Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
$
A
- a - Variable in class javajs.util.Matrix
- a - Variable in class org.jmol.g3d.PrecisionRenderer
- a - Variable in class org.jmol.util.SimpleUnitCell
- a_ - Variable in class org.jmol.util.SimpleUnitCell
- A4 - Class in javajs.util
-
A 4 element axis angle represented by single precision floating point x,y,z,angle components.
- A4() - Constructor for class javajs.util.A4
-
Constructs and initializes a AxisAngle4f to (0,0,1,0).
- aaTest1 - Variable in class org.jmol.viewer.TransformManager
- aatoken - Variable in class org.jmol.script.ScriptEval
- AB - Enum constant in enum class jspecview.common.PanelData.LinkMode
- ABC - Enum constant in enum class jspecview.common.PanelData.LinkMode
- abcFor(M4) - Method in class org.jmol.symmetry.CLEG.ClegData
- abFace - Static variable in class org.jmol.util.Triangulator
- ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
- ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
- AbinitReader - Class in org.jmol.adapter.readers.xtal
- AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
- aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
- AboutDialog - Class in jspecview.application
-
The
About Dialogclass is the help | about window for JSpecView. - AboutDialog - Class in org.openscience.jmol.app.jmolpanel
- AboutDialog(Frame) - Constructor for class jspecview.application.AboutDialog
-
Constructor that initalises the Dialog a parent frame, no title and modality to true
- AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
- abs - Static variable in class org.jmol.script.T
- absolute - Static variable in class org.jmol.script.T
- ABSOLUTE - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
- AbstractButton - Class in org.jmol.awtjs.swing
- AbstractButton(String) - Constructor for class org.jmol.awtjs.swing.AbstractButton
- AbstractTableModel - Interface in org.jmol.awtjs.swing
- ac - Variable in class org.jmol.adapter.readers.cif.CifReader
- ac - Variable in class org.jmol.adapter.readers.simple.InputReader
- ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- ac - Variable in class org.jmol.atomdata.AtomData
- ac - Variable in class org.jmol.jvxl.readers.JvxlReader
- ac - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- ac - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- ac - Variable in class org.jmol.modelset.AtomCollection
- ac - Variable in class org.jmol.util.JmolMolecule
- accept(File) - Method in class jspecview.java.AwtDialogFileFilter
-
Implementation of method from interface
FileFilter. - accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
- accept(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- ACCEPTOR - Enum constant in enum class org.jmol.c.HB
- acm - Variable in class org.jmol.viewer.Viewer
- acos - Static variable in class org.jmol.script.T
- act - Variable in class org.jmol.modelset.Model
-
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- action(String) - Method in interface org.jmol.api.JmolAudioPlayer
- action(String) - Method in class org.jmol.util.JmolAudio
-
Execute an action from load audio "xxxxx.wav" filter "id=a1 action=xxx"
- 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
- ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
- actionCommand - Variable in class org.jmol.awtjs.swing.JComponent
- actionListener - Variable in class org.jmol.awtjs.swing.JComponent
- actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- ActionManager - Class in org.jmol.viewer
- ActionManager() - Constructor for class org.jmol.viewer.ActionManager
- ActionManagerMT - Class in org.jmol.multitouch
- ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
- actionPerformed(ActionEvent) - Method in class jspecview.application.PreferencesDialog
-
Sets the color of the selected element on the current color button
- actionPerformed(ActionEvent) - Method in class jspecview.java.AwtDialogManager
-
ActionListener callback
- actionPerformed(ActionEvent) - Method in class org.jmol.awt.AwtPopupHelper
- actionPerformed(ActionEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ImageDialog
- actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- 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.CreditsAction
- 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.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.TwoDEditorAction
- 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.webexport.Test
- actionPerformed(String) - Method in class jspecview.js2d.JsDialogManager
-
Jmol.Swing.click() callback (via SwingController)
- actionRotateBond(int, int, int, int, boolean) - Method in class org.jmol.modelkit.ModelKit
-
Actually rotate the bond.
- activate() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- activate() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- activateQuery() - Method in class jme.JME
- active_selections - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- add - Static variable in class org.jmol.script.T
- add(float) - Method in class javajs.util.Quat
- add(int, V) - Method in class javajs.util.Lst
- add(String) - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- add(Map<String, Object>, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
- add(M3) - Method in class javajs.util.M3
-
Sets the value of this matrix to sum of itself and matrix m1.
- add(Matrix) - Method in class javajs.util.Matrix
-
add two matrices
- add(T3) - Method in class javajs.util.M4
-
add to translation
- add(T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the vector sum of itself and tuple t1.
- add(T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the vector sum of itself and tuple t1.
- add(T3i) - Method in class javajs.util.T3i
-
Sets the value of this tuple to the sum of itself and t1.
- add(SC) - Method in interface org.jmol.api.SC
- add(SC) - Method in class org.jmol.awt.AwtSwingComponent
- add(SC) - Method in class org.jmol.awtjs.swing.AbstractButton
- add(SC) - Method in class org.jmol.awtjs.swing.ButtonGroup
- add(Component) - Method in class org.jmol.awtjs.swing.Container
- add(JComponent, Object) - Method in class org.jmol.awtjs.swing.JPanel
- add(JComponent, GridBagConstraints) - Method in class org.jmol.awtjs.swing.Grid
- add(V) - Method in class javajs.util.Lst
-
Deprecated.
- ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
- add2(T3d, T3d) - Method in class javajs.util.T3d
-
Sets the value of this tuple to the vector sum of tuples t1 and t2.
- add2(T3, T3) - Method in class javajs.util.T3
-
Sets the value of this tuple to the vector sum of tuples t1 and t2.
- add3(float, float, float) - Method in class javajs.util.T3
-
Add {a b c}
- add33(M34) - Method in class javajs.util.M34
- addActionListener(Object) - Method in interface org.jmol.api.SC
- addActionListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addActionListener(Object) - Method in class org.jmol.awtjs.swing.JComponent
-
Note that it will be the job of the JavaScript on the page to do with actionListener what is desired.
- addActions(List<Action>) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- addAlpha(int) - Method in interface javajs.api.GenericColor
- addAlpha(int) - Method in class jspecview.java.AwtColor
- addAlpha(int) - Method in class org.jmol.awt.AwtColor
- addAlpha(int) - Method in class org.jmol.awtjs.swing.Color
- addAnnotation(Lst<String>) - Method in class jspecview.common.PanelData
- addApplyBtn - Variable in class jspecview.dialog.JSVDialog
- addAssembly(String[]) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addAtom(double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
-
add a proton to the atom list
- addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst<Object>, boolean, boolean, byte, BS, float) - Method in class org.jmol.modelset.ModelSet
- addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtoms(int) - Method in class org.jmol.modelset.Group
- addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
- addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
turns this into a SPHERICAL iterator for "within Distance" measures
- addAtoms(BS) - Method in class org.jmol.symmetry.UnitCellIterator
- addAtomSet(String) - Method in class org.jmol.modelkit.ModelKit
- addAtomstoMatrix() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Generate noeMatrix and map fields for DistanceJMolecule.
- addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addAttribute(SB, String, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- addAttributes(SB, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
- addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
- addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
- addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
- addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
- addBondNoCheck(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addBonds - Variable in class org.jmol.adapter.writers.CMLWriter
- addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
- addButton(String, String) - Method in interface jspecview.api.PlatformDialog
- addButton(String, String) - Method in class jspecview.java.AwtDialog
- addButton(String, String) - Method in class jspecview.js2d.JsDialog
- addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
- addBytes(byte[], int, int) - Method in class javajs.util.ZipData
- addCheckBox(String, String, int, boolean) - Method in interface jspecview.api.PlatformDialog
- addCheckBox(String, String, int, boolean) - Method in class jspecview.java.AwtDialog
- addCheckBox(String, String, int, boolean) - Method in class jspecview.js2d.JsDialog
- addCifAtom(Atom, String, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- addCoef(Map<String, Object>, float[], String, float, float, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- addColix(int) - Method in class org.jmol.shapecgo.CGOMesh
- addCommand(int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- 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
- addComponent(Component) - Method in class org.jmol.awtjs.swing.Container
- addConnectedHAtoms(Atom, BS) - Method in class org.jmol.modelset.BondCollection
- addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
- addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
- addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
- addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
- addContourPoints(Lst<Object>, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- addCouple(int, int, int, int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- addData(MOCalculation, boolean) - Method in interface org.jmol.quantum.mo.DataAdder
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder11H
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder13I
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder7F
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder9G
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderF
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderG
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderH
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderI
- addDialog(int, Annotation.AType, AnnotationData) - Method in class jspecview.common.PanelData
- addDisplayedBackbone(Atom, boolean) - Method in class org.jmol.shapebio.Backbone
- addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addEquiv(double[], double[], double[]) - Method in class org.jmol.quantum.NMRNoeMatrix
- addExplicitLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addExtension(String) - Method in class jspecview.java.AwtDialogFileFilter
-
Adds an extension to the JSpecViewFileFilter
- addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
- addFunction(ScriptFunction) - Method in class org.jmol.script.ScriptEval
- addGroup(Group, int) - Method in class org.jmol.modelset.Chain
- addHallOperationCheckDuplicates(M4) - Method in interface org.jmol.symmetry.HallInfo.HallReceiver
-
Add a (possibly) new operation, checking for duplicates.
- addHallOperationCheckDuplicates(M4) - Method in class org.jmol.symmetry.SpaceGroup
- addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
- addHeader() - Method in class org.jmol.adapter.readers.cif.CifReader
- addHeader() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- addHeader(String, String) - Method in class jspecview.source.JDXHeader.DataLDRTable
- addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addHetero(String, String, String, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addHighlight(double, double, int, int, int, int) - Method in interface jspecview.api.JSVAppletInterface
-
Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a
JSVPanel - addHighlight(double, double, int, int, int, int) - Method in class jspecview.app.JSVApp
-
Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a
JSVPanel - addHighlight(double, double, int, int, int, int) - Method in class jspecview.appletjs.JSVApplet
- addHighlight(GraphSet, double, double, Spectrum, int, int, int, int) - Method in class jspecview.common.PanelData
-
Add information about a region of the displayed spectrum to be highlighted applet only right now
- addHistoryWindowDimInfo(String, Component, Dimension) - Method in interface org.jmol.api.JmolAppAPI
- addHistoryWindowDimInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.JmolApp
- addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
- addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
- addHydrogenBond(Lst<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
- addhydrogens - Static variable in class org.jmol.script.T
- addHydrogens(BS, int) - Method in class org.jmol.viewer.Viewer
- addHydrogens(Lst<Atom>, P3[]) - 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
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in interface org.jmol.api.JmolScriptManager
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.script.ScriptManager
-
Add hydrogens to a model
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- addImageResource(Object, int, int, int[], boolean) - Method in class javajs.export.PDFCreator
- addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.BioResolver
-
Get bonding info for double bonds and add implicit hydrogen atoms, if needed.
- addInfo(Map<String, String>) - Method in class javajs.export.PDFCreator
- addIntegralRegion(double, double) - Method in class jspecview.common.IntegralData
- addInversion() - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- addItemListener(Object) - Method in interface org.jmol.api.SC
- addItemListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addItemListener(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
- addItems(String[][]) - Method in class org.jmol.popup.PopupResource
- addJDXSpectrum(String, Spectrum, boolean) - Method in class jspecview.source.JDXSource
-
Adds a Spectrum to the list
- addJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- addJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Add using Jmol atom index
- addJmolProperties(Properties) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addJmolWindowInfo(String, Component, Point) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Deprecated.
- addJmolWindowInnerInfo(String, Component, Dimension) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addLast(V) - Method in class javajs.util.Lst
- addLatticeVector(Lst<float[]>, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addLatticeVector(Lst<float[]>, String) - Method in interface org.jmol.adapter.smarter.MSInterface
- addListener(PanelListener) - Method in class jspecview.common.PanelData
- addListSelectionListener(Object) - Method in class org.jmol.awtjs.swing.JTable
-
It will be the function of the JavaScript on the page to do with selectionListener what is desired.
- addListSelectionListener(Object) - Method in interface org.jmol.awtjs.swing.ListSelectionModel
- addLockedAtoms(SymmetryInterface, BS) - Method in class org.jmol.modelkit.ModelKit
-
Only for the current model
- addMacrosMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addMagLatticeVectors(Lst<float[]>) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- addMagLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.SpaceGroup
- addMarks(String) - Method in class jspecview.common.IntegralData
-
INTEGRATION MARK list where list is a comma-separated list of ppm1-ppm2 with :x.x added to normalize one of them and starting with 0-0 clears the integration
- addMatrix(String, M4, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtJmolPopup
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtModelKitPopup
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.popup.GenericPopup
- addMenuItem(JMenu, String, char, ActionListener) - Static method in class jspecview.application.ApplicationMenu
- addMenuItem(SC, String) - Method in class org.jmol.popup.GenericPopup
- addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericPopup
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
- addMethyl(double, double, double, double, double, double, double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
-
Add a methyl group to the atom list
- addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- addMOData(int, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
- addModulation(Map<String, double[]>, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
- addModulation(Map<String, double[]>, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
- addMol() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- addMol() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
- addMolFile(String, int, SB, BS, BS, boolean, boolean, boolean, Quat, boolean) - Method in class org.jmol.adapter.writers.MOLWriter
- addMoreUnitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addMouseListener(Object) - Method in interface org.jmol.api.SC
- addMouseListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addMouseListener(Object) - Method in class org.jmol.awtjs.swing.Component
- addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNOE(int, int, String, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addNormix(int) - Method in class org.jmol.shapecgo.CGOMesh
- addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
-
addOp The primary driver of the Reverse Polish Notation evaluation engine.
- addOp(SymmetryOperation, String, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addOperation(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addPeakData(String) - Method in class jspecview.source.JDXReader
- addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
- addPeakHighlight(PeakInfo) - Method in class jspecview.common.PanelData
- addPluginMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
- addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
- addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
- addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
- addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
- addPopulation(double[]) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- addPrimitiveTransform(String, String) - Method in class org.jmol.symmetry.CLEG.ClegData
- addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
- addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
- addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the given properties to the history.
- addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the given property to the history.
- addPropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
- addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
- addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
- addRenderer(int) - Method in class org.jmol.export.Export3D
- addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
-
allows core JavaScript loading to not involve these classes
- addRenderer(int) - Method in class org.jmol.util.GData
- 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
- addRotatedTensor(Atom, Tensor, int, boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
- addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
- addSelectOption(String, String, String[], int, boolean) - Method in interface jspecview.api.PlatformDialog
- addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.java.AwtDialog
- addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.js2d.JsDialog
- addSGTransform(String, String) - Method in class org.jmol.symmetry.CLEG.ClegData
- 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, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
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(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
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.AdfReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AmsReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.DgridReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.CsfReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
See MopacSlaterReader
- addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
- addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
- addSpecShift(double) - Method in class jspecview.common.Measurement
- addSpecShift(double) - Method in class jspecview.common.Spectrum
- addSpinLattice(Lst<String>, Map<String, String>) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- addSpinLattice(Lst<String>, Map<String, String>) - Method in class org.jmol.symmetry.SpaceGroup
-
spin space groups only
- addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addStructure(STR, String, String, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructureProtected(STR, String, String, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructureSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
We must add groups to the proper bsStructure element
- addSubSpectrum(Spectrum, boolean) - Method in class jspecview.common.Spectrum
-
adds an nD subspectrum and titles it "Subspectrum
" These spectra can be iterated over using the UP and DOWN keys. - addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
- addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
- addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
- addTextField(String, String, String, String, String, boolean) - Method in interface jspecview.api.PlatformDialog
- addTextField(String, String, String, String, String, boolean) - Method in class jspecview.java.AwtDialog
- addTextField(String, String, String, String, String, boolean) - Method in class jspecview.js2d.JsDialog
- addTo(GenericZipTools, SB) - Method in class javajs.util.ZipData
- addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
- addTo(T3, float) - Method in class org.jmol.util.ModulationSet
- addToken(String, T) - Static method in class org.jmol.script.T
- addToList(int, Lst<Spectrum>) - Method in class jspecview.common.PanelData
- addTracePt(int, Point3fi) - Method in class org.jmol.util.Vibration
- addTransform(int, String) - Method in class org.jmol.symmetry.CLEG.ClegData
- addTransformLink() - Method in class org.jmol.symmetry.CLEG.ClegData
- addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
- addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
- 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.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, P3) - Method in class org.jmol.bspt.Bspf
- addTuple(T3) - Method in class org.jmol.bspt.Bspt
-
Iterate through all of your data points, calling addTuple
- addUniqueControls() - Method in class jspecview.dialog.IntegrationDialog
- addUniqueControls() - Method in class jspecview.dialog.JSVDialog
- addUniqueControls() - Method in class jspecview.dialog.MeasurementsDialog
- addUniqueControls() - Method in class jspecview.dialog.OverlayLegendDialog
- addUniqueControls() - Method in class jspecview.dialog.PeakListDialog
- addUniqueControls() - Method in class jspecview.dialog.ViewsDialog
- addUniqueControls(DialogManager) - Method in class jspecview.dialog.JSVDialog
- addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
- addUTens(String, float) - Method in class org.jmol.util.ModulationSet
- addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
- addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
- addVectors(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addVertexCopy(T3, float, int, boolean) - 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(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
- addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window informations to the history.
- addWindowInfo(String, Component, Point, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowInnerInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowListener() - Method in class org.jmol.console.JmolConsole
- addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
- addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
- addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
- addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
- addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
- addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
- addXList(Lst<?>) - Method in class org.jmol.script.ScriptMathProcessor
- addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
- addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
- addXMap(Map<String, ?>) - Method in class org.jmol.script.ScriptMathProcessor
- addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
- addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
- addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
- addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
- addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
- addZipEntry(Object, String) - Method in interface javajs.api.GenericZipTools
- addZipEntry(Object, String) - Method in class javajs.util.ZipTools
- 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
- adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
- adjustForWindow - Variable in class org.jmol.modelset.Text
- adjustRangeMinMax(T3[], float, P3i, P3i, P3, P3, P3i, P3i) - Method in interface org.jmol.api.SymmetryInterface
- adjustRangeMinMax(T3[], float, P3i, P3i, P3, P3, P3i, P3i) - Method in class org.jmol.symmetry.Symmetry
- adjustRangeMinMax(T3[], float, P3i, P3i, P3, P3, P3i, P3i) - Method in class org.jmol.symmetry.UnitCell
- adjustStrut(P3[], int, int, int) - Method in class org.jmol.renderbio.RocketsRenderer
- adpmax - Static variable in class org.jmol.script.T
- ADPMAX - Enum constant in enum class org.jmol.c.VDW
- adpmin - Static variable in class org.jmol.script.T
- ADPMIN - Enum constant in enum class org.jmol.c.VDW
- adpMode - Variable in class org.jmol.atomdata.AtomData
- advanceSpectrumBy(int) - Method in class jspecview.common.JSViewer
- advanceSubSpectrum(int) - Method in class jspecview.common.PanelData
- advanceSubSpectrum(int) - Method in class jspecview.common.Spectrum
- AFLOWReader - Class in org.jmol.adapter.readers.more
-
A reader for various AFLOW file types.
- AFLOWReader() - Constructor for class org.jmol.adapter.readers.more.AFLOWReader
- afterClear - Variable in class jme.JME
- 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
- AjaxURLConnection - Class in javajs.util
-
A method to allow a JavaScript Ajax
- AjaxURLConnection(URL) - Constructor for class javajs.util.AjaxURLConnection
- AjaxURLStreamHandler - Class in javajs.util
-
A method to allow a JavaScript AJAX adapter to deliver web content to JSmol.
- AjaxURLStreamHandler(String) - Constructor for class javajs.util.AjaxURLStreamHandler
- AjaxURLStreamHandlerFactory - Class in javajs.util
-
For handling URL file IO via AJAX in JavaScript version
- AjaxURLStreamHandlerFactory() - Constructor for class javajs.util.AjaxURLStreamHandlerFactory
- AlchemyReader - Class in org.jmol.adapter.readers.simple
-
TRIPOS simple Alchemy reader.
- AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
- alert(String) - Method in class org.jmol.viewer.Viewer
- align - Variable in class org.jmol.modelset.Text
- align - Static variable in class org.jmol.script.T
- ALIGN_CENTER - Static variable in class jme.JMEUtil
- ALIGN_LEFT - Static variable in class jme.JMEUtil
- ALIGN_RIGHT - Static variable in class jme.JMEUtil
- alignment - Variable in class jme.AtomDisplayLabel
- alignment_as_cylinders - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- all - Static variable in class org.jmol.script.T
- ALL - Enum constant in enum class jspecview.common.PanelData.LinkMode
- ALL - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
- ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- all_states - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- allconnected - Static variable in class org.jmol.script.T
- allEmptyString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- ALLENE - Static variable in class org.jmol.smiles.SmilesStereo
- allfloat - Static variable in class org.jmol.script.T
- allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- allHs - Variable in class jme.JME
- allNaN() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allNull() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allocateColix(int, boolean) - Static method in class org.jmol.util.C
- allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
- allocateExpCouples(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- allocateExpNoes(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.java.AwtPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.js2d.JsPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in interface org.jmol.api.GenericPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
-
Create an "image" that is either a canvas with width/height/buf32 (from g3d.Platform32) or just an associative array with those (image writing
- allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
-
a simpler option
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
-
legacy only
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
-
This is the older main access point for creating an application or applet vwr.
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
-
old way...
- 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.shapecgo.CGO
- allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
- allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
- 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
- allow_a_len_1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- allow300 - Static variable in class org.jmol.symmetry.CLEG
-
allows 300, 400, 500, 600 instead of p/ l/ r/ f/ could be turned on; this is for Jmol testing
- allowAromaticBond(Bond) - Method in class org.jmol.modelset.BondCollection
- allowaudio - Static variable in class org.jmol.script.T
- allowCapture() - Method in class org.jmol.viewer.Viewer
- allowDashed - Variable in class org.jmol.render.MeshRenderer
- allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
- allowembeddedscripts - Static variable in class org.jmol.script.T
- allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
- allowgestures - Static variable in class org.jmol.script.T
- allowJavaConsole - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- allowkeystrokes - Static variable in class org.jmol.script.T
- allowMenu - Variable in class jspecview.common.JSViewer
- allowmodelkit - Static variable in class org.jmol.script.T
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
- allowmoveatoms - Static variable in class org.jmol.script.T
- allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- allowmultitouch - Static variable in class org.jmol.script.T
- allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
- allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allowrotateselected - Static variable in class org.jmol.script.T
- allowSameName - Static variable in class org.jmol.jsv.JDXMOLParser
- allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
- allowSignedFeatures - Variable in class org.jmol.popup.GenericPopup
- allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
- allowSubSpec(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
- allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
- allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
- allSame() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allTrajectories - Variable in class org.jmol.adapter.writers.CMLWriter
- allZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- alpha - Variable in class org.jmol.util.SimpleUnitCell
- ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
- ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
- ALPHA_SHIFT - Static variable in class org.jmol.util.C
- ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
- alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- AlphaMonomer - Class in org.jmol.modelsetbio
- AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
- AlphaPolymer - Class in org.jmol.modelsetbio
- ALT - Static variable in class org.jmol.util.ColorEncoder
- ALT - Static variable in class org.jmol.viewer.binding.Binding
- ALT_MASK - Static variable in class org.jmol.awtjs.Event
- altArgbsCpk - Static variable in class org.jmol.viewer.JC
- 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
- altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
- altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
- altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
- altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
- altloc - Variable in class org.jmol.modelset.Atom
- altloc - Static variable in class org.jmol.script.T
- altLoc - Variable in class org.jmol.adapter.smarter.Atom
- ALTLOC - Enum constant in enum class org.jmol.c.PAL
- altLocCount - Variable in class org.jmol.modelset.Model
- altType - Variable in class org.jmol.util.Tensor
- altVertices - Variable in class org.jmol.util.MeshSurface
- am - Variable in class org.jmol.modelset.ModelSet
- am - Variable in class org.jmol.viewer.Viewer
- ambient - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- ambient_occlusion_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- ambient_occlusion_scale - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- ambient_occlusion_smooth - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- ambientocclusion - Static variable in class org.jmol.script.T
- ambientOcclusion - Variable in class org.jmol.util.GData
- ambientpercent - Static variable in class org.jmol.script.T
- amino - Static variable in class org.jmol.script.T
- AMINO - Enum constant in enum class org.jmol.c.PAL
- AMINO - Static variable in class org.jmol.util.ColorEncoder
- AminoMonomer - Class in org.jmol.modelsetbio
- AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
- AminoPolymer - Class in org.jmol.modelsetbio
- AML - Enum constant in enum class jspecview.common.ExportType
- AMLExporter - Class in jspecview.export
-
class
AnIMLExportercontains static methods to export a Graph as as AnIML. - AMLExporter() - Constructor for class jspecview.export.AMLExporter
- AmpacReader - Class in org.jmol.adapter.readers.simple
-
A reader for AMPAC output.
- AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
- AmsReader - Class in org.jmol.adapter.readers.quantum
-
A reader for AMS output subclassing the older AdfReader.
- AmsReader() - Constructor for class org.jmol.adapter.readers.quantum.AmsReader
- anaglyph_mode - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- anchor - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- and(BS) - Method in class javajs.util.BS
-
Performs a logical AND of this target bit set with the argument bit set.
- andequals - Static variable in class org.jmol.script.T
- andNot(BS) - Method in class javajs.util.BS
-
Clears all of the bits in this
BitSetwhose corresponding bit is set in the specifiedBitSet. - andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
- angle - Variable in class javajs.util.A4
-
The angle.
- angle - Static variable in class org.jmol.script.T
- angle(V3) - Method in class javajs.util.V3
-
Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
- angle(V3d) - Method in class javajs.util.V3d
- angle_color - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- angle_label_position - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- angle_size - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- angstroms - Static variable in class org.jmol.script.T
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
- animation - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- animation - Static variable in class org.jmol.script.T
- animation_duration - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- animationfps - Static variable in class org.jmol.script.T
- animationFps - Variable in class org.jmol.viewer.AnimationManager
- AnimationManager - Class in org.jmol.viewer
- animationmode - Static variable in class org.jmol.script.T
- animationOn - Variable in class org.jmol.viewer.AnimationManager
- animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
- animationThread - Variable in class org.jmol.viewer.AnimationManager
- AnimationThread - Class in org.jmol.thread
- AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
- AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- ANIMFRAME - Enum constant in enum class org.jmol.c.CBK
- AnIMLReader - Class in jspecview.source
-
Representation of a XML Source.
- AnIMLReader() - Constructor for class jspecview.source.AnIMLReader
- anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
- anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
- anisotropy - Static variable in class org.jmol.script.T
- anisotropy() - Method in class org.jmol.util.Tensor
-
anisotropy = directed distance from (center of two closest) to (the furthest)
- Annotation - Class in jspecview.common
-
The
Annotationclass stores the spectral x and pixel y values of an annotation text along with its text - Annotation - Class in org.jmol.modelsetbio
- Annotation() - Constructor for class jspecview.common.Annotation
- Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
- ANNOTATION - Enum constant in enum class org.jmol.c.STR
- Annotation.AType - Enum Class in jspecview.common
- AnnotationData - Interface in jspecview.api
- AnnotationParser - Class in org.jmol.dssx
-
A parser for output from 3DNA web service.
- AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
- antialias - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- antialias - Variable in class org.jmol.render.MeshRenderer
- antialias - Variable in class org.jmol.viewer.TransformManager
- antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- antialiasdisplay - Static variable in class org.jmol.script.T
- antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
- antialiased - Variable in class org.jmol.viewer.Viewer
- antialiasEnabled - Variable in class org.jmol.util.GData
- antialiasimages - Static variable in class org.jmol.script.T
- antialiasThisFrame - Variable in class org.jmol.util.GData
- antialiastranslucent - Static variable in class org.jmol.script.T
- aperatureAngle - Variable in class org.jmol.viewer.TransformManager
- apertureAngle - Variable in class org.jmol.export.___Exporter
- apiPlatform - Variable in class jspecview.common.JSViewer
- apiPlatform - Variable in class org.jmol.api.JmolViewer
- apiPlatform - Variable in class org.jmol.util.GData
- apivot - Static variable in class org.jmol.script.T
- apointx - Variable in class jme.JME
- apointy - Variable in class jme.JME
- apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
- app - Variable in class jspecview.appletjs.JSVApplet
- appCheckItem(String, SC) - Method in class jspecview.popup.JSVGenericPopup
- appCheckItem(String, SC) - Method in class org.jmol.popup.GenericPopup
-
Opportunity to do something special with an item.
- appCheckItem(String, SC) - Method in class org.jmol.popup.JmolPopup
- appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericPopup
-
Opportunity to do something special with a given submenu is created
- appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolPopup
- AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
- appConsole - Variable in class org.jmol.viewer.Viewer
- AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
- AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
- AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
-
general entry point
- append - Static variable in class org.jmol.script.T
- append(String) - Method in class javajs.util.OC
-
will go to string buffer if bw == null and os == null
- append(String) - Method in class javajs.util.SB
- append(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
- append(String) - Method in interface org.jmol.console.GenericTextArea
- append(String) - Method in class org.jmol.util.JSONWriter
- append3(SB, T3) - Method in class org.jmol.adapter.writers.CIFWriter
- appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Appends an AtomSetCollection
- appendAttrib(SB, Object, Object) - Static method in class javajs.util.XmlUtil
- appendB(boolean) - Method in class javajs.util.SB
- appendC(char) - Method in class javajs.util.SB
- appendCB(char[], int, int) - Method in class javajs.util.SB
- appendCdata(SB, String, Object[], String) - Static method in class javajs.util.XmlUtil
-
" will convert ]]> to ]] > - appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
- appendContourTriangleIntersection(int, float, float, SB) - 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.
- appendD(double) - Method in class javajs.util.SB
- appendEmptyTag(SB, String, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
- appendF(float) - Method in class javajs.util.SB
-
note that JavaScript could drop off the ".0" in "1.0"
- appendField(SB, String, int) - Static method in class org.jmol.adapter.writers.CIFWriter
- appendFontCmd(SB) - Method in class org.jmol.modelset.Text
- appendI(int) - Method in class javajs.util.SB
- appendKey(SB, String, int) - Method in class org.jmol.adapter.writers.CIFWriter
- appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appendnew - Static variable in class org.jmol.script.T
- appendNew - Variable in class org.jmol.viewer.GlobalSettings
- appendO(Object) - Method in class javajs.util.SB
- appendSB(SB) - Method in class javajs.util.SB
- appendTag(SB, String, Object) - Static method in class javajs.util.XmlUtil
-
standard
data " standard" - appendTagAll(SB, String, Object[], Object, boolean, boolean) - Static method in class javajs.util.XmlUtil
- appendTagObj(SB, String, Object[], Object) - Static method in class javajs.util.XmlUtil
-
standard
data " - appFixLabel(String) - Method in class jspecview.popup.JSVGenericPopup
- appFixLabel(String) - Method in class org.jmol.popup.GenericPopup
- appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
- appGetBooleanProperty(String) - Method in class jspecview.popup.JSVGenericPopup
- appGetBooleanProperty(String) - Method in class org.jmol.modelkit.ModelKitPopup
- appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericPopup
- appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
- appGetMenuAsString(String) - Method in class jspecview.popup.JSVGenericPopup
- appGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
- appGetMenuAsString(String) - Method in class org.jmol.popup.JmolPopup
- appletCodeBase - Static variable in class org.jmol.viewer.Viewer
- AppletConsole - Class in org.jmol.console
- AppletConsole - Class in org.jmol.consolejs
-
An interface to Jmol.Console.
- AppletConsole() - Constructor for class org.jmol.console.AppletConsole
- AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
- appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- appletDocumentBase - Static variable in class jspecview.common.JSVFileManager
- appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
- appletFrame - Variable in class jspecview.app.JSVApp
- AppletFrame - Interface in jspecview.api
- APPLETID - Enum constant in enum class jspecview.common.ScriptToken
- appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
- appletName - Variable in class jspecview.common.JSViewer
- appletName - Variable in class org.jmol.viewer.Viewer
- appletObject - Variable in class org.jmol.util.GenericApplet
- appletproxy - Static variable in class org.jmol.script.T
- APPLETREADY - Enum constant in enum class org.jmol.c.CBK
- appletReadyCallbackFunctionName - Variable in class jspecview.app.JSVApp
- APPLETREADYCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
- application - Variable in class jme.JME
- ApplicationMenu - Class in jspecview.application
-
The Main Class or Entry point of the JSpecView Application.
- ApplicationMenu(MainFrame) - Constructor for class jspecview.application.ApplicationMenu
- apply(Object[]) - Method in class jspecview.dialog.JSVDialog
- applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
- applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
- applyFromFields() - Method in class jspecview.dialog.IntegrationDialog
- applyFromFields() - Method in class jspecview.dialog.JSVDialog
- applyFromFields() - Method in class jspecview.dialog.ViewsDialog
- applyFunc(Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
- applyLeftMouse(int) - Static method in class jspecview.app.GenericMouse
- applyScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
-
Apply the scale factor to the coordinates
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- applySymmetryBio(Map<String, Object>, boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- applysymmetrytobonds - Static variable in class org.jmol.script.T
- applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appRestorePopupMenu() - Method in class jspecview.popup.JSVGenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.GenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.JmolPopup
- approx(float, float) - Static method in class javajs.util.PT
- approx0(float) - Static method in class org.jmol.util.SimpleUnitCell
- appRunScript(String) - Method in class jspecview.popup.JSVGenericPopup
- appRunScript(String) - Method in class org.jmol.popup.GenericPopup
- appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
- AppToolBar - Class in jspecview.application
- AppToolBar(MainFrame) - Constructor for class jspecview.application.AppToolBar
- appUpdateForShow() - Method in class jspecview.popup.JSVGenericPopup
- appUpdateForShow() - Method in class org.jmol.modelkit.ModelKitPopup
- appUpdateForShow() - Method in class org.jmol.popup.GenericPopup
- appUpdateForShow() - Method in class org.jmol.popup.JmolPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
-
Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
-
(1) setOption --> set setOption true or set setOption false
- arc - Static variable in class org.jmol.script.T
- ARC - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- area - Static variable in class org.jmol.script.T
- areAxesTainted() - Method in class org.jmol.viewer.Viewer
- areEqual(Object, Object) - Method in interface org.jmol.api.SmilesMatcherInterface
- areEqual(Object, Object) - Method in class org.jmol.smiles.SmilesMatcher
- areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
- areEqual(SV, SV) - Static method in class org.jmol.script.SV
-
For legacy reasons, "x" == "X" but see isLike()
- areEqualTest(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
-
for JUnit test, mainly
- areLinkableX(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
- areLinkableY(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
- areXScalesCompatible(Spectrum, Spectrum, boolean, boolean) - Static method in class jspecview.common.Spectrum
- areYScalesSame(int, int) - Method in class jspecview.common.ViewData
- argb - Variable in class org.jmol.awtjs.swing.Color
- argbCurrent - Variable in class org.jmol.util.GData
- argbNoisyDn - Variable in class org.jmol.util.GData
- argbNoisyUp - Variable in class org.jmol.util.GData
- argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
- argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
- argbsCpk - Static variable in enum class org.jmol.c.PAL
-
Default table of CPK atom colors.
- argbsCpkRasmol - Static variable in enum class org.jmol.c.PAL
- argbsFormalCharge - Static variable in class org.jmol.viewer.JC
- argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
- argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
- argbsRoygbScale - Static variable in class org.jmol.viewer.JC
- argbsRwbScale - Static variable in class org.jmol.viewer.JC
- aromatic - Static variable in class org.jmol.script.T
- array - Static variable in class org.jmol.script.T
- arrayAdd(Object) - Method in class org.jmol.util.JSONWriter
- arrayClose(boolean) - Method in class org.jmol.util.JSONWriter
- arrayCopyBool(boolean[], int) - Static method in class javajs.util.AU
- arrayCopyByte(byte[], int) - Static method in class javajs.util.AU
- arrayCopyF(float[], int) - Static method in class javajs.util.AU
- arrayCopyI(int[], int) - Static method in class javajs.util.AU
- arrayCopyII(int[][], int) - Static method in class javajs.util.AU
- arrayCopyObject(Object, int) - Static method in class javajs.util.AU
-
note -- cannot copy if array is null! does not copy if length is unchanged
- arrayCopyPt(T3[], int) - Static method in class javajs.util.AU
- arrayCopyRangeI(int[], int, int) - Static method in class javajs.util.AU
-
a specialized method that allows copying from a starting point either to the end or to the middle (color schemes, especially)
- arrayCopyRangeRevI(int[], int, int) - Static method in class javajs.util.AU
- arrayCopyS(String[], int) - Static method in class javajs.util.AU
- arrayCopyShort(short[], int) - Static method in class javajs.util.AU
- ArrayDataReader - Class in javajs.util
-
ArrayDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with String[] arrays without any further adaptation.
- ArrayDataReader() - Constructor for class javajs.util.ArrayDataReader
- arrayDiv(Quat[], Quat[], int, boolean) - Static method in class javajs.util.Quat
- arrayOpen(boolean) - Method in class org.jmol.util.JSONWriter
- arrayToList(SV) - Method in class org.jmol.script.SV
- arrow - Static variable in class org.jmol.script.T
- ARROW - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
- as - Static variable in class org.jmol.script.T
- asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
- asBoolean() - Method in class org.jmol.script.SV
- asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ASCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- ascent - Variable in class org.jmol.render.LabelsRenderer
- asFloat() - Method in class org.jmol.script.SV
- asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
- ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- asInt() - Method in class org.jmol.script.SV
- asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
- asObject - Variable in class javajs.util.CifDataParser
-
A flag to create and return Java objects, not strings.
- asPDF - Variable in class jspecview.common.PrintLayout
- assign - Static variable in class org.jmol.script.T
- assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
-
algorithm discussed above.
- assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
- assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
- ASSOCIATION - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- asString() - Method in class javajs.util.T3i
- asString() - Method in class org.jmol.script.SV
- asString() - Method in class org.jmol.symmetry.SpaceGroup
- astrType - Static variable in class org.jmol.script.T
- asymMatrix - Variable in class org.jmol.util.Tensor
- asymmetry() - Method in class org.jmol.util.Tensor
-
asymmetry = deviation from a symmetric tensor
- async - Static variable in class org.jmol.script.T
- async - Variable in class org.jmol.viewer.Viewer
- async_builds - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- at - Variable in class org.jmol.modelset.AtomCollection
- ati_bugs - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- atNos - Variable in class org.jmol.util.JmolMolecule
- atokenInfix - Variable in class org.jmol.script.ScriptCompiler
- atom - Variable in class org.jmol.minimize.MinAtom
- Atom - Class in org.jmol.adapter.smarter
- Atom - Class in org.jmol.modelset
- Atom() - Constructor for class org.jmol.adapter.smarter.Atom
- Atom() - Constructor for class org.jmol.modelset.Atom
- ATOM_INFRAME - Static variable in class org.jmol.modelset.Atom
- ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
- atom_name_wildcard - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- ATOM_NOFLAGS - Static variable in class org.jmol.modelset.Atom
- ATOM_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
- ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.modelset.Atom
- atom_type_format - Enum constant in enum class org.jmol.adapter.readers.pymol.PyMOLSettings
- ATOM_VISIBLE - Static variable in class org.jmol.modelset.Atom
- ATOM_VISSET - Static variable in class org.jmol.modelset.Atom
- atom1 - Variable in class org.jmol.modelset.Bond
- atom2 - Variable in class org.jmol.modelset.Bond
- atomCenterOrCoordinateParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
- AtomCollection - Class in org.jmol.modelset
- AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
- AtomCollection.AtomSorter - Class in org.jmol.modelset
- AtomData - Class in org.jmol.atomdata
- AtomData() - Constructor for class org.jmol.atomdata.AtomData
- atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- AtomDataServer - Interface in org.jmol.atomdata
- AtomDisplayLabel - Class in jme
- AtomDisplayLabel(double, double, String, int, int, int, int, int, int, int, int, FontMetrics, double, boolean) - Constructor for class jme.AtomDisplayLabel
- atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
- atomExpression(T[], int, int, boolean, boolean, Object[], boolean) - Method in class org.jmol.script.ScriptEval
- atomExpressionAt(int) - Method in class org.jmol.script.ScriptEval
- atomExpressionAt(int) - Method in class org.jmol.scriptext.ScriptExt
- atomExpressionCommand - Static variable in class org.jmol.script.T
- atomFormats - Variable in class org.jmol.shape.Hover
- atomHighlighted - Variable in class org.jmol.viewer.Viewer
- 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.CsfReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
- atomicorbital - Static variable in class org.jmol.script.T
- atomicSymbols - Static variable in class org.iupac.InchiUtils
- atomid - Static variable in class org.jmol.script.T
- atomID - Variable in class org.jmol.modelset.Atom
- ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
- ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
- ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C2 - Static variable in class org.jmol.viewer.JC
- ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C4 - Static variable in class org.jmol.viewer.JC
- ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C5 - Static variable in class org.jmol.viewer.JC
- ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C5M - Static variable in class org.jmol.viewer.JC
- ATOMID_C6 - Static variable in class org.jmol.viewer.JC
- ATOMID_C7 - Static variable in class org.jmol.viewer.JC
- ATOMID_C8 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
- ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
- ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_MAX - Static variable in class org.jmol.modelsetbio.BioResolver
- ATOMID_N1 - Static variable in class org.jmol.viewer.JC
- ATOMID_N2 - Static variable in class org.jmol.viewer.JC
- ATOMID_N3 - Static variable in class org.jmol.viewer.JC
- ATOMID_N4 - Static variable in class org.jmol.viewer.JC
- ATOMID_N6 - Static variable in class org.jmol.viewer.JC
- ATOMID_N7 - Static variable in class org.jmol.viewer.JC
- ATOMID_N9 - Static variable in class org.jmol.viewer.JC
- ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
- ATOMID_O1 - Static variable in class org.jmol.viewer.JC
- ATOMID_O1P - Static variable in class org.jmol.viewer.JC
- ATOMID_O2 - Static variable in class org.jmol.viewer.JC
- ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O2P - Static variable in class org.jmol.viewer.JC
- ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O4 - Static variable in class org.jmol.viewer.JC
- ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_O6 - Static variable in class org.jmol.viewer.JC
- ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
- ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
- ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_S4 - Static variable in class org.jmol.viewer.JC
- ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
- atomindex - Static variable in class org.jmol.script.T
- atomIndex - Variable in class org.jmol.atomdata.AtomData
- atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
- atomIndex - Variable in class org.jmol.shape.Hover
- atomIndex - Variable in class org.jmol.shape.Mesh
- atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
- atomIndex1 - Variable in class org.jmol.util.Tensor
- atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
- atomIndex2 - Variable in class org.jmol.util.Tensor
- AtomIndexIterator - Interface in org.jmol.api
-
note: YOU MUST RELEASE THE ITERATOR
- AtomIteratorWithinModel - Class in org.jmol.modelset
- AtomIteratorWithinModelSet - Class in org.jmol.modelset
- AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
- atomLabelBoundingBox - Variable in class jme.AtomDisplayLabel
- atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- atomLabels - Variable in class org.jmol.adapter.writers.CIFWriter
- atomList - Variable in class org.jmol.util.JmolMolecule
- atomMapAnyCase - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomMapX - Variable in class jme.AtomDisplayLabel
- atomMapY - Variable in class jme.AtomDisplayLabel
- atomMolecule - Variable in class org.jmol.atomdata.AtomData
- ATOMMOVED - Enum constant in enum class org.jmol.c.CBK
- atomname - Static variable in class org.jmol.script.T
- atomName - Variable in class org.jmol.adapter.smarter.Atom
- atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- atomno - Static variable in class org.jmol.script.T
- atomNo - Variable in class org.jmol.quantum.SlaterData
- atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
- atomPicked(int) - Method in class org.jmol.jsv.JSV
- atompicking - Static variable in class org.jmol.script.T
- <