Uses of Interface
org.simtk.molecularstructure.Residue

Packages that use Residue

org.simtk.moleculargraphics
org.simtk.moleculargraphics.cartoon
org.simtk.molecularstructure
org.simtk.molecularstructure.atom
org.simtk.molecularstructure.nucleicacid
org.simtk.rnaml
org.simtk.toon.secstruct

Uses of Residue in org.simtk.moleculargraphics

Fields in org.simtk.moleculargraphics with type parameters of type Residue

protected java.util.Map<Residue,java.awt.Color>	SequenceCartoonCanvas.highlightedResidues
protected java.util.Map<Residue,java.awt.Color>	TornadoSequenceCanvas.highlightResidues
protected java.util.Map<Residue,java.awt.Color>	Tornado3DCanvas.highlightResidues
protected java.util.Map<java.lang.Integer,Residue>	SequenceCanvas.positionResidues
protected java.util.Map<Residue,java.lang.Integer>	SequenceCanvas.residuePositions
protected java.util.Set<Residue>	TornadoSequenceCanvas.temporarilySelectedResidues

Methods in org.simtk.moleculargraphics that return Residue

Residue	TornadoSequenceCanvas.getFinalVisibleResidue()
Residue	TornadoSequenceCanvas.getFirstVisibleResidue()

Methods in org.simtk.moleculargraphics with parameters of type Residue

void	TornadoSequenceCanvas.add(Residue r)
void	SequencePane.add(Residue r)
void	SequenceCartoonCanvas.add(Residue r)
void	CylinderPanel.addSphere(Vector3D center, double radius, java.awt.Color color, Residue residue)
void	TornadoSequenceCanvas.centerOnResidue(Residue r)
void	Tornado3DCanvas.centerOnResidue(Residue residue)
void	SequencePane.centerOnResidue(Residue residue)
void	ResidueCenterListener.centerOnResidue(Residue r)
void	ResidueCenterBroadcaster.fireCenter(Residue r)
void	ResidueHighlightBroadcaster.fireHighlight(Residue r)
void	ResidueHighlightBroadcaster.fireUnhighlightResidue(Residue r)
void	TornadoSequenceCanvas.highlightResidue(Residue r, java.awt.Color c)
void	Tornado3DCanvas.highlightResidue(Residue residue, java.awt.Color color)
void	Tornado.highlightResidue(Residue residue, java.awt.Color color)
void	SequencePane.highlightResidue(Residue r, java.awt.Color c)
void	SequenceCartoonCanvas.highlightResidue(Residue r, java.awt.Color c)
void	ResidueHighlightListener.highlightResidue(Residue r, java.awt.Color highlightColor)
void	TornadoSequenceCanvas.unhighlightResidue(Residue r)
void	Tornado3DCanvas.unhighlightResidue(Residue residue)
void	Tornado.unhighlightResidue(Residue r)
void	SequencePane.unhighlightResidue(Residue r)
void	SequenceCartoonCanvas.unhighlightResidue(Residue r)
void	ResidueHighlightListener.unhighlightResidue(Residue r)

Uses of Residue in org.simtk.moleculargraphics.cartoon

Methods in org.simtk.moleculargraphics.cartoon with parameters of type Residue

void	BasePairConnectorStick.addNucleotide(Residue res)
void	BaseConnectorTube.addNucleotide(Residue residue)
void	BasePairOval.addNucleotide(Residue res1, Residue res2)
void	ProteinRibbonSphereTest.addResidue(Residue residue)
void	AtomSphereActor.addResidue(Residue residue)
protected static Vector3D	ProteinRibbonSegment.chainDirection(Residue residue)
protected static Vector3D	ProteinRibbonSegment.hBondNormal(Residue residue, int endFlag)
void	WireFrameActor.highlightResidue(Residue residue, java.awt.Color color)
void	BondStickCartoon.highlightResidue(Residue residue, java.awt.Color color)
void	AtomSphereActor.highlightResidue(Residue residue, java.awt.Color color)
void	ActorCartoonClass.highlightResidue(Residue residue, java.awt.Color color)
protected void	ActorCartoonClass.highlightResidueByAtomScalars(Residue residue, java.awt.Color color)
protected void	ActorCartoonClass.highlightResidueByResidueScalars(Residue residue, java.awt.Color color)
void	WireFrameActor.unhighlightResidue(Residue residue)
void	BondStickCartoon.unhighlightResidue(Residue residue)
void	AtomSphereActor.unhighlightResidue(Residue residue)
void	ActorCartoonClass.unhighlightResidue(Residue residue)
protected void	ActorCartoonClass.unhighlightResidueByAtomScalars(Residue residue)
protected void	ActorCartoonClass.unhighlightResidueByResidueScalars(Residue residue)

Method parameters in org.simtk.moleculargraphics.cartoon with type arguments of type Residue

void	BackboneTubeCartoon.addResidues(java.util.List<Residue> residues)
protected void	RichardsonProteinRibbon.addResidues(java.util.List<Residue> residues, org.simtk.moleculargraphics.cartoon.ResType type, int startIndex, Spline3D positionSpline, Spline3D normalSpline)
protected void	ProteinHelix.createAlphaHelix(java.util.List<Residue> residues, double ribbonThickness, double strandWidth, int startIndex, Spline3D positionSpline, Spline3D normalSpline)
protected void	BetaStrandRibbon.createBetaStrand(java.util.List<Residue> residues, double ribbonThickness, double strandWidth, int startIndex, Spline3D positionSpline, Spline3D normalSpline)
protected void	ProteinCoil.createCoil(java.util.List<Residue> residues, double diameter, int startIndex, Spline3D positionSpline, Spline3D normalSpline)
protected void	ProteinHelix.oldCreateAlphaHelix(java.util.List<Residue> residues, double ribbonThickness, double helixWidth)
protected void	BetaStrandRibbon.oldCreateBetaStrand(java.util.List<Residue> residues, double ribbonThickness, double strandWidth, int startIndex, Spline3D positionSpline, Spline3D normalSpline)
protected void	ProteinCoil.oldCreateCoil(java.util.List<Residue> residues, double diameter)

Constructors in org.simtk.moleculargraphics.cartoon with parameters of type Residue

BaseConnectorTubeActor(Residue residue)

Constructor parameters in org.simtk.moleculargraphics.cartoon with type arguments of type Residue

BackboneTubeActor(double radius, java.util.List<Residue> residues)

BetaStrandRibbon(java.util.List<Residue> residues, double ribbonThickness, double strandWidth, int startIndex, Spline3D positionSpline, Spline3D normalSpline)

ProteinCoil(java.util.List<Residue> residues, double diameter, int startIndex, Spline3D positionSpline, Spline3D normalSpline)

ProteinHelix(java.util.List<Residue> residues, double ribbonThickness, double helixWidth, int startIndex, Spline3D positionSpline, Spline3D normalSpline)

Uses of Residue in org.simtk.molecularstructure

Classes in org.simtk.molecularstructure that implement Residue

class

ResidueClass

Fields in org.simtk.molecularstructure declared as Residue

protected Residue	ResidueClass.nextResidue
protected Residue	ResidueClass.previousResidue

Fields in org.simtk.molecularstructure with type parameters of type Residue

protected java.util.Collection<Residue>

SecondaryStructureClass.residues

Methods in org.simtk.molecularstructure that return Residue

Residue	ResidueClass.getNextResidue()
Residue	Residue.getNextResidue()
Residue	ResidueClass.getPreviousResidue()
Residue	Residue.getPreviousResidue()
Residue	BiopolymerClass.getResidue(int i)
Residue	Biopolymer.getResidue(int i)
Residue	BiopolymerClass.getResidueByNumber(int i)
Residue	Biopolymer.getResidueByNumber(int i)
Residue	BiopolymerClass.getResidueByNumber(int i, char insertionCode)
Residue	BiopolymerClass.getResidueByNumber(java.lang.String n)

Methods in org.simtk.molecularstructure that return types with arguments of type Residue

java.util.Iterator<Residue>	SecondaryStructureClass.getResidueIterator()
java.util.Iterator<Residue>	SecondaryStructure.getResidueIterator()
java.util.Collection<Residue>	SecondaryStructureClass.residues()
java.util.Collection<Residue>	SecondaryStructure.residues()
java.util.List<Residue>	BiopolymerClass.residues()
java.util.List<Residue>	Biopolymer.residues()

Methods in org.simtk.molecularstructure with parameters of type Residue

void	SecondaryStructureClass.addResidue(Residue residue)
void	SecondaryStructure.addResidue(Residue residue)
void	ResidueClass.setNextResidue(Residue r)
void	Residue.setNextResidue(Residue r)
void	ResidueClass.setPreviousResidue(Residue r)
void	Residue.setPreviousResidue(Residue r)

Constructor parameters in org.simtk.molecularstructure with type arguments of type Residue

SecondaryStructureClass(java.util.Collection<Residue> residues)

SecondaryStructureClass(java.util.Collection<Residue> residues, int resLimit)

SecondaryStructureClass(java.util.Collection<Residue> residues, int resLimit, java.lang.String source)

Uses of Residue in org.simtk.molecularstructure.atom

Methods in org.simtk.molecularstructure.atom that return Residue

Residue	AtomClass.getResidue()
Residue	Atom.getResidue()

Methods in org.simtk.molecularstructure.atom with parameters of type Residue

void	AtomClass.setResidue(Residue r)

Uses of Residue in org.simtk.molecularstructure.nucleicacid

Fields in org.simtk.molecularstructure.nucleicacid with type parameters of type Residue

protected java.util.HashMap<Residue,BasePair.EdgeType>

BasePair.edges

Methods in org.simtk.molecularstructure.nucleicacid that return Residue

Residue	BasePair.getResidue1()
Residue	BasePair.getResidue2()

Methods in org.simtk.molecularstructure.nucleicacid that return types with arguments of type Residue

java.util.Iterator<Residue>

BasePair.iterator()

Methods in org.simtk.molecularstructure.nucleicacid with parameters of type Residue

void	BasePair.addResidue(Residue r)
static BasePair	BasePair.getBasePair(Residue r1, Residue r2, java.lang.String source)
BasePair.EdgeType	BasePair.getEdge(Residue res)
java.lang.Boolean	BasePair.isBetween(Residue r1, Residue r2)
static BasePair	BasePair.makeBasePair(Residue r1, Residue r2, java.lang.String source)
void	BasePair.setEdge(Residue res, BasePair.EdgeType edgeT)
void	BasePair.setEdge(Residue res, java.lang.String edge)

Constructors in org.simtk.molecularstructure.nucleicacid with parameters of type Residue

BasePair(Residue r1, Residue r2)

Constructor parameters in org.simtk.molecularstructure.nucleicacid with type arguments of type Residue

BaseStack(java.util.Collection<Residue> residues)

BaseStack(java.util.Collection<Residue> residues, java.lang.String source)

Uses of Residue in org.simtk.rnaml

Methods in org.simtk.rnaml with parameters of type Residue

boolean

RnamlDocument.isDeemedNucleotide(Residue res, java.lang.String source)

Uses of Residue in org.simtk.toon.secstruct

Methods in org.simtk.toon.secstruct that return Residue

Residue

BasePosition.getResidue()

Methods in org.simtk.toon.secstruct with parameters of type Residue

void	SecondaryStructureCanvas.highlightResidue(Residue r, java.awt.Color c)
void	SecondaryStructureCanvas.unhighlightResidue(Residue r)

Constructors in org.simtk.toon.secstruct with parameters of type Residue

BasePosition(Residue r, Vector2D pos)