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

abort() - Method in interface org.simtk.gui.MonitoredProcess

abort() - Method in class org.simtk.gui.ProgressManager

accept(File) - Method in class org.simtk.pdb.FileNameFilter

accept(File) - Method in class org.simtk.util.MyJFileFilter

actionPerformed(ActionEvent) - Method in class org.simtk.gui.ProgressPanel

actionPerformed(ActionEvent) - Method in class org.simtk.gui.UndoableDialog

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

An ActionListener that listens to the radio buttons.

actionPerformed(ActionEvent) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

ActiveMoleculeBroadcaster - Class in org.simtk.moleculargraphics

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

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

ActiveMoleculeListener - Interface in org.simtk.moleculargraphics

actor - Variable in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

ActorCartoon - Interface in org.simtk.moleculargraphics.cartoon

ActorCartoonClass - Class in org.simtk.moleculargraphics.cartoon

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

actorSet - Variable in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

add(MassBody) - Method in class org.simtk.geometry3d.MassBodyClass

add(BoundingBox) - Method in class org.simtk.moleculargraphics.cartoon.BoundingBox

add(MoleculeCollection) - Method in interface org.simtk.moleculargraphics.cartoon.MoleculeCartoon

add(MoleculeCollection) - Method in class org.simtk.moleculargraphics.cartoon.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

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

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

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

addAtom(Atom) - Method in class org.simtk.moleculargraphics.cartoon.CappedBondActor

addBasePair(BasePair) - Method in class org.simtk.moleculargraphics.cartoon.BasePairConnectorStick

addBasePair(BasePair) - Method in class org.simtk.moleculargraphics.cartoon.BasePairOval

addBasePair(BasePair) - Method in class org.simtk.moleculargraphics.cartoon.BasePairRod

addBasePair(BasePair) - Method in class org.simtk.molecularstructure.nucleicacid.Duplex

addColor(String, String) - Static method in class org.simtk.util.ColorName

addCylinder(Vector3D, Vector3D, Color, Chemical) - Method in class org.simtk.moleculargraphics.cartoon.CylinderCartoon

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

addDuplex(Duplex) - Method in class org.simtk.moleculargraphics.cartoon.DuplexCylinderCartoon

addEdit(UndoableEdit) - Method in class org.simtk.gui.UndoRedoMechanism

addExtension(String) - Method in class org.simtk.util.MyJFileFilter

addGenericBond(String, String) - Method in class org.simtk.molecularstructure.ResidueTypeClass

addGenericBonds() - Method in class org.simtk.molecularstructure.nucleicacid.Nucleotide

addGenericBonds() - Method in class org.simtk.molecularstructure.nucleicacid.Purine

addGenericBonds() - Method in class org.simtk.molecularstructure.nucleicacid.Pyrimidine

addGenericBonds() - Method in class org.simtk.molecularstructure.protein.AminoAcid

addGenericBonds() - Method in class org.simtk.molecularstructure.protein.Proline

addGenericBonds() - Method in class org.simtk.molecularstructure.ResidueTypeClass

addGenericResidueBond(String, String) - Method in class org.simtk.molecularstructure.BiopolymerClass

addGenericResidueBonds() - Method in class org.simtk.molecularstructure.BiopolymerClass

addGenericResidueBonds() - Method in class org.simtk.molecularstructure.nucleicacid.NucleicAcid

addGenericResidueBonds() - Method in class org.simtk.molecularstructure.protein.PDBProteinClass

addHalfBond(HalfBond) - Method in class org.simtk.moleculargraphics.cartoon.CappedBondActor

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.AtomSphereActor

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.AtomSpheres

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BackboneCurve

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BackboneStick

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BackboneTubeCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BallAndStickCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BaseConnectorTube

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BasePairConnectorStick

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BasePairOval

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BasePairRibbon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BasePairRod

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.BondStickCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.CappedBondActor

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.DuplexCylinderCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.DuplexResidueWedge

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.FineRibbonCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.GlyphCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeBlobActor

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeBlobs

addMolecule(Molecule) - Method in interface org.simtk.moleculargraphics.cartoon.MoleculeCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeTensorCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.NucleotideStickCartoon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.ResidueSphereActor

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.ResidueSpheres

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.RichardsonProteinRibbon

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.RopeAndCylinder

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.TubeAndStickTrace

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.WireFrame

addMolecule(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.WireFrameActor

addMolecule(Biopolymer) - Method in interface org.simtk.molecularstructure.SecondaryStructure

addMolecule(Biopolymer) - Method in class org.simtk.molecularstructure.SecondaryStructureClass

addMouseListener() - Method in class org.simtk.pdb.JLinkLabel

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

addNucleicAcid(NucleicAcid) - Method in class org.simtk.moleculargraphics.cartoon.BasePairConnectorStick

addNucleicAcid(NucleicAcid) - Method in class org.simtk.moleculargraphics.cartoon.BasePairOval

addNucleicAcid(NucleicAcid) - Method in class org.simtk.moleculargraphics.cartoon.DuplexCylinderCartoon

addNucleicAcid(NucleicAcid) - Method in class org.simtk.moleculargraphics.cartoon.RopeAndCylinder

addNucleotide(Residue) - Method in class org.simtk.moleculargraphics.cartoon.BaseConnectorTube

addNucleotide(Residue) - Method in class org.simtk.moleculargraphics.cartoon.BasePairConnectorStick

addNucleotide(Residue, Residue) - Method in class org.simtk.moleculargraphics.cartoon.BasePairOval

addObserver(Observer) - Method in class org.simtk.gui.ProgressManager

addObserver(Observer) - Method in interface org.simtk.mvc.ObservableInterface

addParametersListener(Observer) - Method in class org.simtk.gui.UndoableDialog

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

addPosition(AtomPosition) - Method in interface org.simtk.molecularstructure.atom.Atom

addPosition(AtomPosition) - Method in class org.simtk.molecularstructure.atom.AtomClass

addResidue(Residue) - Method in class org.simtk.moleculargraphics.cartoon.AtomSphereActor

addResidue(Residue) - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbonSphereTest

addResidue(Residue) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

addResidue(Residue) - Method in interface org.simtk.molecularstructure.SecondaryStructure

addResidue(Residue) - Method in class org.simtk.molecularstructure.SecondaryStructureClass

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.moleculargraphics.cartoon.BackboneTubeCartoon

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

addSecondaryStructure(SecondaryStructure) - Method in class org.simtk.molecularstructure.BiopolymerClass

addSelectionListener(SelectionListener) - Method in class org.simtk.util.SelectionBroadcaster

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

addSubToon(BaseCartoon) - Method in interface org.simtk.moleculargraphics.cartoon.MoleculeCartoon

addSubToon(BaseCartoon) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

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

Adenylate - Class in org.simtk.molecularstructure.nucleicacid

Adenylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Adenylate

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

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

Alanine - Class in org.simtk.molecularstructure.protein

Alanine() - Constructor for class org.simtk.molecularstructure.protein.Alanine

ALICE_BLUE - Static variable in class org.simtk.util.ColorName

alignNaively() - Method in class org.simtk.molecularstructure.SequenceAlignment

Creates an alignment where the first residue of the first molecule is aligned with the first residue of the second molecule, the second residue is aligned with the second residue, and so on.

ALPHA - Static variable in class org.simtk.molecularstructure.protein.Helix

AminoAcid - Class in org.simtk.molecularstructure.protein

AminoAcid(char, String, String) - Constructor for class org.simtk.molecularstructure.protein.AminoAcid

Angle - Class in org.simtk.geometry3d

Angle(double, Angle.Units, Angle.Range) - Constructor for class org.simtk.geometry3d.Angle

Angle(double, Angle.Units) - Constructor for class org.simtk.geometry3d.Angle

Angle(double) - Constructor for class org.simtk.geometry3d.Angle

Angle() - Constructor for class org.simtk.geometry3d.Angle

Angle.Range - Class in org.simtk.geometry3d

Angle.Range() - Constructor for class org.simtk.geometry3d.Angle.Range

Angle.Units - Class in org.simtk.geometry3d

Angle.Units() - Constructor for class org.simtk.geometry3d.Angle.Units

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

ANTIQUE_WHITE - Static variable in class org.simtk.util.ColorName

ANTIQUE_WHITE1 - Static variable in class org.simtk.util.ColorName

ANTIQUE_WHITE2 - Static variable in class org.simtk.util.ColorName

ANTIQUE_WHITE3 - Static variable in class org.simtk.util.ColorName

ANTIQUE_WHITE4 - Static variable in class org.simtk.util.ColorName

AQUA - Static variable in class org.simtk.util.ColorName

AQUAMARINE - Static variable in class org.simtk.util.ColorName

AQUAMARINE1 - Static variable in class org.simtk.util.ColorName

AQUAMARINE2 - Static variable in class org.simtk.util.ColorName

AQUAMARINE3 - Static variable in class org.simtk.util.ColorName

AQUAMARINE4 - Static variable in class org.simtk.util.ColorName

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

Arginine - Class in org.simtk.molecularstructure.protein

Arginine() - Constructor for class org.simtk.molecularstructure.protein.Arginine

arrayLeftDivide(Matrix) - Method in class Jama.Matrix

Element-by-element left division, C = A.\B

arrayLeftDivideEquals(Matrix) - Method in class Jama.Matrix

Element-by-element left division in place, A = A.\B

arrayRightDivide(Matrix) - Method in class Jama.Matrix

Element-by-element right division, C = A./B

arrayRightDivideEquals(Matrix) - Method in class Jama.Matrix

Element-by-element right division in place, A = A./B

arrayTimes(Matrix) - Method in class Jama.Matrix

Element-by-element multiplication, C = A.*B

arrayTimesEquals(Matrix) - Method in class Jama.Matrix

Element-by-element multiplication in place, A = A.*B

Asparagine - Class in org.simtk.molecularstructure.protein

Asparagine() - Constructor for class org.simtk.molecularstructure.protein.Asparagine

Aspartate - Class in org.simtk.molecularstructure.protein

Aspartate() - Constructor for class org.simtk.molecularstructure.protein.Aspartate

Atom - Interface in org.simtk.molecularstructure.atom

AtomClass - Class in org.simtk.molecularstructure.atom

AtomClass(String) - Constructor for class org.simtk.molecularstructure.atom.AtomClass

AtomColorScheme - Class in org.simtk.moleculargraphics.cartoon

AtomColorScheme() - Constructor for class org.simtk.moleculargraphics.cartoon.AtomColorScheme

AtomPosition - Class in org.simtk.molecularstructure.atom

AtomPosition(Vector3D) - Constructor for class org.simtk.molecularstructure.atom.AtomPosition

AtomPosition(String) - Constructor for class org.simtk.molecularstructure.atom.AtomPosition

atoms() - Method in interface org.simtk.molecularstructure.Molecular

atoms() - Method in class org.simtk.molecularstructure.MolecularClass

atoms() - Method in class org.simtk.molecularstructure.ResidueClass

Override atoms() method to use a class that can index by atom name

AtomSet - Class in org.simtk.molecularstructure.atom

AtomSet() - Constructor for class org.simtk.molecularstructure.atom.AtomSet

AtomSphereActor - Class in org.simtk.moleculargraphics.cartoon

AtomSphereActor() - Constructor for class org.simtk.moleculargraphics.cartoon.AtomSphereActor

AtomSphereActor(double) - Constructor for class org.simtk.moleculargraphics.cartoon.AtomSphereActor

AtomSpheres - Class in org.simtk.moleculargraphics.cartoon

AtomSpheres() - Constructor for class org.simtk.moleculargraphics.cartoon.AtomSpheres

available() - Method in class org.simtk.util.UncompressInputStream

axisAngle(Vector3D, double) - Static method in class org.simtk.geometry3d.Matrix3DClass

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

AZURE - Static variable in class org.simtk.util.ColorName

AZURE1 - Static variable in class org.simtk.util.ColorName

AZURE2 - Static variable in class org.simtk.util.ColorName

AZURE3 - Static variable in class org.simtk.util.ColorName

AZURE4 - Static variable in class org.simtk.util.ColorName