A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

actionPerformed(ActionEvent) - Method in class org.simtk.moleculargraphics.CylinderPanel

An ActionListener that listens to the radio buttons.

actionPerformed(ActionEvent) - Method in class org.simtk.tornado.command.BackgroundColorAction

actionPerformed(ActionEvent) - Method in class org.simtk.tornado.command.BrowserLaunchAction

actionPerformed(ActionEvent) - Method in class org.simtk.tornado.command.QuitAction

ActiveMoleculeBroadcaster - Class in org.simtk.moleculargraphics

ActiveMoleculeBroadcaster() - Constructor for class org.simtk.moleculargraphics.ActiveMoleculeBroadcaster

activeMoleculeBroadcaster - Variable in class org.simtk.tornado.Tornado

ActiveMoleculeListener - Interface in org.simtk.moleculargraphics

actor - Variable in class org.simtk.mol.toon.ActorCartoonClass

ActorCartoon - Interface in org.simtk.mol.toon

ActorCartoonClass - Class in org.simtk.mol.toon

actorCartoons - Variable in class org.simtk.moleculargraphics.StructureCanvas

actorSet - Variable in class org.simtk.mol.toon.MoleculeCartoonClass

add(BoundingBox) - Method in class org.simtk.mol.toon.BoundingBox

add(MoleculeCollection) - Method in interface org.simtk.mol.toon.MoleculeCartoon

add(MoleculeCollection) - Method in class org.simtk.mol.toon.MoleculeCartoonClass

add(Residue) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

add(Residue) - Method in class org.simtk.moleculargraphics.SequencePane

add(MoleculeCartoon) - Method in class org.simtk.moleculargraphics.StructureCanvas

add(ActorCartoon) - Method in class org.simtk.moleculargraphics.StructureCanvas

Warning: use of this routine might lead to highlighting arifacts.

add(vtkActor, ActorCartoon) - Method in class org.simtk.moleculargraphics.StructureCanvas

add(MoleculeCartoon) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

add(Residue) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

add_escapes(String) - Method in exception org.simtk.parser.ParseException

Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.

addActiveMoleculeListener(ActiveMoleculeListener) - Method in class org.simtk.moleculargraphics.ActiveMoleculeBroadcaster

addAtom(Atom) - Method in class org.simtk.mol.toon.CappedBondActor

addBasePair(BasePair) - Method in class org.simtk.mol.toon.BasePairConnectorStick

addBasePair(BasePair) - Method in class org.simtk.mol.toon.BasePairOval

addBasePair(BasePair) - Method in class org.simtk.mol.toon.BasePairRod

addCylinder(Vector3D, Vector3D, Color, Chemical) - Method in class org.simtk.mol.toon.CylinderCartoon

addCylinder(Vector3D, Vector3D, double, int, Color) - Method in class org.simtk.moleculargraphics.CylinderPanel

addDuplex(Duplex) - Method in class org.simtk.mol.toon.DuplexCylinderCartoon

addEscapes(String) - Static method in error org.simtk.parser.TokenMgrError

Replaces unprintable characters by their espaced (or unicode escaped) equivalents in the given string

addHalfBond(HalfBond) - Method in class org.simtk.mol.toon.CappedBondActor

addMolecule(Molecule) - Method in class org.simtk.mol.toon.AtomSphereActor

addMolecule(Molecule) - Method in class org.simtk.mol.toon.AtomSpheres

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BackboneCurve

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BackboneStick

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BackboneTubeCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BallAndStickCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BaseConnectorTube

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BasePairConnectorStick

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BasePairOval

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BasePairRibbon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BasePairRod

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BaseStickTube

addMolecule(Molecule) - Method in class org.simtk.mol.toon.BondStickCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.CappedBondActor

addMolecule(Molecule) - Method in class org.simtk.mol.toon.DuplexCylinderCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.DuplexResidueWedge

addMolecule(Molecule) - Method in class org.simtk.mol.toon.FineRibbonCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.GlyphCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.MoleculeBlobActor

addMolecule(Molecule) - Method in class org.simtk.mol.toon.MoleculeBlobs

addMolecule(Molecule) - Method in interface org.simtk.mol.toon.MoleculeCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.MoleculeTensorCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.NucleotideStickCartoon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.ProteinRibbon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.ResidueSphereActor

addMolecule(Molecule) - Method in class org.simtk.mol.toon.ResidueSpheres

addMolecule(Molecule) - Method in class org.simtk.mol.toon.RichardsonProteinRibbon

addMolecule(Molecule) - Method in class org.simtk.mol.toon.RopeAndCylinder

addMolecule(Molecule) - Method in class org.simtk.mol.toon.TubeAndStickTrace

addMolecule(Molecule) - Method in class org.simtk.mol.toon.WireFrame

addMolecule(Molecule) - Method in class org.simtk.mol.toon.WireFrameActor

addNotify() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

addNucleicAcid(NucleicAcid) - Method in class org.simtk.mol.toon.BasePairConnectorStick

addNucleicAcid(NucleicAcid) - Method in class org.simtk.mol.toon.BasePairOval

addNucleicAcid(NucleicAcid) - Method in class org.simtk.mol.toon.DuplexCylinderCartoon

addNucleicAcid(NucleicAcid) - Method in class org.simtk.mol.toon.RopeAndCylinder

addNucleotide(Residue) - Method in class org.simtk.mol.toon.BaseConnectorTube

addNucleotide(Residue) - Method in class org.simtk.mol.toon.BasePairConnectorStick

addNucleotide(Residue, Residue) - Method in class org.simtk.mol.toon.BasePairOval

addNucleotide(Residue) - Method in class org.simtk.mol.toon.BaseStickTube

addPoint(double, Vector3D) - Method in class org.simtk.moleculargraphics.Spline3D

addResidue(Residue) - Method in class org.simtk.mol.toon.AtomSphereActor

addResidue(Residue) - Method in class org.simtk.mol.toon.ProteinRibbonSphereTest

addResidueCenterListener(ResidueCenterListener) - Method in class org.simtk.moleculargraphics.ResidueCenterBroadcaster

addResidueHighlightListener(ResidueHighlightListener) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

addResidues(List<Residue>) - Method in class org.simtk.mol.toon.BackboneTubeCartoon

addResidues(List<Residue>, ResType, int, Spline3D, Spline3D) - Method in class org.simtk.mol.toon.RichardsonProteinRibbon

addSphere(Vector3D, double, Color, Residue) - Method in class org.simtk.moleculargraphics.CylinderPanel

addSubToon(BaseCartoon) - Method in interface org.simtk.mol.toon.MoleculeCartoon

addSubToon(BaseCartoon) - Method in class org.simtk.mol.toon.MoleculeCartoonClass

addWindowSetObserver(Observer) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

adjustBeginLineColumn(int, int) - Method in class org.simtk.parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

adjustmentValueChanged(AdjustmentEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

adjustmentValueChanged(AdjustmentEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

animate() - Method in class org.simtk.moleculargraphics.InertialRotationThread

appendString(String) - Method in class org.simtk.console.ConsolePanel

Add a string to the message area of the console

arcHeight - Variable in class org.simtk.toon.secstruct.BasePairPosition

arcRange - Variable in class org.simtk.toon.secstruct.BasePairPosition

arcStart - Variable in class org.simtk.toon.secstruct.BasePairPosition

arcWidth - Variable in class org.simtk.toon.secstruct.BasePairPosition

arcX - Variable in class org.simtk.toon.secstruct.BasePairPosition

arcY - Variable in class org.simtk.toon.secstruct.BasePairPosition

AtomColorScheme - Class in org.simtk.mol.color

AtomColorScheme() - Constructor for class org.simtk.mol.color.AtomColorScheme

AtomSphereActor - Class in org.simtk.mol.toon

AtomSphereActor() - Constructor for class org.simtk.mol.toon.AtomSphereActor

AtomSphereActor(double) - Constructor for class org.simtk.mol.toon.AtomSphereActor

AtomSpheres - Class in org.simtk.mol.toon

AtomSpheres() - Constructor for class org.simtk.mol.toon.AtomSpheres

Azimuth(double) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

B

BackboneCurve - Class in org.simtk.mol.toon

BackboneCurveActor - Class in org.simtk.mol.toon

BackboneCurveActor(double, double, Molecule) - Constructor for class org.simtk.mol.toon.BackboneCurveActor

BackboneStick - Class in org.simtk.mol.toon

BackboneStick() - Constructor for class org.simtk.mol.toon.BackboneStick

BackboneStick(double) - Constructor for class org.simtk.mol.toon.BackboneStick

BackboneStick(double, int) - Constructor for class org.simtk.mol.toon.BackboneStick

BackboneTubeActor - Class in org.simtk.mol.toon

BackboneTubeActor(double, List<Residue>) - Constructor for class org.simtk.mol.toon.BackboneTubeActor

BackboneTubeCartoon - Class in org.simtk.mol.toon

BackgroundColorAction - Class in org.simtk.tornado.command

BackgroundColorAction(Color, String, Colorable, UndoRedoMechanism) - Constructor for class org.simtk.tornado.command.BackgroundColorAction

backup(int) - Method in class org.simtk.parser.SimpleCharStream

BallAndStickCartoon - Class in org.simtk.mol.toon

BallAndStickCartoon() - Constructor for class org.simtk.mol.toon.BallAndStickCartoon

BaseCartoon - Interface in org.simtk.mol.toon

BaseConnectorTube - Class in org.simtk.mol.toon

BaseConnectorTube() - Constructor for class org.simtk.mol.toon.BaseConnectorTube

BaseConnectorTubeActor - Class in org.simtk.mol.toon

BaseConnectorTubeActor() - Constructor for class org.simtk.mol.toon.BaseConnectorTubeActor

BaseConnectorTubeActor(Residue) - Constructor for class org.simtk.mol.toon.BaseConnectorTubeActor

BasePairBrick - Class in org.simtk.mol.toon

BasePairBrick() - Constructor for class org.simtk.mol.toon.BasePairBrick

BasePairConnectorStick - Class in org.simtk.mol.toon

BasePairConnectorStick() - Constructor for class org.simtk.mol.toon.BasePairConnectorStick

BasePairOval - Class in org.simtk.mol.toon

BasePairOval() - Constructor for class org.simtk.mol.toon.BasePairOval

BasePairPosition - Class in org.simtk.toon.secstruct

basePairPositions() - Method in interface org.simtk.toon.secstruct.SecondaryStructureDiagram

basePairPositions() - Method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

BasePairRibbon - Class in org.simtk.mol.toon

BasePairRibbon() - Constructor for class org.simtk.mol.toon.BasePairRibbon

BasePairRod - Class in org.simtk.mol.toon

BasePosition - Class in org.simtk.toon.secstruct

BasePosition(Residue, Vector2D) - Constructor for class org.simtk.toon.secstruct.BasePosition

basePosition - Variable in class org.simtk.toon.secstruct.NumberTick

basePositions() - Method in interface org.simtk.toon.secstruct.SecondaryStructureDiagram

basePositions() - Method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

BaseStickTube - Class in org.simtk.mol.toon

BaseStickTube() - Constructor for class org.simtk.mol.toon.BaseStickTube

BaseStickTubeActor - Class in org.simtk.mol.toon

BaseStickTubeActor(Residue) - Constructor for class org.simtk.mol.toon.BaseStickTubeActor

beginColumn - Variable in class org.simtk.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginLine - Variable in class org.simtk.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

BeginToken() - Method in class org.simtk.parser.SimpleCharStream

BetaStrandRibbon - Class in org.simtk.mol.toon

BetaStrandRibbon(List<Residue>, double, double, int, Spline3D, Spline3D) - Constructor for class org.simtk.mol.toon.BetaStrandRibbon

BlockComplementaryBaseColorScheme - Class in org.simtk.mol.color

BlockComplementaryBaseColorScheme() - Constructor for class org.simtk.mol.color.BlockComplementaryBaseColorScheme

BondStickCartoon - Class in org.simtk.mol.toon

BondStickCartoon() - Constructor for class org.simtk.mol.toon.BondStickCartoon

BondStickCartoon(double) - Constructor for class org.simtk.mol.toon.BondStickCartoon

BoundingBox - Class in org.simtk.mol.toon

BoundingBox(double[]) - Constructor for class org.simtk.mol.toon.BoundingBox

BrowserLaunchAction - Class in org.simtk.tornado.command

BrowserLaunchAction(String) - Constructor for class org.simtk.tornado.command.BrowserLaunchAction

bufcolumn - Variable in class org.simtk.parser.SimpleCharStream

buffer - Variable in class org.simtk.parser.SimpleCharStream

BufferedCanvas - Class in org.simtk.moleculargraphics

BufferedCanvas() - Constructor for class org.simtk.moleculargraphics.BufferedCanvas

bufline - Variable in class org.simtk.parser.SimpleCharStream

bufpos - Variable in class org.simtk.parser.SimpleCharStream

C

cam - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

CameraPanel - Class in org.simtk.moleculargraphics

canvas - Variable in class org.simtk.moleculargraphics.MolApp

CappedBondActor - Class in org.simtk.mol.toon

CappedBondActor() - Constructor for class org.simtk.mol.toon.CappedBondActor

center() - Method in class org.simtk.mol.toon.BoundingBox

centerByBoundingBox() - Method in class org.simtk.moleculargraphics.StructureCanvas

centerOnResidue(Residue) - Method in interface org.simtk.moleculargraphics.ResidueCenterListener

centerOnResidue(Residue) - Method in class org.simtk.moleculargraphics.SequencePane

centerOnResidue(Residue) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

centerOnResidue(Residue) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

chainDirection(Residue) - Static method in class org.simtk.mol.toon.ProteinRibbonSegment

characterDensity - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

checkSize() - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

checkSize() - Method in class org.simtk.moleculargraphics.SequencePane

Set the minimum size to show the entire height

chemicalIndices - Variable in class org.simtk.mol.toon.ToonColors

classLoader - Variable in class org.simtk.moleculargraphics.MolApp

cleanUpNutation() - Method in class org.simtk.moleculargraphics.StructureCanvas

clear() - Method in class org.simtk.mol.toon.ProteinRibbon

clear() - Method in class org.simtk.moleculargraphics.Spline3D

clear() - Method in class org.simtk.moleculargraphics.StructureCanvas

clear() - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

clearResidues() - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

clearResidues() - Method in class org.simtk.moleculargraphics.SequencePane

clearResidues() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

clearResidues() - Method in class org.simtk.tornado.Tornado

color - Variable in class org.simtk.mol.color.ConstantColor

color - Variable in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

Colorable - Interface in org.simtk.mol.color

colorByScalar() - Method in class org.simtk.mol.toon.GlyphCartoon

colorByScalar() - Method in class org.simtk.mol.toon.TensorGlyphCartoon

colorExpression() - Method in class org.simtk.parser.RasmolParser

colorOf(Object) - Method in class org.simtk.mol.color.AtomColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.BlockComplementaryBaseColorScheme

Takes either Residue or ResidueType as an argument

colorOf(Object) - Method in interface org.simtk.mol.color.ColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.ConstantColor

colorOf(Object) - Method in class org.simtk.mol.color.DefaultColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.HighlightColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.MoleculeColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.ResidueColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.SequencingNucleotideColorScheme

colorOf(Object) - Method in class org.simtk.mol.color.TornadoAminoAcidColorScheme

Takes either Residue or ResidueType as an argument

ColorScheme - Interface in org.simtk.mol.color

colorScheme - Variable in class org.simtk.mol.toon.BackboneStick

colorScheme - Variable in class org.simtk.mol.toon.BasePairRod

colorScheme - Variable in class org.simtk.tornado.Tornado

colorToon(Object, ColorScheme) - Method in class org.simtk.mol.toon.ActorCartoonClass

colorToon(ColorScheme) - Method in class org.simtk.mol.toon.ActorCartoonClass

colorToon(Object, ColorScheme) - Method in interface org.simtk.mol.toon.BaseCartoon

colorToon(ColorScheme) - Method in interface org.simtk.mol.toon.BaseCartoon

colorToon(Object, ColorScheme) - Method in class org.simtk.mol.toon.MoleculeCartoonClass

colorToon(ColorScheme) - Method in class org.simtk.mol.toon.MoleculeCartoonClass

column - Variable in class org.simtk.parser.SimpleCharStream

COMMA - Static variable in interface org.simtk.parser.RasmolParserConstants

componentHidden(ComponentEvent) - Method in class org.simtk.moleculargraphics.BufferedCanvas

componentHidden(ComponentEvent) - Method in class org.simtk.moleculargraphics.ScaleBar

componentHidden(ComponentEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

componentHidden(ComponentEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

componentMoved(ComponentEvent) - Method in class org.simtk.moleculargraphics.BufferedCanvas

componentMoved(ComponentEvent) - Method in class org.simtk.moleculargraphics.ScaleBar

componentMoved(ComponentEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

componentMoved(ComponentEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

componentResized(ComponentEvent) - Method in class org.simtk.moleculargraphics.BufferedCanvas

componentResized(ComponentEvent) - Method in class org.simtk.moleculargraphics.ScaleBar

componentResized(ComponentEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

componentResized(ComponentEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

componentShown(ComponentEvent) - Method in class org.simtk.moleculargraphics.BufferedCanvas

componentShown(ComponentEvent) - Method in class org.simtk.moleculargraphics.ScaleBar

componentShown(ComponentEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

componentShown(ComponentEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

CompositeCartoon - Class in org.simtk.mol.toon

CompositeCartoon() - Constructor for class org.simtk.mol.toon.CompositeCartoon

ConsolePanel - Class in org.simtk.console

CONSTANT - Static variable in interface org.simtk.parser.eg1Constants

ConstantColor - Class in org.simtk.mol.color

ConstantColor(Color) - Constructor for class org.simtk.mol.color.ConstantColor

createAlphaHelix(List<Residue>, double, double, int, Spline3D, Spline3D) - Method in class org.simtk.mol.toon.ProteinHelix

createArrow(List<Vector3D>, List<Vector3D>, List<Chemical>, double, double) - Method in class org.simtk.mol.toon.BetaStrandRibbon

createBetaStrand(List<Residue>, double, double, int, Spline3D, Spline3D) - Method in class org.simtk.mol.toon.BetaStrandRibbon

createCoil(List<Residue>, double, int, Spline3D, Spline3D) - Method in class org.simtk.mol.toon.ProteinCoil

createCoil(List<Vector3D>, List<Vector3D>, List<Chemical>, double) - Method in class org.simtk.mol.toon.ProteinCoil

createExtrudedRibbon(vtkPolyData, double, double, double) - Method in class org.simtk.mol.toon.ProteinRibbonSegment

createPolyLine(List<Vector3D>, List<Vector3D>, List<Chemical>) - Method in class org.simtk.mol.toon.ProteinRibbonSegment

createTaperedRibbon(List<Vector3D>, List<Vector3D>, List<Chemical>, double, double) - Method in class org.simtk.mol.toon.ProteinHelix

curChar - Static variable in class org.simtk.parser.eg1TokenManager

curChar - Variable in class org.simtk.parser.RasmolParserTokenManager

currentToken - Variable in exception org.simtk.parser.ParseException

This is the last token that has been consumed successfully.

CylinderCartoon - Class in org.simtk.mol.toon

CylinderCartoon(double, double) - Constructor for class org.simtk.mol.toon.CylinderCartoon

CylinderPanel - Class in org.simtk.moleculargraphics

cylinderRadius - Variable in class org.simtk.mol.toon.CylinderCartoon

cylinderSource - Variable in class org.simtk.mol.toon.CylinderCartoon

D

debugStream - Static variable in class org.simtk.parser.eg1TokenManager

debugStream - Variable in class org.simtk.parser.RasmolParserTokenManager

DEFAULT - Static variable in interface org.simtk.parser.eg1Constants

DEFAULT - Static variable in interface org.simtk.parser.RasmolParserConstants

DEFAULT_COLOR_SCHEME - Static variable in class org.simtk.mol.color.DefaultColorScheme

defaultColor - Variable in class org.simtk.mol.toon.ToonColors

DefaultColorScheme - Class in org.simtk.mol.color

DefaultColorScheme() - Constructor for class org.simtk.mol.color.DefaultColorScheme

diagram - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

DIGIT - Static variable in interface org.simtk.parser.eg1Constants

DIGIT - Static variable in interface org.simtk.parser.RasmolParserConstants

disable_tracing() - Static method in class org.simtk.parser.eg1

disable_tracing() - Method in class org.simtk.parser.RasmolParser

disposeSplash() - Static method in class org.simtk.splashscreen.SplashWindow

distance - Variable in class org.simtk.mol.toon.vtkGrowPointsFilter

DIVIDE - Static variable in interface org.simtk.parser.eg1Constants

Done() - Method in class org.simtk.parser.SimpleCharStream

doubleHelixCylinder(Duplex) - Static method in class org.simtk.mol.toon.DuplexCylinderActor

Given a set of base paired residues, construct cylinder geometry to represent them.

doubleHelixCylinder(Duplex) - Static method in class org.simtk.mol.toon.NewDuplexCylinderActor

Given a set of base paired residues, construct cylinder geometry to represent them.

DuplexCylinderActor - Class in org.simtk.mol.toon

DuplexCylinderCartoon - Class in org.simtk.mol.toon

DuplexCylinderCartoon() - Constructor for class org.simtk.mol.toon.DuplexCylinderCartoon

DuplexResidueWedge - Class in org.simtk.mol.toon

DuplexResidueWedge() - Constructor for class org.simtk.mol.toon.DuplexResidueWedge

DuplexResidueWedge(double) - Constructor for class org.simtk.mol.toon.DuplexResidueWedge

E

eg1 - Class in org.simtk.parser

eg1(InputStream) - Constructor for class org.simtk.parser.eg1

eg1(InputStream, String) - Constructor for class org.simtk.parser.eg1

eg1(Reader) - Constructor for class org.simtk.parser.eg1

eg1(eg1TokenManager) - Constructor for class org.simtk.parser.eg1

eg1Constants - Interface in org.simtk.parser

eg1TokenManager - Class in org.simtk.parser

eg1TokenManager(SimpleCharStream) - Constructor for class org.simtk.parser.eg1TokenManager

eg1TokenManager(SimpleCharStream, int) - Constructor for class org.simtk.parser.eg1TokenManager

element() - Static method in class org.simtk.parser.eg1

enable_tracing() - Static method in class org.simtk.parser.eg1

enable_tracing() - Method in class org.simtk.parser.RasmolParser

endColumn - Variable in class org.simtk.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endLine - Variable in class org.simtk.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

EOF - Static variable in interface org.simtk.parser.eg1Constants

EOF - Static variable in interface org.simtk.parser.RasmolParserConstants

eol - Variable in exception org.simtk.parser.ParseException

The end of line string for this machine.

EthaneDemo - Class in org.simtk.moleculargraphics

EthaneDemo() - Constructor for class org.simtk.moleculargraphics.EthaneDemo

EthaneSplasher - Class in org.simtk.splashscreen

EthaneSplasher() - Constructor for class org.simtk.splashscreen.EthaneSplasher

evaluate(double) - Method in class org.simtk.moleculargraphics.Spline3D

Execute() - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

Execute() - Method in class org.simtk.mol.toon.vtkGrowPointsFilter

Execute() - Method in class org.simtk.mol.toon.vtkPreExtrusionCenteringFilter

Execute() - Method in class org.simtk.mol.toon.vtkRoundScalarsFilter

Execute() - Method in class org.simtk.mol.toon.vtkSetScalarsFilter

Execute() - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

ExpandBuff(boolean) - Method in class org.simtk.parser.SimpleCharStream

expectedTokenSequences - Variable in exception org.simtk.parser.ParseException

Each entry in this array is an array of integers.

F

FillBuff() - Method in class org.simtk.parser.SimpleCharStream

findWorstPseudoknotBasePairs(Set<BasePair>) - Static method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

Identify a set of base pairs, which, if removed, leaves a set that has no pseudoknots and no bases with multiple base pairs.

FineRibbonCartoon - Class in org.simtk.mol.toon

FineRibbonCartoon() - Constructor for class org.simtk.mol.toon.FineRibbonCartoon

finishVtkPipeline(vtkPolyData) - Method in class org.simtk.mol.toon.ProteinRibbonSegment

fireCenter(Residue) - Method in class org.simtk.moleculargraphics.ResidueCenterBroadcaster

fireHighlight(Residue) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

fireSetActiveMolecle(Molecule) - Method in class org.simtk.moleculargraphics.ActiveMoleculeBroadcaster

fireUnhighlightResidue(Residue) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

fireUnhighlightResidues() - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

flushUserIsInteracting() - Method in class org.simtk.tornado.Tornado

font - Variable in class org.simtk.moleculargraphics.SequenceCanvas

fontHeights - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

fonts - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

fontWidths - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

G

generateParseException() - Static method in class org.simtk.parser.eg1

generateParseException() - Method in class org.simtk.parser.RasmolParser

getActor() - Method in interface org.simtk.mol.toon.ActorCartoon

getActor() - Method in class org.simtk.mol.toon.ActorCartoonClass

getBackground() - Method in class org.simtk.moleculargraphics.MolApp

getBackground() - Method in class org.simtk.moleculargraphics.StructureCanvas

getBeginColumn() - Method in class org.simtk.parser.SimpleCharStream

getBeginLine() - Method in class org.simtk.parser.SimpleCharStream

getBoundingBox() - Method in class org.simtk.moleculargraphics.StructureCanvas

getBoundingBox() - Method in interface org.simtk.toon.secstruct.SecondaryStructureDiagram

getBoundingBox() - Method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

getChemicalFromScalar(int) - Method in interface org.simtk.mol.toon.ActorCartoon

getChemicalFromScalar(int) - Method in class org.simtk.mol.toon.ActorCartoonClass

getChemicalFromScalar(int) - Method in class org.simtk.mol.toon.ToonColors

getColor() - Method in interface org.simtk.mol.color.Colorable

getColorIndex(Chemical) - Method in class org.simtk.mol.toon.ActorCartoonClass

getColumn() - Method in class org.simtk.parser.SimpleCharStream

Deprecated.

getConsecutiveBaseDistance() - Method in interface org.simtk.toon.secstruct.SecondaryStructureDiagram

getConsecutiveBaseDistance() - Method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

getCurrentPath() - Method in class org.simtk.tornado.Tornado

getEndColumn() - Method in class org.simtk.parser.SimpleCharStream

getEndLine() - Method in class org.simtk.parser.SimpleCharStream

getFinalVisibleResidue() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

getFirstVisibleResidue() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

getHighlightActor() - Method in interface org.simtk.mol.toon.ActorCartoon

getHighlightActor() - Method in class org.simtk.mol.toon.ActorCartoonClass

getHighlightColor() - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

GetImage() - Method in class org.simtk.parser.SimpleCharStream

getLabelCorner(Graphics2D, String, Vector2D, Vector2D) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

getLeftEdgePixel() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getLine() - Method in class org.simtk.parser.SimpleCharStream

Deprecated.

getMapper() - Method in interface org.simtk.mol.toon.ActorCartoon

getMapper() - Method in class org.simtk.mol.toon.ActorCartoonClass

getMaximumSize() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getMaximumSize() - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

getMaximumSize() - Method in class org.simtk.moleculargraphics.SequencePane

getMaximumSize() - Method in class org.simtk.moleculargraphics.StructureCanvas

getMaximumSize() - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

getMessage() - Method in exception org.simtk.parser.ParseException

This method has the standard behavior when this object has been created using the standard constructors.

getMessage() - Method in error org.simtk.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMinimumSize() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getMinimumSize() - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

getMinimumSize() - Method in class org.simtk.moleculargraphics.SequencePane

getMinimumSize() - Method in class org.simtk.moleculargraphics.StructureCanvas

getMinimumSize() - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

getMolecule() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getNextToken() - Static method in class org.simtk.parser.eg1

getNextToken() - Static method in class org.simtk.parser.eg1TokenManager

getNextToken() - Method in class org.simtk.parser.RasmolParser

getNextToken() - Method in class org.simtk.parser.RasmolParserTokenManager

getNumberOfInputPoints() - Method in class org.simtk.moleculargraphics.Spline3D

getPreferredSize() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getPreferredSize() - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

getPreferredSize() - Method in class org.simtk.moleculargraphics.StructureCanvas

getPreferredSize() - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

GetRenderer() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

GetRenderWindow() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

getResidue() - Method in class org.simtk.toon.secstruct.BasePosition

getResidueWidth() - Method in class org.simtk.moleculargraphics.SequenceCanvas

GetRibbonFilterWidth() - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

GetRibbonFilterWidth() - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

GetRibbonFilterWidthFactor() - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

GetRibbonFilterWidthFactor() - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

getRightEdgePixel() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getSelectedSourceTypes() - Method in class org.simtk.tornado.Tornado

getSequenceCanvas() - Method in class org.simtk.moleculargraphics.SequencePane

getSequenceWidth() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

What is the total width in pixels of the entire sequence?

GetSuffix(int) - Method in class org.simtk.parser.SimpleCharStream

getTabSize(int) - Method in class org.simtk.parser.SimpleCharStream

GetThickness() - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

GetThickness() - Method in class org.simtk.mol.toon.vtkPreExtrusionCenteringFilter

GetThickness() - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

getToken(int) - Static method in class org.simtk.parser.eg1

getToken(int) - Method in class org.simtk.parser.RasmolParser

getTotalSequenceWidth() - Method in class org.simtk.moleculargraphics.SequenceCanvas

Get width of entire sequence, not just the visible canvas

getUserIsInteracting() - Method in class org.simtk.tornado.Tornado

getViewportWidth() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

How wide is the viewport in which the sequence is shown?

getVtkActors() - Method in class org.simtk.moleculargraphics.ScaleBar

getVtkCylinder(Cylinder, Color, int) - Static method in class org.simtk.moleculargraphics.GraphicsCylinder

getVtkCylinderFilter(Cylinder, int) - Static method in class org.simtk.moleculargraphics.GraphicsCylinder

getVtkMeshCylinder(double, double, double) - Static method in class org.simtk.mol.toon.NewDuplexCylinderActor

getVtkMeshCylinder(Cylinder, double) - Static method in class org.simtk.mol.toon.NewDuplexCylinderActor

getVtkMeshCylinder(Cylinder, Color, double) - Method in class org.simtk.mol.toon.NewDuplexCylinderActor

getVtkProp3D() - Method in class org.simtk.mol.toon.ProteinRibbon

getX() - Method in class org.simtk.toon.secstruct.BasePosition

getY() - Method in class org.simtk.toon.secstruct.BasePosition

GlyphCartoon - Class in org.simtk.mol.toon

Cartoon consisting of a single vtkGlyph3D.

GraphicsCylinder - Class in org.simtk.moleculargraphics

GraphicsCylinder() - Constructor for class org.simtk.moleculargraphics.GraphicsCylinder

H

HardCopy(String, int) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

hasVisibleColor() - Method in class org.simtk.mol.toon.ToonColors

hBondNormal(Residue, int) - Static method in class org.simtk.mol.toon.ProteinRibbonSegment

headLength - Variable in class org.simtk.mol.toon.vtkArrowWidthFilter

headWidth - Variable in class org.simtk.mol.toon.vtkArrowWidthFilter

height - Variable in class org.simtk.mol.toon.BasePairOval

helixWidth - Variable in class org.simtk.mol.toon.RichardsonProteinRibbon

Hidable - Interface in org.simtk.mol.toon

HidableActorClass - Class in org.simtk.mol.toon

HidableActorClass(vtkActor) - Constructor for class org.simtk.mol.toon.HidableActorClass

hide() - Method in interface org.simtk.mol.toon.Hidable

hide() - Method in class org.simtk.mol.toon.HidableActorClass

hide() - Method in class org.simtk.mol.toon.ProteinRibbon

hide(Molecule) - Method in class org.simtk.mol.toon.ProteinRibbon

highlightActor - Variable in class org.simtk.mol.toon.ActorCartoonClass

highlightColor - Variable in class org.simtk.tornado.Tornado

HighlightColorScheme - Class in org.simtk.mol.color

Color scheme that blends a particular highlight color with that of another color scheme.

HighlightColorScheme(Color, ColorScheme) - Constructor for class org.simtk.mol.color.HighlightColorScheme

highlightedResidues - Variable in class org.simtk.moleculargraphics.SequenceCartoonCanvas

highlightFactor - Variable in class org.simtk.mol.toon.GlyphCartoon

highlightGap - Variable in class org.simtk.mol.toon.BackboneCurveActor

highlightMapper - Variable in class org.simtk.mol.toon.ActorCartoonClass

highlightPosition(Graphics, int, Color) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.mol.toon.ActorCartoonClass

highlightResidue(Residue, Color) - Method in class org.simtk.mol.toon.AtomSphereActor

highlightResidue(Residue, Color) - Method in class org.simtk.mol.toon.BackboneCurveActor

highlightResidue(Residue, Color) - Method in class org.simtk.mol.toon.BondStickCartoon

highlightResidue(Residue, Color) - Method in class org.simtk.mol.toon.WireFrameActor

highlightResidue(Residue, Color) - Method in interface org.simtk.moleculargraphics.ResidueHighlightListener

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.SequencePane

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.tornado.Tornado

highlightResidueByAtomScalars(Residue, Color) - Method in class org.simtk.mol.toon.ActorCartoonClass

highlightResidueByBackboneScalars(Residue, Color) - Method in class org.simtk.mol.toon.ActorCartoonClass

highlightResidueByResidueScalars(Residue, Color) - Method in class org.simtk.mol.toon.ActorCartoonClass

highlightResidues - Variable in class org.simtk.moleculargraphics.Tornado3DCanvas

highlightResidues - Variable in class org.simtk.moleculargraphics.TornadoSequenceCanvas

highlightToonColors - Variable in class org.simtk.mol.toon.ActorCartoonClass

I

image - Variable in class org.simtk.parser.Token

The string image of the token.

inBuf - Variable in class org.simtk.parser.SimpleCharStream

indexChemicals - Variable in class org.simtk.mol.toon.ToonColors

InertialRotationThread - Class in org.simtk.moleculargraphics

InertialRotationThread(Tornado) - Constructor for class org.simtk.moleculargraphics.InertialRotationThread

initialBackgroundColor - Variable in class org.simtk.tornado.Tornado

initialize() - Method in class org.simtk.moleculargraphics.InertialRotationThread

initialTableSize - Variable in class org.simtk.mol.toon.ToonColors

input_stream - Static variable in class org.simtk.parser.eg1TokenManager

input_stream - Variable in class org.simtk.parser.RasmolParserTokenManager

inputStream - Variable in class org.simtk.parser.SimpleCharStream

INT - Static variable in interface org.simtk.parser.RasmolParserConstants

InteractionMode - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

InteractionModeRotate() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

InteractionModeTranslate() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

InteractionModeZoom() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

invisibleColorScheme - Variable in class org.simtk.mol.toon.ActorCartoonClass

invokeMain(String, String[]) - Static method in class org.simtk.splashscreen.SplashWindow

Uses reflection to avoid loading many classes before this routine is actually called, allowing rapid splash screen display.

isPopulated() - Method in interface org.simtk.mol.toon.ActorCartoon

isPopulated - Variable in class org.simtk.mol.toon.ActorCartoonClass

isPopulated() - Method in class org.simtk.mol.toon.ActorCartoonClass

isWindowSet() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

J

jj_nt - Static variable in class org.simtk.parser.eg1

jj_nt - Variable in class org.simtk.parser.RasmolParser

jjFillToken() - Static method in class org.simtk.parser.eg1TokenManager

jjFillToken() - Method in class org.simtk.parser.RasmolParserTokenManager

jjstrLiteralImages - Static variable in class org.simtk.parser.eg1TokenManager

jjstrLiteralImages - Static variable in class org.simtk.parser.RasmolParserTokenManager

K

keyPressed(KeyEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

keyPressed(KeyEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

keyReleased(KeyEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

keyReleased(KeyEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

keyTyped(KeyEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

kind - Variable in class org.simtk.parser.Token

An integer that describes the kind of this token.

L

L_BRKT - Static variable in interface org.simtk.parser.RasmolParserConstants

label - Variable in class org.simtk.toon.secstruct.NumberTick

labelDirection - Variable in class org.simtk.toon.secstruct.NumberTick

lastX - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

lastY - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

lengthResolution - Variable in class org.simtk.mol.toon.BetaStrandRibbon

lengthResolution - Variable in class org.simtk.mol.toon.ProteinRibbonSegment

LexicalError(boolean, int, int, int, String, char) - Static method in error org.simtk.parser.TokenMgrError

Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.

lexStateNames - Static variable in class org.simtk.parser.eg1TokenManager

lexStateNames - Static variable in class org.simtk.parser.RasmolParserTokenManager

lgt - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

LightFollowCamera - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

LightFollowCameraOff() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

LightFollowCameraOn() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

lightingset - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

line - Variable in class org.simtk.parser.SimpleCharStream

listeners - Variable in class org.simtk.moleculargraphics.ActiveMoleculeBroadcaster

listeners - Variable in class org.simtk.moleculargraphics.ResidueCenterBroadcaster

listeners - Variable in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

load() - Static method in class org.simtk.moleculargraphics.VTKLibraries

loadSStructViewFile(InputStream) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

Lock() - Method in class org.simtk.moleculargraphics.PublicNativeVtkPanel

Lock() - Method in class org.simtk.moleculargraphics.StructureCanvas

Lock() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

lubricateUserInteraction() - Method in class org.simtk.moleculargraphics.SequencePane

lubricateUserInteraction() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

lubricateUserInteraction() - Method in class org.simtk.tornado.Tornado

lut - Variable in class org.simtk.mol.toon.ToonColors

M

main(String[]) - Static method in class org.simtk.moleculargraphics.CameraPanel

Main method for testing the CameraPanel

main(String[]) - Static method in class org.simtk.moleculargraphics.CylinderPanel

main(String[]) - Static method in class org.simtk.moleculargraphics.EthaneDemo

main(String[]) - Static method in class org.simtk.moleculargraphics.TestMenu

main(String[]) - Static method in class org.simtk.parser.eg1

main(String[]) - Static method in class org.simtk.splashscreen.EthaneSplasher

main(String[]) - Static method in class org.simtk.splashscreen.TornadoSplasher

main(String[]) - Static method in class org.simtk.tornado.Tornado

majorTicks() - Method in interface org.simtk.toon.secstruct.SecondaryStructureDiagram

majorTicks() - Method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

mapper - Variable in class org.simtk.mol.toon.ActorCartoonClass

mapper - Variable in class org.simtk.mol.toon.MoleculeCartoonClass

mapper - Variable in class org.simtk.mol.toon.ToonColors

maxNextCharInd - Variable in class org.simtk.parser.SimpleCharStream

minLength - Variable in class org.simtk.mol.toon.CylinderCartoon

minorTicks() - Method in interface org.simtk.toon.secstruct.SecondaryStructureDiagram

minorTicks() - Method in class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

MINUS - Static variable in interface org.simtk.parser.eg1Constants

MolApp - Class in org.simtk.moleculargraphics

MolApp() - Constructor for class org.simtk.moleculargraphics.MolApp

MoleculeBlobActor - Class in org.simtk.mol.toon

MoleculeBlobActor(Molecule, double) - Constructor for class org.simtk.mol.toon.MoleculeBlobActor

MoleculeBlobs - Class in org.simtk.mol.toon

MoleculeBlobs() - Constructor for class org.simtk.mol.toon.MoleculeBlobs

MoleculeCartoon - Interface in org.simtk.mol.toon

MoleculeCartoonClass - Class in org.simtk.mol.toon

MoleculeCartoonClass() - Constructor for class org.simtk.mol.toon.MoleculeCartoonClass

MoleculeColorScheme - Class in org.simtk.mol.color

MoleculeColorScheme() - Constructor for class org.simtk.mol.color.MoleculeColorScheme

MoleculeTensorActor - Class in org.simtk.mol.toon

MoleculeTensorActor(Molecule) - Constructor for class org.simtk.mol.toon.MoleculeTensorActor

MoleculeTensorCartoon - Class in org.simtk.mol.toon

MoleculeTensorCartoon() - Constructor for class org.simtk.mol.toon.MoleculeTensorCartoon

mouseClicked(MouseEvent) - Method in class org.simtk.console.ConsolePanel

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mouseClicked(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.CylinderPanel

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.StructureCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mouseDragged(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.console.ConsolePanel

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mouseEntered(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mouseExited(MouseEvent) - Method in class org.simtk.console.ConsolePanel

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mouseExited(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.CylinderPanel

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mouseMoved(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mousePressed(MouseEvent) - Method in class org.simtk.console.ConsolePanel

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.StructureCanvas

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mousePressed(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mouseReleased(MouseEvent) - Method in class org.simtk.console.ConsolePanel

mouseReleased(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseReleased(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseReleased(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

mouseReleased(MouseEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

mouseWheelMoved(MouseWheelEvent) - Method in class org.simtk.moleculargraphics.StructureCanvas

mouseWheelMoved(MouseWheelEvent) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

MULTIPLY - Static variable in interface org.simtk.parser.eg1Constants

myGraphics - Variable in class org.simtk.moleculargraphics.SequenceCanvas

N

neckLength - Variable in class org.simtk.mol.toon.vtkArrowWidthFilter

NewDuplexCylinderActor - Class in org.simtk.mol.toon

newToken(int) - Static method in class org.simtk.parser.Token

Returns a new Token object, by default.

next - Variable in class org.simtk.parser.Token

A reference to the next regular (non-special) token from the input stream.

nextColorIndex - Variable in class org.simtk.mol.toon.ToonColors

NoCartoonCreatedException - Exception in org.simtk.mol.toon

NucleotideStickCartoon - Class in org.simtk.mol.toon

NucleotideStickCartoon() - Constructor for class org.simtk.mol.toon.NucleotideStickCartoon

NucleotideStickCartoon(double) - Constructor for class org.simtk.mol.toon.NucleotideStickCartoon

numberFont - Variable in class org.simtk.moleculargraphics.SequenceCanvas

NumberTick - Class in org.simtk.toon.secstruct

NussinovDiagram - Class in org.simtk.toon.secstruct

NussinovDiagram(Biopolymer) - Constructor for class org.simtk.toon.secstruct.NussinovDiagram

O

oldCreateAlphaHelix(List<Residue>, double, double) - Method in class org.simtk.mol.toon.ProteinHelix

oldCreateBetaStrand(List<Residue>, double, double, int, Spline3D, Spline3D) - Method in class org.simtk.mol.toon.BetaStrandRibbon

oldCreateCoil(List<Residue>, double) - Method in class org.simtk.mol.toon.ProteinCoil

one_line() - Static method in class org.simtk.parser.eg1

org.simtk.console - package org.simtk.console

org.simtk.mol.color - package org.simtk.mol.color

org.simtk.mol.toon - package org.simtk.mol.toon

org.simtk.moleculargraphics - package org.simtk.moleculargraphics

org.simtk.parser - package org.simtk.parser

org.simtk.splashscreen - package org.simtk.splashscreen

org.simtk.toon.secstruct - package org.simtk.toon.secstruct

org.simtk.tornado - package org.simtk.tornado

org.simtk.tornado.command - package org.simtk.tornado.command

orientByNormal() - Method in class org.simtk.mol.toon.GlyphCartoon

orientByNormal() - Method in class org.simtk.mol.toon.TensorGlyphCartoon

P

paint(Graphics) - Method in class org.simtk.moleculargraphics.BufferedCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.SequenceCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.SequencePane

paint(Graphics) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

paint(Graphics) - Method in class org.simtk.splashscreen.SplashWindow

paint(Graphics) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

ParseException - Exception in org.simtk.parser

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception org.simtk.parser.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception org.simtk.parser.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception org.simtk.parser.ParseException

parseInput() - Method in class org.simtk.parser.RasmolParser

pauseRotation - Variable in class org.simtk.moleculargraphics.InertialRotationThread

pickActor(int, int) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

PLUS - Static variable in interface org.simtk.parser.eg1Constants

position1 - Variable in class org.simtk.toon.secstruct.BasePairPosition

position2 - Variable in class org.simtk.toon.secstruct.BasePairPosition

positionResidues - Variable in class org.simtk.moleculargraphics.SequenceCanvas

prepareNutation(double) - Method in class org.simtk.moleculargraphics.StructureCanvas

prevCharIsCR - Variable in class org.simtk.parser.SimpleCharStream

prevCharIsLF - Variable in class org.simtk.parser.SimpleCharStream

ProteinCoil - Class in org.simtk.mol.toon

ProteinCoil(List<Residue>, double, int, Spline3D, Spline3D) - Constructor for class org.simtk.mol.toon.ProteinCoil

ProteinHelix - Class in org.simtk.mol.toon

ProteinHelix(List<Residue>, double, double, int, Spline3D, Spline3D) - Constructor for class org.simtk.mol.toon.ProteinHelix

ProteinRibbon - Class in org.simtk.mol.toon

ProteinRibbon() - Constructor for class org.simtk.mol.toon.ProteinRibbon

ProteinRibbonSegment - Class in org.simtk.mol.toon

ProteinRibbonSegment() - Constructor for class org.simtk.mol.toon.ProteinRibbonSegment

ProteinRibbonSphereTest - Class in org.simtk.mol.toon

PublicNativeVtkPanel - Class in org.simtk.moleculargraphics

PublicNativeVtkPanel() - Constructor for class org.simtk.moleculargraphics.PublicNativeVtkPanel

Q

QuitAction - Class in org.simtk.tornado.command

QuitAction() - Constructor for class org.simtk.tornado.command.QuitAction

R

R_BRKT - Static variable in interface org.simtk.parser.RasmolParserConstants

radius - Variable in class org.simtk.mol.toon.BackboneTubeCartoon

rasmolColorName() - Method in class org.simtk.parser.RasmolParser

rasmolColorNumbers() - Method in class org.simtk.parser.RasmolParser

RasmolParser - Class in org.simtk.parser

This class is autogenerated from a .jj file by the javacc parser generator

RasmolParser(String) - Constructor for class org.simtk.parser.RasmolParser

RasmolParser(InputStream) - Constructor for class org.simtk.parser.RasmolParser

RasmolParser(InputStream, String) - Constructor for class org.simtk.parser.RasmolParser

RasmolParser(Reader) - Constructor for class org.simtk.parser.RasmolParser

RasmolParser(RasmolParserTokenManager) - Constructor for class org.simtk.parser.RasmolParser

RasmolParserConstants - Interface in org.simtk.parser

RasmolParserTokenManager - Class in org.simtk.parser

RasmolParserTokenManager(SimpleCharStream) - Constructor for class org.simtk.parser.RasmolParserTokenManager

RasmolParserTokenManager(SimpleCharStream, int) - Constructor for class org.simtk.parser.RasmolParserTokenManager

rasMolStatement() - Method in class org.simtk.parser.RasmolParser

readChar() - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream) - Static method in class org.simtk.parser.eg1

ReInit(InputStream, String) - Static method in class org.simtk.parser.eg1

ReInit(Reader) - Static method in class org.simtk.parser.eg1

ReInit(eg1TokenManager) - Method in class org.simtk.parser.eg1

ReInit(SimpleCharStream) - Static method in class org.simtk.parser.eg1TokenManager

ReInit(SimpleCharStream, int) - Static method in class org.simtk.parser.eg1TokenManager

ReInit(InputStream) - Method in class org.simtk.parser.RasmolParser

ReInit(InputStream, String) - Method in class org.simtk.parser.RasmolParser

ReInit(Reader) - Method in class org.simtk.parser.RasmolParser

ReInit(RasmolParserTokenManager) - Method in class org.simtk.parser.RasmolParser

ReInit(SimpleCharStream) - Method in class org.simtk.parser.RasmolParserTokenManager

ReInit(SimpleCharStream, int) - Method in class org.simtk.parser.RasmolParserTokenManager

ReInit(Reader, int, int, int) - Method in class org.simtk.parser.SimpleCharStream

ReInit(Reader, int, int) - Method in class org.simtk.parser.SimpleCharStream

ReInit(Reader) - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream, String, int, int, int) - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream, int, int, int) - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream, String) - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream) - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream, String, int, int) - Method in class org.simtk.parser.SimpleCharStream

ReInit(InputStream, int, int) - Method in class org.simtk.parser.SimpleCharStream

removeActiveMoleculeListener(ActiveMoleculeListener) - Method in class org.simtk.moleculargraphics.ActiveMoleculeBroadcaster

removeNotify() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

removeResidueCenterListener(ResidueCenterListener) - Method in class org.simtk.moleculargraphics.ResidueCenterBroadcaster

removeResidueHighlightListener(ResidueHighlightListener) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

removeWindowSetObserver(Observer) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

ren - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

Render() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

RenderCreate(vtkRenderWindow) - Method in class org.simtk.moleculargraphics.PublicNativeVtkPanel

RenderCreate(vtkRenderWindow) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

rendering - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

Report() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

resetCamera() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

resetCameraClippingRange() - Method in class org.simtk.moleculargraphics.StructureCanvas

resetCameraClippingRange() - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

resetCameraClippingRange() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

ResidueCenterBroadcaster - Class in org.simtk.moleculargraphics

ResidueCenterBroadcaster() - Constructor for class org.simtk.moleculargraphics.ResidueCenterBroadcaster

residueCenterBroadcaster - Variable in class org.simtk.moleculargraphics.Tornado3DCanvas

residueCenterBroadcaster - Variable in class org.simtk.tornado.Tornado

ResidueCenterListener - Interface in org.simtk.moleculargraphics

ResidueColorScheme - Class in org.simtk.mol.color

ResidueColorScheme() - Constructor for class org.simtk.mol.color.ResidueColorScheme

ResidueHighlightBroadcaster - Class in org.simtk.moleculargraphics

ResidueHighlightBroadcaster() - Constructor for class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

residueHighlightBroadcaster - Variable in class org.simtk.moleculargraphics.Tornado3DCanvas

residueHighlightBroadcaster - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

residueHighlightBroadcaster - Variable in class org.simtk.tornado.Tornado

ResidueHighlightListener - Interface in org.simtk.moleculargraphics

residuePositions - Variable in class org.simtk.moleculargraphics.SequenceCanvas

ResidueSphereActor - Class in org.simtk.mol.toon

ResidueSphereActor() - Constructor for class org.simtk.mol.toon.ResidueSphereActor

ResidueSpheres - Class in org.simtk.mol.toon

ResidueSpheres() - Constructor for class org.simtk.mol.toon.ResidueSpheres

ribbonThickness - Variable in class org.simtk.mol.toon.RichardsonProteinRibbon

ribbonWidth - Variable in class org.simtk.mol.toon.vtkTaperedWidthFilter

RichardsonProteinRibbon - Class in org.simtk.mol.toon

RichardsonProteinRibbon() - Constructor for class org.simtk.mol.toon.RichardsonProteinRibbon

RopeAndCylinder - Class in org.simtk.mol.toon

RopeAndCylinder() - Constructor for class org.simtk.mol.toon.RopeAndCylinder

rotationStyle - Variable in class org.simtk.moleculargraphics.InertialRotationThread

RotationStyle - Enum in org.simtk.moleculargraphics

run() - Method in class org.simtk.moleculargraphics.InertialRotationThread

runCommandString(String) - Method in class org.simtk.console.ConsolePanel

Override this method to respond to commands typed by the user.

rw - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

S

scalarsName - Variable in class org.simtk.mol.toon.vtkSetScalarsFilter

ScaleBar - Class in org.simtk.moleculargraphics

ScaleBar(StructureCanvas) - Constructor for class org.simtk.moleculargraphics.ScaleBar

scaleBar - Variable in class org.simtk.moleculargraphics.StructureCanvas

scaleByAtom - Variable in class org.simtk.mol.toon.AtomSphereActor

scaleByBoundingBox() - Method in class org.simtk.moleculargraphics.StructureCanvas

scaleByNormal() - Method in class org.simtk.mol.toon.GlyphCartoon

scaleByNormal() - Method in class org.simtk.mol.toon.TensorGlyphCartoon

scaleNone() - Method in class org.simtk.mol.toon.GlyphCartoon

scaleNone() - Method in class org.simtk.mol.toon.TensorGlyphCartoon

SCHEME - Static variable in class org.simtk.mol.color.BlockComplementaryBaseColorScheme

SCHEME - Static variable in class org.simtk.mol.color.ResidueColorScheme

SCHEME - Static variable in class org.simtk.mol.color.TornadoAminoAcidColorScheme

SecondaryStructureCanvas - Class in org.simtk.toon.secstruct

SecondaryStructureCanvas(ResidueHighlightBroadcaster) - Constructor for class org.simtk.toon.secstruct.SecondaryStructureCanvas

SecondaryStructureDiagram - Interface in org.simtk.toon.secstruct

SecondaryStructureDiagramClass - Class in org.simtk.toon.secstruct

SecondaryStructureDiagramClass() - Constructor for class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

selectedSourceTypes - Variable in class org.simtk.tornado.Tornado

SequenceCanvas - Class in org.simtk.moleculargraphics

SequenceCanvas() - Constructor for class org.simtk.moleculargraphics.SequenceCanvas

SequenceCartoonCanvas - Class in org.simtk.moleculargraphics

SequenceCartoonCanvas(ResidueHighlightBroadcaster, TornadoSequenceCanvas) - Constructor for class org.simtk.moleculargraphics.SequenceCartoonCanvas

SequencePane - Class in org.simtk.moleculargraphics

SequencePane(ResidueHighlightBroadcaster, ResidueCenterBroadcaster, Tornado) - Constructor for class org.simtk.moleculargraphics.SequencePane

SEQUENCING_NUCLEOTIDE_COLOR_SCHEME - Static variable in class org.simtk.mol.color.SequencingNucleotideColorScheme

SequencingNucleotideColorScheme - Class in org.simtk.mol.color

SequencingNucleotideColorScheme() - Constructor for class org.simtk.mol.color.SequencingNucleotideColorScheme

serialVersionUID - Static variable in class org.simtk.moleculargraphics.BufferedCanvas

serialVersionUID - Static variable in class org.simtk.moleculargraphics.CylinderPanel

serialVersionUID - Static variable in class org.simtk.moleculargraphics.SequenceCartoonCanvas

serialVersionUID - Static variable in class org.simtk.moleculargraphics.SequencePane

serialVersionUID - Static variable in class org.simtk.moleculargraphics.Tornado3DCanvas

setActiveMolecule(Molecule) - Method in interface org.simtk.moleculargraphics.ActiveMoleculeListener

setActiveMolecule(Molecule) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setActiveMolecule(Molecule) - Method in class org.simtk.moleculargraphics.SequencePane

setBackground(Color) - Method in class org.simtk.console.ConsolePanel

setBackground(Color) - Method in class org.simtk.moleculargraphics.MolApp

setBackground(Color) - Method in class org.simtk.moleculargraphics.ScaleBar

setBackground(Color) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setBackground(Color) - Method in class org.simtk.moleculargraphics.SequencePane

setBackground(Color) - Method in class org.simtk.moleculargraphics.StructureCanvas

setBackground(Color) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

setBackgroundColorPredicate() - Method in class org.simtk.parser.RasmolParser

setBackgroundCommand() - Method in class org.simtk.parser.RasmolParser

setColor(Object, Color) - Method in class org.simtk.mol.color.AtomColorScheme

setColor(Color) - Method in interface org.simtk.mol.color.Colorable

setCpkColors() - Method in class org.simtk.mol.color.AtomColorScheme

setCurrentPath(String) - Method in class org.simtk.tornado.Tornado

setDebugStream(PrintStream) - Static method in class org.simtk.parser.eg1TokenManager

setDebugStream(PrintStream) - Method in class org.simtk.parser.RasmolParserTokenManager

setDefaultColor(Color) - Method in class org.simtk.mol.toon.ToonColors

setDiagram(SecondaryStructureDiagram) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

SetDistance(double) - Method in class org.simtk.mol.toon.vtkGrowPointsFilter

setFont(Font) - Method in class org.simtk.console.ConsolePanel

setGlyphSource(vtkPolyData) - Method in class org.simtk.mol.toon.GlyphCartoon

setGlyphSource(vtkPolyData) - Method in class org.simtk.mol.toon.TensorGlyphCartoon

setHighlightColor(Color) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

setLeftEdgePixel(int) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setMaximumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setMaximumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequencePane

setMaximumSize(Dimension) - Method in class org.simtk.moleculargraphics.StructureCanvas

setMaximumSize(Dimension) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setMessage(String) - Method in class org.simtk.tornado.Tornado

setMinimumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setMinimumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequencePane

setMinimumSize(Dimension) - Method in class org.simtk.moleculargraphics.StructureCanvas

setMinimumSize(Dimension) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setMolecule(Biopolymer) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setParentContainer(JComponent) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setPreferredSize(Dimension) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setPreferredSize(Dimension) - Method in class org.simtk.moleculargraphics.StructureCanvas

setPreferredSize(Dimension) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setPrompt(String) - Method in class org.simtk.console.ConsolePanel

setResidue(Residue, Atom[]) - Method in class org.simtk.mol.toon.BaseConnectorTubeActor

setResidueCenterBroadcaster(ResidueCenterBroadcaster) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

setResidueHighlightBroadcaster(ResidueHighlightBroadcaster) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

SetScalars(String) - Method in class org.simtk.mol.toon.vtkSetScalarsFilter

setScale(double) - Method in class org.simtk.mol.toon.AtomSphereActor

setSize(int, int) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

setStereoCrossEye() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoInterlaced() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoLeftEye() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoOff() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoRedBlue() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoRightEye() - Method in class org.simtk.moleculargraphics.StructureCanvas

setTabSize(int) - Method in class org.simtk.parser.SimpleCharStream

SetThickness(double) - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

SetThickness(double) - Method in class org.simtk.mol.toon.vtkPreExtrusionCenteringFilter

SetThickness(double) - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

setTorsionAngle(double) - Method in class org.simtk.moleculargraphics.EthaneDemo

setUpLights() - Method in class org.simtk.moleculargraphics.StructureCanvas

setUpMenuBar() - Method in class org.simtk.moleculargraphics.EthaneDemo

setWait(String) - Method in class org.simtk.tornado.Tornado

SetWidth(double) - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

SetWidth(double) - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

show() - Method in interface org.simtk.mol.toon.Hidable

show() - Method in class org.simtk.mol.toon.HidableActorClass

show() - Method in class org.simtk.mol.toon.ProteinRibbon

show(Molecule) - Method in class org.simtk.mol.toon.ProteinRibbon

SimpleCharStream - Class in org.simtk.parser

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(Reader, int, int, int) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(Reader, int, int) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(Reader) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(InputStream, int, int, int) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(InputStream, String, int, int) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(InputStream, int, int) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(InputStream, String) - Constructor for class org.simtk.parser.SimpleCharStream

SimpleCharStream(InputStream) - Constructor for class org.simtk.parser.SimpleCharStream

specialConstructor - Variable in exception org.simtk.parser.ParseException

This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).

specialToken - Variable in class org.simtk.parser.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

splash(URL) - Static method in class org.simtk.splashscreen.SplashWindow

splash(Image) - Static method in class org.simtk.splashscreen.SplashWindow

SplashWindow - Class in org.simtk.splashscreen

Spline3D - Class in org.simtk.moleculargraphics

Spline3D() - Constructor for class org.simtk.moleculargraphics.Spline3D

splineX - Variable in class org.simtk.moleculargraphics.Spline3D

splineY - Variable in class org.simtk.moleculargraphics.Spline3D

splineZ - Variable in class org.simtk.moleculargraphics.Spline3D

stateChanged(ChangeEvent) - Method in class org.simtk.moleculargraphics.EthaneDemo

staticFlag - Static variable in class org.simtk.parser.SimpleCharStream

stepNutation(double) - Method in class org.simtk.moleculargraphics.StructureCanvas

straightLine - Variable in class org.simtk.toon.secstruct.BasePairPosition

strandWidth - Variable in class org.simtk.mol.toon.RichardsonProteinRibbon

StructureCanvas - Class in org.simtk.moleculargraphics

StructureCanvas() - Constructor for class org.simtk.moleculargraphics.StructureCanvas

subToons - Variable in class org.simtk.mol.toon.MoleculeCartoonClass

sum() - Static method in class org.simtk.parser.eg1

SwitchTo(int) - Static method in class org.simtk.parser.eg1TokenManager

SwitchTo(int) - Method in class org.simtk.parser.RasmolParserTokenManager

T

tabSize - Variable in class org.simtk.parser.SimpleCharStream

taperLength - Variable in class org.simtk.mol.toon.vtkTaperedWidthFilter

temporarilySelectedResidues - Variable in class org.simtk.moleculargraphics.TornadoSequenceCanvas

TensorGlyphCartoon - Class in org.simtk.mol.toon

term() - Static method in class org.simtk.parser.eg1

testFullScreen() - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

TestMenu - Class in org.simtk.moleculargraphics

thickness - Variable in class org.simtk.mol.toon.vtkArrowWidthFilter

thickness - Variable in class org.simtk.mol.toon.vtkPreExtrusionCenteringFilter

thickness - Variable in class org.simtk.mol.toon.vtkTaperedWidthFilter

tipWidth - Variable in class org.simtk.mol.toon.vtkArrowWidthFilter

tipWidth - Variable in class org.simtk.mol.toon.vtkTaperedWidthFilter

token - Static variable in class org.simtk.parser.eg1

token - Variable in class org.simtk.parser.RasmolParser

Token - Class in org.simtk.parser

Describes the input token stream.

Token() - Constructor for class org.simtk.parser.Token

token_source - Static variable in class org.simtk.parser.eg1

token_source - Variable in class org.simtk.parser.RasmolParser

tokenImage - Static variable in interface org.simtk.parser.eg1Constants

tokenImage - Variable in exception org.simtk.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Static variable in interface org.simtk.parser.RasmolParserConstants

TokenMgrError - Error in org.simtk.parser

TokenMgrError() - Constructor for error org.simtk.parser.TokenMgrError

TokenMgrError(String, int) - Constructor for error org.simtk.parser.TokenMgrError

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.simtk.parser.TokenMgrError

toonColors - Variable in class org.simtk.mol.toon.MoleculeCartoonClass

ToonColors - Class in org.simtk.mol.toon

toonRange - Variable in class org.simtk.tornado.Tornado

Tornado - Class in org.simtk.tornado

Tornado3DCanvas - Class in org.simtk.moleculargraphics

Tornado3DCanvas() - Constructor for class org.simtk.moleculargraphics.Tornado3DCanvas

TornadoAminoAcidColorScheme - Class in org.simtk.mol.color

TornadoAminoAcidColorScheme() - Constructor for class org.simtk.mol.color.TornadoAminoAcidColorScheme

TornadoSequenceCanvas - Class in org.simtk.moleculargraphics

TornadoSequenceCanvas(String, SequencePane, ResidueHighlightBroadcaster, ResidueCenterBroadcaster) - Constructor for class org.simtk.moleculargraphics.TornadoSequenceCanvas

TornadoSplasher - Class in org.simtk.splashscreen

TornadoSplasher() - Constructor for class org.simtk.splashscreen.TornadoSplasher

toString() - Method in class org.simtk.parser.Token

Returns the image.

transform - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

transformToBoundingBox(BoundingBox) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

translate(double, double) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

TubeAndStickTrace - Class in org.simtk.mol.toon

TubeAndStickTrace() - Constructor for class org.simtk.mol.toon.TubeAndStickTrace

TubeAndStickTrace(double, double) - Constructor for class org.simtk.mol.toon.TubeAndStickTrace

U

unary() - Static method in class org.simtk.parser.eg1

unhighlightResidue(Residue) - Method in class org.simtk.mol.toon.ActorCartoonClass

unhighlightResidue(Residue) - Method in class org.simtk.mol.toon.AtomSphereActor

unhighlightResidue(Residue) - Method in class org.simtk.mol.toon.BackboneCurveActor

unhighlightResidue(Residue) - Method in class org.simtk.mol.toon.BondStickCartoon

unhighlightResidue(Residue) - Method in class org.simtk.mol.toon.WireFrameActor

unhighlightResidue(Residue) - Method in interface org.simtk.moleculargraphics.ResidueHighlightListener

unhighlightResidue(Residue) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

unhighlightResidue(Residue) - Method in class org.simtk.moleculargraphics.SequencePane

unhighlightResidue(Residue) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

unhighlightResidue(Residue) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

unhighlightResidue(Residue) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

unhighlightResidue(Residue) - Method in class org.simtk.tornado.Tornado

unhighlightResidueByAtomScalars(Residue) - Method in class org.simtk.mol.toon.ActorCartoonClass

unhighlightResidueByBackboneScalars(Residue) - Method in class org.simtk.mol.toon.ActorCartoonClass

unhighlightResidueByResidueScalars(Residue) - Method in class org.simtk.mol.toon.ActorCartoonClass

unhighlightResidues() - Method in class org.simtk.mol.toon.ActorCartoonClass

unhighlightResidues() - Method in interface org.simtk.moleculargraphics.ResidueHighlightListener

unhighlightResidues() - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

unhighlightResidues() - Method in class org.simtk.moleculargraphics.SequencePane

unhighlightResidues() - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

unhighlightResidues() - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

unhighlightResidues() - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

unhighlightResidues() - Method in class org.simtk.tornado.Tornado

UnknownObjectColorException - Exception in org.simtk.mol.color

UnknownObjectColorException() - Constructor for exception org.simtk.mol.color.UnknownObjectColorException

UnLock() - Method in class org.simtk.moleculargraphics.PublicNativeVtkPanel

UnLock() - Method in class org.simtk.moleculargraphics.StructureCanvas

UnLock() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

unSetWait(String) - Method in class org.simtk.tornado.Tornado

update(Graphics) - Method in class org.simtk.moleculargraphics.BufferedCanvas

update(Graphics) - Method in class org.simtk.moleculargraphics.SequenceCanvas

update(Observable, Object) - Method in class org.simtk.moleculargraphics.SequenceCanvas

update(Observable, Object) - Method in class org.simtk.moleculargraphics.StructureCanvas

update(Graphics) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

update(Graphics) - Method in class org.simtk.splashscreen.SplashWindow

updateActors() - Method in interface org.simtk.mol.toon.MoleculeCartoon

updateActors() - Method in class org.simtk.mol.toon.MoleculeCartoonClass

updateAtomPositions(Collection<Atom>) - Method in class org.simtk.mol.toon.CappedBondActor

Proposed interface for updating cartoon conformation.

updateCoordinates() - Method in class org.simtk.mol.toon.DuplexCylinderCartoon

updateCoordinates() - Method in class org.simtk.mol.toon.ProteinRibbon

updateFromWidth() - Method in class org.simtk.mol.toon.vtkArrowWidthFilter

updateFromWidth() - Method in class org.simtk.mol.toon.vtkTaperedWidthFilter

UpdateLight() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

UpdateLineColumn(char) - Method in class org.simtk.parser.SimpleCharStream

updateScaleBar(vtkCamera) - Method in class org.simtk.moleculargraphics.ScaleBar

updateTitleBar() - Method in class org.simtk.tornado.Tornado

userAppName - Variable in class org.simtk.moleculargraphics.EthaneDemo

userIsInteracting - Variable in class org.simtk.tornado.Tornado

useScaleBar - Variable in class org.simtk.moleculargraphics.StructureCanvas

V

valueOf(String) - Static method in enum org.simtk.moleculargraphics.RotationStyle

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.simtk.moleculargraphics.RotationStyle

Returns an array containing the constants of this enum type, in the order they're declared.

visibleColorIndices - Variable in class org.simtk.mol.toon.ToonColors

vtkActors() - Method in interface org.simtk.mol.toon.MoleculeCartoon

vtkActors() - Method in class org.simtk.mol.toon.MoleculeCartoonClass

vtkArrowWidthFilter - Class in org.simtk.mol.toon

vtkArrowWidthFilter() - Constructor for class org.simtk.mol.toon.vtkArrowWidthFilter

vtkGrowPointsFilter - Class in org.simtk.mol.toon

vtkGrowPointsFilter() - Constructor for class org.simtk.mol.toon.vtkGrowPointsFilter

VTKLibraries - Class in org.simtk.moleculargraphics

Class to manage loading of native shared libraries for vtk visualization tool kit.

VTKLibraries() - Constructor for class org.simtk.moleculargraphics.VTKLibraries

vtkPreExtrusionCenteringFilter - Class in org.simtk.mol.toon

vtkPreExtrusionCenteringFilter() - Constructor for class org.simtk.mol.toon.vtkPreExtrusionCenteringFilter

vtkRoundScalarsFilter - Class in org.simtk.mol.toon

vtkRoundScalarsFilter() - Constructor for class org.simtk.mol.toon.vtkRoundScalarsFilter

vtkSetScalarsFilter - Class in org.simtk.mol.toon

vtkSetScalarsFilter() - Constructor for class org.simtk.mol.toon.vtkSetScalarsFilter

vtkSwingPanel - Class in org.simtk.moleculargraphics

vtkSwingPanel() - Constructor for class org.simtk.moleculargraphics.vtkSwingPanel

vtkTaperedWidthFilter - Class in org.simtk.mol.toon

vtkTaperedWidthFilter() - Constructor for class org.simtk.mol.toon.vtkTaperedWidthFilter

W

width - Variable in class org.simtk.mol.toon.BasePairOval

width - Variable in class org.simtk.mol.toon.vtkArrowWidthFilter

windowset - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

windowSetObservable - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

WireFrame - Class in org.simtk.mol.toon

WireFrame() - Constructor for class org.simtk.mol.toon.WireFrame

WireFrameActor - Class in org.simtk.mol.toon

WireFrameActor() - Constructor for class org.simtk.mol.toon.WireFrameActor

worstBasePairs - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

X

xMax - Variable in class org.simtk.mol.toon.BoundingBox

xMin - Variable in class org.simtk.mol.toon.BoundingBox

Y

yMax - Variable in class org.simtk.mol.toon.BoundingBox

yMin - Variable in class org.simtk.mol.toon.BoundingBox

Z

zMax - Variable in class org.simtk.mol.toon.BoundingBox

zMin - Variable in class org.simtk.mol.toon.BoundingBox

zoom(double) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

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