
- parseFloat(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- 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) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- parseFloatArray() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- parseFloatArray(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArray(String, int[]) - Static method in class org.jmol.util.Parser
-
- 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
-
- parseFloatArray3d(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
-
- parseFloatStrict(String) - Static method in class org.jmol.util.Parser
-
- parseInt(String) - Method in class org.jmol.adapter.readers.quantum.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.SurfaceFileReader
-
- parseInt(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- 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.SurfaceFileReader
-
- parseKnownToken(String) - Method in class org.jmol.script.ScriptCompiler
-
- parseLattRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- parseLineParameters(String[], byte[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
sets up arrays and variables for tokenizer.getData()
- parseMeasure(SmilesSearch, String, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
-
- parseNested(SmilesSearch, String) - Method in class org.jmol.smiles.SmilesParser
-
- 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(SmilesSearch, int, SmilesAtom, SmilesBond) - Method in class org.jmol.smiles.SmilesParser
-
Parses a ring definition
- parseScript(String) - Method in class org.jmol.console.ScriptEditor
-
- parseScript(boolean) - Method in class org.jmol.script.ScriptCompiler
-
- parseSfacCoefficients(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- parseSfacElementSymbols(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- parseSfacRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
-
- parseSmiles(SmilesSearch, String, SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesParser
-
Parses a part of a SMILES String
- parseStringInfestedFloatArray(String, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- parseStringInfestedFloatArray(String, BitSet, float[]) - Static method in class org.jmol.util.Parser
-
parses a "dirty" string for floats.
- parseSymmRecord() - Method in class org.jmol.adapter.readers.xtal.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
-
- parseVariableLength(String) - Method in class org.jmol.smiles.SmilesParser
-
- parseVariables(String) - Method in class org.jmol.smiles.SmilesParser
-
- 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.script.Token
-
- partialCharges - Variable in class org.jmol.adapter.readers.simple.AmpacReader
-
- 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
-
- partialdots - Static variable in class org.jmol.script.Token
-
- partialDots - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- Pass - Variable in class org.jmol.export.image.GifEncoder
-
- pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- path() - Method in class org.jmol.script.ScriptFlowContext
-
- path - Static variable in class org.jmol.script.Token
-
- PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
AtomSetCollectionReader.readData() will close any BufferedReader
- PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
- PathButton - Variable in class org.openscience.jmol.app.webexport.Test
-
- pattern - Variable in class org.jmol.smiles.SmilesSearch
-
- patternAtoms - Variable in class org.jmol.smiles.SmilesSearch
-
- pause() - Method in class org.jmol.script.ScriptEvaluator
-
- pause - Static variable in class org.jmol.script.Token
-
- PAUSE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- pauseAnimation() - Method in class org.jmol.viewer.AnimationManager
-
- pauseButton - Variable in class org.jmol.console.ScriptEditor
-
- pauseExecution(boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- pauseScript(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- 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.jmolpanel.PreferencesDialog
-
- pc - Variable in class org.jmol.script.ScriptContext
-
- pc - Variable in class org.jmol.script.ScriptEvaluator
-
- pcEnd - Variable in class org.jmol.script.ScriptContext
-
- pcEnd - Variable in class org.jmol.script.ScriptEvaluator
-
- pchrg - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- pcl - Variable in class org.jmol.export.JmolFileDropper
-
- pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- pdb - Static variable in class org.jmol.script.Token
-
- pdbaddhydrogens - Static variable in class org.jmol.script.Token
-
- pdbAddHydrogens - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- pdbBondInfo - Static variable in class org.jmol.viewer.JmolConstants
-
- pdbgetheader - Static variable in class org.jmol.script.Token
-
- pdbGetHeader - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- pdbHeader - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- pdbheader - Static variable in class org.jmol.script.Token
-
- pdbHydrogenCount - Static variable in class org.jmol.viewer.JmolConstants
-
- pdbLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- PDBOnly - Variable in class org.jmol.popup.SimplePopup
-
- 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.modelset.ModelCollection
-
- pdbsequential - Static variable in class org.jmol.script.Token
-
- pdbSequential - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- PdfCreator - Class in org.openscience.jmol.app.jmolpanel
-
- PdfCreator() - Constructor for class org.openscience.jmol.app.jmolpanel.PdfCreator
-
- peekToken() - Method in class org.jmol.util.CifDataReader
-
just look at the next token.
- pending(MeasurementPending) - Method in class org.jmol.shape.Measures
-
- per - Static variable in class org.jmol.script.Token
-
- percent - Static variable in class org.jmol.script.Token
-
- percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
-
- percentvdwatom - Static variable in class org.jmol.script.Token
-
- percentVdwAtom - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- percentVdwAtom - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- period - Static variable in class org.jmol.script.Token
-
- PERIOD_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for the vibration period in seconds.
- PERIOD_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Precision of the vibration period slider in seconds.
- PERIOD_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.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.jmolpanel.AtomSetChooser
-
- perpendicular - Static variable in class org.jmol.script.Token
-
- perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- perspectivedepth - Static variable in class org.jmol.script.Token
-
- 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.jmolpanel.PreferencesDialog
-
- perspectiveFactor - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- perspectivemodel - Static variable in class org.jmol.script.Token
-
- perspectiveModel - Variable in class org.jmol.viewer.TransformManager
-
- perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
-
- perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
-
- pfaatBinding - Variable in class org.jmol.viewer.ActionManager
-
- PfaatBinding - Class in org.jmol.viewer.binding
-
- PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
-
- 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
-
- phase - Static variable in class org.jmol.script.Token
-
- phi - Variable in class org.jmol.modelset.Group
-
- phi - Static variable in class org.jmol.script.Token
-
- phong - Variable in class org.jmol.export._TachyonExporter
-
- phongExponent - Static variable in class org.jmol.g3d.Shade3D
-
- phongexponent - Static variable in class org.jmol.script.Token
-
- phongExponent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- 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
-
- pickAtomAssignType - Variable in class org.jmol.viewer.ActionManager
-
- pickBondAssignType - Variable in class org.jmol.viewer.ActionManager
-
- pickedAtom - Variable in class org.jmol.shape.Labels
-
- pickedMesh - Variable in class org.jmol.shape.MeshCollection
-
- pickedModel - Variable in class org.jmol.shape.MeshCollection
-
- pickedOffset - Variable in class org.jmol.shape.Labels
-
- pickedVertex - Variable in class org.jmol.shape.MeshCollection
-
- pickedX - Variable in class org.jmol.shape.Labels
-
- pickedY - Variable in class org.jmol.shape.Labels
-
- picking - Static variable in class org.jmol.script.Token
-
- PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
-
picking modes set picking....
- PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
-
- PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
-
- pickingModeNames - Static variable in class org.jmol.viewer.ActionManager
-
- pickingspinrate - Static variable in class org.jmol.script.Token
-
- pickingSpinRate - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- pickingstyle - Static variable in class org.jmol.script.Token
-
- pickingStyle - Variable in class org.jmol.viewer.ActionManager
-
- PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
-
- PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
-
- PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
-
- PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
-
- PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
-
picking styles
- PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
-
- PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
-
- pickingStyleMeasure - Variable in class org.jmol.viewer.ActionManager
-
- pickingStyleNames - Static variable in class org.jmol.viewer.ActionManager
-
- pickingStyleSelect - Variable in class org.jmol.viewer.ActionManager
-
- picklabel - Static variable in class org.jmol.script.Token
-
- pickLabel - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- 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 enum org.jmol.constant.EnumPalette
-
- PINK - Static variable in class org.jmol.g3d.Graphics3D
-
- pipedIS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
-
- pipedOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
-
- pixel - Variable in class org.jmol.g3d.Graphics3D
-
- pixelScaleDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- pixelSize - Variable in class org.jmol.export._ObjExporter
-
The size of a pixel based on some assumptions about screen size
- plane - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- plane - Variable in class org.jmol.modelsetbio.Resolver
-
- plane - Static variable in class org.jmol.script.Token
-
- plane - Variable in class org.jmol.shapespecial.Draw
-
- plane_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
-
- plane_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
-
- planeCenter - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- planeExpected() - Method in class org.jmol.script.ScriptEvaluator
-
- planeParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- planeRadius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- 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
-
- planeU - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- planeV - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- planeValue(Token) - Method in class org.jmol.script.ScriptMathProcessor
-
- Platform - Class in org.jmol.awt
-
- Platform() - Constructor for class org.jmol.awt.Platform
-
- 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.script.Token
-
- PLAY - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- playrev - Static variable in class org.jmol.script.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
-
- plot(Token[]) - Method in class org.jmol.script.ScriptEvaluator
-
- plot - Static variable in class org.jmol.script.Token
-
- plot3d - Static variable in class org.jmol.script.Token
-
- Plot3D - Class in org.jmol.shapesurface
-
- Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
-
- Plot3DRenderer - Class in org.jmol.shapesurface
-
- Plot3DRenderer() - Constructor for class org.jmol.shapesurface.Plot3DRenderer
-
- 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 class org.jmol.export.___Exporter
-
- plotImage(int, int, int, Image, short, int, int) - Method in class org.jmol.export.__CartesianExporter
-
- plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- plotImage(int, int, int, Object, 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, 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[], 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, boolean) - Method in class org.jmol.g3d.Cylinder3D
-
- plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export.___Exporter
-
- plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export.__CartesianExporter
-
- plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export._VrmlExporter
-
- plotText(int, int, int, short, String, Font3D) - Method in class org.jmol.export._X3dExporter
-
- 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.script.Token
-
- plusPlus - Static variable in class org.jmol.script.Token
-
- pmesh - Static variable in class org.jmol.script.Token
-
- Pmesh - Class in org.jmol.shapesurface
-
- Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
-
- PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.jvxl.readers.PmeshReader
-
- PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.util.SurfaceFileTyper
-
- pmeshError - Variable in class org.jmol.jvxl.readers.PmeshReader
-
- PmeshReader - Class in org.jmol.jvxl.readers
-
- PmeshReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PmeshReader
-
- PmeshReader(SurfaceGenerator, String, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PmeshReader
-
- 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.
- pocket - Variable in class org.jmol.jvxl.readers.Parameters
-
- pocket - Static variable in class org.jmol.script.Token
-
- 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.script.Token
-
- point3f - Static variable in class org.jmol.script.Token
-
- Point3fi - Class in org.jmol.util
-
the Point3fi class allows storage of critical information involving
an atom, picked bond, or measurement point, including:
xyz position
screen position
screen radius (-1 for a simple point)
index (for atoms or for an associated bond that has be picked)
associated modelIndex (for measurement points)
- Point3fi() - Constructor for class org.jmol.util.Point3fi
-
- Point3fi(Point3f) - Constructor for class org.jmol.util.Point3fi
-
- Point3fi(float, float, float) - 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.script.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() - Method in class org.jmol.script.ScriptEvaluator
-
- pointgroup - Static variable in class org.jmol.script.Token
-
- PointGroup - Class in org.jmol.symmetry
-
- PointGroup() - Constructor for class org.jmol.symmetry.PointGroup
-
- pointGroup - Variable in class org.jmol.symmetry.Symmetry
-
- 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 - Static variable in class org.jmol.script.Token
-
- pointGroupDistanceTolerance - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- pointgrouplineartolerance - Static variable in class org.jmol.script.Token
-
- 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.jvxl.readers.IsoMOReader
-
- points - Variable in class org.jmol.jvxl.readers.Parameters
-
- points - Variable in class org.jmol.modelset.MeasurementData
-
- points - Variable in class org.jmol.quantum.QuantumCalculation
-
- points - Variable in class org.jmol.shapespecial.DipolesRenderer
-
- points - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- points - Variable in class org.jmol.smiles.SmilesMeasure
-
- points - Variable in class org.jmol.symmetry.PointGroup
-
- POINTS_ALL - Static variable in class org.jmol.jvxl.readers.KinemageReader
-
- POINTS_HETS - Static variable in class org.jmol.jvxl.readers.KinemageReader
-
- POINTS_MCMC - Static variable in class org.jmol.jvxl.readers.KinemageReader
-
- POINTS_MCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
-
- POINTS_SCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
-
- pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
-
- pointsperangstrom - Static variable in class org.jmol.script.Token
-
- pointT - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- pointT - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- pointT - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- pointT2 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- pointT2 - Variable in class org.jmol.viewer.TransformManager
-
- pointT3 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- pointTipOffset - Variable in class org.jmol.shapebio.RocketsRenderer
-
- pointTsp - Variable in class org.jmol.viewer.TransformManager
-
- pointType - Variable in class org.jmol.jvxl.readers.KinemageReader
-
- pointVectorEnd - Variable in class org.jmol.shapespecial.VectorsRenderer
-
- polygon - Static variable in class org.jmol.script.Token
-
- polygon - Variable in class org.jmol.shapespecial.Draw
-
- polygonColixes - Variable in class org.jmol.util.MeshSurface
-
- polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
-
- polygonCount - Variable in class org.jmol.util.MeshSurface
-
- polygonCount0 - Variable in class org.jmol.util.MeshSurface
-
- PolygonFileReader - Class in org.jmol.jvxl.readers
-
- PolygonFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.PolygonFileReader
-
- polygonIndexes - Variable in class org.jmol.util.MeshSurface
-
- polyhedra() - Method in class org.jmol.script.ScriptEvaluator
-
- polyhedra - Static variable in class org.jmol.script.Token
-
- Polyhedra - Class in org.jmol.shapespecial
-
- Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
-
- Polyhedra.Polyhedron - Class in org.jmol.shapespecial
-
- Polyhedra.Polyhedron(Atom, int, int, int, Point3f[], short[], byte[]) - Constructor for class org.jmol.shapespecial.Polyhedra.Polyhedron
-
- 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.script.Token
-
- polymerlength - Static variable in class org.jmol.script.Token
-
- pop - Static variable in class org.jmol.script.Token
-
- popContext(boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- popHoldRepaint() - Method in class org.jmol.api.JmolViewer
-
- popHoldRepaint(boolean) - Method in class org.jmol.viewer.RepaintManager
-
- popHoldRepaint() - Method in class org.jmol.viewer.Viewer
-
- popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
-
- popInHeight - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- PopInJmol - Class in org.openscience.jmol.app.webexport
-
- PopInJmol(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.PopInJmol
-
- popInWidth - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- popupMenu(int, int, char) - Method in class org.jmol.viewer.Viewer
-
- PopupResource - Class in org.jmol.popup
-
- PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
-
- port - Variable in class org.openscience.jmol.app.JmolApp
-
The data model.
- port - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- posCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- position - Variable in class org.openscience.jmol.app.surfacetool.Slice
-
- position - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- position - Variable in class org.openscience.jvxl.MonitorInputStream
-
- positionAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- positionBeforePrompt - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- positionMin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- positionSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- positionThicknessPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- postByteArray(String, byte[]) - Static method in class org.jmol.viewer.FileManager
-
not implemented
- postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- potentials - Variable in class org.jmol.quantum.MepCalculation
-
- povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
-
A dialog for controling the creation of a povray input file from a
Chemframe and a display.
- PovrayDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Creates a dialog for getting info related to output frames in
povray format.
- PovrayDialog.PovrayWindowListener - Class in org.openscience.jmol.app.jmolpanel
-
Listener for responding to dialog window events.
- PovrayDialog.PovrayWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
-
- povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- power4 - Static variable in class org.jmol.geodesic.EnvelopeCalculation
-
- 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
-
- pqrLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- PqrReader - Class in org.jmol.adapter.readers.more
-
PQR file reader.
- PqrReader() - Constructor for class org.jmol.adapter.readers.more.PqrReader
-
- precalculateVoxelData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
-
- precision - Variable in class org.jmol.modelset.LabelToken
-
- Precision - Variable in class org.jmol.util.JpegInfo
-
- 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.script.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.script.ScriptCompiler
-
- predragBinding - Variable in class org.jmol.viewer.ActionManager
-
- preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
-
- PreferencesDialog(JmolPanel, JFrame, GuiMap, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- PreferencesDialog.PrefsAction - Class in org.openscience.jmol.app.jmolpanel
-
- PreferencesDialog.PrefsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
-
- prefsAction - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- preloadClassIndex - Variable in class org.jmol.applet.AppletWrapper
-
- preloadClassNames - Variable in class org.jmol.applet.AppletWrapper
-
- preloadImage - Variable in class org.jmol.applet.AppletWrapper
-
- preloadImageName - Variable in class org.jmol.applet.AppletWrapper
-
- preloadImagePainted - Variable in class org.jmol.applet.AppletWrapper
-
- preloadImageReadyForDisplay - Variable in class org.jmol.applet.AppletWrapper
-
- preloadTextMessage - Variable in class org.jmol.applet.AppletWrapper
-
- preloadThreadCount - Variable in class org.jmol.applet.AppletWrapper
-
- preProcessPlanes - Variable in class org.jmol.jvxl.readers.VolumeFileReader
-
- preserveState - Variable in class org.jmol.modelset.AtomCollection
-
- preservestate - Static variable in class org.jmol.script.Token
-
- preserveState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- pressed - Variable in class org.jmol.viewer.ActionManager
-
- PRESSED - Static variable in class org.jmol.viewer.binding.Binding
-
- pressedAtomIndex - Variable in class org.jmol.viewer.ActionManager
-
- pressedCount - Variable in class org.jmol.viewer.ActionManager
-
- prev - Static variable in class org.jmol.script.Token
-
- prevAtom - Variable in class org.jmol.smiles.SmilesGenerator
-
- prevFrame - Variable in class org.jmol.viewer.Viewer
-
- PREVIOUS - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
-
- PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
-
- previousClassName - Variable in class org.jmol.applet.AppletWrapper
-
- previousMeshID - Variable in class org.jmol.shape.MeshCollection
-
- previousScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- previousSpaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- previousUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- previousX - Variable in class org.jmol.viewer.TransformManager
-
- previousY - Variable in class org.jmol.viewer.TransformManager
-
- prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- prevSp2Atoms - Variable in class org.jmol.smiles.SmilesGenerator
-
- prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
-
- pRight - Variable in class org.jmol.g3d.Hermite3D
-
- primitiveCode - Variable in class org.jmol.symmetry.HallInfo.RotationTerm
-
- primitiveData - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- primitiveHallSymbol - Variable in class org.jmol.symmetry.HallInfo
-
- primitives - Variable in class org.jmol.smiles.SmilesAtom
-
- primitives - Variable in class org.jmol.smiles.SmilesBond
-
- primitiveToCryst - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- primitiveToIndex - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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.quantum.MopacSlaterReader
-
- print() - Method in class org.jmol.script.ScriptEvaluator
-
- print - Static variable in class org.jmol.script.Token
-
- print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
added print command, so that it can be used by RasmolScriptHandler
- printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- printProgressbarMessage(Graphics) - Method in class org.jmol.applet.Jmol
-
- priorRow - Variable in class org.jmol.export.image.PngEncoder
-
- privateKey - Variable in class org.jmol.export.___Exporter
-
- privateKey - Variable in class org.jmol.export.Export3D
-
- privateKey - Variable in class org.jmol.export.image.ImageCreator
-
- privateKey - Variable in class org.jmol.shapesurface.Isosurface
-
- privateKey - Variable in class org.jmol.viewer.Viewer
-
- probe - Static variable in class org.jmol.script.Token
-
- proc - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- process(Point3f) - Method in interface org.jmol.api.QuantumCalculationInterface
-
- process(int, int, float) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
-
Data mapping function to radically increase speed and reduce
memory requirements of mapping data when the mapping comes from
the same data set as the points, so isosurface creation and
data mapping can be carried out both in the first (and only) pass.
- process() - Method in class org.jmol.quantum.MepCalculation
-
- process() - Method in class org.jmol.quantum.MOCalculation
-
- process() - Method in class org.jmol.quantum.NciCalculation
-
- process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
-
Passing the grid points of the two ends of an edge and a fraction
to this method returns the value at a triangle point.
- process(Point3f) - Method in class org.jmol.quantum.QuantumCalculation
-
- process() - Method in class org.jmol.quantum.QuantumCalculation
-
- process - Variable in class org.jmol.script.ParallelProcessor.RunProcess
-
- process - Static variable in class org.jmol.script.Token
-
- processAtom() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
-
- processAtomicCharges() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
Reads the section in MOPAC files with atomic charges.
- processAtomObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- processAtoms() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
-
- processAtoms(int, int, int, int) - Method in class org.jmol.quantum.NciCalculation
-
At each grid point we need to calculate the sum of the
atom-based promolecular data.
- processAtomSiteLoopBlock(boolean) - 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.quantum.CsfReader
-
- processBinaryDocument(BinaryDocument) - Method in class org.jmol.adapter.readers.more.BinaryReader
-
- processBinaryDocument(BinaryDocument) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- processBondObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- processBonds() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
-
- processCellParameter() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
unit cell parameters -- two options, so we use MOD 6
- processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
-
incorporates double-click gesture
- processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- processChangeSync(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- processCharges() - Method in class org.jmol.adapter.readers.simple.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.xtal.ShelxReader
-
- processComponentKeyEvent(KeyEvent) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
-
- processConnectorObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- processCoord() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
-
- processCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
Reads the section in MOPAC files with cartesian coordinates.
- processCtab(boolean) - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- processDataParameter() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
initialize a new atom set
- processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- processDeletedModelAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
-
- 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.XmlQEReader
-
- processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- processEndElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- processEndElement2(String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
-
- processes - Variable in class org.jmol.script.ParallelProcessor
-
- processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.api.JmolViewer
-
- processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.multitouch.ActionManagerMT
-
- processEvent(int, int, int, int, Point3f, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
-
- processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
Translate the specialized Sparsh UI information into
a format that Jmol's ActionManager can understand
without any special classes.
- processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.viewer.ActionManager
-
- processEvent(int, int, int, int, Point3f, long) - Method in class org.jmol.viewer.Viewer
-
- processFile(String, File, File, boolean, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
-
- 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.simple.GhemicalMMReader
-
- processInfo() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
-
- processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- processInputCoords() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- processKeyEvent(KeyEvent) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
-
- processKeyEvent(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
Custom key event processing for command 0 implementation.
- processLigandBondLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- processLocalTransform() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- processLock - Variable in class org.jmol.script.ParallelProcessor.RunProcess
-
- processLoopBlock() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
processes loop_ blocks of interest or skips the data
- processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- processMol() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
-
- processMolecularOrbitalObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- processMolecule() - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- processMolSdHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
-
- processName - Variable in class org.jmol.script.ParallelProcessor.Process
-
- processNextMeasure(Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
-
- processNextMeasure(Measurement) - Method in class org.jmol.modelset.MeasurementData
-
if this is the client, then this method is
called by MeasurementData when a measurement is ready
- processNextMeasure(Measurement) - Method in class org.jmol.shape.Measures
-
- 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.
- processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- processOneCubical(int, int[], int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- processPoints() - Method in class org.jmol.quantum.MOCalculation
-
- processPoints() - Method in class org.jmol.quantum.QuantumCalculation
-
- processScript(Object[]) - Method in class org.jmol.viewer.StatusManager
-
- processShapeCommand(int) - Method in class org.jmol.script.ScriptEvaluator
-
- processShell(int) - Method in class org.jmol.quantum.MOCalculation
-
- processSlater(int) - Method in class org.jmol.quantum.MOCalculation
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- processStartElement(String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- processStartElement2(String, Map<String, String>) - 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.xtal.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
- processTokenList(short, boolean) - Method in class org.jmol.script.ScriptCompiler
-
- processTotalEnergy() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
- processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
the PDB transformation matrix cartesian --> fractional
- processVibrationObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
-
- processXml(XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- processXml(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, XMLReader) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- processXml(XmlReader, AtomSetCollection, BufferedReader, JSObject) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
-
- processXml(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- procSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- 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.util.Measure
-
- prompt(String, String, String[], boolean) - Method in interface org.jmol.api.JmolPromptInterface
-
- prompt(String, String, String[], boolean) - Method in class org.jmol.console.JmolPrompt
-
- prompt() - Method in class org.jmol.script.ScriptEvaluator
-
- prompt - Static variable in class org.jmol.script.Token
-
- prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
-
- prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
-
- prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
-
- prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.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_CONSOLE_TEXT - 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_ERROR_MESSAGE - 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_FILE_INFO - 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_ISOSURFACE_INFO - 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_LIGAND_INFO - 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_MOUSE_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, int[][], int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- properties - Variable in class org.jmol.export.history.HistoryFile
-
The data stored in the history file.
- properties - Variable in class org.jmol.modelset.Model
-
- propertiesTextArea - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- property - Static variable in class org.jmol.script.Token
-
- propertyatomnumbercolumncount - Static variable in class org.jmol.script.Token
-
- propertyatomnumberfield - Static variable in class org.jmol.script.Token
-
- propertyChange(PropertyChangeEvent) - Method in class org.jmol.export.dialog.FilePreview
-
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
-
- propertyColorEncoder - Variable in class org.jmol.util.ColorEncoder
-
- propertyColorEncoder - Variable in class org.jmol.viewer.ColorManager
-
- propertycolorscheme - Static variable in class org.jmol.script.Token
-
- propertyColorScheme - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- propertyCount - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- propertydatacolumncount - Static variable in class org.jmol.script.Token
-
- propertydatafield - Static variable in class org.jmol.script.Token
-
- propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
-
- PROPERTYFLAGS - Static variable in class org.jmol.script.Token
-
- propertyItemCounts - Variable in class org.jmol.adapter.readers.quantum.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
-
- propertySmoothingPower - 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.jmolpanel.RecentFilesDialog
-
- propselector - Static variable in class org.jmol.script.Token
-
- protein - Static variable in class org.jmol.script.Token
-
- proteinShape(int) - Method in class org.jmol.script.ScriptEvaluator
-
- proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
-
- ProteinStructure - Class in org.jmol.modelsetbio
-
- ProteinStructure(AlphaPolymer, EnumStructure, int, int, int) - Constructor for class org.jmol.modelsetbio.ProteinStructure
-
- proteinstructurePending - Variable in class org.jmol.shapebio.RocketsRenderer
-
- proteinStructureTainted - Variable in class org.jmol.modelset.ModelCollection
-
- pS - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- psi - Variable in class org.jmol.modelset.Group
-
- psi - Static variable in class org.jmol.script.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_monteCarloCount - 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_normalization - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- 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
-
- psiContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- PsiReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Psi3 output files.
- PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
-
- pt - Variable in enum org.jmol.constant.EnumVdw
-
- pt - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
-
- pt - Variable in class org.jmol.modelset.LabelToken
-
- pt - Variable in class org.jmol.shape.CageRenderer
-
- pt - Variable in class org.jmol.shape.EchoRenderer
-
- pt - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- pt - Variable in class org.jmol.util.ContactPair
-
- pt - Variable in class org.jmol.util.ZipUtil.GZipData
-
- pt - Variable in class org.jmol.viewer.FileManager.ArrayDataReader
-
- pt - Variable in class org.jmol.viewer.FileManager.VectorDataReader
-
- pt - Variable in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
-
- pt - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
-
- pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- pt0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- pt0 - Variable in class org.jmol.script.ScriptFlowContext
-
- pt0 - Variable in class org.jmol.script.ScriptFunction
-
- pt0 - Static variable in class org.jmol.script.ScriptVariable
-
- pt0 - Static variable in class org.jmol.shape.Axes
-
- pt0 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- pt0f - Variable in class org.jmol.shapespecial.DrawRenderer
-
- pt0i - Variable in class org.jmol.shapespecial.DrawRenderer
-
- pt1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- pt1 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- pt1 - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- pt1 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- pt1 - Variable in class org.jmol.shapesurface.Contact
-
- pt1f - Variable in class org.jmol.shape.MeshRenderer
-
- pt1i - Variable in class org.jmol.shape.MeshRenderer
-
- pt2 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- pt2 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- pt2 - Variable in class org.jmol.shapesurface.Contact
-
- pt2f - Variable in class org.jmol.shape.MeshRenderer
-
- pt2i - Variable in class org.jmol.shape.MeshRenderer
-
- pt3i - Variable in class org.jmol.shape.MeshRenderer
-
- pt4Value(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- 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
-
- ptAi - Variable in class org.jmol.export.Export3D
-
- ptAtom - Variable in class org.jmol.shape.EchoRenderer
-
- ptB - Variable in class org.jmol.export.Export3D
-
- 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
-
- ptCommand - Variable in class org.jmol.script.ScriptFlowContext
-
- ptConnect - Variable in class org.jmol.shapebio.CartoonRenderer
-
- ptD - Variable in class org.jmol.export.Export3D
-
- ptDefault - Variable in class org.jmol.script.ScriptFlowContext
-
- ptDefaultLattice - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- ptFloat - Variable in class org.jmol.adapter.readers.more.MdCrdReader
-
- ptid - Variable in class org.jmol.script.ScriptMathProcessor
-
- ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- ptLine - Variable in class org.jmol.script.ScriptFlowContext
-
- ptList - Variable in class org.jmol.shapespecial.Draw
-
- ptMark - Variable in class org.jmol.viewer.FileManager.ArrayDataReader
-
- ptMark - Variable in class org.jmol.viewer.FileManager.VectorDataReader
-
- ptMax - Variable in class org.jmol.export._IdtfExporter
-
- ptMin - Variable in class org.jmol.export._IdtfExporter
-
- ptMoveToCenter - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- ptMoveToCenter - Variable in class org.jmol.viewer.TransformManager11
-
- ptNewSetModifier - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- ptNext - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- ptNext - Variable in class org.jmol.viewer.ActionManager.Gesture
-
- ptOffset - Variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- ptOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- ptOffset - Variable in class org.jmol.util.MeshSurface
-
- ptOffset - Variable in class org.jmol.viewer.RepaintManager
-
- pTopLeft - Variable in class org.jmol.g3d.Hermite3D
-
- pTopRight - Variable in class org.jmol.g3d.Hermite3D
-
- ptOriginShift - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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.calc.MarchingSquares.Triangle
-
- pts - Variable in class org.jmol.modelset.Measurement
-
- ptS1 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- ptS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- ptSemi - Variable in class org.jmol.script.ScriptCompiler
-
- ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.VolumeDataReader
-
- ptTemp - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- ptTemp - Variable in class org.jmol.export._ObjExporter
-
- ptTemp - Variable in class org.jmol.g3d.Sphere3D
-
- ptTemp - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- ptTemp - Variable in class org.jmol.jvxl.data.VolumeData
-
- ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- ptTemp - Variable in class org.jmol.modelset.ModelCollection
-
- ptTemp - Variable in class org.jmol.modelsetbio.AminoMonomer
-
- ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- 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
-
- ptTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- 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
-
- ptTrans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
-
- ptValue(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptMathProcessor
-
- ptValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- ptx - Variable in class org.jmol.script.ScriptMathProcessor
-
- ptXY - Variable in class org.jmol.shape.Sticks
-
- ptXY - Variable in class org.jmol.shapespecial.Draw
-
- ptXY - Variable in class org.jmol.shapesurface.Isosurface
-
- ptXyzTemp - Variable in class org.jmol.jvxl.data.VolumeData
-
- ptXyzTemp - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- ptY0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- ptZ0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- purging - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
- purine - Static variable in class org.jmol.script.Token
-
- PURPLE - Static variable in class org.jmol.g3d.Graphics3D
-
- push - Static variable in class org.jmol.script.Token
-
- pushContext(ContextToken) - Method in class org.jmol.script.ScriptEvaluator
-
- pushCount - Variable in class org.jmol.script.ScriptCompiler
-
- pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
-
- pushHoldRepaint() - Method in class org.jmol.viewer.RepaintManager
-
- pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
-
- pushHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
-
- put(int, int) - Method in class org.jmol.util.Int2IntHash
-
- putBox(int, float[]) - Method in class org.jmol.shape.Labels
-
- Putbyte(byte, OutputStream) - Method in class org.jmol.export.image.GifEncoder
-
- putCoord(Vector3d, double[]) - Static method in class org.jmol.minimize.Util
-
- putFileContents(File, String) - Method in class org.openscience.chimetojmol.ChimePanel
-
- putIf(char) - Method in class org.jmol.script.ScriptMathProcessor
-
- putLabel(int, Text) - Method in class org.jmol.shape.Labels
-
- putOp(Token) - Method in class org.jmol.script.ScriptMathProcessor
-
- Putword(int, OutputStream) - Method in class org.jmol.export.image.GifEncoder
-
- putX(ScriptVariable) - Method in class org.jmol.script.ScriptMathProcessor
-
- Pwr2 - Static variable in class org.jmol.util.TriangleData
-
- Pwr2 - Static variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- pyrimidine - Static variable in class org.jmol.script.Token
-
- r - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- r - Variable in class org.jmol.quantum.SlaterData
-
- r0 - Variable in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
-
- rab - Variable in class org.jmol.minimize.forcefield.Calculation
-
- rad - Static variable in class org.jmol.script.Token
-
- RAD_TO_DEG - Static variable in class org.jmol.minimize.forcefield.Calculations
-
- RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
-
- radialPart(double) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- RADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- radiansPerDegree - Static variable in class org.jmol.smiles.SmilesMeasure
-
- radiansPerDegree - Static variable in class org.jmol.util.Measure
-
- radiansPerDegree - Static variable in class org.jmol.viewer.JmolConstants
-
- radical - Static variable in class org.jmol.script.Token
-
- radii - Variable in class org.jmol.util.ContactPair
-
- 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 - Static variable in class org.jmol.script.Token
-
- radius - Variable in class org.jmol.shapespecial.Polyhedra
-
- radius - Variable in class org.jmol.symmetry.PointGroup
-
- radius2 - Variable in class org.jmol.g3d.Cylinder3D
-
- RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
-
- RADIUS_MAX - Static variable in class org.jmol.shape.Shape
-
- RADIUS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for vector radius.
- RADIUS_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value of vector radius.
- radiusData - Variable in class org.jmol.atomdata.AtomData
-
- RadiusData - Class in org.jmol.atomdata
-
- RadiusData() - Constructor for class org.jmol.atomdata.RadiusData
-
- RadiusData(float, RadiusData.EnumType, EnumVdw) - Constructor for class org.jmol.atomdata.RadiusData
-
- RadiusData(float[]) - Constructor for class org.jmol.atomdata.RadiusData
-
- radiusData - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- radiusData - Variable in class org.jmol.modelset.MeasurementData
-
- radiusData - Variable in class org.jmol.shape.Measures
-
- RadiusData.EnumType - Enum in org.jmol.atomdata
-
- RadiusData.EnumType() - Constructor for enum org.jmol.atomdata.RadiusData.EnumType
-
- radiusHermites - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- radiusI - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- radiusP - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- radiusSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- ramachandran - Static variable in class org.jmol.script.Token
-
- random - Variable in class org.jmol.g3d.Graphics3D
-
- random - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- random - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- random - Static variable in class org.jmol.script.Token
-
- randomizeUnitVector(Vector3d) - Static method in class org.jmol.minimize.Util
-
- randomPoint() - Static method in class org.jmol.shapespecial.Draw
-
- randomPoint - Static variable in class org.jmol.shapespecial.Polyhedra
-
- randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
-
- range - Static variable in class org.jmol.script.Token
-
- range - Variable in class org.jmol.shapebio.BioShape
-
- rangeAll - Variable in class org.jmol.jvxl.readers.Parameters
-
- rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
-
- rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
-
- rangeSelected - Variable in class org.jmol.jvxl.readers.Parameters
-
- rangeselected - Static variable in class org.jmol.script.Token
-
- rangeSelected - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- rasmol - Static variable in class org.jmol.script.Token
-
- RASMOL - Static variable in class org.jmol.util.ColorEncoder
-
- rasmolBinding - Variable in class org.jmol.viewer.ActionManager
-
- RasmolBinding - Class in org.jmol.viewer.binding
-
- RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
-
- rasmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.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.jmolpanel.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
-
- RAW_RGB - Static variable in class org.jmol.g3d.Graphics3D
-
- RAW_RGB_INT - Static variable in class org.jmol.g3d.Colix3D
-
- rd - Variable in class org.jmol.viewer.Viewer
-
- rdLast - Variable in class org.jmol.shapespecial.Dots
-
- rdVDW - Static variable in class org.jmol.shapesurface.Contact
-
- read(char[]) - Method in class org.jmol.viewer.FileManager.ArrayDataReader
-
- read(char[]) - Method in class org.jmol.viewer.FileManager.VectorDataReader
-
- 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
-
- read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
read three vectors, as for unit cube definitions
allows for non-numeric data preceding the number block
- readableTypes - Static variable in class org.jmol.viewer.PropertyManager
-
- readAllData - Variable in class org.jmol.jvxl.readers.Parameters
-
- readAndSetVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- readAparam() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- readArchive(String, boolean, int, boolean) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readArchive() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- readArchiveHeader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- readAtom(String[], boolean) - Method in class org.jmol.adapter.readers.xtal.AimsReader
-
- readAtomCountAndOrigin() - Method in class org.jmol.adapter.readers.simple.CubeReader
-
- readAtomCountAndSetNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readAtomData(float) - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readAtomicOrbitalOrder() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readAtomicPos(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readAtomNames() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- 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.GromacsReader
-
- readAtoms(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads the output coordinates section into a new AtomSet.
- readAtoms(boolean) - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.simple.CubeReader
-
- readAtoms(int) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
-
- readAtoms(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- readAtomsCartGeomThenCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
-
- readAtomSet(String, boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- readAtomsInAngstromCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- readAtSign() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
- readBasis() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- readBasis() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
- readBasis() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readBasis() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- readBasisNormalized() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readBinaryHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- readBonds(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- readBonds(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- readBonds(int) - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- readBonds() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readBonds() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
-
- readBonds(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
-
- readBrickLayer() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
-
- readBuf(char[]) - Method in class org.jmol.viewer.FileManager.DataReader
-
- 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
-
- readCalculationInfo(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- readCalculationType() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readCellParam() - Method in class org.jmol.adapter.readers.xtal.DmolReader
-
- readCellParam(boolean) - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- readCellParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readCellParams(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readCellThenAtomsCartesian() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
-
- readCharges() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readCifData(BufferedReader) - Static method in class org.jmol.util.CifDataReader
-
- readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- readConstraints() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- readCoord() - Method in class org.jmol.adapter.readers.xtal.DmolReader
-
- readCoordinates() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
-
- readCoordinates() - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Reads a set of coordinates
- readCoordinates() - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
Reads a set of coordinates
- readCoordinates() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
Reads a set of coordinates
- readCrystalInfo() - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- readCrystallographicCoords() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readData() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- readData(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- readData() - Method in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
-
- readData() - Method in class org.jmol.util.CompoundDocument.CmpDocHeader
-
- readData31(String, String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- readData46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- readDimensionality() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readDipole() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
- readDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
-
- readDocument() - Method in class org.jmol.adapter.readers.more.BinaryReader
-
- readDots() - Method in class org.jmol.jvxl.readers.KinemageReader
-
- readDouble() - Method in class org.jmol.util.BinaryDocument
-
- readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- readElementNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readEmbeddedScript() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- readEnergy() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
-
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- reader - Variable in class org.jmol.util.CifDataReader
-
A special tokenizer class for dealing with quoted strings in CIF files.
- reader - Variable in class org.jmol.viewer.FileManager.FileReader
-
- readerClosed - Variable in class org.jmol.jvxl.readers.VolumeFileReader
-
- readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- readerSets - Static variable in class org.jmol.adapter.smarter.Resolver
-
- readESym(boolean) - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readEventCount - Variable in class org.openscience.jvxl.MonitorInputStream
-
- readExtents(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
- readFile31() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- readFile46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- readFileData() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readFinalCell() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readFloat() - Method in class org.jmol.util.BinaryDocument
-
- readFloatArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
-
- readFragments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readFreq() - Method in class org.jmol.adapter.readers.xtal.DmolReader
-
- readFreqsAndModes() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Reads a set of vibrations.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interprets the Harmonic frequencies section.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads the AtomSet and projected frequencies in the frequency section.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
Interprets the Harmonic frequencies section.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
-
- readFrequencies() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
Reads a set of vibrations.
- readFrequencies() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
Interprets the Harmonic frequencies section.
- readFrequencies() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readFrequency() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readGeometryOptimization() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- readGradient() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readGradients() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads the energy gradients section into a new AtomSet.
- readHeader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readHeader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readHeader() - Method in class org.jmol.util.CompoundDocument
-
- readInitialCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readInputAtoms() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- readInputHeader() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- readInputRecords() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- readInt() - Method in class org.jmol.util.BinaryDocument
-
- readJaguarMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readKeywords() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- readLatticeAbc() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readLatticeCart() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readLatticeVector(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
-
- readLEInt() - Method in class org.jmol.util.BinaryDocument
-
- readLELong() - Method in class org.jmol.util.BinaryDocument
-
- readLengthUnit(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readLine() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
- readLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- readLine() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- readLine() - Method in interface org.jmol.api.JmolLineReader
-
- readLine() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- readLine() - Method in class org.jmol.util.CifDataReader
-
- readLine() - Method in class org.jmol.viewer.FileManager.ArrayDataReader
-
- readLine() - Method in class org.jmol.viewer.FileManager.VectorDataReader
-
- readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- readLineWithNewline() - Method in class org.jmol.adapter.smarter.LimitedLineReader
-
- readLong() - Method in class org.jmol.util.BinaryDocument
-
- readMagneticMoments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readMdyn() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readMolecularOrbitalAnalysis(boolean) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
- readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- readMolecularOrbitals(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- readMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- readMolecularOrbitalVectors() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- readMOs() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- readMOs(boolean, QchemReader.MOInfo[]) - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readMultipole(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
-
- readNonCommentLine() - Method in class org.jmol.util.LimitedLineReader
-
- readOrbitalData(boolean) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- readOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
- readOutput() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- readOutputAtoms() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readOutputCharges() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readOutputUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.ApbsReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.CastepDensityReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.CubeReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.JaguarReader
-
nothing much here
- readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.PltFormattedReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- readParameters() - Method in class org.jmol.jvxl.readers.XplorReader
-
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Reads partial charges and assigns them only to the last atom set.
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads partial charges and assigns them only to the last atom set.
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readPartialCharges() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
- readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readPhononFractionalCoord() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readPhononFrequencies() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readPhononTrajectories() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readPhononUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readPolygons() - Method in class org.jmol.jvxl.readers.KinemageReader
-
- readPolygons() - Method in class org.jmol.jvxl.readers.MsmsReader
-
- readPolygons() - Method in class org.jmol.jvxl.readers.ObjReader
-
- readPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- readPOSITION() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readPositionsAbs() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readPositionsFrac() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- readPrimitiveMapping() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
create arrays that maps primitive atoms to conventional atoms in a 1:1
fashion.
- readProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- readProperty() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readPsiMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
- readQchemMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
- readResInfo(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
-
- readROHFonly - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
- readSCFDone() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interprets the SCF Done: section.
- readSCFDone() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
Interprets the SCF Done: section.
- readSecondOrderData() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- readShift() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readShort() - Method in class org.jmol.util.BinaryDocument
-
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
- readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- readSpins() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readString(int) - Method in class org.jmol.util.BinaryDocument
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.CastepDensityReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readSurfaceData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
- readSymmetry() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Read the symmetry information and set the property.
- readSymmetry() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- readThisModel - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- readTitleLines() - Method in class org.jmol.adapter.readers.simple.CubeReader
-
- readTotal() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Interpret a line starting with a line with "Total" in it.
- readTotalAtomicCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readTransform() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- readTransform() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- readTransformationMatrix() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readUniqueAtoms() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
- readUnitCell() - Method in class org.jmol.adapter.readers.more.GromacsReader
-
- readUnitCell() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
-
- readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- readUnnormalizedBasis() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
-
- readUnsignedShort() - Method in class org.jmol.util.BinaryDocument
-
- readUserData(int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
- readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readVectors() - Method in class org.jmol.jvxl.readers.KinemageReader
-
- readVertices() - Method in class org.jmol.jvxl.readers.KinemageReader
-
- readVertices() - Method in class org.jmol.jvxl.readers.MsmsReader
-
- readVertices() - Method in class org.jmol.jvxl.readers.ObjReader
-
- readVertices() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- readVibFreqs() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
-
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- readVolumeFileSurfaceData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- readVolumePrimCell() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- readVolumetricHeader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- readVoxelDataIndividually(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- readVoxelVector(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- 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
-
- rebond() - Method in class org.jmol.api.JmolViewer
-
- rebond() - Method in class org.jmol.viewer.Viewer
-
- rebond(boolean) - Method in class org.jmol.viewer.Viewer
-
- rebond() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- recalc() - Method in class org.jmol.shape.Object2d
-
- recalc() - Method in class org.jmol.shape.Text
-
- recalcAltVertices - Variable in class org.jmol.shape.Mesh
-
- reCalculate(BitSet, Matrix3f) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
- 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
-
- recalculatePositionDependentQuantities(BitSet, Matrix4f) - Method in class org.jmol.modelset.ModelSet
-
- recallCommand(boolean) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
-
- recallCommand(boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleTextPane
-
Recall command history.
- recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- RecentFilesDialog - Class in org.openscience.jmol.app.jmolpanel
-
Manages a list of recently opened files.
- RecentFilesDialog(Frame) - Constructor for class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
Creates a hidden recent files dialog
- recordData(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- recordStatus(String) - Method in class org.jmol.viewer.StatusManager
-
- recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- Rectangle - Class in org.jmol.util
-
- Rectangle() - Constructor for class org.jmol.util.Rectangle
-
- rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- rectRubber - Variable in class org.jmol.viewer.ActionManager
-
- red - Variable in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
-
- RED - Static variable in class org.jmol.g3d.Graphics3D
-
- redo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
-
- redoButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- redomove - Static variable in class org.jmol.script.Token
-
- reduceFilename(String) - Static method in class org.jmol.viewer.ModelManager
-
- reference - Variable in class org.jmol.modelset.TickInfo
-
- reference - Static variable in class org.jmol.script.Token
-
- referenceCenter - Variable in class org.jmol.export.___Exporter
-
- 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.script.ScriptEvaluator
-
- refresh - Static variable in class org.jmol.script.Token
-
- refresh() - Method in class org.jmol.viewer.RepaintManager
-
- refresh(int, String) - Method in class org.jmol.viewer.Viewer
-
initiate a repaint/update sequence if it has not already been requested.
- refreshing - Static variable in class org.jmol.script.Token
-
- refreshing - Variable in class org.jmol.viewer.Viewer
-
- refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
-
- refreshShapeTrajectories(int, BitSet, Matrix4f) - Method in class org.jmol.viewer.ShapeManager
-
- registerAllValues(StateManager.GlobalSettings, boolean) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- rehash() - Method in class org.jmol.util.Int2IntHash
-
- reinitializeLightingAndColor() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- release() - Method in interface org.jmol.api.AtomIndexIterator
-
- release() - Method in class org.jmol.bspt.CubeIterator
-
nulls internal references
- release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
- 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
-
- RELEASED - Static variable in class org.jmol.viewer.binding.Binding
-
- 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.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
-
- releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
-
- remapColors(ColorEncoder, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
remaps colors based on a new color scheme or translucency level
- remark290() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- remark350() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- rememberCheckbox(String, JMenuItem) - Method in class org.jmol.popup.SimplePopup
-
- remoteAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- remoteAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
-
- remove - Static variable in class org.jmol.script.Token
-
- remove(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- removeAll(Object) - Method in class org.jmol.popup.SimplePopup
-
- removeAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- removeBinding(Iterator<String>, String) - Method in class org.jmol.viewer.binding.Binding
-
- 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
- removeJmolParameter(String) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- removeMenuItem(Object, int) - Method in class org.jmol.popup.SimplePopup
-
- 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.
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.export.JmolFileDropper
-
- 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
-
- removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
-
- 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.SimplePopup
-
- render(short, short, boolean, boolean, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Cylinder3D
-
- 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(int, Point3f[], Point3f[], int, int, int, float) - Method in class org.jmol.shape.CageRenderer
-
- render() - Method in class org.jmol.shape.EchoRenderer
-
- 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, boolean, 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.DotsRenderer
-
- 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, boolean) - Method in class org.jmol.viewer.RepaintManager
-
- render() - Method in class org.jmol.viewer.Viewer
-
- render1(Atom) - 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(Dots) - Method in class org.jmol.shapespecial.DotsRenderer
-
- render1(Mesh) - Method in class org.jmol.shapespecial.DrawRenderer
-
- render1(Atom, Object[]) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
-
- render1(Polyhedra.Polyhedron, short, Point3i[]) - Method in class org.jmol.shapespecial.PolyhedraRenderer
-
- render1(Graphics3D, ModelSet, boolean) - Method in class org.jmol.viewer.RepaintManager
-
- render1(Object, Object, int, int) - Method in class org.jmol.viewer.Viewer
-
- render1Strand(Point3i[]) - Method in class org.jmol.shapebio.StrandsRenderer
-
- render2(boolean) - Method in class org.jmol.shape.MeshRenderer
-
- render2(boolean) - Method in class org.jmol.shapespecial.DrawRenderer
-
- render2(boolean) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- render2Strand(boolean, float, float) - Method in class org.jmol.shapebio.MeshRibbonRenderer
-
- 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, boolean) - Method in class org.jmol.shapespecial.DrawRenderer
-
- renderArrowHeads - Variable in class org.jmol.shapebio.RocketsRenderer
-
- renderAsRockets - Variable in class org.jmol.shapebio.CartoonRenderer
-
- renderAxes() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
-
- renderBackground() - Method in interface org.jmol.api.JmolRendererInterface
-
- renderBackground() - Method in class org.jmol.export.Export3D
-
- renderBackground() - Method in class org.jmol.g3d.Graphics3D
-
- renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
-
- 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() - Method in class org.jmol.shape.SticksRenderer
-
- renderCone(short, boolean, byte, int, float, float, float, float, float, float, boolean, boolean) - Method in class org.jmol.g3d.Cylinder3D
-
- renderCone(int, Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.shapebio.BioShapeRenderer
-
- renderContourLines() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- renderConvex(short, FastBitSet, int) - Method in class org.jmol.shapespecial.DotsRenderer
-
generic renderer -- dots and geosurface
- renderConvex(short, FastBitSet, int) - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
-
- 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.shapespecial.DotsRenderer
-
also called by GeoSurface when in motion
- renderDots(Point3f) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
-
- renderEdges - Variable in class org.jmol.shapebio.CartoonRenderer
-
- renderEllipsoid(Ellipsoids.Ellipsoid) - Method in class org.jmol.shapespecial.EllipsoidsRenderer
-
- renderers - Variable in class org.jmol.viewer.RepaintManager
-
- 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
-
- 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, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Hermite3D
-
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.shapebio.BioShapeRenderer
-
- renderHermiteRope(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Hermite3D
-
- renderInfo(SymmetryInterface) - Method in class org.jmol.shape.UccageRenderer
-
- renderInfo() - Method in class org.jmol.shapespecial.DrawRenderer
-
- renderInfo() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- renderInfo() - Method in class org.jmol.shapesurface.MolecularOrbitalRenderer
-
- rendering - Variable in class org.jmol.jvxl.data.JvxlData
-
- renderLabel(String, float, float, float, float, float) - Method in class org.jmol.shape.AxesRenderer
-
- renderLarge() - Method in class org.jmol.g3d.Sphere3D
-
- renderLenotisWesthofEdges(NucleicMonomer, short) - Method in class org.jmol.shapebio.CartoonRenderer
-
- renderLine(Point3f, Point3f, int, Point3i, Point3i, boolean) - Method in class org.jmol.shape.FontLineShapeRenderer
-
- renderLonePair(boolean) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- renderMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.MeasuresRenderer
-
- renderMesh(int, int) - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- 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, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
-
- renderOffScreen(String, Font3D, Object, int, int, int) - Static method in class org.jmol.awt.Image
-
- renderOffScreen(String, Font3D, Object, int, int, int) - Method in class org.jmol.awt.Platform
-
- renderParallelPair(boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Hermite3D
-
- 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(JmolViewer, Object, Object) - Method in interface org.jmol.api.ApiPlatform
-
- renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolSimpleViewer
-
- renderScreenImage(Object, Object, int, int) - Method in class org.jmol.api.JmolViewer
-
an added class for rendering stereo in two independent applets
- renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
-
old -- not used in 12.2
- renderScreenImage(JmolViewer, Object, Object) - Static method in class org.jmol.awt.Display
-
legacy apps will use this
- renderScreenImage(JmolViewer, Object, Object) - Method in class org.jmol.awt.Platform
-
legacy apps will use this
- renderScreenImage(Object, Object, int, int) - Method in class org.jmol.viewer.Viewer
-
- renderScreenImage(Object, int, int) - 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, boolean) - 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(FastBitSet) - Method in class org.jmol.shapespecial.GeoSurfaceRenderer
-
- renderTorsion(boolean) - Method in class org.jmol.shape.MeasuresRenderer
-
- renderTriangle() - Method in class org.jmol.shapebio.CartoonRenderer
-
- renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.shape.MeshRenderer
-
- renderTriangles(boolean, 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(Object) - Method in interface org.jmol.api.ApiPlatform
-
- repaint(Object) - Static method in class org.jmol.awt.Display
-
- repaint(Object) - Method in class org.jmol.awt.Platform
-
- repaint() - Method in class org.jmol.viewer.Viewer
-
- repaintClock() - Method in class org.jmol.applet.AppletWrapper
-
- repaintDone() - Method in class org.jmol.viewer.AnimationManager
-
- repaintDone() - Method in class org.jmol.viewer.RepaintManager
-
- RepaintManager - Class in org.jmol.viewer
-
- RepaintManager(Viewer, ShapeManager) - Constructor for class org.jmol.viewer.RepaintManager
-
- repaintManager - Variable in class org.jmol.viewer.Viewer
-
- repaintPending - Variable in class org.jmol.viewer.RepaintManager
-
- repaintwaitms - Static variable in class org.jmol.script.Token
-
- repaintWaitMs - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- repeatCheckBox - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- replace - Static variable in class org.jmol.script.Token
-
- replace(int, int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.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(Token) - Method in class org.jmol.script.ScriptCompiler
-
- replaceCommand(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
Replaces current command on script.
- replaceQuotedStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
-
- replaceStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
-
- report(String, boolean) - Method in class org.jmol.minimize.Minimizer
-
- report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- reportAll - Variable in class org.jmol.shape.Sticks
-
- reportSelection(String) - Method in class org.jmol.viewer.Viewer
-
- repositionWindow(String, Component, int, int, boolean) - Method in class org.jmol.export.history.HistoryFile
-
Uses the informations in the history to reposition the window.
- repositionWindow(String, Component) - Method in class org.jmol.export.history.HistoryFile
-
Uses the informations in the history to reposition the window.
- requestFocusInWindow(Object) - Method in interface org.jmol.api.ApiPlatform
-
- requestFocusInWindow(Object) - Static method in class org.jmol.awt.Display
-
- requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
-
- requestRepaintAndWait() - Method in class org.jmol.viewer.RepaintManager
-
- requestRepaintAndWait() - Method in class org.jmol.viewer.Viewer
-
- REQUIRE_PROGRESSBAR - Static variable in class org.jmol.applet.Jmol
-
- reset() - Method in class org.jmol.bspt.Bspt
-
- reset() - Method in class org.jmol.script.ScriptEvaluator
-
- reset - Static variable in class org.jmol.script.Token
-
- reset() - Method in class org.jmol.util.BoxInfo
-
- reset(int) - Method in class org.jmol.util.CommandHistory
-
Resets instance.
- reset() - Method in class org.jmol.viewer.FileManager.ArrayDataReader
-
- reset() - Method in class org.jmol.viewer.FileManager.VectorDataReader
-
- reset(boolean) - 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
-
- resetBioshapes(BitSet) - Method in class org.jmol.viewer.ShapeManager
-
- resetBioshapes(BitSet) - Method in class org.jmol.viewer.Viewer
-
- resetBoundCount() - Method in class org.jmol.modelset.Model
-
- resetDefaults(String[]) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- resetElementColors() - Method in class org.jmol.viewer.ColorManager
-
- resetError() - Method in class org.jmol.viewer.Viewer
-
- resetFlag - Static variable in class org.openscience.jmol.app.webexport.LogPanel
-
- resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
-
reset some parameters at the "MAP" keyword
- resetFrankMenu() - Method in class org.jmol.popup.JmolPopup
-
- resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
-
- resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
-
- resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
-
- resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- resetIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- resetKey - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- resetMeasurement() - Method in class org.jmol.viewer.ActionManager
-
- resetMolecules() - Method in class org.jmol.modelset.BondCollection
-
- 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
-
- resetNeeded - Variable in class org.jmol.multitouch.ActionManagerMT
-
- resetObjects() - Method in class org.jmol.shapespecial.Draw
-
- resetParameterStringValue(String, StateManager.GlobalSettings) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- resetPlane(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- resetShapes() - Method in class org.jmol.viewer.ShapeManager
-
- resetShapes() - Method in class org.jmol.viewer.Viewer
-
- resetSlab() - Method in class org.jmol.util.MeshSurface
-
- resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- resetVoxelData(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- resetXYCenter(int, int) - Method in class org.jmol.viewer.TransformManager
-
- residue - Static variable in class org.jmol.script.Token
-
- residueChar - Variable in class org.jmol.smiles.SmilesAtom
-
- residueName - Variable in class org.jmol.smiles.SmilesAtom
-
- residueSpecCodeGenerated - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- resizeByteArray(byte[], int) - Method in class org.jmol.export.image.PngEncoder
-
Increase or decrease the length of a byte array.
- resizeDisplay(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- resizeImage(int, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
- resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
-
- resizeInnerPanel(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- resno - Static variable in class org.jmol.script.Token
-
- resolution - Variable in class org.jmol.jvxl.readers.Parameters
-
- resolution - Static variable in class org.jmol.script.Token
-
- 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
-
- Resolver.BondSorter - Class in org.jmol.modelsetbio
-
- Resolver.BondSorter() - Constructor for class org.jmol.modelsetbio.Resolver.BondSorter
-
- resourceName - Variable in class org.jmol.quantum.MepCalculation
-
- resources - Variable in class org.jmol.export._IdtfExporter
-
- 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.script.ScriptEvaluator
-
- restore - Static variable in class org.jmol.script.Token
-
- restore() - Method in class org.jmol.viewer.StateManager.Connections
-
- restore(float, boolean) - Method in class org.jmol.viewer.StateManager.Orientation
-
- 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
-
- restorePopupMenu() - Method in class org.jmol.popup.SimplePopup
-
- restoreRotation(String, float) - Method in class org.jmol.viewer.Viewer
-
- restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- restoreSelection(String) - Method in class org.jmol.viewer.StateManager
-
- restoreSelection(String) - Method in class org.jmol.viewer.Viewer
-
- restrict() - Method in class org.jmol.script.ScriptEvaluator
-
- restrict - Static variable in class org.jmol.script.Token
-
- restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- RESU - Static variable in class org.jmol.util.ColorEncoder
-
- resume - Static variable in class org.jmol.script.Token
-
- resumeAnimation() - Method in class org.jmol.viewer.AnimationManager
-
- resumeButton - Variable in class org.jmol.console.ScriptEditor
-
- resumePausedExecution() - Method in class org.jmol.script.ScriptEvaluator
-
- resumeScriptExecution() - Method in class org.jmol.viewer.Viewer
-
- returnCmd(ScriptVariable) - Method in class org.jmol.script.ScriptEvaluator
-
- returncmd - Static variable in class org.jmol.script.Token
-
- returnToken() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- returnValue - Variable in class org.jmol.script.ScriptFunction
-
- reverse - Static variable in class org.jmol.script.Token
-
- reverseAnimation() - Method in class org.jmol.viewer.AnimationManager
-
- reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
-
- reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
-
- reversecolor - Static variable in class org.jmol.script.Token
-
- revNumber - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
-
- rewind - Static variable in class org.jmol.script.Token
-
- REWIND - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- rewindAnimation() - Method in class org.jmol.viewer.AnimationManager
-
- 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.awt.Image
-
- rgbFractionalFromArgb(int, char) - Static method in class org.jmol.export.___Exporter
-
- rgbFractionalFromColix(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
-
- RGBtoHSL(float, float, float, float[]) - Static method in class org.jmol.util.ColorEncoder
-
- rhoMin - Variable in class org.jmol.quantum.NciCalculation
-
- rhoMolecules - Variable in class org.jmol.quantum.NciCalculation
-
- rhoParam - Variable in class org.jmol.quantum.NciCalculation
-
- rhoPlot - Variable in class org.jmol.quantum.NciCalculation
-
- ribbon - Static variable in class org.jmol.script.Token
-
- ribbonaspectratio - Static variable in class org.jmol.script.Token
-
- ribbonAspectRatio - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- ribbonborder - Static variable in class org.jmol.script.Token
-
- 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
-
- 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.script.Token
-
- RIGHT - Static variable in class org.jmol.viewer.binding.Binding
-
- rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- rightbrace - Static variable in class org.jmol.script.Token
-
- rightDifference(Quaternion) - Method in class org.jmol.util.Quaternion
-
- rightOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- rightparen - Static variable in class org.jmol.script.Token
-
- rightPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
-
- rightsquare - Static variable in class org.jmol.script.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
-
- ringConnections - Variable in class org.jmol.smiles.SmilesSearch
-
- ringConnectivity - Variable in class org.jmol.smiles.SmilesAtom
-
- ringCounts - Variable in class org.jmol.smiles.SmilesSearch
-
- ringData - Variable in class org.jmol.smiles.SmilesSearch
-
- ringDataMax - Variable in class org.jmol.smiles.SmilesSearch
-
- ringMembership - Variable in class org.jmol.smiles.SmilesAtom
-
- ringSets - Variable in class org.jmol.smiles.SmilesGenerator
-
- ringSets - Variable in class org.jmol.smiles.SmilesSearch
-
- ringSize - Variable in class org.jmol.smiles.SmilesAtom
-
- 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.script.Token
-
- rnl - Variable in class org.jmol.jvxl.readers.IsoShapeReader
-
- rocket - Static variable in class org.jmol.script.Token
-
- rocketbarrels - Static variable in class org.jmol.script.Token
-
- rocketBarrels - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- Rockets - Class in org.jmol.shapebio
-
- Rockets() - Constructor for class org.jmol.shapebio.Rockets
-
- 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.adapter.readers.quantum.JaguarReader
-
- ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
-
- rootDir - Variable in class org.openscience.chimetojmol.ChimePanel
-
- rootEntry - Variable in class org.jmol.util.CompoundDocument
-
- rootPickingStyle - Variable in class org.jmol.viewer.ActionManager
-
- rotate(boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- rotate - Static variable in class org.jmol.script.Token
-
- rotate45 - Static variable in class org.jmol.script.Token
-
- ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- rotateAboutPointsInternal(Point3f, Point3f, float, float, boolean, boolean, BitSet, boolean, Vector3f, List<Point3f>) - Method in class org.jmol.viewer.TransformManager
-
- rotateAboutPointsInternal(Point3f, Point3f, float, float, boolean, BitSet, Vector3f, List<Point3f>) - Method in class org.jmol.viewer.Viewer
-
- rotateArcBall(float, float, float) - Method in class org.jmol.viewer.TransformManager
-
- rotateArcBall(int, int, float) - 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
-
- rotateBondIndex - Variable in class org.jmol.viewer.Viewer
-
- 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
-
- rotatePoint(Point3f, Point3f) - Method in class org.jmol.viewer.TransformManager
-
- rotatePoint(Point3f, Point3f) - Method in class org.jmol.viewer.Viewer
-
- rotatePrev1 - Variable in class org.jmol.viewer.Viewer
-
- rotatePrev2 - Variable in class org.jmol.viewer.Viewer
-
- rotateSelected - Static variable in class org.jmol.script.Token
-
- rotateSelected(float, float, BitSet) - Method in class org.jmol.viewer.Viewer
-
- 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(float, float, BitSet) - Method in class org.jmol.viewer.TransformManager
-
- rotateXYBy(float, float) - 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, int, int) - Method in class org.jmol.viewer.TransformManager
-
- rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
-
- rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
-
- rotation - Static variable in class org.jmol.script.Token
-
- 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
-
- 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.viewer.StateManager.Orientation
-
- rotationOrder - Variable in class org.jmol.symmetry.Translation
-
- rotationradius - Static variable in class org.jmol.script.Token
-
- rotationRadius - Variable in class org.jmol.viewer.StateManager.Orientation
-
- rotationRadiusDefault - Variable in class org.jmol.viewer.TransformManager
-
- rotationRadiusDelta - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- 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
-
- round(double) - Static method in class org.jmol.export.___Exporter
-
- round(Tuple3f) - Static method in class org.jmol.export.___Exporter
-
- route - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- row - Static variable in class org.jmol.script.Token
-
- ROYGB - Static variable in class org.jmol.util.ColorEncoder
-
- rpower - Static variable in class org.jmol.quantum.NciCalculation
-
- rScaled - Variable in class org.jmol.g3d.Rgb16
-
- rubberband - Static variable in class org.jmol.script.Token
-
- rubberbandSelectionMode - Variable in class org.jmol.viewer.ActionManager
-
- run() - Method in class org.jmol.applet.ClassPreloader
-
- run() - Method in class org.jmol.applet.TickerThread
-
- run() - Method in class org.jmol.applet.WrappedAppletLoader
-
- run() - Method in class org.jmol.g3d.Platform3D.ClearingThread
-
- run() - Method in class org.jmol.minimize.Minimizer.MinimizationThread
-
- run() - Method in class org.jmol.script.ParallelProcessor.RunProcess
-
- run() - Method in class org.jmol.viewer.ActionManager.HoverWatcher
-
- run() - Method in class org.jmol.viewer.ActionManager.TimeoutThread
-
- run() - Method in class org.jmol.viewer.AnimationManager.AnimationThread
-
- run() - Method in class org.jmol.viewer.FileManager.DOMReader
-
- run() - Method in class org.jmol.viewer.FileManager.FileReader
-
- run() - Method in class org.jmol.viewer.FileManager.FilesReader
-
- 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.MotionThread
-
- 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.jmolpanel.AboutDialog.PageLoader
-
- run() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ExecuteCommandThread
-
- run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- run() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
-
- run() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JsonNioServerThread
-
- run() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService.JsonNioThread
-
- run() - Method in class org.openscience.jmol.app.jmolpanel.WhatsNewDialog.PageLoader
-
- runAllProcesses(Viewer, boolean) - Method in class org.jmol.script.ParallelProcessor
-
- runButton - Variable in class org.jmol.console.JmolConsole
-
- runButton - Variable in class org.jmol.console.ScriptEditor
-
- runFunction(ScriptFunction, String, List<ScriptVariable>, ScriptVariable, boolean, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- runFunction(ScriptFunction, List<ScriptVariable>, ScriptVariable) - Method in class org.jmol.script.ScriptEvaluator
-
- runNextScript() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
-
- runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- runProcess(ParallelProcessor.Process, ShapeManager) - Method in class org.jmol.script.ParallelProcessor
-
- runScript(String, StringBuffer) - Method in class org.jmol.script.ScriptEvaluator
-
runs a script and sends selected output to a provided StringBuffer
- runScript(String) - Method in class org.jmol.script.ScriptEvaluator
-
- runScript(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
-
- runScriptImmediately(String) - Method in class org.jmol.viewer.Viewer
-
- runStatus - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- RWB - Static variable in class org.jmol.util.ColorEncoder
-
- s0 - Variable in class org.jmol.shapespecial.EllipsoidsRenderer
-
- s1 - Variable in class org.jmol.shape.SticksRenderer
-
- 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.shape.SticksRenderer
-
- 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
-
- 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.awt.Image
-
- sasurface - Static variable in class org.jmol.script.Token
-
- SAT - Variable in class org.jmol.util.CompoundDocument
-
- save() - Method in class org.jmol.export.history.HistoryFile
-
Saves properties to the history file.
- save() - Method in class org.jmol.script.ScriptEvaluator
-
- save - Static variable in class org.jmol.script.Token
-
- SAVE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- save() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- save() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- saveAmbient - Variable in class org.jmol.g3d.Graphics3D
-
- 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.jmolpanel.GaussianDialog
-
- 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.jmolpanel.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
-
- saveDiffuse - Variable in class org.jmol.g3d.Graphics3D
-
- saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- saveHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Just saves the path settings from this session.
- saveHistory() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- saveList() - Method in class org.openscience.jmol.app.jmolpanel.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.jmolpanel.PovrayDialog
-
- saveproteinstructurestate - Static variable in class org.jmol.script.Token
-
- saveProteinStructureState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- 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
-
- saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
-
- saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Saves the currently active collection as a multistep XYZ file.
- say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- sb - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- sb - Variable in class org.jmol.util.OutputStringBuffer
-
- sbConect - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- sbIgnored - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- sbSelected - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- sbTemp - Variable in class org.jmol.export._IdtfExporter
-
- 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.jvxl.readers.Parameters
-
- scale - Variable in class org.jmol.modelset.TickInfo
-
- scale - Static variable in class org.jmol.script.Token
-
- 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 - Variable in class org.jmol.symmetry.PointGroup
-
- scale3d - Variable in class org.jmol.jvxl.data.JvxlData
-
- scale3d - Variable in class org.jmol.jvxl.readers.Parameters
-
- scale3d - Static variable in class org.jmol.script.Token
-
- scale3d - Variable in class org.jmol.shapesurface.Isosurface
-
- scale3d - Variable in class org.jmol.util.MeshSurface
-
- 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.jmolpanel.AtomSetChooser
-
Maximum value for vector scale.
- SCALE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Precision of the vector scale slider
- SCALE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value of vector scale.
- scaleangstromsperinch - Static variable in class org.jmol.script.Token
-
- scaleBox(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
-
- 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.export.___Exporter
-
- scalePixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
-
- scalePixelsPerMicron - Variable in class org.jmol.shape.Labels
-
- scalePixelsPerMicron - Variable in class org.jmol.shape.MeshRenderer
-
- scalePixelsPerMicron - Variable in class org.jmol.shape.Object2d
-
- scalePrimitiveData(int, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of
the radial exponent differently depending upon position in
the periodic table -- noble gases and transition metals
and for the fact that these are spherical functions (5D, not 6D)
ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
Perform implementation-specific scaling.
- scaleSlider - Variable in class org.openscience.jmol.app.jmolpanel.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.quantum.GaussianReader
-
The scan point, where -1 denotes no scan information.
- schemes - Variable in class org.jmol.util.ColorEncoder
-
- score - Variable in class org.jmol.util.ContactPair
-
- 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.shapespecial.DotsRenderer
-
- screenCorners - Variable in class org.jmol.shapebio.RocketsRenderer
-
- screenDiameter - Variable in class org.jmol.util.Point3fi
-
- screenDotCount - Variable in class org.jmol.shapespecial.DotsRenderer
-
- screenHeight - Variable in class org.jmol.export.___Exporter
-
- screenHeight - Static variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- screenHeight - Variable in class org.jmol.viewer.TransformManager
-
- screenLevel - Variable in class org.jmol.shapespecial.DotsRenderer
-
- screenPixelCount - Variable in class org.jmol.viewer.TransformManager
-
- screens - Variable in class org.jmol.shape.AxesRenderer
-
- screens - Variable in class org.jmol.shape.CageRenderer
-
- screens - Variable in class org.jmol.shape.MeshRenderer
-
- 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.jmolpanel.JmolPanel
-
- screenVectorEnd - Variable in class org.jmol.shapespecial.VectorsRenderer
-
- screenWidth - Variable in class org.jmol.export.___Exporter
-
- screenWidth - Static variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- 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 class org.jmol.api.JmolViewer
-
- script(String) - Method in class org.jmol.applet.Jmol
-
- script(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- script - Variable in class org.jmol.jvxl.readers.Parameters
-
- script - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- script - Variable in class org.jmol.script.ScriptContext
-
- script - Variable in class org.jmol.script.ScriptEvaluator
-
- script(int, String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- script - Variable in class org.jmol.script.ScriptFunction
-
- script - Static variable in class org.jmol.script.Token
-
- script - Variable in class org.jmol.shape.Object2d
-
- script - Variable in class org.jmol.shapesurface.Isosurface
-
- script - Variable in class org.jmol.viewer.ActionManager.TimeoutThread
-
- script(String) - Method in class org.jmol.viewer.Viewer
-
- script - Variable in class org.openscience.jmol.app.JmolApp
-
- script - Variable in class org.openscience.jmol.app.webexport.JmolInstance
-
- script1 - Variable in class org.jmol.modelset.ModelCollection.StateScript
-
- script1 - Variable in class org.openscience.jmol.app.JmolApp
-
- script2 - Variable in class org.jmol.modelset.ModelCollection.StateScript
-
- script2 - Variable in class org.openscience.jmol.app.JmolApp
-
- SCRIPT_CHECK - Static variable in class org.jmol.applet.Jmol
-
- SCRIPT_COMPLETED - Static variable in class org.jmol.script.ScriptEvaluator
-
- SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JmolConstants
-
- 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.jmolpanel.JmolPanel
-
- scriptAppendix - Variable in class org.jmol.shapesurface.Isosurface
-
- scriptButtonPercent - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- ScriptButtons - Class in org.openscience.jmol.app.webexport
-
- ScriptButtons(JmolViewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.ScriptButtons
-
- scriptCallback(String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
from StatusManager
- scriptCheck(String) - Method in class org.jmol.api.JmolViewer
-
- scriptCheck(String) - Method in class org.jmol.applet.Jmol
-
- scriptCheck(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- scriptCheck(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- scriptCheck(String) - Method in class org.jmol.viewer.Viewer
-
- scriptCommand - Static variable in class org.jmol.script.Token
-
- scriptCommand - Variable in class org.jmol.shape.Mesh
-
- ScriptCompilationTokenParser - Class in org.jmol.script
-
- ScriptCompilationTokenParser() - Constructor for class org.jmol.script.ScriptCompilationTokenParser
-
- ScriptCompiler - Class in org.jmol.script
-
- ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
-
- ScriptCompiler(ScriptCompiler) - Constructor for class org.jmol.script.ScriptCompiler
-
- ScriptContext - Class in org.jmol.script
-
- ScriptContext() - Constructor for class org.jmol.script.ScriptContext
-
- scriptDelay - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- scriptEcho(String) - Method in class org.jmol.viewer.Viewer
-
- scriptEditor - Variable in class org.jmol.console.JmolConsole
-
- ScriptEditor - Class in org.jmol.console
-
- ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
-
- ScriptEditor(JmolViewer, JFrame, JmolConsole) - Constructor for class org.jmol.console.ScriptEditor
-
- scriptEditor - Variable in class org.jmol.viewer.Viewer
-
- ScriptEditor.EditorDocument - Class in org.jmol.console
-
- ScriptEditor.EditorDocument() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument
-
- ScriptEditor.EditorDocument.MyUndoableEditListener - Class in org.jmol.console
-
- ScriptEditor.EditorDocument.MyUndoableEditListener() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
-
- ScriptEditor.EditorTextPane - Class in org.jmol.console
-
- ScriptEditor.EditorTextPane() - Constructor for class org.jmol.console.ScriptEditor.EditorTextPane
-
- scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
-
- ScriptEvaluator - Class in org.jmol.script
-
- ScriptEvaluator(Viewer) - Constructor for class org.jmol.script.ScriptEvaluator
-
- ScriptEvaluator.ScriptException - Exception in org.jmol.script
-
- ScriptEvaluator.ScriptException(String, String) - Constructor for exception org.jmol.script.ScriptEvaluator.ScriptException
-
- scriptExtensions - Variable in class org.jmol.script.ScriptCompiler
-
- scriptExtensions - Variable in class org.jmol.script.ScriptContext
-
- scriptExtensions - Variable in class org.jmol.script.ScriptEvaluator
-
- scriptFilename - Variable in class org.openscience.jmol.app.JmolApp
-
- scriptFilePrefixes - Static variable in class org.jmol.viewer.FileManager
-
- ScriptFlowContext - Class in org.jmol.script
-
- ScriptFlowContext(ScriptCompiler, ContextToken, int, ScriptFlowContext) - Constructor for class org.jmol.script.ScriptFlowContext
-
- ScriptFunction - Class in org.jmol.script
-
- ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
-
- scriptIndex - Variable in class org.jmol.viewer.Viewer
-
- scriptLevel - Variable in class org.jmol.script.ScriptContext
-
- scriptLevel - Variable in class org.jmol.script.ScriptEvaluator
-
- scriptLevelMax - Static variable in class org.jmol.script.ScriptEvaluator
-
- 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
-
- ScriptMathProcessor - Class in org.jmol.script
-
- ScriptMathProcessor(ScriptEvaluator, boolean, boolean, boolean) - Constructor for class org.jmol.script.ScriptMathProcessor
-
- scriptNoWait(String) - Method in class org.jmol.applet.Jmol
-
- scriptNoWait(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- scriptProcessor(String, String, int) - Method in class org.jmol.applet.Jmol
-
- scriptqueue - Static variable in class org.jmol.script.Token
-
- scriptQueue - Variable in class org.jmol.viewer.ScriptManager
-
- scriptQueueRunning - Variable in class org.jmol.viewer.ScriptManager
-
- scriptReportingLevel - Variable in class org.jmol.script.ScriptEvaluator
-
- scriptreportinglevel - Static variable in class org.jmol.script.Token
-
- scriptStatus(String) - Method in class org.jmol.viewer.Viewer
-
- scriptStatus(String, String) - Method in class org.jmol.viewer.Viewer
-
- scriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
-
- scriptStatusOrBuffer(String) - Method in class org.jmol.script.ScriptEvaluator
-
- ScriptVariable - Class in org.jmol.script
-
- ScriptVariable() - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable(int) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable(int, int, Object) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable(int, Object) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable(int, int) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable(BitSet, int) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable(Token) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable.Sort - Class in org.jmol.script
-
- ScriptVariable.Sort(int) - Constructor for class org.jmol.script.ScriptVariable.Sort
-
- 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 interface org.jmol.applet.JmolAppletInterface
-
- scriptWait(String, String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- scriptWait(String) - Method in class org.jmol.viewer.Viewer
-
- scriptWaitOutput(String) - Method in class org.jmol.applet.Jmol
-
- scriptWaitOutput(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
-
- scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
-
- SDIM - Static variable in class org.jmol.g3d.Sphere3D
-
- Se - Variable in class org.jmol.util.JpegInfo
-
- search - Static variable in class org.jmol.script.Token
-
- search - Variable in class org.jmol.smiles.SmilesMeasure
-
- search(boolean) - Method in class org.jmol.smiles.SmilesSearch
-
the start of the search.
- searchForTurns(AlphaPolymer.Code[], float[], EnumStructure[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
- secondCharOnly - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
-
- 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.util.MeshSurface
-
- 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(int) - Method in class org.jmol.script.ScriptEvaluator
-
- select - Static variable in class org.jmol.script.Token
-
- select(BitSet, Boolean, boolean) - Method in class org.jmol.viewer.SelectionManager
-
- select(BitSet, boolean, Boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
- select - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- 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 - Static variable in class org.jmol.script.Token
-
- 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.script.Token
-
- selected - Variable in class org.jmol.smiles.SmilesAtom
-
- selectedAtomCount - Variable in class org.jmol.smiles.SmilesSearch
-
- selectedBonds - Variable in class org.jmol.shape.Sticks
-
- selectedFileName - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
- selectedfloat - Static variable in class org.jmol.script.Token
-
- selectedGroupCount - Variable in class org.jmol.modelset.Chain
-
- selectedIndex - Variable in class org.jmol.modelset.Group
-
- selectedMeasurementRow - Variable in class org.openscience.jmol.app.jmolpanel.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
-
- selectField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- selecthetero - Static variable in class org.jmol.script.Token
-
- selecthydrogen - Static variable in class org.jmol.script.Token
-
- selection - Static variable in class org.jmol.script.Token
-
- 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.script.ScriptEvaluator
-
- selectionHaloEnabled - Variable in class org.jmol.modelset.ModelSet
-
- selectionhalos - Static variable in class org.jmol.script.Token
-
- SelectionManager - Class in org.jmol.viewer
-
- SelectionManager(Viewer) - Constructor for class org.jmol.viewer.SelectionManager
-
- selectionManager - Variable in class org.jmol.viewer.Viewer
-
- selectionWorking - Variable in class org.jmol.viewer.ActionManager
-
- selectItem(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- selectItem(Token) - Static method in class org.jmol.script.ScriptVariable
-
- selectItem(ScriptVariable, int) - Static method in class org.jmol.script.ScriptVariable
-
- selectItem(Token, int) - Static method in class org.jmol.script.ScriptVariable
-
- selectPocket(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- 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.jmolpanel.AtomSetChooser
-
- semicolon - Static variable in class org.jmol.script.Token
-
- send(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
from JmolPanel and SYNC command
- sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
-
- sendConsoleEcho(String) - Method in class org.jmol.console.AppletConsole
-
- sendConsoleEcho(String) - Method in class org.jmol.console.JmolConsole
-
- sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
-
- sendConsoleMessage(String) - Method in class org.jmol.console.AppletConsole
-
- sendConsoleMessage(String) - Method in class org.jmol.console.JmolConsole
-
- sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- sendJsTextareaStatus(String) - Method in class org.jmol.applet.Jmol
-
- sendJsTextStatus(String) - Method in class org.jmol.applet.Jmol
-
- sendKeyBuffer() - Method in class org.jmol.awt.Mouse
-
- sendMessage(JsonNioService.JSONObject, String, NIOSocket) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- sendNioMessage(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- sendScript(String, String, boolean, boolean) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- sep - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- 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.script.Token
-
- seqcodes - Variable in class org.jmol.modelset.ModelLoader
-
- sequence - Static variable in class org.jmol.script.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
-
- serial - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- SERIAL_NO - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- serialArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
-
- serialID - Variable in class org.jmol.adapter.smarter.Structure
-
- serialID - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- 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
-
- serverConnection - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
- serverService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- serverSocket - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- serverThread - Variable in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- service - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- service - Variable in class org.openscience.molecularplayground.MPJmolApp
-
- SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- set(ModelCollection, int, int, int, Point3f, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
-
- set(Point3f, float) - Method in interface org.jmol.api.AtomIndexIterator
-
- set(Bspt) - Method in class org.jmol.bspt.CubeIterator
-
- 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(ModelCollection, int, int, int, Point3f, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
- set(Point3f, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
- set(Point3f, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
-
- set(int) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
-
- set(JmolViewer) - Method in class org.jmol.popup.SimplePopup
-
- set() - Method in class org.jmol.script.ScriptEvaluator
-
- set(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptVariable
-
creates a NEW version of the variable
- set - Static variable in class org.jmol.script.Token
-
- 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(SmilesBond) - Method in class org.jmol.smiles.SmilesBond
-
- set(int, boolean) - Method in class org.jmol.smiles.SmilesBond
-
- set(SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
-
- set(PointGroup, Atom[], BitSet, boolean, float, float) - Method in class org.jmol.symmetry.PointGroup
-
- set(int) - Method in class org.jmol.util.FastBitSet
-
- set(int, boolean) - Method in class org.jmol.util.FastBitSet
-
- set(int, int) - Method in class org.jmol.util.FastBitSet
-
- set(int, int, boolean) - Method in class org.jmol.util.FastBitSet
-
- set(float, float, float) - Method in interface org.jmol.util.JmolNode
-
- set(Quaternion) - Method in class org.jmol.util.Quaternion
-
- set(Point4f) - Method in class org.jmol.util.Quaternion
-
{x y z w} --> {q1 q2 q3 q0} and factored
- set(Tuple3f, float) - Method in class org.jmol.util.Quaternion
-
q = (cos(theta/2), sin(theta/2) * n)
- set(AxisAngle4f) - Method in class org.jmol.util.Quaternion
-
- set(Matrix3f) - Method in class org.jmol.util.Quaternion
-
- set(int, int, int, long) - Method in class org.jmol.viewer.ActionManager.MotionPoint
-
- set(long, int, int, int) - Method in class org.jmol.viewer.ActionManager.Mouse
-
- set(int, String) - Method in class org.jmol.viewer.ActionManager.TimeoutThread
-
- set(float, Point3f, Matrix3f, float, float, float, float, Point3f, float, float, float) - Method in class org.jmol.viewer.TransformManager.MotionThread
-
- set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- set2dZ(int, int) - Method in class org.jmol.modelset.ModelLoader
-
- set3dContourVector(List<Object>, int[][], Point3f[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
Interpret fractional data in terms of actual vertex positions and
create the elements of a Vector in Vector[] vContours starting at
the CONTOUR_POINTS position.
- setAaTokenCompiled() - Method in class org.jmol.script.ScriptCompiler
-
- setABC(int) - Method in class org.jmol.util.MeshSurface
-
- setAbstractButtonLabels(Map<String, AbstractButton>, Map<String, String>) - Static method in class org.jmol.console.KeyJMenuItem
-
- setAction(int, long) - Method in class org.jmol.viewer.ActionManager.Gesture
-
- setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
-
Changes the activation state for a logging level.
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
adaptable via subclassing
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.more.P2nReader
-
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.more.PqrReader
-
- 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
-
- setAllFractionalRelative(boolean) - Method in class org.jmol.symmetry.UnitCell
-
- setAllowStatusReporting(boolean) - Method in class org.jmol.viewer.StatusManager
-
- setAmbientPercent(int) - Static method in class org.jmol.g3d.Graphics3D
-
fractional distance from black for ambient color
- setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.g3d.Rgb16
-
- setAngleUnits(int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setAnimation(int) - Method in class org.jmol.viewer.Viewer
-
- setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
-
- 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.AnimationManager
-
- setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
-
- setAnimationLast() - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationOff(boolean) - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
-
- setAnimationPrevious() - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationRange(int, int) - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
-
- setAnimationRelative(int) - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationReplayMode(EnumAnimationMode, float, float) - Method in class org.jmol.viewer.AnimationManager
-
- setAnimationReplayMode(EnumAnimationMode, float, float) - Method in class org.jmol.viewer.Viewer
-
- setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- 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.applet.WrappedApplet
-
- setApplySymmetryToBonds(boolean) - Method in class org.jmol.viewer.Viewer
-
- setAtom2(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
-
- setAtom2dZ(Atom, Atom, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.modelset.ModelLoader
-
- setAtomArray() - Method in class org.jmol.smiles.SmilesSearch
-
- setAtomBitSet(BitSet) - Method in class org.jmol.modelset.Chain
-
- 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.ModelSet
-
- 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(Tuple3f, BitSet) - Method in class org.jmol.modelset.ModelSet
-
- setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.viewer.Viewer
-
- setAtomCoordRelative(Tuple3f, BitSet) - Method in class org.jmol.viewer.Viewer
-
- setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
-
- setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
-
- setAtomI(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
- setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
-
- setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the atomic mass of the atom.
- setAtomicOrbital(float[]) - Method in class org.jmol.jvxl.readers.Parameters
-
- setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
-
- setAtomLabel(String, int) - Method in class org.jmol.viewer.Viewer
-
- setAtomName(Atom, String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
-
- setAtomName(int, String) - Method in class org.jmol.modelset.AtomCollection
-
- setAtomName(String) - Method in class org.jmol.smiles.SmilesAtom
-
- setAtomNames(Properties) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setAtomNamesAndNumbers(int, int, AtomCollection) - Method in class org.jmol.modelset.ModelCollection
-
- setAtomNumber(int, int) - Method in class org.jmol.modelset.AtomCollection
-
- setAtomPickingOption(String) - Method in class org.jmol.viewer.ActionManager
-
- setAtomPickingOption(String) - Method in class org.jmol.viewer.Viewer
-
- setAtomPositions() - Method in class org.jmol.minimize.Minimizer
-
- setAtomProperties() - Method in class org.jmol.modelset.ModelLoader
-
- setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
-
- setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelCollection
-
- setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
-
- setAtomProperty(BitSet, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
-
- setAtomSetAtomProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- 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 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
- setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setAtomSetFrequency(String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setAtomSetInfo() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- setAtomSetInfoMd() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets a property for the current AtomSet
used specifically for creating directories and plots of frequencies and
moleular energies
- setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the name for the current 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, 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, float) - Method in class org.jmol.script.ScriptEvaluator
-
- setAtomSymmetry(BitSet) - Method in class org.jmol.modelset.Atom
-
- setAtomType(int, String) - Method in class org.jmol.modelset.AtomCollection
-
- 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
-
- setAttributes() - Method in class org.jmol.console.ScriptEditor
-
- 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.SimplePopup
-
- setAxes(DrawMesh) - Static method in class org.jmol.shapespecial.Draw
-
- setAxes(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
-
- 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(Object) - Method in class org.jmol.g3d.Graphics3D
-
- setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
-
- setBackgroundModelIndex(int) - Method in class org.jmol.viewer.AnimationManager
-
- 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
-
- setBanner(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- setBannerLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- setBannerLabel(String) - Method in interface org.openscience.jmol.app.jmolpanel.JsonNioClient
-
- setBannerLabel(String) - Method in class org.openscience.molecularplayground.MPJmolApp
-
- setBaseSymmetryAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setBbcage(float) - Method in class org.jmol.util.BoxInfo
-
- setBf(int) - Method in class org.jmol.modelset.AtomCollection
-
- 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
-
- setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
-
- setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
-
- setBioAtom(char) - Method in class org.jmol.smiles.SmilesAtom
-
- setBiomoleculeAtomCounts() - Method in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- setBioPolymer(BioPolymer, int) - Method in class org.jmol.modelsetbio.Monomer
-
- setBit(int) - Static method in class org.jmol.util.BitSetUtil
-
- setBitmap(String, Font3D, Graphics3D, boolean) - Method in class org.jmol.g3d.Text3D
-
- setBitsetProperty(BitSet, int, int, float, Token) - Method in class org.jmol.script.ScriptEvaluator
-
- setBond(Bond, int[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
- setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
-
- setBondArray() - Method in class org.jmol.smiles.SmilesAtom
-
- setBondDirections() - Method in class org.jmol.smiles.SmilesGenerator
-
Creates global BitSets bsBondsUp and bsBondsDown.
- setBondingAndMolecules() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
(1) If GEOM_BOND records are present, we
(a) use them to generate bonds
(b) add H atoms to bonds if necessary
(c) turn off autoBonding ("hasBonds")
(2) If MOLECULAR, then we
(a) use {1 1 1} if lattice is not defined
(b) use atomSetCollection.bonds[] to construct
a preliminary molecule and connect as we go
(c) check symmetry for connections to molecule in any
one of the 27 3x3 adjacent cells
(d) move those atoms and their connected branch set
(e) iterate as necessary to get all atoms desired
(f) delete unselected atoms
(g) set all coordinates as Cartesians
(h) remove all unit cell information
- setBondmode() - Method in class org.jmol.script.ScriptEvaluator
-
- setBondOrder(int, char) - Method in class org.jmol.modelset.BondCollection
-
- setBondPickingOption(String) - Method in class org.jmol.viewer.ActionManager
-
- setBondPickingOption(String) - Method in class org.jmol.viewer.Viewer
-
- setBonds(Bond[]) - Method in class org.jmol.modelset.Atom
-
- setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
-
- setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
-
- setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
-
- setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
-
- setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- setBooleanProperty(String, int, boolean) - Method in class org.jmol.viewer.Viewer
-
- setBorder() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.modelset.ModelCollection
-
- setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.util.BoxInfo
-
- setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.viewer.Viewer
-
- setBoundingBox() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setBoundingBox(Point3f, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.shape.Object2d
-
- setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.shape.Text
-
- setBraceCount - Variable in class org.jmol.script.ScriptCompiler
-
- setBranch2dZ(Atom, BitSet, BitSet, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.modelset.ModelLoader
-
- setBs(Atom[], int, BitSet[], BitSet) - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
iteratively run through connected atoms, adding them to the set
- setBsHidden(BitSet) - Method in class org.jmol.modelset.AtomCollection
-
- setBsVdw() - Method in class org.jmol.shapesurface.Isosurface
-
- setButton(String) - Method in class org.jmol.console.JmolConsole
-
- setButton(String) - Method in class org.jmol.console.ScriptEditor
-
- setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
- setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
-
- setCallbackFunction(String, String) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- setCallbackFunction(String, String) - Method in class org.jmol.console.JmolConsole
-
- setCallbackFunction(String, String) - Method in class org.jmol.viewer.StatusManager
-
- setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- 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
- setCapOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setCE(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
-
- setCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
-
- setCellParams() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- 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
-
- setCenters() - Method in class org.jmol.shapespecial.DrawMesh
-
- 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.
- setCharges() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- setCheckBoxOption(JMenuItem, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
-
- setCheckBoxOption(JMenuItem, String, String) - Method in class org.jmol.popup.SimplePopup
-
- setCheckBoxState(Object, boolean) - Method in class org.jmol.popup.SimplePopup
-
- setCheckBoxValue(JMenuItem, String, boolean) - Method in class org.jmol.popup.JmolPopup
-
(1) setOption --> set setOption true or set setOption false
- setCheckBoxValue(JMenuItem, String, boolean) - Method in class org.jmol.popup.SimplePopup
-
(1) setOption --> set setOption true or set setOption false
- setCheckBoxValue(Object) - Method in class org.jmol.popup.SimplePopup
-
- setCheckSpecial(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setChiralClass(int) - 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
-
- 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.
- setCoeffs(boolean) - Method in class org.jmol.quantum.MOCalculation
-
- 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.MeshRenderer
-
- 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, int, Bond) - Method in class org.jmol.shape.Shape
-
- setColix(short, byte, BitSet) - Method in class org.jmol.shapebio.BioShape
-
- setColix(short) - Method in class org.jmol.util.MeshSurface
-
- 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, int, BitSet) - Method in class org.jmol.shapespecial.Dipoles
-
- setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setColor(int) - Method in interface org.jmol.api.JmolRendererInterface
-
- setColor(int) - Method in class org.jmol.export.Export3D
-
- setColor(int) - Method in class org.jmol.g3d.Graphics3D
-
- setColor(short) - Method in class org.jmol.shape.Measures
-
- setColorBackground(String) - Method in class org.jmol.api.JmolViewer
-
- setColorBackground(String) - Method in class org.jmol.viewer.Viewer
-
- setColorByScore(float, int) - Method in class org.jmol.shapesurface.Contact
-
- setColorCommand() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
just sets the color command for this isosurface.
- setColorModel(ColorModel) - Method in class org.jmol.export.image.ImageEncoder
-
- setColorNoisy(int) - Method in class org.jmol.g3d.Graphics3D
-
- setColorOptions(StringBuffer, int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
-
- setColorsFromJvxlData(int) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
from Isosurface.notifySurfaceGenerationCompleted()
starting with Jmol 12.1.50, JVXL files contain color, translucency, color
scheme information, and vertex color mappings (as from COLOR ISOSURFACE
{hydrophobic} WHITE), returning these settings when the JVXL file is
opened.
- setCommand(Token) - Method in class org.jmol.script.ScriptCompiler
-
- 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(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- setConformation(BitSet) - Method in class org.jmol.modelset.Polymer
-
- setConformation(BitSet) - Method in class org.jmol.modelsetbio.BioPolymer
-
- setConformation() - Method in class org.jmol.viewer.Viewer
-
- setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
-
sets a custom console -- should be called IMMEDIATELY following allocateViewer
create your console with, perhaps:
new org.openscience.jmol.app.jmolPanel.AppConsole(viewer, displayFrame,
externalJPanel, buttonsEnabled);
(see examples/basic/org/jmol/Integration.java
- setConsoleTextPane(AppConsole.ConsoleTextPane) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- setConstraints(List<Object[]>) - Method in class org.jmol.minimize.forcefield.Calculations
-
- setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
-
- setContactBitSets(BitSet, BitSet, boolean, float, RadiusData, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- setContacts(Object[]) - Method in class org.jmol.shapesurface.Contact
-
- setContext(ScriptContext) - Method in class org.jmol.console.ScriptEditor
-
- setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- setContourVector(List<Object>, int, BitSet, float, short, int, StringBuffer) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
- setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setCount(int) - Method in class org.jmol.modelset.Measurement
-
- setCount(int) - Method in class org.jmol.modelset.MeasurementPending
-
- setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelCollection
-
- setCrystallographicDefaults() - Method in class org.jmol.viewer.StateManager
-
- setCurrent(int) - Method in class org.jmol.viewer.ActionManager.Mouse
-
- setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
-
- setCurrentAtomSetIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- 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.AnimationManager
-
- setCurrentModelIndex(int, boolean) - Method in class org.jmol.viewer.AnimationManager
-
- 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, Object) - Method in interface org.jmol.api.ApiPlatform
-
- setCursor(int, Object) - Static method in class org.jmol.awt.Display
-
- setCursor(int, Object) - Method in class org.jmol.awt.Platform
-
- setCursor(int) - Method in class org.jmol.viewer.Viewer
-
- setCursorWait(boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.MapFileReader
-
- setData(String, String, int, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- setData(List<Object[]>, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.AngleCalc
-
- setData(List<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.DistanceCalc
-
- setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.ESCalc
-
- setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.OOPCalc
-
- setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.PairCalc
-
- setData(List<Object[]>, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.TorsionCalc
-
- setData(List<Object[]>, int, int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF.VDWCalc
-
- setData(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.script.ScriptEvaluator
-
- setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
-
- setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
-
- setDefaultColors(boolean) - Method in class org.jmol.viewer.ColorManager
-
- setDefaultColors(boolean) - 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
-
- setDefaultRendering(int) - Method in class org.jmol.modelset.ModelLoader
-
- setDefaults - Variable in class org.jmol.shape.Labels
-
- setDefaults(String) - Method in class org.jmol.viewer.Viewer
-
- setDefaults() - Method in class org.jmol.viewer.Viewer
-
- setDefaultStructure(BitSet) - Method in class org.jmol.modelset.ModelCollection
-
- setDefaultVdw(EnumVdw) - Method in class org.jmol.viewer.DataManager
-
- setDefaultVdw(String) - Method in class org.jmol.viewer.Viewer
-
- setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setDepth(Vector3f, Point3f, Point3f, Point3f, float) - Method in class org.jmol.g3d.Hermite3D
-
- setDesiredQpt(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- 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
-
df in I = df * (N dot L) + sf * (R dot V)^p
- setDimensions(int, int) - Method in class org.jmol.export.image.ImageEncoder
-
- setDipole(String[]) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- setDipole() - Method in class org.jmol.shapespecial.Dipoles
-
- setDipole(Atom, Atom, float, float) - Method in class org.jmol.shapespecial.Dipoles
-
- setDirect() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- setDisplayMenuState() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- setDoFixPeriodic() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
-
- setDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
-
- setDrawing(int[]) - 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
-
- setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
-
- setEccentricity(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
-
- setEcho() - Method in class org.jmol.script.ScriptEvaluator
-
- setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
-
- setEchoStateActive(boolean) - Method in class org.jmol.viewer.Viewer
-
- setEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Face
-
- setEdges() - Method in class org.jmol.shape.BbcageRenderer
-
- setEdges() - Method in class org.jmol.shape.CageRenderer
-
- setEdges() - Method in class org.jmol.shape.UccageRenderer
-
- setEditorTextPane(ScriptEditor.EditorTextPane) - Method in class org.jmol.console.ScriptEditor.EditorDocument
-
- setElement(Atom, int) - Method in class org.jmol.modelset.AtomCollection
-
- 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
-
- setEnabled(JButton, boolean) - Method in class org.jmol.console.JmolConsole
-
- setEncodeAlpha(boolean) - Method in class org.jmol.export.image.PngEncoder
-
Set the alpha encoding on or off.
- setEnergies(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- setEnergy() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interpret the Energy= line for non SCF type energy output
- setEnergy(String, String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
-
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
-
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- setEqualPt - Variable in class org.jmol.script.ScriptCompiler
-
- setError(Throwable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setError(boolean) - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- setErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptEvaluator
-
- setErrorMessage(String) - Method in class org.jmol.script.ScriptEvaluator
-
- setErrorMessage(String) - Method in class org.jmol.viewer.Viewer
-
- setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
-
- setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of explicit hydrogen atoms bonded with this atom.
- setFid(byte) - Method in class org.jmol.shape.Text
-
- setFile() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- 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
-
- setFileLoadStatus(String, String, String, String, int, boolean) - Method in class org.jmol.viewer.StatusManager
-
- setFileLoadStatus(FileManager.EnumFileStatus, String, String, String, String) - Method in class org.jmol.viewer.Viewer
-
- setFilename(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
-
- setFilename(String) - Method in class org.jmol.console.ScriptEditor
-
- setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- 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.script.ScriptEvaluator
-
- setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
-
- setFloatProperty(String, int, float) - Method in class org.jmol.viewer.Viewer
-
- setFocus() - 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
-
- setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
-
- setFractionalCoord(int, float, boolean) - Method in class org.jmol.modelset.Atom
-
- setFractionalCoord(Point3f, boolean) - Method in class org.jmol.modelset.Atom
-
- setFractionalCoord(Point3f, Point3f, boolean) - Method in class org.jmol.modelset.Atom
-
- setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setFrameOffset(int) - Method in class org.jmol.viewer.TransformManager
-
- setFrameOffset(int) - Method in class org.jmol.viewer.Viewer
-
- setFrameOffsets(Point3f[]) - Method in class org.jmol.viewer.TransformManager
-
- setFrameOffsets(BitSet) - Method in class org.jmol.viewer.Viewer
-
- setFrameRangeVisible() - Method in class org.jmol.viewer.AnimationManager
-
- setFrameTitle(BitSet, Object) - Method in class org.jmol.modelset.ModelCollection
-
- setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
-
- setFrameTitle(Object) - 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
-
- setFreqValue(float, String[]) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
- setFromBits(int, BitSet) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
- setFront(int, boolean) - Method in class org.jmol.shape.Labels
-
- setFunction(ScriptFunction) - Method in class org.jmol.script.ScriptFlowContext
-
- setFunction(ScriptFunction, String, int, int, short[], int[][], List<Token[]>) - Static method in class org.jmol.script.ScriptFunction
-
- setFunctionXY(List<Object>) - Method in class org.jmol.jvxl.readers.Parameters
-
- setFunctionXYZ(List<Object>) - Method in class org.jmol.jvxl.readers.Parameters
-
- setGeneralBindings() - Method in class org.jmol.viewer.binding.JmolBinding
-
- setGestureSwipeFactor(float) - Method in class org.jmol.viewer.ActionManager
-
- setGhostOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setGlobal() - Method in class org.jmol.script.ScriptVariable
-
- setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setGouraud(int, int, int) - Method in class org.jmol.g3d.Triangle3D
-
- setGreyscaleMode(boolean) - Method in class org.jmol.g3d.Graphics3D
-
controls greyscale rendering
- setGridLimitsForAtom(Point3f, float, Point3i, Point3i) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- setGroup(Group) - Method in class org.jmol.modelset.Atom
-
- setGroup(int, boolean) - Method in class org.jmol.shape.Labels
-
- setGroupIndex(int) - Method in class org.jmol.modelset.Group
-
- setGroupParameter(int, float) - Method in class org.jmol.modelset.Group
-
- setHandler(XMLReader, XmlReader.JmolXmlHandler) - Method in class org.jmol.adapter.readers.xml.XmlReader.JmolXmlHandler
-
- setHaveHsAlready(boolean) - Method in interface org.jmol.api.JmolBioResolver
-
- setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.Resolver
-
- setHaveStraightness(boolean) - Method in class org.jmol.modelset.AtomCollection
-
- setHbond() - Method in class org.jmol.script.ScriptEvaluator
-
- setHeader(String, String) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- setHeader(String) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- setHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
-
- setHeading(Point3f, Vector3f, int) - Method in class org.jmol.shapesurface.Isosurface
-
- 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
-
- setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
-
- setHydrogen(int, int, String, Point3f) - Method in class org.jmol.modelsetbio.Resolver
-
- setHydrogenCount(SmilesSearch) - Method in class org.jmol.smiles.SmilesAtom
-
Finalizes the hydrogen count hydrogens in a SmilesMolecule.
- setHydrophobicity(int, float) - Method in class org.jmol.modelset.AtomCollection
-
- setImage(Image) - Method in class org.jmol.export.image.PngEncoder
-
Set the image to be encoded
- setImage(Object) - Method in class org.jmol.shape.Text
-
- setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Sets the output image dimensions.
- setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
-
- setImageInfo(int, int, String) - Method in class org.jmol.export.dialog.Dialog
-
- setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of implicit hydrogen atoms bonded with this atom.
- 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.jmolpanel.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.quantum.SpartanArchive
-
- setInMotion(boolean) - Method in class org.jmol.viewer.AnimationManager
-
- setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
-
- setIntersectData() - Method in class org.jmol.shapespecial.Draw
-
- setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
-
- setIntProperty(String, int) - Method in class org.jmol.script.ScriptEvaluator
-
- setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
-
- setIntProperty(String, int, int) - Method in class org.jmol.viewer.Viewer
-
- setIonicRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
-
- setIsBigEndian(boolean) - Method in class org.jmol.util.BinaryDocument
-
- setIsDna(boolean) - Method in class org.jmol.modelset.Chain
-
- setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setIsRna(boolean) - Method in class org.jmol.modelset.Chain
-
- setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
-
- setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelCollection
-
- setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
-
- setIteratorForPoint(AtomIndexIterator, int, Point3f, float) - Method in interface org.jmol.atomdata.AtomDataServer
-
- setIteratorForPoint(AtomIndexIterator, int, Point3f, float) - Method in class org.jmol.modelset.ModelCollection
-
- setIteratorForPoint(AtomIndexIterator, int, Point3f, float) - Method in class org.jmol.viewer.Viewer
-
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
-
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.StatusManager
-
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
-
- 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, JmolCallbackListener) - Method in class org.jmol.viewer.StatusManager
-
- setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
-
- setJvxlColorMap(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
set up the jvxlData fields needed for either just the
header (isAll = false) or the full file (isAll = true)
- setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- setJvxlDataRendering() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- 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.SimplePopup
-
- setLabel(String) - Method in class org.jmol.script.ScriptEvaluator
-
- setLabel(LabelToken[][], String, int) - Method in class org.jmol.shape.Labels
-
- setLabel(String, BitSet) - Method in class org.jmol.viewer.ShapeManager
-
- setLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.BannerFrame
-
- setLabels() - Method in class org.jmol.console.AppletConsole
-
- setLanguagePath(String) - Static method in class org.jmol.i18n.GT
-
- setLastError(String) - Static method in exception org.jmol.smiles.InvalidSmilesException
-
- setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
-
set symmetry lattice type using Hall rotations
- 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, boolean, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
- 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
-
- setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
-
- setLighting(int) - Method in class org.jmol.shape.Mesh
-
- setLine() - Method in class org.jmol.script.ScriptFlowContext
-
- setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- setLinearOffsets() - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- setLineBits(float, float) - Method in class org.jmol.g3d.Line3D
-
- setLoadFormat(String, char, boolean) - Method in class org.jmol.viewer.Viewer
-
- setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
-
- setLoadState(Map<String, Object>) - Method in class org.jmol.viewer.FileManager
-
- setLobe(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
-
- setLocalPath(JmolViewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
-
called by getImageFileNameFromDialog
called by getOpenFileNameFromDialog
called by getSaveFileNameFromDialog
called by classifyName for any full file load
called from the CD command
currentLocalPath is set in all cases
and is used specifically for dialogs as a first try
defaultDirectoryLocal is set only when not from a dialog
and is used only in getLocalPathForWritingFile or
from an open/save dialog.
- setLogFile(String) - Method in class org.jmol.viewer.Viewer
-
- 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.
- setLp(Point4f) - Method in class org.jmol.jvxl.readers.Parameters
-
- setMad(short) - Method in class org.jmol.modelset.Bond
-
- setMad(short, BitSet, float[]) - Method in class org.jmol.shapebio.BioShape
-
- setMad(int, short) - Method in class org.jmol.shapebio.BioShape
-
- setMadAtom(Viewer, RadiusData) - 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
-
- setMappingPlane(Point4f) - Method in class org.jmol.jvxl.data.VolumeData
-
- setMapRanges(SurfaceReader, boolean) - 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 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
-
- setMeasurementUnits(String) - Method in class org.jmol.script.ScriptEvaluator
-
- setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- setMep(float[], boolean) - Method in class org.jmol.jvxl.readers.Parameters
-
- setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- setMesh(String) - Method in class org.jmol.shape.MeshCollection
-
- setMesh() - Method in class org.jmol.shapesurface.Isosurface
-
- setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
-
an external applet or app with class that extends org.jmol.jvxl.MeshCreator
might execute:
org.jmol.viewer.Viewer viewer = applet.getViewer();
viewer.setMeshCreator(this);
then that class's updateMesh(String id) method will be called whenever a
mesh is rendered.
- setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEvaluator
-
- setMeshTokenProperty(Mesh, int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
-
- 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
-
- setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
-
- setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
-
- setMinMaxLatticeParameters(Point3i, Point3i) - Method in interface org.jmol.api.SymmetryInterface
-
- setMinMaxLatticeParameters(Point3i, Point3i) - Method in class org.jmol.symmetry.Symmetry
-
- setMinMaxLatticeParameters(Point3i, Point3i) - Method in class org.jmol.symmetry.UnitCell
-
- setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- setMO(int, float[]) - Method in class org.jmol.jvxl.readers.Parameters
-
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- setMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setMoData(List<Object[]>, int, float[], int, boolean, int, String) - Method in class org.jmol.script.ScriptEvaluator
-
- 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.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
-
- setModelClickability() - Method in class org.jmol.shapespecial.Dots
-
- setModelIndex(int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- setModelIndex(short) - Method in class org.jmol.modelset.Measurement
-
- setModelIndex(int) - Method in class org.jmol.modelset.ModelCollection.StateScript
-
- setModelIndex() - Method in class org.jmol.shapespecial.Dipoles
-
- setModelKitMode(boolean) - Method in class org.jmol.viewer.Viewer
-
- setModelkitMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- setModelNameNumberProperties(int, int, String, int, Properties, Map<String, Object>, String) - Method in class org.jmol.modelset.ModelLoader
-
- setModelParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- 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
-
- setModelVisibility() - Method in class org.jmol.viewer.ShapeManager
-
- 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.ActionManager
-
only NONE (-1) is implemented; it just stops the
hoverWatcher thread so that the viewer references are all removed
- setModeMouse(int) - Method in class org.jmol.viewer.Viewer
-
- setMonitor() - Method in class org.jmol.script.ScriptEvaluator
-
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
- setMotionFixedAtoms(BitSet) - Method in class org.jmol.viewer.SelectionManager
-
- setMotionFixedAtoms(BitSet) - Method in class org.jmol.viewer.Viewer
-
- setMOType(Map<String, Object>, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
-
- setMouseDragFactor(float) - Method in class org.jmol.viewer.ActionManager
-
- setMouseEnabled(boolean) - Method in class org.jmol.viewer.Viewer
-
- setMouseMode() - Method in class org.jmol.awt.Mouse
-
- setMouseMode() - Method in class org.jmol.viewer.ActionManager
-
- setMouseWheelFactor(float) - Method in class org.jmol.viewer.ActionManager
-
- setMovableBitSet(BitSet, boolean) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
-
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
-
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
- setNAltLocs(int) - Method in class org.jmol.modelset.Model
-
- setName(String) - Method in class org.jmol.script.ScriptVariable
-
- setNavFps(int) - Method in class org.jmol.viewer.TransformManager
-
- setNavFps(int) - Method in class org.jmol.viewer.TransformManager11
-
- 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
-
- setNavigationOffsetRelative(boolean) - Method in class org.jmol.viewer.TransformManager
-
- setNavigationOffsetRelative(boolean) - Method in class org.jmol.viewer.TransformManager11
-
- setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager
-
- setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager11
-
- setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
-
- setNavOn(boolean) - Method in class org.jmol.viewer.Viewer
-
- setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
-
- setNavXYZ(float, float, float) - Method in class org.jmol.viewer.Viewer
-
- setNci(boolean) - Method in class org.jmol.jvxl.readers.Parameters
-
- setNeighbors(int) - Method in class org.jmol.shapebio.BioShapeRenderer
-
- setNested(int, Object) - Method in class org.jmol.smiles.SmilesSearch
-
- setNewRotationCenter(Point3f, boolean) - Method in class org.jmol.viewer.TransformManager
-
- setNewRotationCenter(Point3f) - Method in class org.jmol.viewer.Viewer
-
- setNewSetCommand(boolean, String) - Method in class org.jmol.script.ScriptCompiler
-
- setNewWindowParametersForExport() - Method in class org.jmol.g3d.Graphics3D
-
- setNext(String, String, int[], int) - Static method in class org.jmol.util.XmlReader
-
shift pointer to a new tag or field contents
- setNInsertions(int) - Method in class org.jmol.modelset.Model
-
- setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in interface org.jmol.api.JmolRendererInterface
-
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.export.Export3D
-
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to
assign a noisy shade to the surface it will render
- setNoneSelected(boolean) - Method in class org.jmol.viewer.Viewer
-
- setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setNoPrompt() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- setNotionalUnitCell(float[], Matrix3f, Point3f) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setObjectArgb(String, int) - Method in class org.jmol.script.ScriptEvaluator
-
- 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.script.ScriptEvaluator
-
- setObjectMad(int, String, int) - Method in class org.jmol.viewer.Viewer
-
- setObjectProperty() - Method in class org.jmol.script.ScriptEvaluator
-
- 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.jmolpanel.AppConsole.ConsoleDocument
-
- setOffsets(int, int, boolean) - Method in class org.jmol.shape.Labels
-
- setOrbital(int, float[]) - Method in class org.jmol.shapesurface.MolecularOrbital
-
- setOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
- setOrder(int) - Method in class org.jmol.modelset.Bond
-
- setOrientation(Matrix3f) - Method in class org.jmol.symmetry.UnitCell
-
- setOutputStream(BinaryDocument, OutputStream) - Method in interface org.jmol.jvxl.api.MeshDataServer
-
- setOutputStream(OutputStream) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- setOutputStream(BinaryDocument, OutputStream) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- setOutputStream(OutputStream) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setOutputStream(BinaryDocument, OutputStream) - Method in class org.jmol.shapesurface.Isosurface
-
- setOutputStream(OutputStream, Viewer, double) - Method in class org.jmol.util.BinaryDocument
-
- setPaletteID(byte) - Method in class org.jmol.modelset.Atom
-
- setPaletteID(byte) - Method in class org.jmol.modelset.Bond
-
- setPaletteID(byte) - Method in class org.jmol.modelset.HBond
-
- setPanel(JPanel) - Method in class org.openscience.jmol.app.jmolpanel.KioskFrame
-
- setParallel(boolean) - Method in class org.jmol.viewer.Viewer
-
- setparam - Static variable in class org.jmol.script.Token
-
- setParameter(String, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
-
- 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
-
- setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
-
- 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(Map<String, FFParam>) - Method in class org.jmol.minimize.forcefield.Calculations
-
- setParent(SmilesSearch) - Method in class org.jmol.smiles.SmilesSearch
-
- setPartialCharge(int, float) - Method in class org.jmol.modelset.AtomCollection
-
- setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setPdb() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setPdbConectBonding(int, int, BitSet) - Method in class org.jmol.modelset.ModelSet
-
- setPdbConectBonding(boolean, 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
-
- setPhongExponent(int) - Static method in class org.jmol.g3d.Graphics3D
-
p in I = df * (N dot L) + sf * (R dot V)^p
- setPhononVector(float[], Atom, Vector3f, Vector3f, Vector3f) - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
transform complex vibration vector to a real vector by applying the
appropriate translation, storing the results in v
- setPickBindings() - Method in class org.jmol.viewer.binding.JmolBinding
-
- setPicked(int) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- setPicked(int) - Method in class org.jmol.viewer.Viewer
-
- setPicking() - Method in class org.jmol.script.ScriptEvaluator
-
- setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
-
- setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
-
- setPickingStyle() - Method in class org.jmol.script.ScriptEvaluator
-
- setPickingStyle(int) - Method in class org.jmol.viewer.ActionManager
-
- setPickingStyle(String, int) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- 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
-
- setPlanes(float[][]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
-
Planes to use for holding raw file data.
- setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
-
Raw file data planes are passed to us here from VolumeFileReader
- setPoint(Point3f, Point3f, Vector3f, int) - Method in class org.jmol.g3d.Hermite3D
-
- setPoint(float[], int, int, int) - Static method in class org.jmol.util.MeshSurface
-
- 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
-
- setPolygonColix(int, short) - Method in class org.jmol.util.MeshSurface
-
- setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
-
- setPopInDim(int, int) - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- setPosition(float) - Method in class org.jmol.shape.Text
-
- setPositions() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
- setPreliminary(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
-
- setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
-
- setPrincipalAxis(int, int) - Method in class org.jmol.symmetry.PointGroup
-
- setPrincipalPlane(int, int) - Method in class org.jmol.symmetry.PointGroup
-
- setPrivateKeyForShape(int) - Method in class org.jmol.viewer.Viewer
-
- setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.ConsoleDocument
-
- setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole.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.Echo
-
- setProperty(String, Object, BitSet) - Method in class org.jmol.shape.FontLineShape
-
- setProperty(String, Object, BitSet) - Method in class org.jmol.shape.FontShape
-
- 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(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
-
may come from any source -- executed AFTER a shape's own setProperty method
- 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.Dots
-
- 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.Contact
-
- 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
-
- setPropertyColorRange(float[], BitSet, String) - Method in class org.jmol.viewer.ColorManager
-
- setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
-
- setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.ColorManager
-
- setPropertyColorScheme(String, boolean, 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
-
- setProteinStructureId(int) - Method in class org.jmol.modelset.Group
-
- setProteinStructureId(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- setProteinStructureId(int) - Method in class org.jmol.modelsetbio.Monomer
-
- setProteinStructureType(EnumStructure, int) - Method in class org.jmol.modelset.Group
-
- setProteinStructureType(EnumStructure, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- setProteinType(BitSet, EnumStructure) - Method in class org.jmol.modelset.ModelCollection
-
- setProteinType(EnumStructure, BitSet) - Method in class org.jmol.viewer.Viewer
-
- setPt0(int, boolean) - Method in class org.jmol.script.ScriptFlowContext
-
- setQuality(int) - Method in class org.jmol.util.JpegEncoder
-
- setRadical(Point4f) - 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, float, boolean) - Method in class org.jmol.util.ColorEncoder
-
- setRanges(float, 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 class org.jmol.export.___Exporter
-
- setRgb(byte[], byte[], byte[]) - Method in class org.jmol.export.image.GifEncoder.AdaptiveColorCollection
-
- setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setRingData(BitSet) - Method in class org.jmol.smiles.SmilesSearch
-
- setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setRotateBondIndex(int) - Method in class org.jmol.viewer.Viewer
-
- setRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- 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
-
- setRotationMatrix(Matrix3f) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- setScaling() - Method in class org.jmol.shape.Labels
-
- setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
-
- setScreenDimension(int, int) - 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.script.ScriptFunction
-
- setScript(String) - Method in class org.jmol.shape.Object2d
-
- setScriptButtonPercent(int) - Static method in class org.openscience.jmol.app.webexport.WebExport
-
- setScriptEcho(String, boolean) - Method in class org.jmol.viewer.StatusManager
-
- setScriptEditor(ScriptEditor) - Method in class org.jmol.console.JmolConsole
-
- setScriptExtensions() - Method in class org.jmol.script.ScriptEvaluator
-
- setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
-
- setScriptFileReferences(String, String, boolean) - Static method in class org.jmol.viewer.FileManager
-
Sets all local file references in a script file to point to files within
dataPath.
- setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
-
- setScriptQueue(boolean) - Method in class org.jmol.viewer.Viewer
-
- setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.StatusManager
-
- setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
-
- setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
-
- setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
-
- setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
-
- setSelected(BitSet) - Method in class org.jmol.smiles.SmilesSearch
-
- setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
-
- setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
-
- setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.Viewer
-
- setSelectedFloats(float, BitSet, float[]) - Static method in class org.jmol.util.Parser
-
- setSelectedOctant() - Method in class org.jmol.shapespecial.EllipsoidsRenderer
-
- setSelectedTranslation(BitSet, char, int) - Method in class org.jmol.viewer.RepaintManager
-
- setSelectedValue(int, ScriptVariable) - Method in class org.jmol.script.ScriptVariable
-
- 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, Boolean) - 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
-
- setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
-
- setShapeId(int, int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- setShapeModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
-
- setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEvaluator
-
- setShapeProperty(int, String, Object, BitSet) - Method in class org.jmol.script.ScriptEvaluator
-
- setShapeProperty(String, Object, BitSet) - Method in class org.jmol.shape.Shape
-
specifically from modelSet.setShapeProperty, mostly from ScriptEvaluation,
but not always -- definitely not from "super.setProperty"
- setShapeProperty(int, String, Object, BitSet) - Method in class org.jmol.viewer.ShapeManager
-
- setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
-
- setShapeSize(int, int, BitSet) - Method in class org.jmol.script.ScriptEvaluator
-
- setShapeSize(int, RadiusData) - Method in class org.jmol.script.ScriptEvaluator
-
- setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.shape.Shape
-
- setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.shapebio.Backbone
-
- setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.shapebio.BioShapeCollection
-
- setShapeSize(int, int, RadiusData, BitSet) - Method in class org.jmol.viewer.ShapeManager
-
- setShapeSize(int, int, BitSet) - Method in class org.jmol.viewer.Viewer
-
- setShapeSize(int, RadiusData, BitSet) - Method in class org.jmol.viewer.Viewer
-
- setShapeState(Map<String, BitSet>, Map<String, BitSet>) - Method in class org.jmol.shapebio.BioShape
-
- setShapeTranslucency(int, String, String, float, BitSet) - Method in class org.jmol.script.ScriptEvaluator
-
- setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
-
- setShapeVisibility(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
-
- setShowWithin(List<Point3f>, float, boolean) - Method in class org.jmol.shape.Mesh
-
- setSilent(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
-
- setSingleItem(List<Object>) - Method in class org.jmol.shape.Measures
-
- setSize(int, BitSet) - Method in class org.jmol.shape.AtomShape
-
- setSize(RadiusData, BitSet) - Method in class org.jmol.shape.AtomShape
-
- setSize(RadiusData, BitSet) - Method in class org.jmol.shape.Balls
-
- setSize(int, BitSet) - Method in class org.jmol.shape.Measures
-
- setSize(int, BitSet) - Method in class org.jmol.shape.Shape
-
- setSize(RadiusData, 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(RadiusData, BitSet) - Method in class org.jmol.shapespecial.Dots
-
- 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
-
- setSlab(BitSet, BitSet, String, String, float) - Method in class org.jmol.util.MeshSurface
-
- setSlabAndDepthValues(int, int, boolean, int, int) - Method in class org.jmol.g3d.Graphics3D
-
clipping from the front and the back
- setSlabData() - Method in class org.jmol.shapespecial.Draw
-
- 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
-
- setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
-
- setSlaters(boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlice(float, float, float, float, Point3f, Vector3f, boolean) - Method in class org.openscience.jmol.app.surfacetool.Slice
-
Sets the right plane and left plane bounding a slice.
- setSlice(float, float, float, float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
Defines a slice within which isosurfaces (and in future? atoms) are
displayed.
- setSliceAnglefromZ(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setSliceAngleXY(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setSlicePosition(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setSliceThickness(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setSmilesBondCoordinates(SmilesAtom, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
-
- setSmilesCoordinates(JmolNode, SmilesAtom, SmilesAtom, JmolNode[]) - Method in class org.jmol.smiles.SmilesSearch
-
- setSmilesString(String) - Method in class org.jmol.viewer.Viewer
-
- 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
-
- setSpecularExponent(int) - Static method in class org.jmol.g3d.Graphics3D
-
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p
for faster calculation of shades
- setSpecularPercent(int) - Static method in class org.jmol.g3d.Graphics3D
-
sf in I = df * (N dot L) + sf * (R dot V)^p
not a percent of anything, really
- setSpecularPower(int) - Static method in class org.jmol.g3d.Graphics3D
-
fractional distance to white for specular dot
- setSphere(float) - Method in class org.jmol.jvxl.readers.Parameters
-
- setSphereMatrix(Point3f, float, float, float, AxisAngle4f, Matrix4f) - Method in class org.jmol.export.__CartesianExporter
-
- 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, List<Point3f>, BitSet, boolean) - Method in class org.jmol.viewer.TransformManager
-
- setSpinOn(boolean) - Method in class org.jmol.viewer.Viewer
-
- setSpinXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
-
- setSsbond() - Method in class org.jmol.script.ScriptEvaluator
-
- setsSuccessful - Variable in class org.jmol.jvxl.data.MeshData
-
- setStateInfo(Map<String, BitSet>, int, String) - Static method in class org.jmol.shape.Shape
-
- setStateInfo(Map<String, BitSet>, int, int, String) - Static method in class org.jmol.shape.Shape
-
- setStateInfo(Map<String, BitSet>, int, int, String) - Static method in class org.jmol.viewer.StateManager
-
- setStatement(int) - Method in class org.jmol.script.ScriptEvaluator
-
provides support for @x and @{....} in statements.
- setStateScriptVersion(String) - Method in class org.jmol.viewer.Viewer
-
- setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
-
- setStatusAppletReady(String, boolean) - Method in class org.jmol.viewer.StatusManager
-
- setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.StatusManager
-
- setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.Viewer
-
- setStatusAtomMoved(BitSet) - Method in class org.jmol.viewer.StatusManager
-
- setStatusAtomPicked(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
-
- setStatusClicked(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
-
- setStatusFrameChanged() - Method in class org.jmol.viewer.AnimationManager
-
- setStatusFrameChanged(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
-
- setStatusFrameChanged(int) - Method in class org.jmol.viewer.Viewer
-
- setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.StatusManager
-
- setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
-
- setStatusPicked(int, Point3f) - Method in class org.jmol.shape.MeshCollection
-
- setStatusResized(int, int) - Method in class org.jmol.viewer.StatusManager
-
- setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
-
- setStereoDegrees(float) - Method in class org.jmol.viewer.TransformManager
-
- setStereoGraphics(boolean) - Method in class org.jmol.applet.Jmol
-
- setStereoGraphics(boolean) - Method in interface org.jmol.applet.JmolAppletInterface
-
- setStereoMode(int[]) - Method in class org.jmol.viewer.TransformManager
-
- setStereoMode(EnumStereoMode) - Method in class org.jmol.viewer.TransformManager
-
- setStereoMode(int[], EnumStereoMode, float) - Method in class org.jmol.viewer.Viewer
-
- setStrandCount() - Method in class org.jmol.shapebio.StrandsRenderer
-
- setStrandCount(int, int) - Method in class org.jmol.viewer.Viewer
-
- setStream(BufferedInputStream, boolean) - Method in class org.jmol.util.BinaryDocument
-
- setStream(DataInputStream) - Method in class org.jmol.util.BinaryDocument
-
- setString(String) - Method in class org.jmol.util.CifDataReader
-
sets a string to be parsed from the beginning
- setStringNextLine() - Method in class org.jmol.util.CifDataReader
-
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.script.ScriptEvaluator
-
- setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
-
- setStringProperty(String, int, String) - Method in class org.jmol.viewer.Viewer
-
- setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.AlphaMonomer
-
- setStructure(BitSet, EnumStructure) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.Monomer
-
- setStructure(String) - Method in class org.jmol.popup.PopupResource
-
- setStructureIds() - Method in class org.jmol.modelset.ModelCollection
-
- setStructureList(Map<EnumStructure, float[]>) - Method in class org.jmol.modelset.ModelCollection
-
- setStructureList(Map<EnumStructure, float[]>) - Method in class org.jmol.modelset.Polymer
-
- setStructureList(Map<EnumStructure, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- setStructureList(float[], EnumStructure) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- setStructureList(float[], EnumStructure) - Method in class org.jmol.viewer.Viewer
-
- setStructureTypes() - Method in class org.jmol.shapebio.BioShapeRenderer
-
- setStrut(int, int, int, List<Atom>, BitSet, BitSet, List<Atom[]>, BitSet, BitSet, BitSet, int) - Static method in class org.jmol.modelsetbio.AlphaPolymer
-
- setSuperCell(String, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setSurfaceInfo(Point4f, int, String) - Method in class org.jmol.jvxl.data.JvxlData
-
- setSurfaceInfoFromBitSet(BitSet, Point4f) - Method in class org.jmol.jvxl.data.JvxlData
-
- setSurfaceToolParam() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setSym(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the symbol of the atm.
- setSymmetry() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- setSymmetryInfo(int, Map<String, Object>) - Method in interface org.jmol.api.SymmetryInterface
-
- setSymmetryInfo(int, Map<String, Object>) - Method in class org.jmol.symmetry.Symmetry
-
- setSymmetryInfo(Map<String, Object>) - 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
-
- setSymmetryOps() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- 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
-
- setSyncStarting() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setSyncTarget(int, boolean) - Method in class org.jmol.viewer.Viewer
-
- settable - Static variable in class org.jmol.script.Token
-
- setTag(char[], BitSet, char) - Method in class org.jmol.modelsetbio.AminoPolymer
-
- 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
-
- setTemp() - Method in class org.jmol.quantum.MOCalculation
-
- setTempPoints(Point3f, Point3f, boolean) - Method in class org.jmol.export.__CartesianExporter
-
- setTempVertex(Point3f, Point3f, Point3f) - Static method in class org.jmol.export.___Exporter
-
- setTempZSlab(int) - Method in class org.jmol.g3d.Graphics3D
-
- setText(String) - Method in class org.jmol.shape.Text
-
- setThisScheme(String, int[]) - Method in class org.jmol.util.ColorEncoder
-
- setTimeout(String, int, String) - Method in class org.jmol.viewer.ActionManager
-
- setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
-
- setTitle() - Method in class org.jmol.console.JmolConsole
-
- setToken(Viewer, String, LabelToken, int, int, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
-
sets a label token based on a label string
- setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
-
- setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
-
- setTorsionData(Point3f, Point3f, Point3f, Point3f, SmilesSearch.VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
-
- 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
-
- setTrajectoryName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
- setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setTransformManager(TransformManager) - Method in class org.jmol.viewer.Viewer
-
for an external application
- 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
-
- setTranslucentCoverOnly(boolean) - Method in interface org.jmol.api.JmolRendererInterface
-
- setTranslucentCoverOnly(boolean) - Method in class org.jmol.export.Export3D
-
- setTranslucentCoverOnly(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setTransparentColor(int) - Method in class org.jmol.export.image.PngEncoder
-
- setTransparentCursor(Object) - Method in interface org.jmol.api.ApiPlatform
-
- setTransparentCursor(Object) - Static method in class org.jmol.awt.Display
-
- setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
-
- setTriangleColixAndShadeIndex(short, int) - Method in class org.jmol.g3d.Graphics3D
-
- setTriangleTranslucency(short, short, short) - Method in class org.jmol.g3d.Graphics3D
-
- setUnitCell() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- 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
-
- setUnitCellAllFractionalRelative(boolean) - Method in interface org.jmol.api.SymmetryInterface
-
- setUnitCellAllFractionalRelative(boolean) - Method in class org.jmol.symmetry.Symmetry
-
- setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setUnitCellOffset(Point3f) - Method in interface org.jmol.api.SymmetryInterface
-
- setUnitCellOffset(int, Point3f, int) - Method in class org.jmol.modelset.ModelCollection
-
- setUnitCellOffset(Point3f) - Method in class org.jmol.symmetry.Symmetry
-
- setUnitCellOrientation(Matrix3f) - Method in interface org.jmol.api.SymmetryInterface
-
- setUnitCellOrientation(Matrix3f) - Method in class org.jmol.symmetry.Symmetry
-
- setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
-
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- setup(String) - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMepReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
-
- setup(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- setup(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- setup() - Method in class org.jmol.minimize.forcefield.ForceField
-
- setup(int, float[], Point3f[], BitSet) - Method in class org.jmol.quantum.MepCalculation
-
- setupCalculation(VolumeDataInterface, BitSet, BitSet, BitSet[], String, Point3f[], int, List<int[]>, float[][], int[][], Object, float[], float[], float[][], float[], boolean, Point3f[], float[], int) - Method in interface org.jmol.api.QuantumCalculationInterface
-
- setupCalculation() - Method in class org.jmol.jvxl.readers.IsoMOReader
-
- setupCalculation(VolumeDataInterface, BitSet, BitSet, BitSet[], String, Point3f[], int, List<int[]>, float[][], int[][], Object, float[], float[], float[][], float[], boolean, Point3f[], float[], int) - Method in class org.jmol.quantum.MOCalculation
-
- setupCalculation(VolumeDataInterface, BitSet, BitSet, BitSet[], String, Point3f[], int, List<int[]>, float[][], int[][], Object, float[], float[], float[][], float[], boolean, Point3f[], float[], int) - Method in class org.jmol.quantum.NciCalculation
-
- setupCalculations() - Method in class org.jmol.minimize.forcefield.Calculations
-
- setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
-
- setupCoordinates(float[], float[], BitSet, Point3f[], Point3f[], boolean) - 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.console.AppletConsole
-
- setupLabels() - Method in class org.jmol.console.AppletConsole
-
- setupLabels() - Method in class org.jmol.console.JmolConsole
-
- setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
-
- setupMinimization() - Method in class org.jmol.minimize.Minimizer
-
- setupOutput() - Method in class org.jmol.console.AppletConsole
-
- 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)
- setUseMolecular(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- setUseNumberLocalization(boolean) - Static method in class org.jmol.util.TextFormat
-
- setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
-
- setUserColors() - Method in class org.jmol.script.ScriptEvaluator
-
- setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
-
- setUserScale(int[]) - Method in class org.jmol.viewer.ColorManager
-
- setUserScale(int[]) - Method in class org.jmol.viewer.Viewer
-
- setUserVariable(String, ScriptVariable) - Method in class org.jmol.viewer.StateManager.GlobalSettings
-
- setUserVariable(String, ScriptVariable) - Method in class org.jmol.viewer.Viewer
-
- setUserVdw(EnumVdw) - Method in class org.jmol.viewer.DataManager
-
- setValence(int) - Method in class org.jmol.modelset.Atom
-
- setValence(int) - Method in class org.jmol.smiles.SmilesAtom
-
- setValue(String, String) - Method in class org.jmol.applet.Jmol
-
- setValue(float) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
-
- setValueMinMax() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
- setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
-
- setVariable(int, int, String, int) - Method in class org.jmol.script.ScriptEvaluator
-
- setVariables(Map<String, ScriptVariable>, List<ScriptVariable>) - Method in class org.jmol.script.ScriptFunction
-
- setVariables() - Method in class org.jmol.shape.MeshRenderer
-
- setVectorAnisotropy(Vector3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setVectorScale(float) - Method in class org.jmol.api.JmolViewer
-
- setVectorScale(float) - Method in class org.jmol.viewer.Viewer
-
- setVersion(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
- setVertexAnisotropy(Point3f) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
-
- setVertexSource() - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- 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
-
- setVibrationsFromProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- 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, double) - Method in interface org.jmol.api.JmolImageCreatorInterface
-
- setViewer(JmolViewer, double) - Method in class org.jmol.export.image.ImageCreator
-
- setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
-
- setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
-
- setViewer(Viewer, int, int) - Method in class org.jmol.viewer.TransformManager
-
- setViewer(JmolViewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- setViewer(JmolViewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- 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 interface org.jmol.api.JmolAppConsoleInterface
-
- setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
-
- setVisible(boolean) - Method in class org.jmol.console.AppletConsole
-
- setVisible(boolean) - Method in class org.jmol.console.JmolConsole
-
- setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
-
- setVisible(boolean) - Method in class org.jmol.modelset.Measurement
-
- setVisible(boolean) - Method in class org.jmol.shapespecial.Polyhedra
-
- setVisualRange(float) - Method in class org.jmol.viewer.TransformManager
-
- setVolumeData() - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- setVolumeData() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- setVolumeData() - Method in class org.jmol.jvxl.readers.IsoFxyReader
-
- setVolumeData() - Method in class org.jmol.jvxl.readers.IsoShapeReader
-
- setVolumeData(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setVolumeData() - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- setVolumeData(int, VolumeData, ContactPair, float, int) - Method in class org.jmol.shapesurface.Contact
-
- setVolumeDataParams() - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- setVolumeForPlane() - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setVolumetricOrigin(float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
-
- setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
-
- setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- setVolumetricVector(int, float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
-
- setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
-
- setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
-
- setVoxel(int, int, int, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
-
- 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 interface org.jmol.api.VolumeDataInterface
-
- setVoxelData(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
-
- setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
-
- setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
-
- setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
-
for sparse data mapping, as for a plane
- setVoxelRange(int, float, float, float, int) - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
-
- 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
-
- setXmlProperty(String, Object, BitSet) - Method in class org.jmol.shape.Shape
-
may NOT be over-ridden by shape; executed BEFORE shape's setProperty
- setXY(int, int) - Method in class org.jmol.shape.Object2d
-
- setXYZ(boolean) - Method in class org.jmol.quantum.QuantumCalculation.QMAtom
-
- setXYZ(Point3f) - Method in class org.jmol.shape.Object2d
-
- setXYZBohr(Point3f[]) - Method in class org.jmol.quantum.QuantumCalculation
-
- setXYZBohr(float[], int, int, Point3f[]) - Method in class org.jmol.quantum.QuantumCalculation
-
- 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
-
- setZs(int, int) - Method in class org.jmol.shape.Object2d
-
- setZShadeEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
-
- setZShadePower(int) - Static method in class org.jmol.g3d.Graphics3D
-
fractional distance from black for ambient color
- setZslab() - Method in class org.jmol.script.ScriptEvaluator
-
- setZslabPoint(Point3f) - Method in class org.jmol.viewer.TransformManager
-
- setZslabPoint(Point3f) - Method in class org.jmol.viewer.Viewer
-
- sfacElementSymbols - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
-
- sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- sg - Variable in class org.jmol.shapesurface.Isosurface
-
- sgIndex - Static variable in class org.jmol.symmetry.SpaceGroup
-
- Shade3D - Class in org.jmol.g3d
-
All static functions.
- Shade3D() - Constructor for class org.jmol.g3d.Shade3D
-
- SHADE_SLAB_CLIPPED - Static variable in class org.jmol.g3d.Sphere3D
-
- shadeIndexes - Variable in class org.jmol.g3d.Normix3D
-
- shadeIndexes2Sided - Variable in class org.jmol.g3d.Normix3D
-
- shadeIndexLast - Static variable in class org.jmol.g3d.Shade3D
-
- shadeIndexMax - Static variable in class org.jmol.g3d.Shade3D
-
- shadeIndexNoisyLimit - Static variable in class org.jmol.g3d.Shade3D
-
- shadeIndexNormal - 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 - Static variable in class org.jmol.script.Token
-
- Shape - Class in org.jmol.shape
-
Shape now encompasses:
AtomShape (abstract)
|
Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors
|
GeoSurface
BioShapeCollection (abstract)
|
Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace
Dipoles
FontLineShape (abstract)
|
Axes, Bbcage, Frank, Uccage
Measures
MeshCollection (abstract)
| |
Draw Isosurface
|
LcaoCartoon, MolecularOrbital, Pmesh
Sticks
|
Hsticks, Sssticks
TextShape (abstract)
|
Echo, Hover
- Shape() - Constructor for class org.jmol.shape.Shape
-
- shape - Variable in class org.jmol.shape.ShapeRenderer
-
- shape - Variable in class org.jmol.shapebio.BioShape
-
- 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_CONTACT - 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_PLOT3D - 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_STRUTS - 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
-
- shapeCommand - Static variable in class org.jmol.script.Token
-
- shapeID - Variable in class org.jmol.shape.Shape
-
- shapeID - Variable in class org.jmol.shape.ShapeRenderer
-
- shapely - Static variable in class org.jmol.script.Token
-
- SHAPELY - Static variable in class org.jmol.util.ColorEncoder
-
- shapeManager - Variable in class org.jmol.modelset.ModelCollection
-
- shapeManager - Variable in class org.jmol.script.ParallelProcessor.RunProcess
-
- shapeManager - Variable in class org.jmol.script.ScriptEvaluator
-
- shapeManager - Variable in class org.jmol.viewer.RepaintManager
-
- ShapeManager - Class in org.jmol.viewer
-
- ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
-
- ShapeManager(Viewer, ModelSet) - Constructor for class org.jmol.viewer.ShapeManager
-
- shapeManager - Variable in class org.jmol.viewer.Viewer
-
- ShapeRenderer - Class in org.jmol.shape
-
- ShapeRenderer() - Constructor for class org.jmol.shape.ShapeRenderer
-
- shapes - Variable in class org.jmol.viewer.ShapeManager
-
- shapeTokenIndex(int) - Static method 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, int, EnumStructure) - Constructor for class org.jmol.modelsetbio.Sheet
-
- sheet - Static variable in class org.jmol.script.Token
-
- SHEET_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- sheetOffsets - Static variable in class org.jmol.modelsetbio.AminoPolymer
-
- sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
-
- sheetsmoothing - Static variable in class org.jmol.script.Token
-
- 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.quantum.CsfReader
-
- SHELL_D_CARTESIAN - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_D_SPHERICAL - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_F_CARTESIAN - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_F_SPHERICAL - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_L - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_P - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_S - Static variable in class org.jmol.api.JmolAdapter
-
- SHELL_SP - Static variable in class org.jmol.api.JmolAdapter
-
- shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
-
- shellCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
-
- shellOrder - Static variable in class org.jmol.quantum.MOCalculation
-
- shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
- shells - Variable in class org.jmol.quantum.MOCalculation
-
- shellsByUniqueAtom - Variable in class org.jmol.adapter.readers.quantum.PsiReader
-
- shelxLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- ShelxReader - Class in org.jmol.adapter.readers.xtal
-
A reader for SHELX output (RES) files.
- ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
-
- SHIFT - Static variable in class org.jmol.viewer.binding.Binding
-
- SHIFT_MASK - Static variable in class org.jmol.api.Event
-
- shortSectorPower - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
-
- shortSectorSize - Variable in class org.jmol.util.CompoundDocument
-
- shouldDisplay() - Method in class org.jmol.i18n.GT.Language
-
- show(int, int, char) - Method in interface org.jmol.api.JmolModelKitInterface
-
- show(int, int) - Method in interface org.jmol.api.JmolPopupInterface
-
- show(int, int, char) - Method in class org.jmol.modelkit.ModelKit
-
- show(int, int) - Method in class org.jmol.popup.JmolPopup
-
- show(int, int, boolean) - Method in class org.jmol.popup.SimplePopup
-
- show() - Method in class org.jmol.script.ScriptEvaluator
-
- show - Static variable in class org.jmol.script.Token
-
- show - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- show2D(String) - Method in class org.jmol.viewer.Viewer
-
- showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Show an atom set from the indexes array
- showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Shows the auxiliary information in the propertiesPane of the
AtomSetChooser window
- showaxes - Static variable in class org.jmol.script.Token
-
- showAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- showboundbox - Static variable in class org.jmol.script.Token
-
- showBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- showBox(JmolRendererInterface, short, int, int, int, int, int, int, float, boolean) - Static method in class org.jmol.shape.Text
-
- showConsole(boolean) - Method in class org.jmol.viewer.Viewer
-
- showContourLines - Variable in class org.jmol.shape.Mesh
-
- showEditor(String[]) - Method in class org.jmol.viewer.Viewer
-
- showfrank - Static variable in class org.jmol.script.Token
-
- showFrankMenu(int, int) - Method in class org.jmol.popup.JmolPopup
-
- showGridInfo() - Method in class org.jmol.jvxl.readers.VolumeDataReader
-
- showhiddenselectionhalos - Static variable in class org.jmol.script.Token
-
- showHiddenSelectionHalos - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- showHide(boolean) - Method in class org.jmol.shape.Measures
-
- showHide(Measurement, boolean) - Method in class org.jmol.shape.Measures
-
- showhydrogens - Static variable in class org.jmol.script.Token
-
- showHydrogens - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- showHydrogens - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- showInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
-
- showKey - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
-
- showKey() - Method in class org.jmol.shapesurface.IsosurfaceRenderer
-
- showkeystrokes - Static variable in class org.jmol.script.Token
-
- showKeyStrokes - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- showmeasurements - Static variable in class org.jmol.script.Token
-
- showMeasurements - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- showMeasurements - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- showMessage(String) - Method in class org.jmol.viewer.Viewer
-
- 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 - Static variable in class org.jmol.script.Token
-
- showMultipleBonds - Variable in class org.jmol.shape.SticksRenderer
-
- showMultipleBonds - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- shownavigationpointalways - Static variable in class org.jmol.script.Token
-
- showNavigationPointAlways - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- showNumbers - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
-
- showPaintTime - Variable in class org.jmol.applet.Jmol
-
- showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.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.SimplePopup
-
- showPovrayPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Show a file selector when the savePath button is pressed.
- showProgress() - Method in class org.openscience.chimetojmol.ChimePanel
-
- showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Shows the properties in the propertiesPane of the
AtomSetChooser window
- showRebondTimes - Static variable in class org.jmol.modelset.ModelCollection
-
- showSaveDialog(Component, JFileChooser, File) - Method in class org.jmol.export.dialog.Dialog
-
- showSavePathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Show a file selector when the savePath button is pressed.
- showscript - Static variable in class org.jmol.script.Token
-
- showSelected - Variable in class org.jmol.viewer.Viewer
-
- showSliceBoundaryPlanes(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
-
- showStatus(String) - Method in class org.jmol.applet.Jmol.MyStatusListener
-
- showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
-
- showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
-
- showString(String) - Method in class org.jmol.script.ScriptEvaluator
-
- showString(String, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- showString(String, boolean) - Method in class org.jmol.viewer.Viewer
-
- showTimeout(String) - Method in class org.jmol.viewer.ActionManager
-
- showTimeout(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.jmolpanel.DisplayPanel
-
- showTriangles - Variable in class org.jmol.shape.Mesh
-
- showunitcell - Static variable in class org.jmol.script.Token
-
- 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.jmolpanel.StatusListener
-
- 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.script.Token
-
- SIDfirstSector - Variable in class org.jmol.util.CompoundDocument.CmpDocDirectoryEntry
-
- siestaContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SiestaReader - Class in org.jmol.adapter.readers.xtal
-
SIESTA
http://www.icmab.es/siesta/
- SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
-
- sigma - Variable in class org.jmol.jvxl.readers.Parameters
-
- sigma - Static variable in class org.jmol.script.Token
-
- sign - Static variable in class org.jmol.script.Token
-
- SignedOnly - Variable in class org.jmol.popup.SimplePopup
-
- signFactor - Variable in class org.jmol.modelset.TickInfo
-
- silent - Variable in class org.jmol.minimize.forcefield.Calculations
-
- silent - Static variable in class org.jmol.script.Token
-
- SILVER - Static variable in class org.jmol.g3d.Graphics3D
-
- simpleAverage(Quaternion[]) - Static method in class org.jmol.util.Quaternion
-
Just a starting point.
- SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
-
- SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, List<Point3f>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
-
- SimpleMarchingCubesOld(VoxelDataCreator, VolumeData, float, boolean, boolean) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- SimplePopup - Class in org.jmol.popup
-
- SimplePopup() - Constructor for class org.jmol.popup.SimplePopup
-
- SimplePopup(JmolViewer) - Constructor for class org.jmol.popup.SimplePopup
-
- SimplePopup(JmolViewer, String, PopupResource, boolean) - Constructor for class org.jmol.popup.SimplePopup
-
- SimplePopup.CheckboxMenuItemListener - Class in org.jmol.popup
-
- SimplePopup.CheckboxMenuItemListener() - Constructor for class org.jmol.popup.SimplePopup.CheckboxMenuItemListener
-
- SimplePopup.MenuItemListener - Class in org.jmol.popup
-
- SimplePopup.MenuItemListener() - Constructor for class org.jmol.popup.SimplePopup.MenuItemListener
-
- simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.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.
- SimpleUnitCell - Class in org.jmol.util
-
general-purpose simple unit cell for calculations
and as a super-class of unitcell, which is only part of Symmetry
allows one-dimensional (polymer) and two-dimensional (slab)
periodicity
- SimpleUnitCell(float[]) - Constructor for class org.jmol.util.SimpleUnitCell
-
- simulationPhase - Variable in class org.jmol.multitouch.ActionManagerMT
-
- simulator - Variable in class org.jmol.multitouch.ActionManagerMT
-
- sin - Static variable in class org.jmol.script.Token
-
- sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
-
- sinBeta - Variable in class org.jmol.util.SimpleUnitCell
-
- sinGamma - Variable in class org.jmol.util.SimpleUnitCell
-
- SINGLE_CLICK - Static variable in class org.jmol.viewer.binding.Binding
-
- SINGLE_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- SingleModelOnly - Variable in class org.jmol.popup.SimplePopup
-
- SinglePointGesture - Class in org.jmol.multitouch.sparshui
-
SINGLE_POINT_GESTURE
only passes single-touch gestures.
- SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
-
- 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.script.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
-
- siteScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- sixdots - Static variable in class org.jmol.shape.SticksRenderer
-
- size - Variable in class org.jmol.g3d.Text3D
-
- size - Static variable in class org.jmol.script.Token
-
- size() - Method in class org.jmol.util.FastBitSet
-
- sizeCorrection - Variable in class org.jmol.g3d.Circle3D
-
- sizeOf(Token) - Static method in class org.jmol.script.ScriptVariable
-
- 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.Dsn6BinaryReader
-
- skipData(int) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
-
- skipData(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
- skipFloats(int) - Method in class org.jmol.adapter.readers.more.MdCrdReader
-
- skipHeader() - Method in class org.jmol.jvxl.readers.MsmsReader
-
- skipLoop() - Method in class org.jmol.adapter.readers.cifpdb.CifReader
-
skips all associated loop data
- skipping - Variable in class org.jmol.script.ScriptMathProcessor
-
- skipPoints(int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
-
- skipTag(String) - Method in class org.jmol.util.XmlReader
-
- skipTo(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
- skipTo(String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
-
- skipTo(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
-
- skipTo(String) - Method in class org.jmol.util.XmlReader
-
- 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.script.ScriptEvaluator
-
- slab - Static variable in class org.jmol.script.Token
-
- slabbing - Variable in class org.jmol.shape.SticksRenderer
-
- slabbingObject - Variable in class org.jmol.shape.Mesh
-
- slabbingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
-
- slabbyatom - Static variable in class org.jmol.script.Token
-
- slabByAtom - Variable in class org.jmol.shape.SticksRenderer
-
- slabByAtom - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- slabbymolecule - Static variable in class org.jmol.script.Token
-
- slabByMolecule - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- slabByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
-
- slabByPixels(int) - Method in class org.jmol.viewer.Viewer
-
- slabColix - Variable in class org.jmol.util.MeshSurface
-
- slabData - Variable in class org.jmol.shapespecial.Draw
-
- slabDepthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
-
- slabDepthByPixels(int) - Method in class org.jmol.viewer.Viewer
-
- slabDepthChanged() - Method in class org.jmol.viewer.TransformManager
-
- slabenabled - Static variable in class org.jmol.script.Token
-
- slabEnabled - Variable in class org.jmol.viewer.TransformManager
-
- slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
-
- slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
-
- slabInternal(Point4f, boolean) - Method in class org.jmol.viewer.TransformManager
-
- slabInternal(Point4f, boolean) - Method in class org.jmol.viewer.Viewer
-
- slabIsosurface(List<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
- slabMeshType - Variable in class org.jmol.util.MeshSurface
-
- slabOptions - Variable in class org.jmol.util.MeshSurface
-
- slabPercentSetting - Variable in class org.jmol.viewer.TransformManager
-
- slabPlane - Variable in class org.jmol.viewer.TransformManager
-
- slabPlaneOffset - Variable in class org.jmol.jvxl.readers.Parameters
-
- slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
-
- slabPolygons(List<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
-
- slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSurface
-
- slabrange - Static variable in class org.jmol.script.Token
-
- slabRange - 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.jvxl.data.JvxlData
-
- slabValue - Variable in class org.jmol.viewer.TransformManager
-
- slabZ - Variable in class org.jmol.export.___Exporter
-
- slaterArray - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
-
- SlaterData - Class in org.jmol.quantum
-
- SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
-
- SlaterReader - Class in org.jmol.adapter.readers.quantum
-
- SlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader
-
- SlaterReader.OrbitalSorter - Class in org.jmol.adapter.readers.quantum
-
- SlaterReader.OrbitalSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
-
- SlaterReader.SlaterSorter - Class in org.jmol.adapter.readers.quantum
-
- SlaterReader.SlaterSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
-
- slaters - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
-
- slaters - Variable in class org.jmol.quantum.MOCalculation
-
- sLeft - Variable in class org.jmol.g3d.Hermite3D
-
- Slice - Class in org.openscience.jmol.app.surfacetool
-
- Slice() - Constructor for class org.openscience.jmol.app.surfacetool.Slice
-
- slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- sliceObject(String, int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- slicer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- slicerFrame - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- sliceSelected() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- SLIDE_ZOOM_X_PERCENT - Static variable in class org.jmol.viewer.ActionManager
-
- slider - Variable in class org.jmol.export.dialog.Dialog.QualityListener
-
- sliderPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- 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
-
- SlowBitSet - Class in org.jmol.util
-
- SlowBitSet() - Constructor for class org.jmol.util.SlowBitSet
-
- SmallAtomDot - Static variable in class org.openscience.jmol.app.webexport.Orbitals
-
- smallmoleculemaxatoms - Static variable in class org.jmol.script.Token
-
- smallMoleculeMaxAtoms - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- smartaromatic - Static variable in class org.jmol.script.Token
-
- 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
-
- smiles - Static variable in class org.jmol.script.Token
-
- smiles2dimageformat - Static variable in class org.jmol.script.Token
-
- SmilesAromatic - Class in org.jmol.smiles
-
- SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
-
- SmilesAtom - Class in org.jmol.smiles
-
This class represents an atom in a SmilesMolecule.
- SmilesAtom(int) - Constructor for class org.jmol.smiles.SmilesAtom
-
Constructs a SmilesAtom.
- SmilesAtom(int, int, int, short, int) - Constructor for class org.jmol.smiles.SmilesAtom
-
- SmilesBond - Class in org.jmol.smiles
-
Bond in a SmilesMolecule
- SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
-
SmilesBond constructor
- SmilesBond(int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
-
- SmilesGenerator - Class in org.jmol.smiles
-
Double bond, allene, square planar and tetrahedral stereochemistry only
not octahedral or trigonal bipyramidal.
- SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
-
- SmilesMatcher - Class in org.jmol.smiles
-
Originating author: Nicholas Vervelle
A class to handle a variety of SMILES/SMARTS-related functions, including:
-- determining if two SMILES strings are equivalent
-- determining the molecular formula of a SMILES or SMARTS string
-- searching for specific runs of atoms in a 3D model
-- searching for specific runs of atoms in a SMILES description
-- generating valid (though not canonical) SMILES and bioSMILES strings
-- getting atom-atom correlation maps to be used with biomolecular alignment methods
- SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
-
- smilesMatcher - Variable in class org.jmol.viewer.Viewer
-
- SmilesMatcherInterface - Interface in org.jmol.api
-
- SmilesMeasure - Class in org.jmol.smiles
-
- SmilesMeasure(SmilesSearch, int, int, float, float, boolean) - Constructor for class org.jmol.smiles.SmilesMeasure
-
- SmilesParser - Class in org.jmol.smiles
-
Parses a SMILES String to create a SmilesMolecule.
- SmilesParser(boolean) - Constructor for class org.jmol.smiles.SmilesParser
-
- SmilesSearch - Class in org.jmol.smiles
-
-- was SmilesMolecule,
but this now includes more data than that and the search itself
so as to keep this thread safe
- SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
-
- SmilesSearch.VTemp - Class in org.jmol.smiles
-
- SmilesSearch.VTemp() - Constructor for class org.jmol.smiles.SmilesSearch.VTemp
-
- smilesurlformat - Static variable in class org.jmol.script.Token
-
- smilesUrlFormat - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- smoothingPower - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
-
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
-
- solid - Static variable in class org.jmol.script.Token
-
- solvent - Static variable in class org.jmol.script.Token
-
- solvent_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
-
- solvent_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
-
- solventDistance(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
-
- solventprobe - Static variable in class org.jmol.script.Token
-
- solventproberadius - Static variable in class org.jmol.script.Token
-
- 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
-
- sort - Static variable in class org.jmol.script.Token
-
- sortedItem(List<String>, int) - Static method in class org.jmol.util.ArrayUtil
-
- sortInorganic(JmolNode, List<JmolEdge>) - Method in class org.jmol.smiles.SmilesGenerator
-
We must sort the bond vector such that a diaxial pair is
first and last.
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
sorts coefficients by atomic number for speed later
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
sorts orbitals by energy rather than by symmetry
so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrReverse(int) - Method in class org.jmol.script.ScriptVariable
-
- sortSurfaceSets() - Method in class org.jmol.jvxl.data.MeshData
-
- 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_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
-
- spacebeforesquare - Static variable in class org.jmol.script.Token
-
- spacefill - Static variable in class org.jmol.script.Token
-
- Spacefilling - Static variable in class org.openscience.jmol.app.webexport.Molecules
-
- spaceGroup - Variable in class org.jmol.adapter.readers.xtal.GulpReader
-
- spaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- spacegroup - Static variable in class org.jmol.script.Token
-
- 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
-
- spaceGroupDefinitions - Static variable in class org.jmol.symmetry.SpaceGroup
-
- spaceGroupName - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- SpartanArchive - Class in org.jmol.adapter.readers.quantum
-
- SpartanArchive(BasisFunctionReader) - Constructor for class org.jmol.adapter.readers.quantum.SpartanArchive
-
- SpartanArchive(BasisFunctionReader, String, String) - Constructor for class org.jmol.adapter.readers.quantum.SpartanArchive
-
- spartanArchive - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- spartanBinaryContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- spartanContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SpartanInputReader - Class in org.jmol.adapter.readers.quantum
-
- SpartanInputReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanInputReader
-
- SpartanReader - Class in org.jmol.adapter.readers.quantum
-
- SpartanReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanReader
-
- spartanSmolLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SpartanSmolReader - Class in org.jmol.adapter.readers.quantum
-
- SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanSmolReader
-
- spec_alternate - Static variable in class org.jmol.script.Token
-
- spec_atom - Static variable in class org.jmol.script.Token
-
- spec_chain - Static variable in class org.jmol.script.Token
-
- spec_model - Static variable in class org.jmol.script.Token
-
- spec_model2 - Static variable in class org.jmol.script.Token
-
- spec_name_pattern - Static variable in class org.jmol.script.Token
-
- spec_resid - Static variable in class org.jmol.script.Token
-
- spec_seqcode - Static variable in class org.jmol.script.Token
-
- spec_seqcode_range - Static variable in class org.jmol.script.Token
-
- SPECIAL_AIMS - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_ALCHEMY - Static variable in class org.jmol.adapter.smarter.Resolver
-
- 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_CASTEP - 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_CRYSTAL - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_CUBE - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_FOLDINGXYZ - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_GENNBO - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_GROMACS - 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_QE_XML - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_VASP_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_VASP_XML - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_WIEN - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_XSD_DOM - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_XSD_XML - Static variable in class org.jmol.adapter.smarter.Resolver
-
- SPECIAL_XYZ - Static variable in class org.jmol.adapter.smarter.Resolver
-
- specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
-
- specialAtomNames - Static variable in class org.jmol.viewer.JmolConstants
-
- specialLabel - Variable in class org.jmol.shape.Hover
-
- specialLoad(String, String) - Static method in class org.jmol.adapter.smarter.Resolver
-
Special loading for file directories.
- 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.script.Token
-
- specialTags - Static variable in class org.jmol.adapter.smarter.Resolver
-
- specialTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
-
- specular - Static variable in class org.jmol.script.Token
-
- specular - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- specularExponent - Static variable in class org.jmol.g3d.Shade3D
-
- specularexponent - Static variable in class org.jmol.script.Token
-
- specularExponent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- specularFactor - Static variable in class org.jmol.g3d.Shade3D
-
- specularOn - Static variable in class org.jmol.g3d.Shade3D
-
- specularPercent - Static variable in class org.jmol.g3d.Shade3D
-
- specularpercent - Static variable in class org.jmol.script.Token
-
- specularPercent - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- specularPower - Static variable in class org.jmol.g3d.Shade3D
-
- specularpower - Static variable in class org.jmol.script.Token
-
- specularPower - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- sphere - Static variable in class org.jmol.script.Token
-
- 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
-
- sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
-
- sphereMean(Quaternion[], float[], float) - Static method in class org.jmol.util.Quaternion
-
- sphereNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- sphereShadeIndexes - 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
-
- sphericalDValues - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
- spin - Static variable in class org.jmol.script.Token
-
- SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
-
- spine - Static variable in class org.jmol.script.Token
-
- spinfps - Static variable in class org.jmol.script.Token
-
- spinFps - Variable in class org.jmol.viewer.TransformManager
-
- spinOn - Variable in class org.jmol.viewer.TransformManager
-
- spinOn - Variable in class org.openscience.jmol.app.webexport.JmolInstance
-
- spinThread - Variable in class org.jmol.viewer.TransformManager
-
- spinx - Static variable in class org.jmol.script.Token
-
- spinX - Variable in class org.jmol.viewer.TransformManager
-
- spinXYBy(int, int, float) - Method in class org.jmol.viewer.TransformManager
-
- spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
-
- spiny - Static variable in class org.jmol.script.Token
-
- spinY - Variable in class org.jmol.viewer.TransformManager
-
- spinz - Static variable in class org.jmol.script.Token
-
- spinZ - Variable in class org.jmol.viewer.TransformManager
-
- splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- Splash - Class in org.openscience.jmol.app.jmolpanel
-
- Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
-
- Splash.WindowListener - Class in org.openscience.jmol.app.jmolpanel
-
- Splash.WindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
-
- splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
-
- splashImage - Variable in class org.openscience.jmol.app.jmolpanel.Splash
-
- SplashInterface - Interface in org.openscience.jmol.app
-
- split - Static variable in class org.jmol.script.Token
-
- 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
-
- splitCommandLine(String) - Static method in class org.jmol.script.ScriptCompiler
-
used by app to separate a command line into three sections:
prefix....;cmd ........
- sprintf(String, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- sprintf(String, ScriptVariable, Object[], int[], float[], double[], boolean, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- sprintf(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable
-
sprintf accepts arguments from the format() function
First argument is a format string.
- sprintf(String, Object[]) - Static method in class org.jmol.util.TextFormat
-
sprintf emulation uses (almost) c++ standard string formats 's' string 'i'
or 'd' integer 'f' float/decimal 'p' point3f 'q' quaternion/plane/axisangle
' with added "i" in addion to the insipid "d" (digits?)
- sptContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- sqrt - Static variable in class org.jmol.script.Token
-
- sqrt3_2 - Static variable in class org.jmol.modelset.AtomCollection
-
- squareCount - Variable in class org.jmol.script.ScriptMathProcessor
-
- squared - Static variable in class org.jmol.script.Token
-
- sr - Variable in class org.jmol.jvxl.data.VolumeData
-
- 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.script.ScriptEvaluator
-
- ssbond - Static variable in class org.jmol.script.Token
-
- ssbondsbackbone - Static variable in class org.jmol.script.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
-
- STAND_ALONE - Static variable in class org.openscience.jmol.app.webexport.WebExport
-
- STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
-
- standardLevel - Static variable in class org.jmol.geodesic.Geodesic
-
3 levels, 0 through 3
- star - Static variable in class org.jmol.script.Token
-
- Stars - Class in org.jmol.shape
-
- Stars() - Constructor for class org.jmol.shape.Stars
-
- 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.openscience.jmol.app.jmolpanel.DisplayPanel
-
- startByteArrayReaderThread() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
-
- startChainID - Variable in class org.jmol.adapter.smarter.Structure
-
- startCommandWatcher(boolean) - Method in class org.jmol.viewer.ScriptManager
-
- startConsoleReaderThread(InputStream) - Method in class org.openscience.jmol.app.jmolpanel.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
-
- startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
-
- startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
-
- startIndexPending - Variable in class org.jmol.shapebio.RocketsRenderer
-
- startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
-
- startJmol(JmolApp) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- startJsonNioKiosk(int) - Method in class org.openscience.molecularplayground.MPJmolApp
-
- startMinimization() - Method in class org.jmol.minimize.Minimizer
-
- startMotion(boolean) - Method in class org.jmol.viewer.TransformManager.MotionThread
-
- startMotion() - Method in class org.jmol.viewer.TransformManager.MotionThread
-
- startPaintClock() - Method in class org.jmol.applet.Jmol
-
- startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- startPixelScale - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
-
- startRotationRadius - Variable in class org.jmol.viewer.TransformManager.MotionThread
-
- startScriptQueue(boolean) - Method in class org.jmol.viewer.ScriptManager
-
- startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
-
- startServerService() - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- startService(int, JsonNioClient, JmolViewer, String) - Method in class org.openscience.jmol.app.jmolpanel.JsonNioService
-
- startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
-
- startSparshUIService(boolean) - Method in class org.jmol.multitouch.ActionManagerMT
-
- startSpinningAxis(Point3f, Point3f, boolean) - Method in class org.jmol.viewer.Viewer
-
- startTime - Variable in class org.jmol.applet.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.jmolpanel.DisplayPanel
-
- startupHeight - Variable in class org.openscience.jmol.app.JmolApp
-
- startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- startupWidth - Variable in class org.openscience.jmol.app.JmolApp
-
- startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- startViewer(JmolViewer, SplashInterface) - Method in class org.openscience.jmol.app.JmolApp
-
- 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.script.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.console.JmolConsole
-
- stateButton - Variable in class org.jmol.console.ScriptEditor
-
- 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.jmolpanel.AtomSetChooser
-
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.webexport.PopInJmol
-
- 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, int, float, 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(StateManager.GlobalSettings, boolean) - Constructor for class org.jmol.viewer.StateManager.GlobalSettings
-
- StateManager.Orientation - Class in org.jmol.viewer
-
- StateManager.Orientation(boolean) - Constructor for class org.jmol.viewer.StateManager.Orientation
-
- statement - Variable in class org.jmol.script.ScriptContext
-
- statement - Variable in class org.jmol.script.ScriptEvaluator
-
- statementAsString(Token[], int, boolean) - Static method in class org.jmol.script.ScriptEvaluator
-
- statementLength - Variable in class org.jmol.script.ScriptContext
-
- statementLength - Variable in class org.jmol.script.ScriptEvaluator
-
- stateScripts - Variable in class org.jmol.modelset.ModelCollection
-
- stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
-
- StaticConstants - Class in org.jmol.constant
-
- StaticConstants() - Constructor for class org.jmol.constant.StaticConstants
-
- staticFunctions - Static variable in class org.jmol.viewer.StateManager
-
- staticGetAtomSetCollectionOrBufferedReaderFromZip(InputStream, String, String[], Map<String, Object>, int, boolean, 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.jmol.viewer.ActionManager.TimeoutThread
-
- status - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- status - Variable in class org.openscience.jmol.app.jmolpanel.Splash
-
- status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
-
- StatusBar - Class in org.openscience.jmol.app.jmolpanel
-
- StatusBar() - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
-
- statusForm - Variable in class org.jmol.applet.Jmol
-
- statusList - Variable in class org.jmol.viewer.StatusManager
-
- statusListener - Variable in class org.jmol.export.JmolFileDropper
-
- StatusListener - Class in org.openscience.jmol.app.jmolpanel
-
- StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
-
- StatusManager - Class in org.jmol.viewer
-
The StatusManager class handles all details of status reporting, including:
1) saving the message in a queue that replaces the "callback" mechanism,
2) sending messages off to the console, and
3) delivering messages back to the main Jmol.java class in app or applet
to handle differences in capabilities, including true callbacks.
- 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 - Static variable in class org.jmol.script.Token
-
- statusReporting - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- STATUSSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
-
- statusText - Variable in class org.jmol.applet.Jmol
-
- statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
-
- statusTextarea - Variable in class org.jmol.applet.Jmol
-
- statusTop - Variable in class org.openscience.jmol.app.jmolpanel.Splash
-
- STD_ORIENTATION_ATOMIC_NUMBER_OFFSET - Static variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
Word index of atomic number in line with atom coordinates in an
orientation block.
- stddev - Static variable in class org.jmol.script.Token
-
- stdDev(Quaternion[], Quaternion) - Static method in class org.jmol.util.Quaternion
-
- steepestDescentInitialize(int, double) - Method in class org.jmol.minimize.forcefield.ForceField
-
- steepestDescentTakeNSteps(int) - Method in class org.jmol.minimize.forcefield.ForceField
-
- step - Static variable in class org.jmol.script.Token
-
- stepAxisCoordinates() - Method in class org.jmol.shape.SticksRenderer
-
- stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
-
- stepButton - Variable in class org.jmol.console.ScriptEditor
-
- stepButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- stepMax - Variable in class org.jmol.minimize.forcefield.ForceField
-
- stepMinimization() - Method in class org.jmol.minimize.Minimizer
-
- stepNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
- stepPausedExecution() - Method in class org.jmol.script.ScriptEvaluator
-
- steps - Variable in class org.jmol.jvxl.readers.Parameters
-
- steps - Variable in class org.jmol.minimize.Minimizer
-
- stepScriptExecution() - Method in class org.jmol.viewer.Viewer
-
- stereo() - Method in class org.jmol.script.ScriptEvaluator
-
- stereo - Static variable in class org.jmol.script.Token
-
- STEREOCHEMISTRY_ALLENE - Static variable in class org.jmol.smiles.SmilesAtom
-
- STEREOCHEMISTRY_DEFAULT - Static variable in class org.jmol.smiles.SmilesAtom
-
- STEREOCHEMISTRY_OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
-
- STEREOCHEMISTRY_SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesAtom
-
- STEREOCHEMISTRY_TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
-
- STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesAtom
-
- stereoColors - Variable in class org.jmol.viewer.TransformManager
-
- stereodegrees - Static variable in class org.jmol.script.Token
-
- stereoDegrees - Variable in class org.jmol.viewer.TransformManager
-
- stereoFrame - Variable in class org.jmol.viewer.TransformManager
-
- stereoMode - Variable in class org.jmol.viewer.TransformManager
-
- stereoRadians - Variable in class org.jmol.viewer.TransformManager
-
- stereoState - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- stereoSync - Variable in class org.jmol.viewer.StatusManager
-
- Sticks - Class in org.jmol.shape
-
- Sticks() - Constructor for class org.jmol.shape.Sticks
-
- SticksRenderer - Class in org.jmol.shape
-
- SticksRenderer() - Constructor for class org.jmol.shape.SticksRenderer
-
- sto_exp - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- stop() - Method in class org.jmol.export.image.ImageEncoder
-
- stop - Static variable in class org.jmol.script.Token
-
- stop() - Method in class org.jmol.viewer.ScriptManager.ScriptQueueRunnable
-
- stopAnimationThreads(String) - Method in class org.jmol.viewer.Viewer
-
- stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
-
- stopMinimization() - Method in class org.jmol.viewer.Viewer
-
- stopMotion() - Method in class org.jmol.viewer.TransformManager
-
- stopMotion() - Method in class org.jmol.viewer.Viewer
-
- stopPaintClock() - Method in class org.jmol.applet.Jmol
-
- stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- str - Variable in class org.jmol.util.CifDataReader
-
- straightness - Variable in class org.jmol.modelset.Group
-
- straightness - Static variable in class org.jmol.script.Token
-
- STRAND_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- strandCount - Variable in class org.jmol.adapter.smarter.Structure
-
- strandCount - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- strandcount - Static variable in class org.jmol.script.Token
-
- strandCount - Variable in class org.jmol.shapebio.StrandsRenderer
-
- strandcountformeshribbon - Static variable in class org.jmol.script.Token
-
- strandCountForMeshRibbon - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- strandcountforstrands - Static variable in class org.jmol.script.Token
-
- strandCountForStrands - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- strands - Static variable in class org.jmol.script.Token
-
- Strands - Class in org.jmol.shapebio
-
- Strands() - Constructor for class org.jmol.shapebio.Strands
-
- strandSeparation - Variable in class org.jmol.shapebio.StrandsRenderer
-
- StrandsRenderer - Class in org.jmol.shapebio
-
- StrandsRenderer() - Constructor for class org.jmol.shapebio.StrandsRenderer
-
- strAtomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- strCommand - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole.ExecuteCommandThread
-
- stream - Variable in class org.jmol.util.BinaryDocument
-
- streamFileData(String, String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
-
- strFormat - Variable in class org.jmol.modelset.Measurement
-
- strFormat - Variable in class org.jmol.modelset.MeasurementData
-
- strFormat - Variable in class org.jmol.shape.Measures
-
- strFractionTemp - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- strID - Variable in class org.jmol.shapesurface.MolecularOrbital
-
- string - Static variable in class org.jmol.script.Token
-
- stringClass - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- stringParameter(int) - Method in class org.jmol.script.ScriptEvaluator
-
- stringParameterSet(int) - Method in class org.jmol.script.ScriptEvaluator
-
- stringReaders - Variable in class org.jmol.viewer.FileManager.FilesReader
-
- strings - Variable in class org.jmol.shape.Labels
-
- stringSetting(int, boolean) - Method in class org.jmol.script.ScriptEvaluator
-
- stringsResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
-
- StringtoScriptButton - Variable in class org.openscience.jmol.app.webexport.Test
-
- stringWidth(Object, String) - Static method in class org.jmol.awt.Font
-
- stringWidth(String) - Method in class org.jmol.g3d.Font3D
-
- 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
-
- strMenuStructure - Static variable in class org.jmol.popup.JmolPopup
-
- strOSName - Variable in class org.jmol.viewer.Viewer
-
- strparam - Static variable in class org.jmol.script.Token
-
- strPeeked - Variable in class org.jmol.util.CifDataReader
-
- strproperty - Static variable in class org.jmol.script.Token
-
- strucid - Static variable in class org.jmol.script.Token
-
- strucno - Static variable in class org.jmol.script.Token
-
- STRUCT_ID - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- 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(EnumStructure) - Constructor for class org.jmol.adapter.smarter.Structure
-
- Structure(int, EnumStructure, EnumStructure, String, int, int, char, int, char, char, int, char) - Constructor for class org.jmol.adapter.smarter.Structure
-
- structure - Variable in class org.jmol.popup.PopupResource
-
- structure() - Method in class org.jmol.script.ScriptEvaluator
-
- structure - Static variable in class org.jmol.script.Token
-
- structureContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
-
- structureContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
-
- structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- structureCount - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- structureID - Variable in class org.jmol.adapter.smarter.Structure
-
- structureID - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- structureList - Variable in class org.jmol.modelsetbio.AminoPolymer
-
- structureList - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- structures - Variable in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator
-
- structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
-
- structureTainted - Variable in class org.jmol.modelset.Model
-
- structureType - Variable in class org.jmol.adapter.smarter.Structure
-
- structureTypes - Variable in class org.jmol.shapebio.BioShapeRenderer
-
- strutdefaultradius - Static variable in class org.jmol.script.Token
-
- strutDefaultRadius - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- strutlengthmaximum - Static variable in class org.jmol.script.Token
-
- strutLengthMaximum - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- strutPoint(int, int, int) - Static method in class org.jmol.modelsetbio.AlphaPolymer
-
- struts() - Method in class org.jmol.script.ScriptEvaluator
-
- struts - Static variable in class org.jmol.script.Token
-
- strutsmultiple - Static variable in class org.jmol.script.Token
-
- strutsMultiple - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- strutspacing - Static variable in class org.jmol.script.Token
-
- strutSpacing - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- stub - Variable in class org.jmol.console.JmolConsole.FileChecker
-
- sub(double[], double[], Vector3d) - Static method in class org.jmol.minimize.Util
-
- sub - Static variable in class org.jmol.script.Token
-
- subSearches - Variable in class org.jmol.smiles.SmilesSearch
-
- subset() - Method in class org.jmol.script.ScriptEvaluator
-
- subset - Static variable in class org.jmol.script.Token
-
- substructure - Static variable in class org.jmol.script.Token
-
- substructureType - Variable in class org.jmol.adapter.smarter.Structure
-
- subtype - Variable in class org.jmol.modelsetbio.ProteinStructure
-
- sum - Variable in class org.jmol.quantum.MOCalculation
-
- sum - Static variable in class org.jmol.script.Token
-
- sum2 - Static variable in class org.jmol.script.Token
-
- sumVertexNormals(Point3f[], Vector3f[]) - Method in class org.jmol.shape.Mesh
-
- sumVertexNormals(Point3f[], Vector3f[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
- supercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- supercell - Static variable in class org.jmol.script.Token
-
- SUPPORTED_BASIS_FUNCTIONS - Static variable in class org.jmol.api.JmolAdapter
-
- SUPPORTED_BASIS_FUNCTIONS - Static variable in enum org.jmol.constant.EnumQuantumShell
-
- supportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
-
- surface - Static variable in class org.jmol.script.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.shapespecial.Dots
-
- SURFACE_ELLIPSOID2 - Static variable in class org.jmol.jvxl.readers.Parameters
-
- SURFACE_ELLIPSOID3 - Static variable in class org.jmol.jvxl.readers.Parameters
-
- SURFACE_FUNCTIONXY - Static variable in class org.jmol.jvxl.readers.Parameters
-
- SURFACE_FUNCTIONXYZ - Static variable in class org.jmol.jvxl.readers.Parameters
-
- SURFACE_INTERSECT - 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_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
-
- SURFACE_MEP - Static variable in class org.jmol.jvxl.readers.Parameters
-
- SURFACE_MLP - 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_NCI - 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_RADICAL - 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.JvxlXmlReader
-
- surfacedistance - Static variable in class org.jmol.script.Token
-
- surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
-
- surfaceDistanceMax - Variable in class org.jmol.modelset.AtomCollection
-
- SurfaceFileReader - Class in org.jmol.jvxl.readers
-
- SurfaceFileReader(SurfaceGenerator, BufferedReader) - Constructor for class org.jmol.jvxl.readers.SurfaceFileReader
-
- SurfaceFileTyper - Class in org.jmol.util
-
- SurfaceFileTyper() - Constructor for class org.jmol.util.SurfaceFileTyper
-
- SurfaceGenerator - Class in org.jmol.jvxl.readers
-
- SurfaceGenerator() - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
-
- SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
-
- surfaceList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- surfaceNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- surfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingSquares
-
- surfaceReader - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- SurfaceReader - Class in org.jmol.jvxl.readers
-
- SurfaceReader(SurfaceGenerator) - Constructor for class org.jmol.jvxl.readers.SurfaceReader
-
- surfaces - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- surfaceScrollPane - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- surfaceSet - Variable in class org.jmol.util.MeshSurface
-
- surfacesOnly - Variable in class org.jmol.export._ObjExporter
-
Flag to cause only surfaces to be output.
- SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
-
Class that holds the surface status information that the surface tool needs.
- SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
-
- surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- SurfaceTool - Class in org.openscience.jmol.app.surfacetool
-
- SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- SurfaceToolGUI - Class in org.openscience.jmol.app.surfacetool
-
GUI for the Jmol surfaceTool
- SurfaceToolGUI(JmolViewer, HistoryFile, String, SurfaceTool) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
Builds and opens a GUI to control slicing.
- SurfaceToolGUI(LayoutManager) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- SurfaceToolGUI(boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- SurfaceToolGUI(LayoutManager, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- SurfaceToolGUI.SurfaceListCellRenderer - Class in org.openscience.jmol.app.surfacetool
-
- SurfaceToolGUI.SurfaceListCellRenderer() - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
-
- 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.script.ScriptVariable
-
- sValueArray(StringBuffer, ScriptVariable, Map<Object, Boolean>, int, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- swap(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
-
- swapBytes(int) - Static method in class org.jmol.util.BinaryDocument
-
- swapBytes(short) - Static method in class org.jmol.util.BinaryDocument
-
- swingPopup - Variable in class org.jmol.popup.SimplePopup
-
- switchAtoms() - Method in class org.jmol.smiles.SmilesBond
-
- switchAtoms() - Method in class org.jmol.util.ContactPair
-
- switchCmd(ContextToken, int) - Method in class org.jmol.script.ScriptEvaluator
-
- switchcmd - Static variable in class org.jmol.script.Token
-
- sym - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
-
- sym - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- SYM_EQUIV_XYZ - Static variable in class org.jmol.adapter.readers.cifpdb.CifReader
-
- symbol - Static variable in class org.jmol.script.Token
-
- symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
-
- symmetries - Variable in class org.jmol.adapter.readers.quantum.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 - Static variable in class org.jmol.script.Token
-
- Symmetry - Class in org.jmol.symmetry
-
- Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
-
- symmetry - Variable in class org.jmol.viewer.Viewer
-
- 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.SimplePopup
-
- SymmetryOperation - Class in org.jmol.symmetry
-
- SymmetryOperation() - Constructor for class org.jmol.symmetry.SymmetryOperation
-
- SymmetryOperation(boolean, int) - 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.script.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.script.ScriptEvaluator
-
- sync - Static variable in class org.jmol.script.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_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
-
- SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
-
- SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
-
- SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
-
- SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
-
- syncDisabled - Variable in class org.jmol.viewer.StatusManager
-
- syncDone() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- 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
-
- syncmouse - Static variable in class org.jmol.script.Token
-
- syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
-
- syncScript(String) - Method in class org.jmol.applet.Jmol
-
- syncScript(String) - Method in interface org.jmol.applet.JmolAppletInterface
-
- syncscript - Static variable in class org.jmol.script.Token
-
- syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
-
- syncSend(String, String, int) - Method in class org.jmol.viewer.StatusManager
-
- v - Variable in class org.jmol.console.JmolConsole.FileChecker
-
- v - Variable in class org.jmol.smiles.SmilesSearch
-
- V - Variable in class org.jmol.util.Eigen
-
Array for internal storage of eigenvectors.
- 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
-
- vA - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vAB - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- vAB - Variable in class org.jmol.modelsetbio.Resolver
-
- vAB - Variable in class org.jmol.shape.Mesh
-
- vAB - Variable in class org.jmol.shapespecial.Draw
-
- vAB - Variable in class org.jmol.shapespecial.Polyhedra
-
- vAB - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- vAC - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- vAC - Variable in class org.jmol.modelsetbio.Resolver
-
- vAC - Variable in class org.jmol.shape.Mesh
-
- vAC - Variable in class org.jmol.shapespecial.Draw
-
- vAC - Variable in class org.jmol.shapespecial.Polyhedra
-
- vAC - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- val - Static variable in class org.jmol.script.Token
-
- 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.script.Token
-
- valence - Variable in class org.jmol.smiles.SmilesAtom
-
- validate(boolean) - Method in class org.jmol.bspt.Bspf
-
- validate(int, boolean) - Method in class org.jmol.bspt.Bspf
-
- VALIDATE - Static variable in class org.jmol.geodesic.Geodesic
-
- validateAndAllocate(Chain, String, int, int, int, int[]) - 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) - Static method in class org.jmol.modelsetbio.CarbohydrateMonomer
-
- validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
-
- validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.PhosphorusMonomer
-
- validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
-
- validateBspf(int, boolean) - Method in class org.jmol.modelset.AtomCollection
-
- validateFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
- validatePolyhedronNew(Atom, int, Point3f[]) - Method in class org.jmol.shapespecial.Polyhedra
-
- validSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- 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
-
- vAll - Static variable in class org.jmol.script.ScriptVariable
-
- value - Variable in class org.jmol.atomdata.RadiusData
-
- value - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
-
- value - Variable in class org.jmol.modelset.Measurement
-
- value - Variable in class org.jmol.script.Token
-
- value - Variable in class org.jmol.util.Int2IntHash.Entry
-
- valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
-
- valueCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- valueExtended - Variable in class org.jmol.atomdata.RadiusData
-
- valueFor(float, float, int) - Method in interface org.jmol.api.MepCalculationInterface
-
- valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
-
- 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
-
- valueMin - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- valueOf(String) - Static method in enum org.jmol.atomdata.RadiusData.EnumType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumAnimationMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumAxesMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumCallback
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumHBondType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumPalette
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumQuantumShell
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumStereoMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumStructure
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumVdw
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.viewer.FileManager.Encoding
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.viewer.FileManager.EnumFileStatus
-
Returns the enum constant of this type with the specified name.
- valuePeek() - Method in class org.jmol.script.ScriptCompilationTokenParser
-
- valueRange - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
-
- values() - Static method in enum org.jmol.atomdata.RadiusData.EnumType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values - Variable in class org.jmol.atomdata.RadiusData
-
- values() - Static method in enum org.jmol.constant.EnumAnimationMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumAxesMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumCallback
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumHBondType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumPalette
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumQuantumShell
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumStereoMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumStructure
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumVdw
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values - Variable in class org.jmol.jvxl.readers.IsoFxyReader
-
- values - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
-
- values() - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.util.JmolEdge.EnumBondOrder
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.viewer.FileManager.Encoding
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.viewer.FileManager.EnumFileStatus
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- vanderwaals - Static variable in class org.jmol.script.Token
-
- vanderwaalsMars - Static variable in class org.jmol.util.Elements
-
Default table of van der Waals Radii.
- var - Variable in class org.jmol.script.ScriptFlowContext
-
- var - Static variable in class org.jmol.script.Token
-
- varButton - Variable in class org.openscience.jmol.app.jmolpanel.AppConsole
-
- varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
-
- variable - Static variable in class org.jmol.script.Token
-
- variables - Variable in class org.jmol.script.ScriptFunction
-
- variables - Static variable in class org.jmol.script.Token
-
- varray - Static variable in class org.jmol.script.Token
-
- vaspImplementedAttributes - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
-
- vaspOutcarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
-
- VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
-
http://cms.mpi.univie.ac.at/vasp/
- VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
-
- vB - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vBraces - Variable in class org.jmol.script.ScriptCompiler
-
- vButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- vCompnds - Variable in class org.jmol.adapter.readers.cifpdb.PdbReader
-
- vConnect - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- vContours - Variable in class org.jmol.jvxl.data.JvxlData
-
- vd - Variable in class org.jmol.quantum.QuantumCalculation
-
- vData - Variable in class org.jmol.shapespecial.Draw
-
- vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- vDist - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- vdw1 - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
-
- vdwPercentSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- VdwPROBE - Static variable in class org.jmol.viewer.JmolConstants
-
- vdws - Variable in class org.jmol.util.ContactPair
-
- vdwType - Variable in class org.jmol.atomdata.RadiusData
-
- vdwVolume - Variable in class org.jmol.util.ContactPair
-
- vector() - Method in class org.jmol.script.ScriptEvaluator
-
- vector - Static variable in class org.jmol.script.Token
-
- vector - Variable in class org.jmol.shapespecial.Dipole
-
- VECTOR - Static variable in class org.openscience.jmol.app.jmolpanel.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 - Variable in class org.jmol.jvxl.readers.MapFileReader
-
- Vectors - Class in org.jmol.shapespecial
-
- Vectors() - Constructor for class org.jmol.shapespecial.Vectors
-
- vectorscale - Static variable in class org.jmol.script.Token
-
- vectorScale - Variable in class org.jmol.shapespecial.VectorsRenderer
-
- vectorScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- 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.shape.FontLineShapeRenderer
-
- vectorT - Variable in class org.jmol.viewer.TransformManager
-
- vectorT2 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- vectorT2 - Variable in class org.jmol.viewer.TransformManager
-
- vectorT3 - Variable in class org.jmol.shape.FontLineShapeRenderer
-
- 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
-
- vEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- VERIFY - Static variable in class org.jmol.g3d.Triangle3D
-
- verNumber - Variable in class org.jmol.util.CompoundDocument.CmpDocHeader
-
- version - Variable in class org.jmol.jvxl.data.JvxlData
-
- version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- version - Static variable in class org.jmol.viewer.JmolConstants
-
- VERSION - Static variable in class org.openscience.jvxl.Jvxl
-
- VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
-
- vertexBase - Variable in class org.jmol.jvxl.readers.PmeshReader
-
- vertexColixes - Variable in class org.jmol.util.MeshSurface
-
- vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
-
- vertexColorMap - Variable in class org.jmol.shape.Mesh
-
- vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
-
- vertexCount - Variable in class org.jmol.shape.MeshRenderer
-
- vertexCount - Variable in class org.jmol.util.MeshSurface
-
- vertexCount0 - Variable in class org.jmol.util.MeshSurface
-
- vertexCounts - Static variable in class org.jmol.geodesic.Geodesic
-
- vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
-
- vertexDataOnly - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- VertexDataServer - Interface in org.jmol.jvxl.api
-
- vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
-
- vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- vertexMap - Variable in class org.jmol.jvxl.readers.PmeshReader
-
- vertexNext - Static variable in class org.jmol.geodesic.Geodesic
-
- vertexPoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- vertexSets - Variable in class org.jmol.util.MeshSurface
-
- vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
-
- vertexSource - Variable in class org.jmol.util.MeshSurface
-
- vertexTest - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- vertexValues - Variable in class org.jmol.shapesurface.IsosurfaceRenderer
-
- vertexValues - Variable in class org.jmol.util.MeshSurface
-
- vertexValues - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- vertexVectors - Static variable in class org.jmol.g3d.Normix3D
-
- vertexVectors - Static variable in class org.jmol.geodesic.Geodesic
-
- vertices - Static variable in class org.jmol.script.Token
-
- 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
-
- vertices - Variable in class org.jmol.util.MeshSurface
-
- verticesT - Variable in class org.jmol.shape.UccageRenderer
-
- verticesTransformed - Variable in class org.jmol.shapespecial.DotsRenderer
-
- vF - Static variable in class org.jmol.script.ScriptVariable
-
- vFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- vFunctionStack - Variable in class org.jmol.script.ScriptCompiler
-
- vibEnergy - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- vibFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- vibFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
-
- vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
-
- vibration() - Method in class org.jmol.script.ScriptEvaluator
-
- vibration - Static variable in class org.jmol.script.Token
-
- VIBRATION_VECTOR_FLAG - Static variable in class org.jmol.modelset.Atom
-
- vibrationAmplitude - Variable in class org.jmol.viewer.TransformManager
-
- vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- vibrationOn - Variable in class org.jmol.viewer.TransformManager
-
- VibrationOnly - Variable in class org.jmol.popup.SimplePopup
-
- vibrationperiod - Static variable in class org.jmol.script.Token
-
- 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 - Static variable in class org.jmol.script.Token
-
- vibrationScale - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- vibrationScale - Variable in class org.jmol.viewer.TransformManager
-
- vibrationSteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
-
- vibrationSteps - Variable in class org.jmol.modelset.ModelCollection
-
- vibrationThread - Variable in class org.jmol.viewer.TransformManager
-
- vibrationVectors - Variable in class org.jmol.modelset.AtomCollection
-
- vibx - Static variable in class org.jmol.script.Token
-
- vibxyz - Static variable in class org.jmol.script.Token
-
- viby - Static variable in class org.jmol.script.Token
-
- vibz - Static variable in class org.jmol.script.Token
-
- viewCenterButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
- viewer - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
- viewer - Variable in class org.jmol.applet.Jmol
-
- viewer - Variable in class org.jmol.awt.Mouse
-
- viewer - Variable in class org.jmol.console.JmolConsole
-
- viewer - Variable in class org.jmol.console.ScriptEditor
-
- viewer - Variable in class org.jmol.export.___Exporter
-
- viewer - Variable in class org.jmol.export.dialog.Dialog
-
- viewer - Variable in class org.jmol.export.dialog.FilePreview.FPPanel
-
- viewer - Variable in class org.jmol.export.image.ImageCreator
-
- viewer - Variable in class org.jmol.export.JmolFileDropper
-
- viewer - Variable in class org.jmol.geodesic.EnvelopeCalculation
-
- viewer - Variable in class org.jmol.minimize.Minimizer
-
- viewer - Variable in class org.jmol.modelkit.ModelKit
-
- viewer - Variable in class org.jmol.modelset.AtomCollection
-
- viewer - Variable in class org.jmol.modelset.AtomIteratorWithinModel
-
- viewer - Variable in class org.jmol.modelset.Measurement
-
- viewer - Variable in class org.jmol.modelset.MeasurementData
-
- viewer - Variable in class org.jmol.modelset.ModelLoader
-
- viewer - Variable in class org.jmol.popup.SimplePopup
-
- viewer - Variable in class org.jmol.script.ParallelProcessor
-
- viewer - Variable in class org.jmol.script.ScriptCompilationTokenParser
-
- viewer - Variable in class org.jmol.script.ScriptEvaluator
-
- viewer - Variable in class org.jmol.script.ScriptMathProcessor
-
- 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.ActionManager
-
- viewer - Variable in class org.jmol.viewer.AnimationManager
-
- viewer - Variable in class org.jmol.viewer.ColorManager
-
- viewer - Variable in class org.jmol.viewer.DataManager
-
- viewer - Variable in class org.jmol.viewer.FileManager
-
- viewer - Variable in class org.jmol.viewer.ModelManager
-
- 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.ShapeManager
-
- 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(Object, JmolAdapter, String) - Constructor for class org.jmol.viewer.Viewer
-
- viewer - Variable in class org.openscience.jmol.app.JmolApp
-
- viewer - Variable in class org.openscience.jmol.app.JmolData
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
-
- viewer - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
-
- viewer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
- 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
-
- viewerFrame - Variable in class org.jmol.console.JmolConsole
-
- viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
- viewpoint - Variable in class org.jmol.export.__CartesianExporter
-
- vInputCoords - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
- 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 - Static variable in class org.jmol.script.Token
-
- 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
-
- visualrange - Static variable in class org.jmol.script.Token
-
- visualRange - Variable in class org.jmol.viewer.StateManager.GlobalSettings
-
- visualRange - Variable in class org.jmol.viewer.TransformManager
-
- VK_ALT - Static variable in class org.jmol.api.Event
-
- VK_CONTROL - Static variable in class org.jmol.api.Event
-
- VK_DOWN - Static variable in class org.jmol.api.Event
-
- VK_LEFT - Static variable in class org.jmol.api.Event
-
- VK_PERIOD - Static variable in class org.jmol.api.Event
-
- VK_RIGHT - Static variable in class org.jmol.api.Event
-
- VK_SHIFT - Static variable in class org.jmol.api.Event
-
- VK_SPACE - Static variable in class org.jmol.api.Event
-
- VK_UP - Static variable in class org.jmol.api.Event
-
- vMax - Variable in class org.jmol.jvxl.readers.KinemageReader
-
- vMin - Variable in class org.jmol.jvxl.readers.KinemageReader
-
- vNorm - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- vNorm - Variable in class org.jmol.modelsetbio.Resolver
-
- vNorm1 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vNorm2 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vNorm3 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- volume - Variable in class org.jmol.quantum.QuantumCalculation
-
- volume - Static variable in class org.jmol.script.Token
-
- volume - Variable in class org.jmol.util.ContactPair
-
- volume - Variable in class org.jmol.util.SimpleUnitCell
-
- 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.Parameters
-
- volumeData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
-
- volumeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- volumeData - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
-
- volumeData - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
-
- 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
-
- volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
-
- volumeRender(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
- volumeRender(boolean) - Method in class org.jmol.export.Export3D
-
- volumeRender(int, int, int, int) - Method in class org.jmol.export.Export3D
-
- volumeRender(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- volumeRender - Variable in class org.jmol.shape.MeshRenderer
-
- volumeRenderPointSize - Variable in class org.jmol.shapesurface.IsosurfaceMesh
-
- 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.SurfaceReader
-
- volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
-
- volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
-
- volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
-
- voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- voxelData - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- voxelData - Variable in class org.jmol.jvxl.data.VolumeData
-
- voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
-
- voxelData - Variable in class org.jmol.quantum.QuantumCalculation
-
- VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
-
- VoxelDataCreator(VolumeData) - Constructor for class org.openscience.jvxl.simplewriter.VoxelDataCreator
-
- voxelDataTemp - Variable in class org.jmol.quantum.MOCalculation
-
- voxelIsInTrough(float, float, float, float, float) - Static method in class org.jmol.jvxl.readers.IsoSolventReader
-
- voxelMap - Variable in class org.jmol.jvxl.data.VolumeData
-
- 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
-
- voxelSource - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
- voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
-
- voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
-
- voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
-
- vProcess - Variable in class org.jmol.script.ScriptEvaluator
-
- vpt0 - Variable in class org.jmol.shapespecial.DrawRenderer
-
- vpt1 - Variable in class org.jmol.shapespecial.DrawRenderer
-
- vpt2 - Variable in class org.jmol.shapespecial.DrawRenderer
-
- vPush - Variable in class org.jmol.script.ScriptCompiler
-
- vRef - Static variable in class org.jmol.modelset.AtomCollection
-
- vReturn - Variable in class org.jmol.smiles.SmilesSearch
-
- VsampFactor - Variable in class org.jmol.util.JpegInfo
-
- vStereo - Variable in class org.jmol.modelset.ModelLoader
-
- vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
-
- vT - Static variable in class org.jmol.script.ScriptVariable
-
- vTemp - Variable in class org.jmol.jvxl.readers.IsoMOReader
-
- vTemp - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- vTemp - Variable in class org.jmol.modelset.ModelSet
-
- vTemp - Variable in class org.jmol.shape.Mesh
-
- vTemp - Variable in class org.jmol.shapespecial.DrawRenderer
-
- vTemp - Variable in class org.jmol.smiles.SmilesGenerator
-
- vTemp - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vTemp - Variable in class org.jmol.symmetry.PointGroup
-
- vTemp - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
-
- vTemp1 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- vTemp2 - Variable in class org.jmol.shapespecial.DrawRenderer
-
- vTemp2 - Variable in class org.jmol.smiles.SmilesSearch.VTemp
-
- vTemp3 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
-
- vX - Variable in class org.jmol.shapesurface.Contact
-
- vY - Variable in class org.jmol.shapesurface.Contact
-
- vZ - Variable in class org.jmol.shapesurface.Contact
-