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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.pdb.MoleculeAcquisitionMethodDialog
 
add(MassBody) - Method in class org.simtk.geometry3d.MassBodyClass
 
addBasePair(BasePair) - Method in class org.simtk.molecularstructure.nucleicacid.Duplex
 
addColor(String, String) - Static method in class org.simtk.util.ColorName
 
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
 
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
 
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
 
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.molecularstructure.nucleicacid.BasePair
 
addResidue(Residue) - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
addResidue(Residue) - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
addSecondaryStructure(SecondaryStructure) - Method in class org.simtk.molecularstructure.BiopolymerClass
 
addSelectionListener(SelectionListener) - Method in class org.simtk.util.SelectionBroadcaster
 
Adenylate - Class in org.simtk.molecularstructure.nucleicacid
 
Adenylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Adenylate
 
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
 
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
 
Arginine - Class in org.simtk.molecularstructure.protein
 
Arginine() - Constructor for class org.simtk.molecularstructure.protein.Arginine
 
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
 
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
 
available() - Method in class org.simtk.util.UncompressInputStream
 
axisAngle(Vector3D, double) - Static method in class org.simtk.geometry3d.Matrix3DClass
 
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
 

B

backboneGroup - Static variable in class org.simtk.molecularstructure.protein.AminoAcid
 
baseGroup - Static variable in class org.simtk.molecularstructure.nucleicacid.Nucleotide
 
BasePair - Class in org.simtk.molecularstructure.nucleicacid
 
BasePair(Residue, Residue) - Constructor for class org.simtk.molecularstructure.nucleicacid.BasePair
 
BasePair.BondOrientation - Enum in org.simtk.molecularstructure.nucleicacid
 
BasePair.EdgeType - Enum in org.simtk.molecularstructure.nucleicacid
 
basePairs() - Method in class org.simtk.molecularstructure.nucleicacid.BaseTriple
 
basePairs() - Method in class org.simtk.molecularstructure.nucleicacid.Duplex
 
BaseStack - Class in org.simtk.molecularstructure.nucleicacid
 
BaseStack() - Constructor for class org.simtk.molecularstructure.nucleicacid.BaseStack
 
BaseStack(Collection<Residue>) - Constructor for class org.simtk.molecularstructure.nucleicacid.BaseStack
 
BaseStack(Collection<Residue>, String) - Constructor for class org.simtk.molecularstructure.nucleicacid.BaseStack
 
BaseTriple - Class in org.simtk.molecularstructure.nucleicacid
 
BaseTriple(Collection<BasePair>) - Constructor for class org.simtk.molecularstructure.nucleicacid.BaseTriple
 
BaseTriple(Collection<BasePair>, String) - Constructor for class org.simtk.molecularstructure.nucleicacid.BaseTriple
 
BaseTriple(BasePair, BasePair, BasePair) - Constructor for class org.simtk.molecularstructure.nucleicacid.BaseTriple
 
BEIGE - Static variable in class org.simtk.util.ColorName
 
bestLine3D(Vector<Vector3D>) - Static method in class org.simtk.geometry3d.Line3D
 
bestPlane3D(Collection<Vector3D>) - Static method in class org.simtk.geometry3d.Plane3D
Create a plane that minimizes the sum of squared distances to a set of points
bestPlane3D(Vector3D[], double[]) - Static method in class org.simtk.geometry3d.Plane3D
 
bestPlane3D() - Method in interface org.simtk.molecularstructure.Molecular
 
bestPlane3D() - Method in class org.simtk.molecularstructure.MolecularClass
 
BetaStrand - Class in org.simtk.molecularstructure.protein
 
BetaStrand() - Constructor for class org.simtk.molecularstructure.protein.BetaStrand
 
Biopolymer - Interface in org.simtk.molecularstructure
 
BiopolymerClass - Class in org.simtk.molecularstructure
 
BiopolymerClass(char) - Constructor for class org.simtk.molecularstructure.BiopolymerClass
 
BISQUE - Static variable in class org.simtk.util.ColorName
 
BISQUE1 - Static variable in class org.simtk.util.ColorName
 
BISQUE2 - Static variable in class org.simtk.util.ColorName
 
BISQUE3 - Static variable in class org.simtk.util.ColorName
 
BISQUE4 - Static variable in class org.simtk.util.ColorName
 
BLACK - Static variable in class org.simtk.util.ColorName
 
BLANCHED_ALMOND - Static variable in class org.simtk.util.ColorName
 
BLUE - Static variable in class org.simtk.util.ColorName
 
BLUE1 - Static variable in class org.simtk.util.ColorName
 
BLUE2 - Static variable in class org.simtk.util.ColorName
 
BLUE3 - Static variable in class org.simtk.util.ColorName
 
BLUE4 - Static variable in class org.simtk.util.ColorName
 
BLUE_VIOLET - Static variable in class org.simtk.util.ColorName
 
bond_orient - Variable in class org.simtk.molecularstructure.nucleicacid.BasePair
 
bonds() - Method in interface org.simtk.molecularstructure.atom.Atom
 
bonds() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
BORON - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
BROMINE - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
BROWN - Static variable in class org.simtk.util.ColorName
 
BROWN1 - Static variable in class org.simtk.util.ColorName
 
BROWN2 - Static variable in class org.simtk.util.ColorName
 
BROWN3 - Static variable in class org.simtk.util.ColorName
 
BROWN4 - Static variable in class org.simtk.util.ColorName
 
BURLYWOOD - Static variable in class org.simtk.util.ColorName
 
BURLYWOOD1 - Static variable in class org.simtk.util.ColorName
 
BURLYWOOD2 - Static variable in class org.simtk.util.ColorName
 
BURLYWOOD3 - Static variable in class org.simtk.util.ColorName
 
BURLYWOOD4 - Static variable in class org.simtk.util.ColorName
 
byteValue() - Method in class org.simtk.geometry3d.Angle
 

C

CADET_BLUE - Static variable in class org.simtk.util.ColorName
 
CADET_BLUE1 - Static variable in class org.simtk.util.ColorName
 
CADET_BLUE2 - Static variable in class org.simtk.util.ColorName
 
CADET_BLUE3 - Static variable in class org.simtk.util.ColorName
 
CADET_BLUE4 - Static variable in class org.simtk.util.ColorName
 
CALCIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
CARBON - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
centroid(Collection<Vector2D>) - Static method in class org.simtk.geometry3d.Vector2DClass
Compute the centroid or mean point
centroid(Vector2D[], double[]) - Static method in class org.simtk.geometry3d.Vector2DClass
 
centroid(Collection<Vector3D>) - Static method in class org.simtk.geometry3d.Vector3DClass
Compute the centroid or mean point
centroid(Vector3D[], double[]) - Static method in class org.simtk.geometry3d.Vector3DClass
 
chainId - Variable in class org.simtk.molecularstructure.MoleculeClass
 
CHARTREUSE - Static variable in class org.simtk.util.ColorName
 
CHARTREUSE1 - Static variable in class org.simtk.util.ColorName
 
CHARTREUSE2 - Static variable in class org.simtk.util.ColorName
 
CHARTREUSE3 - Static variable in class org.simtk.util.ColorName
 
CHARTREUSE4 - Static variable in class org.simtk.util.ColorName
 
Chemical - Interface in org.simtk.molecularstructure
 
ChemicalElement - Interface in org.simtk.molecularstructure.atom
 
ChemicalElementClass - Class in org.simtk.molecularstructure.atom
Instantiates interface for ChemicalElement, using a single set of parameters for each element in the periodic table
CHLORINE - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
CHOCOLATE - Static variable in class org.simtk.util.ColorName
 
CHOCOLATE1 - Static variable in class org.simtk.util.ColorName
 
CHOCOLATE2 - Static variable in class org.simtk.util.ColorName
 
CHOCOLATE3 - Static variable in class org.simtk.util.ColorName
 
CHOCOLATE4 - Static variable in class org.simtk.util.ColorName
 
clear() - Method in class org.simtk.geometry3d.Hash3D
 
clear() - Method in class org.simtk.geometry3d.MassBodyClass
 
clone() - Method in class org.simtk.geometry3d.Hash3D
 
ColorName - Class in org.simtk.util
 
CommandLineInterface - Class in org.simtk.util
 
CommandLineInterface() - Constructor for class org.simtk.util.CommandLineInterface
 
computeBaseHydrogenBonds() - Method in class org.simtk.molecularstructure.nucleicacid.NucleicAcid
 
COPPER - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
copy(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
copy(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
copy contents of argument vector into this one
copy(MathMatrix) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
copy(MathVector) - Method in interface org.simtk.geometry3d.MutableMathVector
 
copy(MathVector) - Method in class org.simtk.geometry3d.Vector2DClass
 
copy(MathVector) - Method in class org.simtk.geometry3d.Vector3DClass
 
CORAL - Static variable in class org.simtk.util.ColorName
 
CORAL1 - Static variable in class org.simtk.util.ColorName
 
CORAL2 - Static variable in class org.simtk.util.ColorName
 
CORAL3 - Static variable in class org.simtk.util.ColorName
 
CORAL4 - Static variable in class org.simtk.util.ColorName
 
CORN_SILK - Static variable in class org.simtk.util.ColorName
 
CORN_SILK1 - Static variable in class org.simtk.util.ColorName
 
CORN_SILK2 - Static variable in class org.simtk.util.ColorName
 
CORN_SILK3 - Static variable in class org.simtk.util.ColorName
 
CORN_SILK4 - Static variable in class org.simtk.util.ColorName
 
CORNFLOWER_BLUE - Static variable in class org.simtk.util.ColorName
 
cos() - Method in class org.simtk.geometry3d.Angle
 
createFactoryPDBMolecule(URL) - Static method in class org.simtk.molecularstructure.MoleculeClass
 
createFactoryPDBMolecule(String) - Static method in class org.simtk.molecularstructure.MoleculeClass
 
createFactoryPDBMolecule(LineNumberReader) - Static method in class org.simtk.molecularstructure.MoleculeClass
Read one molecule from a PDB format stream.
CRIMSON - Static variable in class org.simtk.util.ColorName
 
cross(Vector2D) - Method in interface org.simtk.geometry3d.Vector2D
 
cross(Vector2D) - Method in class org.simtk.geometry3d.Vector2DClass
 
cross(Vector3D) - Method in interface org.simtk.geometry3d.Vector3D
 
cross(Vector3D) - Method in class org.simtk.geometry3d.Vector3DClass
 
currentPathUpdated() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
CYAN - Static variable in class org.simtk.util.ColorName
 
CYAN1 - Static variable in class org.simtk.util.ColorName
 
CYAN2 - Static variable in class org.simtk.util.ColorName
 
CYAN3 - Static variable in class org.simtk.util.ColorName
 
CYAN4 - Static variable in class org.simtk.util.ColorName
 
Cylinder - Class in org.simtk.geometry3d
 
Cylinder(Vector3D, Vector3D, double) - Constructor for class org.simtk.geometry3d.Cylinder
 
Cysteine - Class in org.simtk.molecularstructure.protein
 
Cysteine() - Constructor for class org.simtk.molecularstructure.protein.Cysteine
 
Cytidylate - Class in org.simtk.molecularstructure.nucleicacid
 
Cytidylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Cytidylate
 

D

DARK_BLUE - Static variable in class org.simtk.util.ColorName
 
DARK_CYAN - Static variable in class org.simtk.util.ColorName
 
DARK_GOLDENROD - Static variable in class org.simtk.util.ColorName
 
DARK_GOLDENROD1 - Static variable in class org.simtk.util.ColorName
 
DARK_GOLDENROD2 - Static variable in class org.simtk.util.ColorName
 
DARK_GOLDENROD3 - Static variable in class org.simtk.util.ColorName
 
DARK_GOLDENROD4 - Static variable in class org.simtk.util.ColorName
 
DARK_GRAY - Static variable in class org.simtk.util.ColorName
 
DARK_GREEN - Static variable in class org.simtk.util.ColorName
 
DARK_GREY - Static variable in class org.simtk.util.ColorName
 
DARK_KHAKI - Static variable in class org.simtk.util.ColorName
 
DARK_MAGENTA - Static variable in class org.simtk.util.ColorName
 
DARK_OLIVE_GREEN - Static variable in class org.simtk.util.ColorName
 
DARK_OLIVE_GREEN1 - Static variable in class org.simtk.util.ColorName
 
DARK_OLIVE_GREEN2 - Static variable in class org.simtk.util.ColorName
 
DARK_OLIVE_GREEN3 - Static variable in class org.simtk.util.ColorName
 
DARK_OLIVE_GREEN4 - Static variable in class org.simtk.util.ColorName
 
DARK_ORANGE - Static variable in class org.simtk.util.ColorName
 
DARK_ORANGE1 - Static variable in class org.simtk.util.ColorName
 
DARK_ORANGE2 - Static variable in class org.simtk.util.ColorName
 
DARK_ORANGE3 - Static variable in class org.simtk.util.ColorName
 
DARK_ORANGE4 - Static variable in class org.simtk.util.ColorName
 
DARK_ORCHID - Static variable in class org.simtk.util.ColorName
 
DARK_ORCHID1 - Static variable in class org.simtk.util.ColorName
 
DARK_ORCHID2 - Static variable in class org.simtk.util.ColorName
 
DARK_ORCHID3 - Static variable in class org.simtk.util.ColorName
 
DARK_ORCHID4 - Static variable in class org.simtk.util.ColorName
 
DARK_RED - Static variable in class org.simtk.util.ColorName
 
DARK_SALMON - Static variable in class org.simtk.util.ColorName
 
DARK_SEA_GREEN - Static variable in class org.simtk.util.ColorName
 
DARK_SEA_GREEN1 - Static variable in class org.simtk.util.ColorName
 
DARK_SEA_GREEN2 - Static variable in class org.simtk.util.ColorName
 
DARK_SEA_GREEN3 - Static variable in class org.simtk.util.ColorName
 
DARK_SEA_GREEN4 - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_BLUE - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_GRAY - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_GRAY1 - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_GRAY2 - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_GRAY3 - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_GRAY4 - Static variable in class org.simtk.util.ColorName
 
DARK_SLATE_GREY - Static variable in class org.simtk.util.ColorName
 
DARK_TURQUOISE - Static variable in class org.simtk.util.ColorName
 
DARK_VIOLET - Static variable in class org.simtk.util.ColorName
 
DEEP_PINK - Static variable in class org.simtk.util.ColorName
 
DEEP_PINK1 - Static variable in class org.simtk.util.ColorName
 
DEEP_PINK2 - Static variable in class org.simtk.util.ColorName
 
DEEP_PINK3 - Static variable in class org.simtk.util.ColorName
 
DEEP_PINK4 - Static variable in class org.simtk.util.ColorName
 
DEEP_SKY_BLUE - Static variable in class org.simtk.util.ColorName
 
DEEP_SKY_BLUE1 - Static variable in class org.simtk.util.ColorName
 
DEEP_SKY_BLUE2 - Static variable in class org.simtk.util.ColorName
 
DEEP_SKY_BLUE3 - Static variable in class org.simtk.util.ColorName
 
DEEP_SKY_BLUE4 - Static variable in class org.simtk.util.ColorName
 
DEGREES - Static variable in class org.simtk.geometry3d.Angle.Units
 
DEGREES_PER_RADIAN - Static variable in class org.simtk.geometry3d.Angle
 
deleteObserver(Observer) - Method in class org.simtk.gui.ProgressManager
 
deleteObserver(Observer) - Method in interface org.simtk.mvc.ObservableInterface
 
deleteObservers() - Method in class org.simtk.gui.ProgressManager
 
deleteObservers() - Method in interface org.simtk.mvc.ObservableInterface
 
designations - Variable in enum org.simtk.molecularstructure.nucleicacid.BasePair.BondOrientation
 
designations - Variable in enum org.simtk.molecularstructure.nucleicacid.BasePair.EdgeType
 
designations - Variable in enum org.simtk.molecularstructure.SecondaryStructureClass.SourceType
 
DIM_GRAY - Static variable in class org.simtk.util.ColorName
 
DIM_GREY - Static variable in class org.simtk.util.ColorName
 
direction - Variable in class org.simtk.geometry3d.Line3D
 
displayableStructures() - Method in class org.simtk.molecularstructure.BiopolymerClass
 
displaySourceTypes - Variable in class org.simtk.molecularstructure.MoleculeClass
 
distance(MathVector) - Method in interface org.simtk.geometry3d.MathVector
 
distance(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
distance(Vector3D) - Method in class org.simtk.geometry3d.Plane3D
Distance between a point and a plane
distance(Atom) - Method in interface org.simtk.molecularstructure.atom.Atom
 
distance(Atom) - Method in class org.simtk.molecularstructure.atom.AtomClass
 
distanceSquared(MathVector) - Method in interface org.simtk.geometry3d.MathVector
 
distanceSquared(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
DNA - Class in org.simtk.molecularstructure.nucleicacid
 
DNA(char) - Constructor for class org.simtk.molecularstructure.nucleicacid.DNA
 
DODGER_BLUE - Static variable in class org.simtk.util.ColorName
 
DODGER_BLUE1 - Static variable in class org.simtk.util.ColorName
 
DODGER_BLUE2 - Static variable in class org.simtk.util.ColorName
 
DODGER_BLUE3 - Static variable in class org.simtk.util.ColorName
 
DODGER_BLUE4 - Static variable in class org.simtk.util.ColorName
 
dot(MathVector) - Method in interface org.simtk.geometry3d.MathVector
 
dot(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
DoubleRing - Class in org.simtk.util
 
DoubleRing(int) - Constructor for class org.simtk.util.DoubleRing
 
doubleValue() - Method in class org.simtk.geometry3d.Angle
 
Duplex - Class in org.simtk.molecularstructure.nucleicacid
 
Duplex() - Constructor for class org.simtk.molecularstructure.nucleicacid.Duplex
 

E

edges - Variable in class org.simtk.molecularstructure.nucleicacid.BasePair
 
equals(Object) - Method in class org.simtk.geometry3d.Angle
 
equals(Angle) - Method in class org.simtk.geometry3d.Angle
 
equals(Number) - Method in class org.simtk.geometry3d.Angle
 
equals(Object) - Method in class org.simtk.geometry3d.Vector2DClass
 
equals(Object) - Method in class org.simtk.geometry3d.Vector3DClass
 
equals(Object) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
execute(String[], Object) - Method in interface org.simtk.util.LineCommand
 

F

fileLoadObservable - Variable in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
FileNameFilter - Class in org.simtk.pdb
 
FIREBRICK - Static variable in class org.simtk.util.ColorName
 
FIREBRICK1 - Static variable in class org.simtk.util.ColorName
 
FIREBRICK2 - Static variable in class org.simtk.util.ColorName
 
FIREBRICK3 - Static variable in class org.simtk.util.ColorName
 
FIREBRICK4 - Static variable in class org.simtk.util.ColorName
 
fireSelect(Selectable) - Method in class org.simtk.util.SelectionBroadcaster
 
fireUnSelect() - Method in class org.simtk.util.SelectionBroadcaster
 
fireUnSelect(Selectable) - Method in class org.simtk.util.SelectionBroadcaster
 
floatValue() - Method in class org.simtk.geometry3d.Angle
 
FLORAL_WHITE - Static variable in class org.simtk.util.ColorName
 
FLUORINE - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
FOREST_GREEN - Static variable in class org.simtk.util.ColorName
 
FUCHSIA - Static variable in class org.simtk.util.ColorName
 
FunctionalGroup - Class in org.simtk.molecularstructure
 
FunctionalGroup(String[]) - Constructor for class org.simtk.molecularstructure.FunctionalGroup
 

G

GAINSBORO - Static variable in class org.simtk.util.ColorName
 
genericBonds() - Method in class org.simtk.molecularstructure.ResidueClass
 
genericBonds() - Method in interface org.simtk.molecularstructure.ResidueType
 
genericBonds - Variable in class org.simtk.molecularstructure.ResidueTypeClass
 
genericBonds() - Method in class org.simtk.molecularstructure.ResidueTypeClass
 
get(int, int) - Method in class org.simtk.geometry3d.JamaMatrix
 
get(int, int) - Method in interface org.simtk.geometry3d.MathMatrix
 
get(int, int) - Method in class org.simtk.geometry3d.MathMatrixClass
 
get(int) - Method in interface org.simtk.geometry3d.MathVector
 
get(int) - Method in class org.simtk.geometry3d.MathVectorClass
 
get(int) - Method in class org.simtk.geometry3d.Vector3DFloatArrayWrapper
 
get(FunctionalGroup) - Method in interface org.simtk.molecularstructure.Residue
 
get(FunctionalGroup) - Method in class org.simtk.molecularstructure.ResidueClass
 
getAtom(String) - Method in interface org.simtk.molecularstructure.Residue
 
getAtom(String) - Method in class org.simtk.molecularstructure.ResidueClass
Get the atom with the given name.
getAtomName() - Method in interface org.simtk.molecularstructure.atom.Atom
 
getAtomName() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getAtomNames() - Method in class org.simtk.molecularstructure.FunctionalGroup
 
getBackbone() - Method in interface org.simtk.molecularstructure.Residue
 
getBackbone() - Method in class org.simtk.molecularstructure.ResidueClass
 
getBackbonePosition() - Method in interface org.simtk.molecularstructure.Residue
 
getBackbonePosition() - Method in class org.simtk.molecularstructure.ResidueClass
Return preferred location of backbone trace in molecular representations
getBasePair(Residue, Residue, String) - Static method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getBasePlane() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getBond_orient() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getBondOrienation(String) - Static method in enum org.simtk.molecularstructure.nucleicacid.BasePair.BondOrientation
 
getCenterOfMass() - Method in interface org.simtk.geometry3d.MassBody
 
getCenterOfMass() - Method in class org.simtk.geometry3d.MassBodyClass
 
getCenterOfMass() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getCenterOfMass() - Method in class org.simtk.molecularstructure.MolecularClass
 
getCenterOfMass() - Method in class org.simtk.molecularstructure.MoleculeCollection
 
getClosest(Vector3D, double) - Method in class org.simtk.geometry3d.Hash3D
Return the closest object to a particular position If no object is within the specified radius, return null.
getClosestPoint(Vector3D) - Method in class org.simtk.geometry3d.Line3D
 
getColor(String) - Static method in class org.simtk.util.ColorName
 
getColumn(int) - Method in interface org.simtk.geometry3d.MathMatrix
 
getColumn(int) - Method in class org.simtk.geometry3d.MathMatrixClass
 
getColumn(int) - Method in interface org.simtk.geometry3d.Matrix3D
 
getColumn(int) - Method in class org.simtk.geometry3d.Matrix3DClass
 
getColumnCount() - Method in class org.simtk.geometry3d.JamaMatrix
 
getColumnCount() - Method in interface org.simtk.geometry3d.MathMatrix
 
getColumnCount() - Method in class org.simtk.geometry3d.MathMatrixClass
 
getContentPane() - Method in class org.simtk.gui.UndoableDialog
 
getCoordinates() - Method in interface org.simtk.molecularstructure.atom.Atom
 
getCoordinates() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getCoordinates() - Method in class org.simtk.molecularstructure.atom.AtomPosition
 
getCovalentRadius() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getCovalentRadius() - Method in interface org.simtk.molecularstructure.atom.ChemicalElement
 
getCovalentRadius() - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
getCurrentPath() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
getDefaultPdbId() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
getDescription() - Method in class org.simtk.pdb.FileNameFilter
 
getDescription() - Method in class org.simtk.util.MyJFileFilter
 
getDiagonal() - Method in interface org.simtk.geometry3d.MathMatrix
 
getDiagonal() - Method in class org.simtk.geometry3d.MathMatrixClass
 
getDiagonal() - Method in interface org.simtk.geometry3d.Matrix3D
 
getDiagonal() - Method in class org.simtk.geometry3d.Matrix3DClass
 
getDimension() - Method in interface org.simtk.geometry3d.MathVector
 
getDimension() - Method in class org.simtk.geometry3d.MathVectorClass
 
getDirection() - Method in class org.simtk.geometry3d.Line3D
 
getDisplaySourceTypes() - Method in interface org.simtk.molecularstructure.Molecule
 
getDisplaySourceTypes() - Method in class org.simtk.molecularstructure.MoleculeClass
 
getEdge(Residue) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getEdgeType(String) - Static method in enum org.simtk.molecularstructure.nucleicacid.BasePair.EdgeType
 
getEigenvalueDecomposition() - Method in class org.simtk.geometry3d.JamaMatrix
 
getElement(int) - Method in interface org.simtk.geometry3d.MathVector
 
getElement(int) - Method in class org.simtk.geometry3d.MathVectorClass
 
getElementName() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getElementName() - Method in interface org.simtk.molecularstructure.atom.ChemicalElement
 
getElementName() - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
getElementSymbol() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getElementSymbol() - Method in interface org.simtk.molecularstructure.atom.ChemicalElement
 
getElementSymbol() - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
getExtension(File) - Static method in class org.simtk.util.MyJFileFilter
 
getGlycosyl() - Method in class org.simtk.molecularstructure.ResidueClass
 
getHead() - Method in class org.simtk.geometry3d.Cylinder
 
getHelixCenter() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
Estimate position at center of a double helix containing this base pair
getHelixType() - Method in class org.simtk.molecularstructure.protein.Helix
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Adenylate
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Cytidylate
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Nucleotide
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Purine
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Pyrimidine
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Thymidylate
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Uridylate
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.ResidueClass
 
getHydrogenBondAcceptorAtomNames() - Method in interface org.simtk.molecularstructure.ResidueType
 
getHydrogenBondAcceptorAtomNames() - Method in class org.simtk.molecularstructure.ResidueTypeClass
 
getHydrogenBondAcceptors() - Method in interface org.simtk.molecularstructure.Residue
 
getHydrogenBondAcceptors() - Method in class org.simtk.molecularstructure.ResidueClass
 
getHydrogenBondDonorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Guanylate
 
getHydrogenBondDonorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Inositate
 
getHydrogenBondDonorAtomNames() - Method in class org.simtk.molecularstructure.nucleicacid.Nucleotide
 
getHydrogenBondDonorAtomNames() - Method in class org.simtk.molecularstructure.ResidueClass
 
getHydrogenBondDonorAtomNames() - Method in interface org.simtk.molecularstructure.ResidueType
 
getHydrogenBondDonorAtomNames() - Method in class org.simtk.molecularstructure.ResidueTypeClass
 
getHydrogenBondDonors() - Method in interface org.simtk.molecularstructure.Residue
 
getHydrogenBondDonors() - Method in class org.simtk.molecularstructure.ResidueClass
 
getInputStream() - Method in class org.simtk.pdb.LoadPdbUrlProcess
 
getInputStructureFileName() - Method in class org.simtk.molecularstructure.MoleculeCollection
 
getMass() - Method in interface org.simtk.geometry3d.MassBody
 
getMass() - Method in class org.simtk.geometry3d.MassBodyClass
 
getMass() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getMass() - Method in interface org.simtk.molecularstructure.atom.ChemicalElement
 
getMass() - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
getMass() - Method in class org.simtk.molecularstructure.MolecularClass
 
getMass() - Method in class org.simtk.molecularstructure.MoleculeCollection
 
getMaximum() - Method in interface org.simtk.gui.MonitoredProcess
 
getMidpoint() - Method in class org.simtk.geometry3d.Cylinder
 
getMilliseconds() - Method in class org.simtk.util.Stopwatch
 
getMinimum() - Method in interface org.simtk.gui.MonitoredProcess
 
getMolecule(int) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
getMolecules() - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
getMolecules() - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
getName(Color) - Static method in class org.simtk.util.ColorName
 
getNames(Color) - Static method in class org.simtk.util.ColorName
 
getNextResidue() - Method in interface org.simtk.molecularstructure.Residue
 
getNextResidue() - Method in class org.simtk.molecularstructure.ResidueClass
 
getNormal() - Method in class org.simtk.geometry3d.Plane3D
 
getNormal() - Method in class org.simtk.geometry3d.SemiCylinder
 
getOccupancy() - Method in interface org.simtk.molecularstructure.atom.Atom
 
getOccupancy() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getOccupancy() - Method in class org.simtk.molecularstructure.atom.AtomPosition
 
getOneLetterCode() - Method in class org.simtk.molecularstructure.ResidueClass
Create an empty Residue object with no atoms.
getOneLetterCode() - Method in interface org.simtk.molecularstructure.ResidueType
 
getOneLetterCode() - Method in class org.simtk.molecularstructure.ResidueTypeClass
 
getOrigin() - Method in class org.simtk.geometry3d.Line3D
 
getParameters() - Method in class org.simtk.gui.ParameterSetModel
 
getPdbAltLoc() - Method in class org.simtk.molecularstructure.atom.AtomPosition
 
getPdbChainId() - Method in interface org.simtk.molecularstructure.Molecule
 
getPdbChainId() - Method in class org.simtk.molecularstructure.MoleculeClass
 
getPdbId() - Method in class org.simtk.molecularstructure.MoleculeCollection
 
getPdbId() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
getPdbInsertionCode() - Method in interface org.simtk.molecularstructure.Residue
 
getPdbInsertionCode() - Method in class org.simtk.molecularstructure.ResidueClass
 
getPreviousResidue() - Method in interface org.simtk.molecularstructure.Residue
 
getPreviousResidue() - Method in class org.simtk.molecularstructure.ResidueClass
 
getProgress() - Method in interface org.simtk.gui.MonitoredProcess
 
getProgressPanel() - Method in class org.simtk.gui.ProgressDialogClass
 
getPucker() - Method in class org.simtk.molecularstructure.ResidueClass
 
getRadius() - Method in class org.simtk.geometry3d.Cylinder
 
getRange() - Method in class org.simtk.geometry3d.Angle
 
getRedoAction() - Method in class org.simtk.gui.UndoRedoMechanism
 
getResidue() - Method in interface org.simtk.molecularstructure.atom.Atom
 
getResidue() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getResidue(int) - Method in interface org.simtk.molecularstructure.Biopolymer
 
getResidue(int) - Method in class org.simtk.molecularstructure.BiopolymerClass
 
getResidue1() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getResidue2() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getResidueByNumber(int) - Method in interface org.simtk.molecularstructure.Biopolymer
 
getResidueByNumber(int) - Method in class org.simtk.molecularstructure.BiopolymerClass
 
getResidueByNumber(int, char) - Method in class org.simtk.molecularstructure.BiopolymerClass
 
getResidueByNumber(String) - Method in class org.simtk.molecularstructure.BiopolymerClass
 
getResidueIterator() - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
getResidueIterator() - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
getResidueName() - Method in class org.simtk.molecularstructure.ResidueClass
 
getResidueName() - Method in interface org.simtk.molecularstructure.ResidueType
 
getResidueName() - Method in class org.simtk.molecularstructure.ResidueTypeClass
 
getResidueNumber() - Method in interface org.simtk.molecularstructure.Residue
 
getResidueNumber() - Method in class org.simtk.molecularstructure.ResidueClass
 
getResidueType() - Method in interface org.simtk.molecularstructure.Residue
 
getResidueType() - Method in class org.simtk.molecularstructure.ResidueClass
 
getRotation() - Method in interface org.simtk.geometry3d.HomogeneousTransform
 
getRotation() - Method in class org.simtk.geometry3d.HomogeneousTransformClass
 
getRow(int) - Method in interface org.simtk.geometry3d.MathMatrix
 
getRow(int) - Method in class org.simtk.geometry3d.MathMatrixClass
 
getRow(int) - Method in interface org.simtk.geometry3d.Matrix3D
 
getRow(int) - Method in class org.simtk.geometry3d.Matrix3DClass
 
getRowCount() - Method in class org.simtk.geometry3d.JamaMatrix
 
getRowCount() - Method in interface org.simtk.geometry3d.MathMatrix
 
getRowCount() - Method in class org.simtk.geometry3d.MathMatrixClass
 
getSeconds() - Method in class org.simtk.util.Stopwatch
 
getSelected() - Method in class org.simtk.util.SelectionBroadcaster
Return a list of those objects that have been selected through this object
getSideChainPosition() - Method in interface org.simtk.molecularstructure.Residue
 
getSideChainPosition() - Method in class org.simtk.molecularstructure.ResidueClass
 
getSource() - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
getSource() - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
getSourceType(String) - Static method in enum org.simtk.molecularstructure.SecondaryStructureClass.SourceType
 
getStrand_orient() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
getSuperposition() - Method in class org.simtk.molecularstructure.SequenceAlignment
Generates rigid-body transformation that when applied to the first molecule's residues, minimizes the least squared deviation from the second molecule's residues.
getTail() - Method in class org.simtk.geometry3d.Cylinder
 
getTemperatureFactor() - Method in interface org.simtk.molecularstructure.atom.Atom
 
getTemperatureFactor() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getTemperatureFactor() - Method in class org.simtk.molecularstructure.atom.AtomPosition
 
getThreeLetterCode() - Method in class org.simtk.molecularstructure.ResidueClass
 
getThreeLetterCode() - Method in interface org.simtk.molecularstructure.ResidueType
 
getThreeLetterCode() - Method in class org.simtk.molecularstructure.ResidueTypeClass
 
getTitle() - Method in class org.simtk.molecularstructure.MoleculeCollection
 
getTranslation() - Method in interface org.simtk.geometry3d.HomogeneousTransform
 
getTranslation() - Method in class org.simtk.geometry3d.HomogeneousTransformClass
 
getType(String) - Static method in class org.simtk.molecularstructure.ResidueTypeClass
 
getUndoAction() - Method in class org.simtk.gui.UndoRedoMechanism
 
getUnits() - Method in class org.simtk.geometry3d.Angle
 
getValue(Angle.Units) - Method in class org.simtk.geometry3d.Angle
 
getValue() - Method in class org.simtk.geometry3d.Angle
 
getVanDerWaalsRadius() - Method in class org.simtk.molecularstructure.atom.AtomClass
 
getVanDerWaalsRadius() - Method in interface org.simtk.molecularstructure.atom.ChemicalElement
 
getVanDerWaalsRadius() - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
getX() - Method in interface org.simtk.geometry3d.Vector2D
 
getX() - Method in class org.simtk.geometry3d.Vector2DClass
 
getX() - Method in interface org.simtk.geometry3d.Vector3D
 
getX() - Method in class org.simtk.geometry3d.Vector3DClass
 
getY() - Method in interface org.simtk.geometry3d.Vector2D
 
getY() - Method in class org.simtk.geometry3d.Vector2DClass
 
getY() - Method in interface org.simtk.geometry3d.Vector3D
 
getY() - Method in class org.simtk.geometry3d.Vector3DClass
 
getZ() - Method in interface org.simtk.geometry3d.Vector3D
 
getZ() - Method in class org.simtk.geometry3d.Vector3DClass
 
GHOST_WHITE - Static variable in class org.simtk.util.ColorName
 
Glutamate - Class in org.simtk.molecularstructure.protein
 
Glutamate() - Constructor for class org.simtk.molecularstructure.protein.Glutamate
 
Glutamine - Class in org.simtk.molecularstructure.protein
 
Glutamine() - Constructor for class org.simtk.molecularstructure.protein.Glutamine
 
Glycine - Class in org.simtk.molecularstructure.protein
 
Glycine() - Constructor for class org.simtk.molecularstructure.protein.Glycine
 
GOLD - Static variable in class org.simtk.util.ColorName
 
GOLD1 - Static variable in class org.simtk.util.ColorName
 
GOLD2 - Static variable in class org.simtk.util.ColorName
 
GOLD3 - Static variable in class org.simtk.util.ColorName
 
GOLD4 - Static variable in class org.simtk.util.ColorName
 
GOLDENROD - Static variable in class org.simtk.util.ColorName
 
GOLDENROD1 - Static variable in class org.simtk.util.ColorName
 
GOLDENROD2 - Static variable in class org.simtk.util.ColorName
 
GOLDENROD3 - Static variable in class org.simtk.util.ColorName
 
GOLDENROD4 - Static variable in class org.simtk.util.ColorName
 
GRADS - Static variable in class org.simtk.geometry3d.Angle.Units
 
GRADS_PER_RADIAN - Static variable in class org.simtk.geometry3d.Angle
 
GRAY - Static variable in class org.simtk.util.ColorName
 
GRAY0 - Static variable in class org.simtk.util.ColorName
 
GRAY1 - Static variable in class org.simtk.util.ColorName
 
GRAY10 - Static variable in class org.simtk.util.ColorName
 
GRAY100 - Static variable in class org.simtk.util.ColorName
 
GRAY11 - Static variable in class org.simtk.util.ColorName
 
GRAY12 - Static variable in class org.simtk.util.ColorName
 
GRAY13 - Static variable in class org.simtk.util.ColorName
 
GRAY14 - Static variable in class org.simtk.util.ColorName
 
GRAY15 - Static variable in class org.simtk.util.ColorName
 
GRAY16 - Static variable in class org.simtk.util.ColorName
 
GRAY17 - Static variable in class org.simtk.util.ColorName
 
GRAY18 - Static variable in class org.simtk.util.ColorName
 
GRAY19 - Static variable in class org.simtk.util.ColorName
 
GRAY2 - Static variable in class org.simtk.util.ColorName
 
GRAY20 - Static variable in class org.simtk.util.ColorName
 
GRAY21 - Static variable in class org.simtk.util.ColorName
 
GRAY22 - Static variable in class org.simtk.util.ColorName
 
GRAY23 - Static variable in class org.simtk.util.ColorName
 
GRAY24 - Static variable in class org.simtk.util.ColorName
 
GRAY25 - Static variable in class org.simtk.util.ColorName
 
GRAY26 - Static variable in class org.simtk.util.ColorName
 
GRAY27 - Static variable in class org.simtk.util.ColorName
 
GRAY28 - Static variable in class org.simtk.util.ColorName
 
GRAY29 - Static variable in class org.simtk.util.ColorName
 
GRAY3 - Static variable in class org.simtk.util.ColorName
 
GRAY30 - Static variable in class org.simtk.util.ColorName
 
GRAY31 - Static variable in class org.simtk.util.ColorName
 
GRAY32 - Static variable in class org.simtk.util.ColorName
 
GRAY33 - Static variable in class org.simtk.util.ColorName
 
GRAY34 - Static variable in class org.simtk.util.ColorName
 
GRAY35 - Static variable in class org.simtk.util.ColorName
 
GRAY36 - Static variable in class org.simtk.util.ColorName
 
GRAY37 - Static variable in class org.simtk.util.ColorName
 
GRAY38 - Static variable in class org.simtk.util.ColorName
 
GRAY39 - Static variable in class org.simtk.util.ColorName
 
GRAY4 - Static variable in class org.simtk.util.ColorName
 
GRAY40 - Static variable in class org.simtk.util.ColorName
 
GRAY41 - Static variable in class org.simtk.util.ColorName
 
GRAY42 - Static variable in class org.simtk.util.ColorName
 
GRAY43 - Static variable in class org.simtk.util.ColorName
 
GRAY44 - Static variable in class org.simtk.util.ColorName
 
GRAY45 - Static variable in class org.simtk.util.ColorName
 
GRAY46 - Static variable in class org.simtk.util.ColorName
 
GRAY47 - Static variable in class org.simtk.util.ColorName
 
GRAY48 - Static variable in class org.simtk.util.ColorName
 
GRAY49 - Static variable in class org.simtk.util.ColorName
 
GRAY5 - Static variable in class org.simtk.util.ColorName
 
GRAY50 - Static variable in class org.simtk.util.ColorName
 
GRAY51 - Static variable in class org.simtk.util.ColorName
 
GRAY52 - Static variable in class org.simtk.util.ColorName
 
GRAY53 - Static variable in class org.simtk.util.ColorName
 
GRAY54 - Static variable in class org.simtk.util.ColorName
 
GRAY55 - Static variable in class org.simtk.util.ColorName
 
GRAY56 - Static variable in class org.simtk.util.ColorName
 
GRAY57 - Static variable in class org.simtk.util.ColorName
 
GRAY58 - Static variable in class org.simtk.util.ColorName
 
GRAY59 - Static variable in class org.simtk.util.ColorName
 
GRAY6 - Static variable in class org.simtk.util.ColorName
 
GRAY60 - Static variable in class org.simtk.util.ColorName
 
GRAY61 - Static variable in class org.simtk.util.ColorName
 
GRAY62 - Static variable in class org.simtk.util.ColorName
 
GRAY63 - Static variable in class org.simtk.util.ColorName
 
GRAY64 - Static variable in class org.simtk.util.ColorName
 
GRAY65 - Static variable in class org.simtk.util.ColorName
 
GRAY66 - Static variable in class org.simtk.util.ColorName
 
GRAY67 - Static variable in class org.simtk.util.ColorName
 
GRAY68 - Static variable in class org.simtk.util.ColorName
 
GRAY69 - Static variable in class org.simtk.util.ColorName
 
GRAY7 - Static variable in class org.simtk.util.ColorName
 
GRAY70 - Static variable in class org.simtk.util.ColorName
 
GRAY71 - Static variable in class org.simtk.util.ColorName
 
GRAY72 - Static variable in class org.simtk.util.ColorName
 
GRAY73 - Static variable in class org.simtk.util.ColorName
 
GRAY74 - Static variable in class org.simtk.util.ColorName
 
GRAY75 - Static variable in class org.simtk.util.ColorName
 
GRAY76 - Static variable in class org.simtk.util.ColorName
 
GRAY77 - Static variable in class org.simtk.util.ColorName
 
GRAY78 - Static variable in class org.simtk.util.ColorName
 
GRAY79 - Static variable in class org.simtk.util.ColorName
 
GRAY8 - Static variable in class org.simtk.util.ColorName
 
GRAY80 - Static variable in class org.simtk.util.ColorName
 
GRAY81 - Static variable in class org.simtk.util.ColorName
 
GRAY82 - Static variable in class org.simtk.util.ColorName
 
GRAY83 - Static variable in class org.simtk.util.ColorName
 
GRAY84 - Static variable in class org.simtk.util.ColorName
 
GRAY85 - Static variable in class org.simtk.util.ColorName
 
GRAY86 - Static variable in class org.simtk.util.ColorName
 
GRAY87 - Static variable in class org.simtk.util.ColorName
 
GRAY88 - Static variable in class org.simtk.util.ColorName
 
GRAY89 - Static variable in class org.simtk.util.ColorName
 
GRAY9 - Static variable in class org.simtk.util.ColorName
 
GRAY90 - Static variable in class org.simtk.util.ColorName
 
GRAY91 - Static variable in class org.simtk.util.ColorName
 
GRAY92 - Static variable in class org.simtk.util.ColorName
 
GRAY93 - Static variable in class org.simtk.util.ColorName
 
GRAY94 - Static variable in class org.simtk.util.ColorName
 
GRAY95 - Static variable in class org.simtk.util.ColorName
 
GRAY96 - Static variable in class org.simtk.util.ColorName
 
GRAY97 - Static variable in class org.simtk.util.ColorName
 
GRAY98 - Static variable in class org.simtk.util.ColorName
 
GRAY99 - Static variable in class org.simtk.util.ColorName
 
GREEN - Static variable in class org.simtk.util.ColorName
 
GREEN1 - Static variable in class org.simtk.util.ColorName
 
GREEN2 - Static variable in class org.simtk.util.ColorName
 
GREEN3 - Static variable in class org.simtk.util.ColorName
 
GREEN4 - Static variable in class org.simtk.util.ColorName
 
GREEN_YELLOW - Static variable in class org.simtk.util.ColorName
 
GREY - Static variable in class org.simtk.util.ColorName
 
GREY0 - Static variable in class org.simtk.util.ColorName
 
GREY1 - Static variable in class org.simtk.util.ColorName
 
GREY10 - Static variable in class org.simtk.util.ColorName
 
GREY100 - Static variable in class org.simtk.util.ColorName
 
GREY11 - Static variable in class org.simtk.util.ColorName
 
GREY12 - Static variable in class org.simtk.util.ColorName
 
GREY13 - Static variable in class org.simtk.util.ColorName
 
GREY14 - Static variable in class org.simtk.util.ColorName
 
GREY15 - Static variable in class org.simtk.util.ColorName
 
GREY16 - Static variable in class org.simtk.util.ColorName
 
GREY17 - Static variable in class org.simtk.util.ColorName
 
GREY18 - Static variable in class org.simtk.util.ColorName
 
GREY19 - Static variable in class org.simtk.util.ColorName
 
GREY2 - Static variable in class org.simtk.util.ColorName
 
GREY20 - Static variable in class org.simtk.util.ColorName
 
GREY21 - Static variable in class org.simtk.util.ColorName
 
GREY22 - Static variable in class org.simtk.util.ColorName
 
GREY23 - Static variable in class org.simtk.util.ColorName
 
GREY24 - Static variable in class org.simtk.util.ColorName
 
GREY25 - Static variable in class org.simtk.util.ColorName
 
GREY26 - Static variable in class org.simtk.util.ColorName
 
GREY27 - Static variable in class org.simtk.util.ColorName
 
GREY28 - Static variable in class org.simtk.util.ColorName
 
GREY29 - Static variable in class org.simtk.util.ColorName
 
GREY3 - Static variable in class org.simtk.util.ColorName
 
GREY30 - Static variable in class org.simtk.util.ColorName
 
GREY31 - Static variable in class org.simtk.util.ColorName
 
GREY32 - Static variable in class org.simtk.util.ColorName
 
GREY33 - Static variable in class org.simtk.util.ColorName
 
GREY34 - Static variable in class org.simtk.util.ColorName
 
GREY35 - Static variable in class org.simtk.util.ColorName
 
GREY36 - Static variable in class org.simtk.util.ColorName
 
GREY37 - Static variable in class org.simtk.util.ColorName
 
GREY38 - Static variable in class org.simtk.util.ColorName
 
GREY39 - Static variable in class org.simtk.util.ColorName
 
GREY4 - Static variable in class org.simtk.util.ColorName
 
GREY40 - Static variable in class org.simtk.util.ColorName
 
GREY41 - Static variable in class org.simtk.util.ColorName
 
GREY42 - Static variable in class org.simtk.util.ColorName
 
GREY43 - Static variable in class org.simtk.util.ColorName
 
GREY44 - Static variable in class org.simtk.util.ColorName
 
GREY45 - Static variable in class org.simtk.util.ColorName
 
GREY46 - Static variable in class org.simtk.util.ColorName
 
GREY47 - Static variable in class org.simtk.util.ColorName
 
GREY48 - Static variable in class org.simtk.util.ColorName
 
GREY49 - Static variable in class org.simtk.util.ColorName
 
GREY5 - Static variable in class org.simtk.util.ColorName
 
GREY50 - Static variable in class org.simtk.util.ColorName
 
GREY51 - Static variable in class org.simtk.util.ColorName
 
GREY52 - Static variable in class org.simtk.util.ColorName
 
GREY53 - Static variable in class org.simtk.util.ColorName
 
GREY54 - Static variable in class org.simtk.util.ColorName
 
GREY55 - Static variable in class org.simtk.util.ColorName
 
GREY56 - Static variable in class org.simtk.util.ColorName
 
GREY57 - Static variable in class org.simtk.util.ColorName
 
GREY58 - Static variable in class org.simtk.util.ColorName
 
GREY59 - Static variable in class org.simtk.util.ColorName
 
GREY6 - Static variable in class org.simtk.util.ColorName
 
GREY60 - Static variable in class org.simtk.util.ColorName
 
GREY61 - Static variable in class org.simtk.util.ColorName
 
GREY62 - Static variable in class org.simtk.util.ColorName
 
GREY63 - Static variable in class org.simtk.util.ColorName
 
GREY64 - Static variable in class org.simtk.util.ColorName
 
GREY65 - Static variable in class org.simtk.util.ColorName
 
GREY66 - Static variable in class org.simtk.util.ColorName
 
GREY67 - Static variable in class org.simtk.util.ColorName
 
GREY68 - Static variable in class org.simtk.util.ColorName
 
GREY69 - Static variable in class org.simtk.util.ColorName
 
GREY7 - Static variable in class org.simtk.util.ColorName
 
GREY70 - Static variable in class org.simtk.util.ColorName
 
GREY71 - Static variable in class org.simtk.util.ColorName
 
GREY72 - Static variable in class org.simtk.util.ColorName
 
GREY73 - Static variable in class org.simtk.util.ColorName
 
GREY74 - Static variable in class org.simtk.util.ColorName
 
GREY75 - Static variable in class org.simtk.util.ColorName
 
GREY76 - Static variable in class org.simtk.util.ColorName
 
GREY77 - Static variable in class org.simtk.util.ColorName
 
GREY78 - Static variable in class org.simtk.util.ColorName
 
GREY79 - Static variable in class org.simtk.util.ColorName
 
GREY8 - Static variable in class org.simtk.util.ColorName
 
GREY80 - Static variable in class org.simtk.util.ColorName
 
GREY81 - Static variable in class org.simtk.util.ColorName
 
GREY82 - Static variable in class org.simtk.util.ColorName
 
GREY83 - Static variable in class org.simtk.util.ColorName
 
GREY84 - Static variable in class org.simtk.util.ColorName
 
GREY85 - Static variable in class org.simtk.util.ColorName
 
GREY86 - Static variable in class org.simtk.util.ColorName
 
GREY87 - Static variable in class org.simtk.util.ColorName
 
GREY88 - Static variable in class org.simtk.util.ColorName
 
GREY89 - Static variable in class org.simtk.util.ColorName
 
GREY9 - Static variable in class org.simtk.util.ColorName
 
GREY90 - Static variable in class org.simtk.util.ColorName
 
GREY91 - Static variable in class org.simtk.util.ColorName
 
GREY92 - Static variable in class org.simtk.util.ColorName
 
GREY93 - Static variable in class org.simtk.util.ColorName
 
GREY94 - Static variable in class org.simtk.util.ColorName
 
GREY95 - Static variable in class org.simtk.util.ColorName
 
GREY96 - Static variable in class org.simtk.util.ColorName
 
GREY97 - Static variable in class org.simtk.util.ColorName
 
GREY98 - Static variable in class org.simtk.util.ColorName
 
GREY99 - Static variable in class org.simtk.util.ColorName
 
Guanylate - Class in org.simtk.molecularstructure.nucleicacid
 
Guanylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Guanylate
 

H

Hairpin - Class in org.simtk.molecularstructure.nucleicacid
 
Hairpin() - Constructor for class org.simtk.molecularstructure.nucleicacid.Hairpin
 
handleMoleculeUrl(URL) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
hasChanged() - Method in class org.simtk.gui.ProgressManager
 
hasChanged() - Method in interface org.simtk.mvc.ObservableInterface
 
Hash3D<V> - Class in org.simtk.geometry3d
Container class to speed up finding objects that are near one another in 3D Cartesian space.
Hash3D(double) - Constructor for class org.simtk.geometry3d.Hash3D
 
hashCode() - Method in class org.simtk.geometry3d.Angle
 
hashCode() - Method in class org.simtk.geometry3d.Vector2DClass
 
hashCode() - Method in class org.simtk.geometry3d.Vector3DClass
 
hashCode() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
Helix - Class in org.simtk.molecularstructure.protein
 
Helix() - Constructor for class org.simtk.molecularstructure.protein.Helix
 
helixString() - Method in class org.simtk.molecularstructure.nucleicacid.Duplex
 
hide() - Method in interface org.simtk.gui.ProgressDialog
 
hideDialog() - Method in class org.simtk.gui.ProgressManager
 
Histidine - Class in org.simtk.molecularstructure.protein
 
Histidine() - Constructor for class org.simtk.molecularstructure.protein.Histidine
 
HomogeneousTransform - Interface in org.simtk.geometry3d
 
HomogeneousTransformClass - Class in org.simtk.geometry3d
 
HomogeneousTransformClass() - Constructor for class org.simtk.geometry3d.HomogeneousTransformClass
 
HomogeneousTransformClass(MathMatrix) - Constructor for class org.simtk.geometry3d.HomogeneousTransformClass
 
HONEYDEW - Static variable in class org.simtk.util.ColorName
 
HONEYDEW1 - Static variable in class org.simtk.util.ColorName
 
HONEYDEW2 - Static variable in class org.simtk.util.ColorName
 
HONEYDEW3 - Static variable in class org.simtk.util.ColorName
 
HONEYDEW4 - Static variable in class org.simtk.util.ColorName
 
HOT_PINK - Static variable in class org.simtk.util.ColorName
 
HOT_PINK1 - Static variable in class org.simtk.util.ColorName
 
HOT_PINK2 - Static variable in class org.simtk.util.ColorName
 
HOT_PINK3 - Static variable in class org.simtk.util.ColorName
 
HOT_PINK4 - Static variable in class org.simtk.util.ColorName
 
HYDROGEN - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 

I

identifyBasePairs() - Method in class org.simtk.molecularstructure.nucleicacid.NucleicAcid
 
identifyHairpins() - Method in class org.simtk.molecularstructure.nucleicacid.NucleicAcid
 
identity - Static variable in class org.simtk.geometry3d.Matrix3DClass
 
importSecondaryStructures() - Method in class org.simtk.rnaml.RnamlDocument
 
inactivate() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
increment() - Method in class org.simtk.gui.Throbber
Change image to the next one in the animation sequence
INDIAN_RED - Static variable in class org.simtk.util.ColorName
 
INDIAN_RED1 - Static variable in class org.simtk.util.ColorName
 
INDIAN_RED2 - Static variable in class org.simtk.util.ColorName
 
INDIAN_RED3 - Static variable in class org.simtk.util.ColorName
 
INDIAN_RED4 - Static variable in class org.simtk.util.ColorName
 
INDIGO - Static variable in class org.simtk.util.ColorName
 
initialize(Vector2D) - Method in class org.simtk.geometry3d.Vector2DClass
 
initialize(Vector3D) - Method in class org.simtk.geometry3d.Vector3DClass
 
Inositate - Class in org.simtk.molecularstructure.nucleicacid
 
Inositate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Inositate
 
InsufficientAtomsException - Exception in org.simtk.molecularstructure
 
InsufficientAtomsException() - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException
 
InsufficientAtomsException(String) - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException
 
InsufficientAtomsException(String, Throwable) - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException
 
InsufficientAtomsException(Throwable) - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException
 
InsufficientPointsException - Exception in org.simtk.geometry3d
 
InsufficientPointsException() - Constructor for exception org.simtk.geometry3d.InsufficientPointsException
 
InsufficientPointsException(String) - Constructor for exception org.simtk.geometry3d.InsufficientPointsException
 
InsufficientPointsException(String, Throwable) - Constructor for exception org.simtk.geometry3d.InsufficientPointsException
 
InsufficientPointsException(Throwable) - Constructor for exception org.simtk.geometry3d.InsufficientPointsException
 
intValue() - Method in class org.simtk.geometry3d.Angle
 
IODINE - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
IRON - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
isAlive() - Method in interface org.simtk.gui.MonitoredProcess
 
isAlphaHelix() - Method in interface org.simtk.molecularstructure.Residue
 
isAlphaHelix() - Method in class org.simtk.molecularstructure.ResidueClass
 
isBetween(Residue, Residue) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
isCancelled() - Method in interface org.simtk.gui.ProgressDialog
 
isCancelled() - Method in class org.simtk.gui.ProgressDialogClass
 
isCancelled() - Method in class org.simtk.gui.ProgressPanel
 
isDeemedNucleotide(Residue, String) - Method in class org.simtk.rnaml.RnamlDocument
 
isDNA(String) - Static method in class org.simtk.molecularstructure.ResidueClass
 
isEmpty() - Method in class org.simtk.util.DoubleRing
 
isFailed() - Method in interface org.simtk.gui.MonitoredProcess
 
isHelix() - Method in interface org.simtk.molecularstructure.Residue
 
isHelix() - Method in class org.simtk.molecularstructure.ResidueClass
 
isKnownHetatm(String) - Static method in class org.simtk.molecularstructure.ResidueClass
 
isNucleicAcid(String) - Static method in class org.simtk.molecularstructure.ResidueClass
 
Isoleucine - Class in org.simtk.molecularstructure.protein
 
Isoleucine() - Constructor for class org.simtk.molecularstructure.protein.Isoleucine
 
isProtein(String) - Static method in class org.simtk.molecularstructure.ResidueClass
 
isRNA(String) - Static method in class org.simtk.molecularstructure.ResidueClass
 
isRnaviewNA(Biopolymer) - Method in class org.simtk.rnaml.RnamlDocument
 
isSolvent() - Method in interface org.simtk.molecularstructure.Molecule
 
isSolvent() - Method in class org.simtk.molecularstructure.MoleculeClass
 
isSolvent(String) - Static method in class org.simtk.molecularstructure.ResidueClass
 
isStrand() - Method in interface org.simtk.molecularstructure.Residue
 
isStrand() - Method in class org.simtk.molecularstructure.ResidueClass
 
isSuccessful() - Method in interface org.simtk.gui.MonitoredProcess
 
iterator() - Method in class org.simtk.geometry3d.MathVectorClass
 
iterator() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
iterator() - Method in class org.simtk.molecularstructure.SequenceAlignment
 
IVORY - Static variable in class org.simtk.util.ColorName
 
IVORY1 - Static variable in class org.simtk.util.ColorName
 
IVORY2 - Static variable in class org.simtk.util.ColorName
 
IVORY3 - Static variable in class org.simtk.util.ColorName
 
IVORY4 - Static variable in class org.simtk.util.ColorName
 

J

JamaMatrix - Class in org.simtk.geometry3d
 
JLinkLabel - Class in org.simtk.pdb
 
JLinkLabel(String) - Constructor for class org.simtk.pdb.JLinkLabel
 
JLinkLabel() - Constructor for class org.simtk.pdb.JLinkLabel
 

K

kabsch78(Vector3D[], Vector3D[], double[]) - Static method in class org.simtk.geometry3d.Superposition
Return a transformation that can place one set of vectors onto another while minimizing the least-squares distance between the corresponding points.
KHAKI - Static variable in class org.simtk.util.ColorName
 
KHAKI1 - Static variable in class org.simtk.util.ColorName
 
KHAKI2 - Static variable in class org.simtk.util.ColorName
 
KHAKI3 - Static variable in class org.simtk.util.ColorName
 
KHAKI4 - Static variable in class org.simtk.util.ColorName
 
knownHetatms - Static variable in class org.simtk.molecularstructure.ResidueClass
 

L

LAVENDER - Static variable in class org.simtk.util.ColorName
 
LAVENDER_BLUSH - Static variable in class org.simtk.util.ColorName
 
LAVENDER_BLUSH1 - Static variable in class org.simtk.util.ColorName
 
LAVENDER_BLUSH2 - Static variable in class org.simtk.util.ColorName
 
LAVENDER_BLUSH3 - Static variable in class org.simtk.util.ColorName
 
LAVENDER_BLUSH4 - Static variable in class org.simtk.util.ColorName
 
LAWN_GREEN - Static variable in class org.simtk.util.ColorName
 
LEFT_HANDED_ALPHA - Static variable in class org.simtk.molecularstructure.protein.Helix
 
LEFT_HANDED_GAMMA - Static variable in class org.simtk.molecularstructure.protein.Helix
 
LEFT_HANDED_OMEGA - Static variable in class org.simtk.molecularstructure.protein.Helix
 
LEMON_CHIFFON - Static variable in class org.simtk.util.ColorName
 
LEMON_CHIFFON1 - Static variable in class org.simtk.util.ColorName
 
LEMON_CHIFFON2 - Static variable in class org.simtk.util.ColorName
 
LEMON_CHIFFON3 - Static variable in class org.simtk.util.ColorName
 
LEMON_CHIFFON4 - Static variable in class org.simtk.util.ColorName
 
length() - Method in interface org.simtk.geometry3d.MathVector
 
length() - Method in class org.simtk.geometry3d.MathVectorClass
 
lengthSquared() - Method in interface org.simtk.geometry3d.MathVector
 
lengthSquared() - Method in class org.simtk.geometry3d.MathVectorClass
 
Leucine - Class in org.simtk.molecularstructure.protein
 
Leucine() - Constructor for class org.simtk.molecularstructure.protein.Leucine
 
LIGHT_BLUE - Static variable in class org.simtk.util.ColorName
 
LIGHT_BLUE1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_BLUE2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_BLUE3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_BLUE4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_CORAL - Static variable in class org.simtk.util.ColorName
 
LIGHT_CYAN - Static variable in class org.simtk.util.ColorName
 
LIGHT_CYAN1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_CYAN2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_CYAN3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_CYAN4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_GOLDENROD - Static variable in class org.simtk.util.ColorName
 
LIGHT_GOLDENROD1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_GOLDENROD2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_GOLDENROD3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_GOLDENROD4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_GOLDENROD_YELLOW - Static variable in class org.simtk.util.ColorName
 
LIGHT_GRAY - Static variable in class org.simtk.util.ColorName
 
LIGHT_GREEN - Static variable in class org.simtk.util.ColorName
 
LIGHT_GREY - Static variable in class org.simtk.util.ColorName
 
LIGHT_PINK - Static variable in class org.simtk.util.ColorName
 
LIGHT_PINK1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_PINK2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_PINK3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_PINK4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SALMON - Static variable in class org.simtk.util.ColorName
 
LIGHT_SALMON1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SALMON2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SALMON3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SALMON4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SEA_GREEN - Static variable in class org.simtk.util.ColorName
 
LIGHT_SKY_BLUE - Static variable in class org.simtk.util.ColorName
 
LIGHT_SKY_BLUE1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SKY_BLUE2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SKY_BLUE3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SKY_BLUE4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_SLATE_BLUE - Static variable in class org.simtk.util.ColorName
 
LIGHT_SLATE_GRAY - Static variable in class org.simtk.util.ColorName
 
LIGHT_SLATE_GREY - Static variable in class org.simtk.util.ColorName
 
LIGHT_STEEL_BLUE - Static variable in class org.simtk.util.ColorName
 
LIGHT_STEEL_BLUE1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_STEEL_BLUE2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_STEEL_BLUE3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_STEEL_BLUE4 - Static variable in class org.simtk.util.ColorName
 
LIGHT_YELLOW - Static variable in class org.simtk.util.ColorName
 
LIGHT_YELLOW1 - Static variable in class org.simtk.util.ColorName
 
LIGHT_YELLOW2 - Static variable in class org.simtk.util.ColorName
 
LIGHT_YELLOW3 - Static variable in class org.simtk.util.ColorName
 
LIGHT_YELLOW4 - Static variable in class org.simtk.util.ColorName
 
LIME - Static variable in class org.simtk.util.ColorName
 
LIME_GREEN - Static variable in class org.simtk.util.ColorName
 
Line3D - Class in org.simtk.geometry3d
 
Line3D() - Constructor for class org.simtk.geometry3d.Line3D
 
Line3D(Vector3D, Vector3D) - Constructor for class org.simtk.geometry3d.Line3D
 
LineCommand - Interface in org.simtk.util
 
LINEN - Static variable in class org.simtk.util.ColorName
 
listeners - Variable in class org.simtk.util.SelectionBroadcaster
 
LITHIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
loadMolecules() - Method in class org.simtk.pdb.LoadPdbUrlProcess
 
loadPDBFormat(String) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
loadPDBFormat(URL) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
loadPDBFormat(InputStream) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
LoadPdbUrlProcess - Class in org.simtk.pdb
 
LoadPdbUrlProcess(URL, SimpleObservable) - Constructor for class org.simtk.pdb.LoadPdbUrlProcess
 
LocatedProtein - Interface in org.simtk.molecularstructure.protein
 
Location - Interface in org.simtk.geometry3d
 
longValue() - Method in class org.simtk.geometry3d.Angle
 
Lysine - Class in org.simtk.molecularstructure.protein
 
Lysine() - Constructor for class org.simtk.molecularstructure.protein.Lysine
 

M

MAGENTA - Static variable in class org.simtk.util.ColorName
 
MAGENTA1 - Static variable in class org.simtk.util.ColorName
 
MAGENTA2 - Static variable in class org.simtk.util.ColorName
 
MAGENTA3 - Static variable in class org.simtk.util.ColorName
 
MAGENTA4 - Static variable in class org.simtk.util.ColorName
 
MAGNESIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
main(String[]) - Static method in class org.simtk.geometry3d.TestSuperposition
 
main(String[]) - Static method in class org.simtk.util.UncompressInputStream
 
makeBasePair(Residue, Residue, String) - Static method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
MANGANESE - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
MAROON - Static variable in class org.simtk.util.ColorName
 
MAROON1 - Static variable in class org.simtk.util.ColorName
 
MAROON2 - Static variable in class org.simtk.util.ColorName
 
MAROON3 - Static variable in class org.simtk.util.ColorName
 
MAROON4 - Static variable in class org.simtk.util.ColorName
 
MassBody - Interface in org.simtk.geometry3d
 
MassBodyClass - Class in org.simtk.geometry3d
 
MassBodyClass() - Constructor for class org.simtk.geometry3d.MassBodyClass
 
matchesPdbLine(String) - Method in class org.simtk.molecularstructure.ResidueClass
 
MathMatrix - Interface in org.simtk.geometry3d
 
MathMatrixClass - Class in org.simtk.geometry3d
 
MathMatrixClass(int, int) - Constructor for class org.simtk.geometry3d.MathMatrixClass
 
MathMatrixClass(int, int, double) - Constructor for class org.simtk.geometry3d.MathMatrixClass
 
MathMatrixClass(MathMatrix) - Constructor for class org.simtk.geometry3d.MathMatrixClass
 
MathVector - Interface in org.simtk.geometry3d
 
MathVectorClass - Class in org.simtk.geometry3d
 
MathVectorClass(int) - Constructor for class org.simtk.geometry3d.MathVectorClass
 
Matrix3D - Interface in org.simtk.geometry3d
 
Matrix3DClass - Class in org.simtk.geometry3d
 
Matrix3DClass() - Constructor for class org.simtk.geometry3d.Matrix3DClass
 
Matrix3DClass(MathMatrix) - Constructor for class org.simtk.geometry3d.Matrix3DClass
 
Matrix3DClass(double, double, double, double, double, double, double, double, double) - Constructor for class org.simtk.geometry3d.Matrix3DClass
 
MatrixSizeMismatchException - Exception in org.simtk.geometry3d
 
mean() - Method in class org.simtk.util.DoubleRing
Compute mean value of the elements in the ring.
MEDIUM_AQUAMARINE - Static variable in class org.simtk.util.ColorName
 
MEDIUM_BLUE - Static variable in class org.simtk.util.ColorName
 
MEDIUM_ORCHID - Static variable in class org.simtk.util.ColorName
 
MEDIUM_ORCHID1 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_ORCHID2 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_ORCHID3 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_ORCHID4 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_PURPLE - Static variable in class org.simtk.util.ColorName
 
MEDIUM_PURPLE1 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_PURPLE2 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_PURPLE3 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_PURPLE4 - Static variable in class org.simtk.util.ColorName
 
MEDIUM_SEA_GREEN - Static variable in class org.simtk.util.ColorName
 
MEDIUM_SLATE_BLUE - Static variable in class org.simtk.util.ColorName
 
MEDIUM_SPRING_GREEN - Static variable in class org.simtk.util.ColorName
 
MEDIUM_TURQUOISE - Static variable in class org.simtk.util.ColorName
 
MEDIUM_VIOLET_RED - Static variable in class org.simtk.util.ColorName
 
Methionine - Class in org.simtk.molecularstructure.protein
 
Methionine() - Constructor for class org.simtk.molecularstructure.protein.Methionine
 
MIDNIGHT_BLUE - Static variable in class org.simtk.util.ColorName
 
MINT_CREAM - Static variable in class org.simtk.util.ColorName
 
minus(Angle) - Method in class org.simtk.geometry3d.Angle
 
minus(MathMatrix) - Method in interface org.simtk.geometry3d.MathMatrix
 
minus(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
minus(MathVector) - Method in interface org.simtk.geometry3d.MathVector
 
minus(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
minus(MathMatrix) - Method in interface org.simtk.geometry3d.Matrix3D
 
minus(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass
 
minus(MathVector) - Method in interface org.simtk.geometry3d.Vector2D
 
minus(MathVector) - Method in class org.simtk.geometry3d.Vector2DClass
 
minus(MathVector) - Method in interface org.simtk.geometry3d.Vector3D
 
minus(MathVector) - Method in class org.simtk.geometry3d.Vector3DClass
 
minusEquals(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
minusEquals(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
minusEquals(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass
 
minusEquals(MathMatrix) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
minusEquals(MathVector) - Method in interface org.simtk.geometry3d.MutableMathVector
 
MISTY_ROSE - Static variable in class org.simtk.util.ColorName
 
MISTY_ROSE1 - Static variable in class org.simtk.util.ColorName
 
MISTY_ROSE2 - Static variable in class org.simtk.util.ColorName
 
MISTY_ROSE3 - Static variable in class org.simtk.util.ColorName
 
MISTY_ROSE4 - Static variable in class org.simtk.util.ColorName
 
MOCCASIN - Static variable in class org.simtk.util.ColorName
 
modifiedAdenylates - Static variable in class org.simtk.molecularstructure.ResidueClass
 
modifiedCytidylates - Static variable in class org.simtk.molecularstructure.ResidueClass
 
modifiedGuanylates - Static variable in class org.simtk.molecularstructure.ResidueClass
 
modifiedInositates - Static variable in class org.simtk.molecularstructure.ResidueClass
 
modifiedThymidylates - Static variable in class org.simtk.molecularstructure.ResidueClass
 
modifiedUridylates - Static variable in class org.simtk.molecularstructure.ResidueClass
 
Molecular - Interface in org.simtk.molecularstructure
 
MolecularClass - Class in org.simtk.molecularstructure
 
MolecularClass() - Constructor for class org.simtk.molecularstructure.MolecularClass
 
MolecularClass(AtomSet) - Constructor for class org.simtk.molecularstructure.MolecularClass
 
Molecule - Interface in org.simtk.molecularstructure
 
MoleculeAcquisitionMethodDialog - Class in org.simtk.pdb
 
MoleculeAcquisitionMethodDialog(JFrame, ProgressDialog) - Constructor for class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
MoleculeAcquisitionMethodDialog(JFrame, ProgressDialog, String) - Constructor for class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
MoleculeClass - Class in org.simtk.molecularstructure
 
MoleculeClass(char) - Constructor for class org.simtk.molecularstructure.MoleculeClass
 
MoleculeCollection - Class in org.simtk.molecularstructure
 
MoleculeCollection() - Constructor for class org.simtk.molecularstructure.MoleculeCollection
 
MoleculeMVCModel - Class in org.simtk.mvc
 
MoleculeMVCModel() - Constructor for class org.simtk.mvc.MoleculeMVCModel
 
molecules() - Method in class org.simtk.molecularstructure.MoleculeCollection
 
MonitoredProcess - Interface in org.simtk.gui
 
MutableHomogeneousTransform - Interface in org.simtk.geometry3d
 
MutableMathMatrix - Interface in org.simtk.geometry3d
 
MutableMathVector - Interface in org.simtk.geometry3d
 
MutableMatrix3D - Interface in org.simtk.geometry3d
 
MutableVector2D - Interface in org.simtk.geometry3d
 
MutableVector3D - Interface in org.simtk.geometry3d
 
MVCModel - Interface in org.simtk.mvc
 
MVCView - Interface in org.simtk.mvc
 
MyJFileFilter - Class in org.simtk.util
 
MyJFileFilter() - Constructor for class org.simtk.util.MyJFileFilter
 

N

NAVAJO_WHITE - Static variable in class org.simtk.util.ColorName
 
NAVAJO_WHITE1 - Static variable in class org.simtk.util.ColorName
 
NAVAJO_WHITE2 - Static variable in class org.simtk.util.ColorName
 
NAVAJO_WHITE3 - Static variable in class org.simtk.util.ColorName
 
NAVAJO_WHITE4 - Static variable in class org.simtk.util.ColorName
 
NAVY - Static variable in class org.simtk.util.ColorName
 
NAVY_BLUE - Static variable in class org.simtk.util.ColorName
 
neighborKeys(Vector3D, double) - Method in class org.simtk.geometry3d.Hash3D
Find positions of all objects within a specified radius of a specified point.
neighborValues(Vector3D, double) - Method in class org.simtk.geometry3d.Hash3D
Find all objects within a specified radius of a specified point This method has constant asymptotic time complexity.
nextResidue - Variable in class org.simtk.molecularstructure.ResidueClass
 
NICKEL - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
NITROGEN - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
notifyObservers(Object) - Method in class org.simtk.gui.ProgressManager
 
notifyObservers() - Method in class org.simtk.gui.ProgressManager
 
notifyObservers() - Method in interface org.simtk.mvc.ObservableInterface
 
notifyObservers(Object) - Method in interface org.simtk.mvc.ObservableInterface
 
NucleicAcid - Class in org.simtk.molecularstructure.nucleicacid
 
NucleicAcid(char) - Constructor for class org.simtk.molecularstructure.nucleicacid.NucleicAcid
 
Nucleotide - Class in org.simtk.molecularstructure.nucleicacid
 
Nucleotide(char, String, String) - Constructor for class org.simtk.molecularstructure.nucleicacid.Nucleotide
 

O

ObservableInterface - Interface in org.simtk.mvc
 
OLD_LACE - Static variable in class org.simtk.util.ColorName
 
OLIVE - Static variable in class org.simtk.util.ColorName
 
OLIVE_DRAB - Static variable in class org.simtk.util.ColorName
 
OLIVE_DRAB1 - Static variable in class org.simtk.util.ColorName
 
OLIVE_DRAB2 - Static variable in class org.simtk.util.ColorName
 
OLIVE_DRAB3 - Static variable in class org.simtk.util.ColorName
 
OLIVE_DRAB4 - Static variable in class org.simtk.util.ColorName
 
oneLetterCode - Variable in class org.simtk.molecularstructure.ResidueTypeClass
 
ORANGE - Static variable in class org.simtk.util.ColorName
 
ORANGE1 - Static variable in class org.simtk.util.ColorName
 
ORANGE2 - Static variable in class org.simtk.util.ColorName
 
ORANGE3 - Static variable in class org.simtk.util.ColorName
 
ORANGE4 - Static variable in class org.simtk.util.ColorName
 
ORANGE_RED - Static variable in class org.simtk.util.ColorName
 
ORANGE_RED1 - Static variable in class org.simtk.util.ColorName
 
ORANGE_RED2 - Static variable in class org.simtk.util.ColorName
 
ORANGE_RED3 - Static variable in class org.simtk.util.ColorName
 
ORANGE_RED4 - Static variable in class org.simtk.util.ColorName
 
ORCHID - Static variable in class org.simtk.util.ColorName
 
ORCHID1 - Static variable in class org.simtk.util.ColorName
 
ORCHID2 - Static variable in class org.simtk.util.ColorName
 
ORCHID3 - Static variable in class org.simtk.util.ColorName
 
ORCHID4 - Static variable in class org.simtk.util.ColorName
 
org.simtk.geometry3d - package org.simtk.geometry3d
 
org.simtk.gui - package org.simtk.gui
 
org.simtk.molecularstructure - package org.simtk.molecularstructure
 
org.simtk.molecularstructure.atom - package org.simtk.molecularstructure.atom
 
org.simtk.molecularstructure.nucleicacid - package org.simtk.molecularstructure.nucleicacid
 
org.simtk.molecularstructure.protein - package org.simtk.molecularstructure.protein
 
org.simtk.mvc - package org.simtk.mvc
 
org.simtk.pdb - package org.simtk.pdb
 
org.simtk.rnaml - package org.simtk.rnaml
 
org.simtk.util - package org.simtk.util
 
origin - Variable in class org.simtk.geometry3d.Line3D
 
outputter - Variable in class org.simtk.rnaml.RnamlExportDocument
 
OXYGEN - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 

P

paint(Graphics) - Method in class org.simtk.pdb.JLinkLabel
 
PALE_GOLDENROD - Static variable in class org.simtk.util.ColorName
 
PALE_GREEN - Static variable in class org.simtk.util.ColorName
 
PALE_GREEN1 - Static variable in class org.simtk.util.ColorName
 
PALE_GREEN2 - Static variable in class org.simtk.util.ColorName
 
PALE_GREEN3 - Static variable in class org.simtk.util.ColorName
 
PALE_GREEN4 - Static variable in class org.simtk.util.ColorName
 
PALE_TURQUOISE - Static variable in class org.simtk.util.ColorName
 
PALE_TURQUOISE1 - Static variable in class org.simtk.util.ColorName
 
PALE_TURQUOISE2 - Static variable in class org.simtk.util.ColorName
 
PALE_TURQUOISE3 - Static variable in class org.simtk.util.ColorName
 
PALE_TURQUOISE4 - Static variable in class org.simtk.util.ColorName
 
PALE_VIOLET_RED - Static variable in class org.simtk.util.ColorName
 
PALE_VIOLET_RED1 - Static variable in class org.simtk.util.ColorName
 
PALE_VIOLET_RED2 - Static variable in class org.simtk.util.ColorName
 
PALE_VIOLET_RED3 - Static variable in class org.simtk.util.ColorName
 
PALE_VIOLET_RED4 - Static variable in class org.simtk.util.ColorName
 
PAPAYA_WHIP - Static variable in class org.simtk.util.ColorName
 
ParameterSetModel - Class in org.simtk.gui
 
ParameterSetModel() - Constructor for class org.simtk.gui.ParameterSetModel
 
parentMolecules - Variable in class org.simtk.molecularstructure.SecondaryStructureClass
 
PDBProteinClass - Class in org.simtk.molecularstructure.protein
 
PDBProteinClass(char) - Constructor for class org.simtk.molecularstructure.protein.PDBProteinClass
 
PEACH_PUFF - Static variable in class org.simtk.util.ColorName
 
PEACH_PUFF1 - Static variable in class org.simtk.util.ColorName
 
PEACH_PUFF2 - Static variable in class org.simtk.util.ColorName
 
PEACH_PUFF3 - Static variable in class org.simtk.util.ColorName
 
PEACH_PUFF4 - Static variable in class org.simtk.util.ColorName
 
PERU - Static variable in class org.simtk.util.ColorName
 
Phenylalanine - Class in org.simtk.molecularstructure.protein
 
Phenylalanine() - Constructor for class org.simtk.molecularstructure.protein.Phenylalanine
 
phosphateGroup - Static variable in class org.simtk.molecularstructure.nucleicacid.Nucleotide
 
PHOSPHORUS - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
PINK - Static variable in class org.simtk.util.ColorName
 
PINK1 - Static variable in class org.simtk.util.ColorName
 
PINK2 - Static variable in class org.simtk.util.ColorName
 
PINK3 - Static variable in class org.simtk.util.ColorName
 
PINK4 - Static variable in class org.simtk.util.ColorName
 
Plane3D - Class in org.simtk.geometry3d
 
Plane3D() - Constructor for class org.simtk.geometry3d.Plane3D
 
PLUM - Static variable in class org.simtk.util.ColorName
 
PLUM1 - Static variable in class org.simtk.util.ColorName
 
PLUM2 - Static variable in class org.simtk.util.ColorName
 
PLUM3 - Static variable in class org.simtk.util.ColorName
 
PLUM4 - Static variable in class org.simtk.util.ColorName
 
plus(Angle) - Method in class org.simtk.geometry3d.Angle
 
plus(MathMatrix) - Method in interface org.simtk.geometry3d.MathMatrix
 
plus(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
plus(MathVector) - Method in interface org.simtk.geometry3d.MathVector
 
plus(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
plus(MathMatrix) - Method in interface org.simtk.geometry3d.Matrix3D
 
plus(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass
 
plus(MathVector) - Method in interface org.simtk.geometry3d.Vector2D
 
plus(MathVector) - Method in class org.simtk.geometry3d.Vector2DClass
 
plus(MathVector) - Method in interface org.simtk.geometry3d.Vector3D
 
plus(MathVector) - Method in class org.simtk.geometry3d.Vector3DClass
 
plusEquals(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
plusEquals(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass
 
plusEquals(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass
 
plusEquals(MathMatrix) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
plusEquals(MathVector) - Method in interface org.simtk.geometry3d.MutableMathVector
 
POLYPROLINE - Static variable in class org.simtk.molecularstructure.protein.Helix
 
pop() - Method in class org.simtk.util.DoubleRing
 
POTASSIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
POWDER_BLUE - Static variable in class org.simtk.util.ColorName
 
previousResidue - Variable in class org.simtk.molecularstructure.ResidueClass
 
ProgrammerLogicProblem - Exception in org.simtk.util
 
ProgrammerLogicProblem() - Constructor for exception org.simtk.util.ProgrammerLogicProblem
 
ProgrammerLogicProblem(String) - Constructor for exception org.simtk.util.ProgrammerLogicProblem
 
ProgressDialog - Interface in org.simtk.gui
 
ProgressDialogClass - Class in org.simtk.gui
 
ProgressManager - Class in org.simtk.gui
 
ProgressManager(MonitoredProcess, ProgressDialog) - Constructor for class org.simtk.gui.ProgressManager
 
ProgressManager(MonitoredProcess, JFrame, String) - Constructor for class org.simtk.gui.ProgressManager
 
ProgressPanel - Class in org.simtk.gui
 
ProgressPanel(String) - Constructor for class org.simtk.gui.ProgressPanel
 
Proline - Class in org.simtk.molecularstructure.protein
 
Proline() - Constructor for class org.simtk.molecularstructure.protein.Proline
 
Protein - Interface in org.simtk.molecularstructure.protein
 
Pseudoknot - Class in org.simtk.molecularstructure.nucleicacid
 
Pseudoknot(Duplex, Duplex) - Constructor for class org.simtk.molecularstructure.nucleicacid.Pseudoknot
 
Pseudoknot(Duplex, Duplex, String) - Constructor for class org.simtk.molecularstructure.nucleicacid.Pseudoknot
 
Purine - Class in org.simtk.molecularstructure.nucleicacid
 
Purine(char, String, String) - Constructor for class org.simtk.molecularstructure.nucleicacid.Purine
 
PURPLE - Static variable in class org.simtk.util.ColorName
 
PURPLE1 - Static variable in class org.simtk.util.ColorName
 
PURPLE2 - Static variable in class org.simtk.util.ColorName
 
PURPLE3 - Static variable in class org.simtk.util.ColorName
 
PURPLE4 - Static variable in class org.simtk.util.ColorName
 
push(double) - Method in class org.simtk.util.DoubleRing
 
put(Vector3D, V) - Method in class org.simtk.geometry3d.Hash3D
Inserts an object into the data structure at a particular position.
Pyrimidine - Class in org.simtk.molecularstructure.nucleicacid
 
Pyrimidine(char, String, String) - Constructor for class org.simtk.molecularstructure.nucleicacid.Pyrimidine
 

R

RADIANS - Static variable in class org.simtk.geometry3d.Angle.Units
 
RADIANS_PER_DEGREE - Static variable in class org.simtk.geometry3d.Angle
 
RADIANS_PER_GRAD - Static variable in class org.simtk.geometry3d.Angle
 
RADIANS_PER_REV - Static variable in class org.simtk.geometry3d.Angle
 
reactivate() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
read() - Method in class org.simtk.util.UncompressInputStream
 
read(byte[], int, int) - Method in class org.simtk.util.UncompressInputStream
 
readPdbLine(String) - Method in class org.simtk.molecularstructure.atom.AtomClass
 
readStructureFromMoleculeCollection(MoleculeCollection) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
Overload this to make use of preloaded molecule collection
RED - Static variable in class org.simtk.util.ColorName
 
RED1 - Static variable in class org.simtk.util.ColorName
 
RED2 - Static variable in class org.simtk.util.ColorName
 
RED3 - Static variable in class org.simtk.util.ColorName
 
RED4 - Static variable in class org.simtk.util.ColorName
 
remove(Vector3D) - Method in class org.simtk.geometry3d.Hash3D
Remove the object at a particular position
Residue - Interface in org.simtk.molecularstructure
 
ResidueBackbone - Class in org.simtk.molecularstructure
 
ResidueBackbone(Residue) - Constructor for class org.simtk.molecularstructure.ResidueBackbone
 
ResidueClass - Class in org.simtk.molecularstructure
 
ResidueClass(ResidueType) - Constructor for class org.simtk.molecularstructure.ResidueClass
 
ResidueClass(String) - Constructor for class org.simtk.molecularstructure.ResidueClass
 
residueName - Variable in class org.simtk.molecularstructure.ResidueTypeClass
 
residueNumber - Variable in class org.simtk.molecularstructure.ResidueClass
 
residues() - Method in interface org.simtk.molecularstructure.Biopolymer
 
residues() - Method in class org.simtk.molecularstructure.BiopolymerClass
 
residues() - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
residues - Variable in class org.simtk.molecularstructure.SecondaryStructureClass
 
residues() - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
ResidueType - Interface in org.simtk.molecularstructure
 
ResidueTypeClass - Class in org.simtk.molecularstructure
 
ResidueTypeClass(char, String, String) - Constructor for class org.simtk.molecularstructure.ResidueTypeClass
 
resLimit - Variable in class org.simtk.molecularstructure.SecondaryStructureClass
 
respondToClick() - Method in class org.simtk.pdb.JLinkLabel
 
restart() - Method in class org.simtk.util.Stopwatch
 
REVS - Static variable in class org.simtk.geometry3d.Angle.Units
 
REVS_PER_RADIAN - Static variable in class org.simtk.geometry3d.Angle
 
RIBBON_HELIX_27 - Static variable in class org.simtk.molecularstructure.protein.Helix
 
RIGHT_HANDED_310 - Static variable in class org.simtk.molecularstructure.protein.Helix
 
RIGHT_HANDED_ALPHA - Static variable in class org.simtk.molecularstructure.protein.Helix
 
RIGHT_HANDED_GAMMA - Static variable in class org.simtk.molecularstructure.protein.Helix
 
RIGHT_HANDED_OMEGA - Static variable in class org.simtk.molecularstructure.protein.Helix
 
RIGHT_HANDED_PI - Static variable in class org.simtk.molecularstructure.protein.Helix
 
RNA - Class in org.simtk.molecularstructure.nucleicacid
 
RNA(char) - Constructor for class org.simtk.molecularstructure.nucleicacid.RNA
 
RnamlDocument - Class in org.simtk.rnaml
 
RnamlDocument(File, MoleculeCollection) - Constructor for class org.simtk.rnaml.RnamlDocument
 
RnamlExportDocument - Class in org.simtk.rnaml
 
RnamlExportDocument(String, String) - Constructor for class org.simtk.rnaml.RnamlExportDocument
 
RnamlExportDocument(String, String, MoleculeCollection) - Constructor for class org.simtk.rnaml.RnamlExportDocument
 
rnamlIndexMolecules - Variable in class org.simtk.rnaml.RnamlDocument
 
rnamlMolecules - Variable in class org.simtk.rnaml.RnamlExportDocument
 
ROSY_BROWN - Static variable in class org.simtk.util.ColorName
 
ROSY_BROWN1 - Static variable in class org.simtk.util.ColorName
 
ROSY_BROWN2 - Static variable in class org.simtk.util.ColorName
 
ROSY_BROWN3 - Static variable in class org.simtk.util.ColorName
 
ROSY_BROWN4 - Static variable in class org.simtk.util.ColorName
 
rotate(double) - Method in interface org.simtk.geometry3d.Vector2D
 
rotate(double) - Method in class org.simtk.geometry3d.Vector2DClass
 
rotate(Vector3D, double) - Method in interface org.simtk.geometry3d.Vector3D
 
rotate(Vector3D, double) - Method in class org.simtk.geometry3d.Vector3DClass
 
ROYAL_BLUE - Static variable in class org.simtk.util.ColorName
 
ROYAL_BLUE1 - Static variable in class org.simtk.util.ColorName
 
ROYAL_BLUE2 - Static variable in class org.simtk.util.ColorName
 
ROYAL_BLUE3 - Static variable in class org.simtk.util.ColorName
 
ROYAL_BLUE4 - Static variable in class org.simtk.util.ColorName
 
run() - Method in class org.simtk.gui.ProgressManager
 

S

SADDLE_BROWN - Static variable in class org.simtk.util.ColorName
 
SALMON - Static variable in class org.simtk.util.ColorName
 
SALMON1 - Static variable in class org.simtk.util.ColorName
 
SALMON2 - Static variable in class org.simtk.util.ColorName
 
SALMON3 - Static variable in class org.simtk.util.ColorName
 
SALMON4 - Static variable in class org.simtk.util.ColorName
 
SANDY_BROWN - Static variable in class org.simtk.util.ColorName
 
SEA_GREEN - Static variable in class org.simtk.util.ColorName
 
SEA_GREEN1 - Static variable in class org.simtk.util.ColorName
 
SEA_GREEN2 - Static variable in class org.simtk.util.ColorName
 
SEA_GREEN3 - Static variable in class org.simtk.util.ColorName
 
SEA_GREEN4 - Static variable in class org.simtk.util.ColorName
 
SEASHELL - Static variable in class org.simtk.util.ColorName
 
SEASHELL1 - Static variable in class org.simtk.util.ColorName
 
SEASHELL2 - Static variable in class org.simtk.util.ColorName
 
SEASHELL3 - Static variable in class org.simtk.util.ColorName
 
SEASHELL4 - Static variable in class org.simtk.util.ColorName
 
SecondaryStructure - Interface in org.simtk.molecularstructure
Base class for alpha helices, beta strands, beta sheets, and RNA duplexes
SecondaryStructureClass - Class in org.simtk.molecularstructure
 
SecondaryStructureClass() - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass
 
SecondaryStructureClass(int) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass
 
SecondaryStructureClass(Collection<Residue>) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass
 
SecondaryStructureClass(Collection<Residue>, int) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass
 
SecondaryStructureClass(Collection<Residue>, int, String) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass
 
SecondaryStructureClass.SourceType - Enum in org.simtk.molecularstructure
 
secondaryStructures() - Method in interface org.simtk.molecularstructure.Biopolymer
 
secondaryStructures() - Method in class org.simtk.molecularstructure.BiopolymerClass
 
secondaryStructures() - Method in interface org.simtk.molecularstructure.Residue
 
secondaryStructures() - Method in class org.simtk.molecularstructure.ResidueClass
 
select(Selectable) - Method in interface org.simtk.util.SelectionListener
 
Selectable - Interface in org.simtk.util
 
selectedObjects - Variable in class org.simtk.util.SelectionBroadcaster
 
SelectionBroadcaster - Class in org.simtk.util
 
SelectionBroadcaster() - Constructor for class org.simtk.util.SelectionBroadcaster
 
SelectionListener - Interface in org.simtk.util
 
SELENIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
selfUnit() - Method in class org.simtk.geometry3d.MathVectorClass
 
selfUnit() - Method in interface org.simtk.geometry3d.MutableMathVector
 
SemiCylinder - Class in org.simtk.geometry3d
 
SemiCylinder(Vector3D, Vector3D, double, Vector3DClass) - Constructor for class org.simtk.geometry3d.SemiCylinder
 
SequenceAlignment - Class in org.simtk.molecularstructure
 
SequenceAlignment(Biopolymer, Biopolymer) - Constructor for class org.simtk.molecularstructure.SequenceAlignment
 
serialVersionUID - Static variable in exception org.simtk.util.ProgrammerLogicProblem
 
Serine - Class in org.simtk.molecularstructure.protein
 
Serine() - Constructor for class org.simtk.molecularstructure.protein.Serine
 
set(int, int, double) - Method in class org.simtk.geometry3d.JamaMatrix
 
set(int, int, double) - Method in class org.simtk.geometry3d.MathMatrixClass
 
set(int, double) - Method in class org.simtk.geometry3d.MathVectorClass
 
set(int, int, double) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
set(int, double) - Method in interface org.simtk.geometry3d.MutableMathVector
 
set(int, double) - Method in class org.simtk.geometry3d.Vector3DFloatArrayWrapper
 
setAtomName(String) - Method in interface org.simtk.molecularstructure.atom.Atom
 
setAtomName(String) - Method in class org.simtk.molecularstructure.atom.AtomClass
 
setBond_orient(BasePair.BondOrientation) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
setBond_orient(String) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
setCancelled(boolean) - Method in interface org.simtk.gui.ProgressDialog
 
setCancelled(boolean) - Method in class org.simtk.gui.ProgressDialogClass
 
setCancelled(boolean) - Method in class org.simtk.gui.ProgressPanel
 
setChanged() - Method in class org.simtk.mvc.SimpleObservable
 
setColumn(int, MathVector) - Method in class org.simtk.geometry3d.MathMatrixClass
 
setColumn(int, MathVector) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
setCoordinates(Vector3D) - Method in interface org.simtk.molecularstructure.atom.Atom
 
setCoordinates(Vector3D) - Method in class org.simtk.molecularstructure.atom.AtomClass
 
setCoordinates(Vector3D) - Method in class org.simtk.molecularstructure.atom.AtomPosition
 
setCovalentRadius(double) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
setCurrentPath(String) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
setDefaultPdbId(String) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
setDescription(String) - Method in class org.simtk.util.MyJFileFilter
 
setDisplaySourceTypes(Collection<SecondaryStructureClass.SourceType>) - Method in interface org.simtk.molecularstructure.Molecule
 
setDisplaySourceTypes(Collection<SecondaryStructureClass.SourceType>) - Method in class org.simtk.molecularstructure.MoleculeClass
 
setEdge(Residue, BasePair.EdgeType) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
setEdge(Residue, String) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
setElement(ChemicalElement) - Method in class org.simtk.molecularstructure.atom.AtomClass
 
setElementName(String) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
setElementSymbol(String) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
setGlycosyl(String) - Method in class org.simtk.molecularstructure.ResidueClass
 
setHelixType(HelixType) - Method in class org.simtk.molecularstructure.protein.Helix
 
setInputStructureFileName(String) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
setMass(double) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
setMolecule(Biopolymer) - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
setMolecule(Biopolymer) - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
setNewParameters(Object) - Method in class org.simtk.gui.UndoableDialog
 
setNextResidue(Residue) - Method in interface org.simtk.molecularstructure.Residue
 
setNextResidue(Residue) - Method in class org.simtk.molecularstructure.ResidueClass
 
setParameters(Object) - Method in class org.simtk.gui.ParameterSetModel
 
setPdbChainId(String) - Method in class org.simtk.molecularstructure.MoleculeClass
 
setPdbId(String) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
setPdbId(String) - Method in class org.simtk.pdb.LoadPdbUrlProcess
 
setPdbId(String) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
setPdbInsertionCode(char) - Method in class org.simtk.molecularstructure.ResidueClass
 
setPreviousResidue(Residue) - Method in interface org.simtk.molecularstructure.Residue
 
setPreviousResidue(Residue) - Method in class org.simtk.molecularstructure.ResidueClass
 
setPucker(String) - Method in class org.simtk.molecularstructure.ResidueClass
 
setRange(Angle.Range) - Method in class org.simtk.geometry3d.Angle
 
setResidue(Residue) - Method in class org.simtk.molecularstructure.atom.AtomClass
 
setResidueNumber(int) - Method in interface org.simtk.molecularstructure.Residue
 
setResidueNumber(int) - Method in class org.simtk.molecularstructure.ResidueClass
 
setRotation(Matrix3D) - Method in class org.simtk.geometry3d.HomogeneousTransformClass
 
setRotation(Matrix3D) - Method in interface org.simtk.geometry3d.MutableHomogeneousTransform
 
setRow(int, MathVector) - Method in class org.simtk.geometry3d.MathMatrixClass
 
setRow(int, MathVector) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
setSource(String) - Method in interface org.simtk.molecularstructure.SecondaryStructure
 
setSource(String) - Method in class org.simtk.molecularstructure.SecondaryStructureClass
 
setStartTime(Date) - Method in interface org.simtk.gui.ProgressDialog
 
setStartTime(Date) - Method in class org.simtk.gui.ProgressDialogClass
 
setStartTime(Date) - Method in class org.simtk.gui.ProgressPanel
 
setStrand_orient(String) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
setTitle(String) - Method in class org.simtk.molecularstructure.MoleculeCollection
 
setTranslation(Vector3D) - Method in class org.simtk.geometry3d.HomogeneousTransformClass
 
setTranslation(Vector3D) - Method in interface org.simtk.geometry3d.MutableHomogeneousTransform
 
setUnits(Angle.Units) - Method in class org.simtk.geometry3d.Angle
 
setValue(double, Angle.Units) - Method in class org.simtk.geometry3d.Angle
 
setValue(double) - Method in class org.simtk.geometry3d.Angle
 
setVanDerWaalsRadius(double) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
setX(double) - Method in interface org.simtk.geometry3d.MutableVector2D
 
setX(double) - Method in interface org.simtk.geometry3d.MutableVector3D
 
setX(double) - Method in class org.simtk.geometry3d.Vector2DClass
 
setX(double) - Method in class org.simtk.geometry3d.Vector3DClass
 
setY(double) - Method in interface org.simtk.geometry3d.MutableVector2D
 
setY(double) - Method in interface org.simtk.geometry3d.MutableVector3D
 
setY(double) - Method in class org.simtk.geometry3d.Vector2DClass
 
setY(double) - Method in class org.simtk.geometry3d.Vector3DClass
 
setZ(double) - Method in interface org.simtk.geometry3d.MutableVector3D
 
setZ(double) - Method in class org.simtk.geometry3d.Vector3DClass
 
shortValue() - Method in class org.simtk.geometry3d.Angle
 
sideChainGroup - Static variable in class org.simtk.molecularstructure.protein.AminoAcid
 
SIENNA - Static variable in class org.simtk.util.ColorName
 
SIENNA1 - Static variable in class org.simtk.util.ColorName
 
SIENNA2 - Static variable in class org.simtk.util.ColorName
 
SIENNA3 - Static variable in class org.simtk.util.ColorName
 
SIENNA4 - Static variable in class org.simtk.util.ColorName
 
SIGNED - Static variable in class org.simtk.geometry3d.Angle.Range
 
SILVER - Static variable in class org.simtk.util.ColorName
 
SimpleObservable - Class in org.simtk.mvc
Observable with public setChanged() method
SimpleObservable() - Constructor for class org.simtk.mvc.SimpleObservable
 
sin() - Method in class org.simtk.geometry3d.Angle
 
skip(long) - Method in class org.simtk.util.UncompressInputStream
 
SKY_BLUE - Static variable in class org.simtk.util.ColorName
 
SKY_BLUE1 - Static variable in class org.simtk.util.ColorName
 
SKY_BLUE2 - Static variable in class org.simtk.util.ColorName
 
SKY_BLUE3 - Static variable in class org.simtk.util.ColorName
 
SKY_BLUE4 - Static variable in class org.simtk.util.ColorName
 
SLATE_BLUE - Static variable in class org.simtk.util.ColorName
 
SLATE_BLUE1 - Static variable in class org.simtk.util.ColorName
 
SLATE_BLUE2 - Static variable in class org.simtk.util.ColorName
 
SLATE_BLUE3 - Static variable in class org.simtk.util.ColorName
 
SLATE_BLUE4 - Static variable in class org.simtk.util.ColorName
 
SLATE_GRAY - Static variable in class org.simtk.util.ColorName
 
SLATE_GRAY1 - Static variable in class org.simtk.util.ColorName
 
SLATE_GRAY2 - Static variable in class org.simtk.util.ColorName
 
SLATE_GRAY3 - Static variable in class org.simtk.util.ColorName
 
SLATE_GRAY4 - Static variable in class org.simtk.util.ColorName
 
SLATE_GREY - Static variable in class org.simtk.util.ColorName
 
SNOW - Static variable in class org.simtk.util.ColorName
 
SNOW1 - Static variable in class org.simtk.util.ColorName
 
SNOW2 - Static variable in class org.simtk.util.ColorName
 
SNOW3 - Static variable in class org.simtk.util.ColorName
 
SNOW4 - Static variable in class org.simtk.util.ColorName
 
SODIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
sourceType - Variable in class org.simtk.molecularstructure.SecondaryStructureClass
 
SPRING_GREEN - Static variable in class org.simtk.util.ColorName
 
SPRING_GREEN1 - Static variable in class org.simtk.util.ColorName
 
SPRING_GREEN2 - Static variable in class org.simtk.util.ColorName
 
SPRING_GREEN3 - Static variable in class org.simtk.util.ColorName
 
SPRING_GREEN4 - Static variable in class org.simtk.util.ColorName
 
STEEL_BLUE - Static variable in class org.simtk.util.ColorName
 
STEEL_BLUE1 - Static variable in class org.simtk.util.ColorName
 
STEEL_BLUE2 - Static variable in class org.simtk.util.ColorName
 
STEEL_BLUE3 - Static variable in class org.simtk.util.ColorName
 
STEEL_BLUE4 - Static variable in class org.simtk.util.ColorName
 
Stopwatch - Class in org.simtk.util
 
Stopwatch() - Constructor for class org.simtk.util.Stopwatch
 
strand_orient - Variable in class org.simtk.molecularstructure.nucleicacid.BasePair
 
sugarGroup - Static variable in class org.simtk.molecularstructure.nucleicacid.Nucleotide
 
SULFUR - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
Superposition - Class in org.simtk.geometry3d
 
Superposition() - Constructor for class org.simtk.geometry3d.Superposition
 

T

tan() - Method in class org.simtk.geometry3d.Angle
 
TAN - Static variable in class org.simtk.util.ColorName
 
TAN1 - Static variable in class org.simtk.util.ColorName
 
TAN2 - Static variable in class org.simtk.util.ColorName
 
TAN3 - Static variable in class org.simtk.util.ColorName
 
TAN4 - Static variable in class org.simtk.util.ColorName
 
TEAL - Static variable in class org.simtk.util.ColorName
 
TestSuperposition - Class in org.simtk.geometry3d
 
TestSuperposition() - Constructor for class org.simtk.geometry3d.TestSuperposition
 
THISTLE - Static variable in class org.simtk.util.ColorName
 
THISTLE1 - Static variable in class org.simtk.util.ColorName
 
THISTLE2 - Static variable in class org.simtk.util.ColorName
 
THISTLE3 - Static variable in class org.simtk.util.ColorName
 
THISTLE4 - Static variable in class org.simtk.util.ColorName
 
threeLetterCode - Variable in class org.simtk.molecularstructure.ResidueTypeClass
 
Threonine - Class in org.simtk.molecularstructure.protein
 
Threonine() - Constructor for class org.simtk.molecularstructure.protein.Threonine
 
Throbber - Class in org.simtk.gui
 
Throbber(Icon[]) - Constructor for class org.simtk.gui.Throbber
 
Thymidylate - Class in org.simtk.molecularstructure.nucleicacid
 
Thymidylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Thymidylate
 
times(Vector3D) - Method in interface org.simtk.geometry3d.HomogeneousTransform
 
times(HomogeneousTransform) - Method in interface org.simtk.geometry3d.HomogeneousTransform
 
times(Vector3D) - Method in class org.simtk.geometry3d.HomogeneousTransformClass
 
times(HomogeneousTransform) - Method in class org.simtk.geometry3d.HomogeneousTransformClass
 
times(double) - Method in interface org.simtk.geometry3d.MathMatrix
 
times(MathVector) - Method in interface org.simtk.geometry3d.MathMatrix
 
times(MathMatrix) - Method in interface org.simtk.geometry3d.MathMatrix
 
times(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
times(MathVector) - Method in class org.simtk.geometry3d.MathMatrixClass
 
times(double) - Method in class org.simtk.geometry3d.MathMatrixClass
 
times(double) - Method in interface org.simtk.geometry3d.MathVector
 
times(double) - Method in class org.simtk.geometry3d.MathVectorClass
 
times(double) - Method in interface org.simtk.geometry3d.Matrix3D
 
times(MathVector) - Method in interface org.simtk.geometry3d.Matrix3D
 
times(MathMatrix) - Method in interface org.simtk.geometry3d.Matrix3D
 
times(MathVector) - Method in class org.simtk.geometry3d.Matrix3DClass
 
times(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass
 
times(double) - Method in class org.simtk.geometry3d.Matrix3DClass
 
times(double) - Method in interface org.simtk.geometry3d.Vector2D
 
times(double) - Method in class org.simtk.geometry3d.Vector2DClass
 
times(double) - Method in interface org.simtk.geometry3d.Vector3D
 
times(double) - Method in class org.simtk.geometry3d.Vector3DClass
 
timesEquals(double) - Method in class org.simtk.geometry3d.MathMatrixClass
 
timesEquals(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass
 
timesEquals(double) - Method in class org.simtk.geometry3d.MathVectorClass
 
timesEquals(double) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
timesEquals(MathMatrix) - Method in interface org.simtk.geometry3d.MutableMathMatrix
 
timesEquals(double) - Method in interface org.simtk.geometry3d.MutableMathVector
 
toArray() - Method in interface org.simtk.geometry3d.Matrix3D
 
toArray() - Method in class org.simtk.geometry3d.Matrix3DClass
 
toArray() - Method in interface org.simtk.geometry3d.Vector2D
 
toArray() - Method in class org.simtk.geometry3d.Vector2DClass
 
toArray() - Method in interface org.simtk.geometry3d.Vector3D
 
toArray() - Method in class org.simtk.geometry3d.Vector3DClass
 
TOMATO - Static variable in class org.simtk.util.ColorName
 
TOMATO1 - Static variable in class org.simtk.util.ColorName
 
TOMATO2 - Static variable in class org.simtk.util.ColorName
 
TOMATO3 - Static variable in class org.simtk.util.ColorName
 
TOMATO4 - Static variable in class org.simtk.util.ColorName
 
toString() - Method in class org.simtk.geometry3d.Angle
 
toString() - Method in class org.simtk.geometry3d.MathMatrixClass
 
toString() - Method in class org.simtk.geometry3d.MathVectorClass
 
toString() - Method in class org.simtk.geometry3d.Vector2DClass
 
toString() - Method in class org.simtk.geometry3d.Vector3DClass
 
toString() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair
 
trace() - Method in interface org.simtk.geometry3d.MathMatrix
 
trace() - Method in class org.simtk.geometry3d.MathMatrixClass
 
trace() - Method in interface org.simtk.geometry3d.Matrix3D
 
transpose() - Method in interface org.simtk.geometry3d.MathMatrix
 
transpose() - Method in class org.simtk.geometry3d.MathMatrixClass
 
transpose() - Method in interface org.simtk.geometry3d.Matrix3D
 
transpose() - Method in class org.simtk.geometry3d.Matrix3DClass
 
Tryptophan - Class in org.simtk.molecularstructure.protein
 
Tryptophan() - Constructor for class org.simtk.molecularstructure.protein.Tryptophan
 
TURQUOISE - Static variable in class org.simtk.util.ColorName
 
TURQUOISE1 - Static variable in class org.simtk.util.ColorName
 
TURQUOISE2 - Static variable in class org.simtk.util.ColorName
 
TURQUOISE3 - Static variable in class org.simtk.util.ColorName
 
TURQUOISE4 - Static variable in class org.simtk.util.ColorName
 
TWO_PI - Static variable in class org.simtk.geometry3d.Angle
 
Tyrosine - Class in org.simtk.molecularstructure.protein
 
Tyrosine() - Constructor for class org.simtk.molecularstructure.protein.Tyrosine
 

U

UncompressInputStream - Class in org.simtk.util
This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UncompressInputStream(InputStream) - Constructor for class org.simtk.util.UncompressInputStream
 
UndoableDialog - Class in org.simtk.gui
 
UndoableDialog(Frame) - Constructor for class org.simtk.gui.UndoableDialog
 
UndoableDialog() - Constructor for class org.simtk.gui.UndoableDialog
 
UndoRedoMechanism - Class in org.simtk.gui
 
UndoRedoMechanism() - Constructor for class org.simtk.gui.UndoRedoMechanism
 
unit() - Method in interface org.simtk.geometry3d.MathVector
 
unit() - Method in class org.simtk.geometry3d.MathVectorClass
 
unit() - Method in interface org.simtk.geometry3d.Vector2D
 
unit() - Method in class org.simtk.geometry3d.Vector2DClass
 
unit() - Method in interface org.simtk.geometry3d.Vector3D
 
unit() - Method in class org.simtk.geometry3d.Vector3DClass
 
UNKNOWN_ELEMENT - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
UNKNOWN_RESIDUE_TYPE - Static variable in class org.simtk.molecularstructure.ResidueTypeClass
 
UnknownAminoAcid - Class in org.simtk.molecularstructure.protein
 
UnknownAminoAcid() - Constructor for class org.simtk.molecularstructure.protein.UnknownAminoAcid
 
UNLIMITED - Static variable in class org.simtk.geometry3d.Angle.Range
 
unSelect() - Method in interface org.simtk.util.SelectionListener
 
unSelect(Selectable) - Method in interface org.simtk.util.SelectionListener
 
UNSIGNED - Static variable in class org.simtk.geometry3d.Angle.Range
 
update(Observable, Object) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog
 
updateAtomPosition(Atom) - Method in interface org.simtk.molecularstructure.Residue
 
updateAtomPosition(Atom) - Method in class org.simtk.molecularstructure.ResidueClass
 
updateState() - Method in interface org.simtk.gui.ProgressDialog
 
updateState() - Method in class org.simtk.gui.ProgressDialogClass
 
updateState() - Method in class org.simtk.gui.ProgressPanel
 
Uridylate - Class in org.simtk.molecularstructure.nucleicacid
 
Uridylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Uridylate
 
url - Variable in class org.simtk.pdb.LoadPdbUrlProcess
 

V

Valine - Class in org.simtk.molecularstructure.protein
 
Valine() - Constructor for class org.simtk.molecularstructure.protein.Valine
 
valueOf(String) - Static method in enum org.simtk.molecularstructure.nucleicacid.BasePair.BondOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simtk.molecularstructure.nucleicacid.BasePair.EdgeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.simtk.molecularstructure.SecondaryStructureClass.SourceType
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.simtk.molecularstructure.nucleicacid.BasePair.BondOrientation
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.simtk.molecularstructure.nucleicacid.BasePair.EdgeType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.simtk.molecularstructure.SecondaryStructureClass.SourceType
Returns an array containing the constants of this enum type, in the order they're declared.
Vector2D - Interface in org.simtk.geometry3d
 
Vector2DClass - Class in org.simtk.geometry3d
 
Vector2DClass() - Constructor for class org.simtk.geometry3d.Vector2DClass
 
Vector2DClass(double, double) - Constructor for class org.simtk.geometry3d.Vector2DClass
 
Vector2DClass(double[]) - Constructor for class org.simtk.geometry3d.Vector2DClass
 
Vector2DClass(MathVector) - Constructor for class org.simtk.geometry3d.Vector2DClass
 
Vector3D - Interface in org.simtk.geometry3d
 
Vector3DClass - Class in org.simtk.geometry3d
 
Vector3DClass() - Constructor for class org.simtk.geometry3d.Vector3DClass
 
Vector3DClass(double, double, double) - Constructor for class org.simtk.geometry3d.Vector3DClass
 
Vector3DClass(double[]) - Constructor for class org.simtk.geometry3d.Vector3DClass
 
Vector3DClass(MathVector) - Constructor for class org.simtk.geometry3d.Vector3DClass
 
Vector3DFloatArrayWrapper - Class in org.simtk.geometry3d
 
Vector3DFloatArrayWrapper(float[], int) - Constructor for class org.simtk.geometry3d.Vector3DFloatArrayWrapper
 
VectorSizeException - Exception in org.simtk.geometry3d
 
VIOLET - Static variable in class org.simtk.util.ColorName
 
VIOLET_RED - Static variable in class org.simtk.util.ColorName
 
VIOLET_RED1 - Static variable in class org.simtk.util.ColorName
 
VIOLET_RED2 - Static variable in class org.simtk.util.ColorName
 
VIOLET_RED3 - Static variable in class org.simtk.util.ColorName
 
VIOLET_RED4 - Static variable in class org.simtk.util.ColorName
 

W

WebPDB - Class in org.simtk.pdb
 
WebPDB() - Constructor for class org.simtk.pdb.WebPDB
 
WHEAT - Static variable in class org.simtk.util.ColorName
 
WHEAT1 - Static variable in class org.simtk.util.ColorName
 
WHEAT2 - Static variable in class org.simtk.util.ColorName
 
WHEAT3 - Static variable in class org.simtk.util.ColorName
 
WHEAT4 - Static variable in class org.simtk.util.ColorName
 
WHITE - Static variable in class org.simtk.util.ColorName
 
WHITE_SMOKE - Static variable in class org.simtk.util.ColorName
 
writeTo(OutputStream) - Method in class org.simtk.rnaml.RnamlExportDocument
 
writeTo(File) - Method in class org.simtk.rnaml.RnamlExportDocument
 

X

x() - Method in interface org.simtk.geometry3d.Vector2D
 
x() - Method in class org.simtk.geometry3d.Vector2DClass
 
x() - Method in interface org.simtk.geometry3d.Vector3D
 
x() - Method in class org.simtk.geometry3d.Vector3DClass
 
X_AXIS - Static variable in class org.simtk.geometry3d.Vector3DClass
 

Y

y() - Method in interface org.simtk.geometry3d.Vector2D
 
y() - Method in class org.simtk.geometry3d.Vector2DClass
 
y() - Method in interface org.simtk.geometry3d.Vector3D
 
y() - Method in class org.simtk.geometry3d.Vector3DClass
 
Y_AXIS - Static variable in class org.simtk.geometry3d.Vector3DClass
 
YELLOW - Static variable in class org.simtk.util.ColorName
 
YELLOW1 - Static variable in class org.simtk.util.ColorName
 
YELLOW2 - Static variable in class org.simtk.util.ColorName
 
YELLOW3 - Static variable in class org.simtk.util.ColorName
 
YELLOW4 - Static variable in class org.simtk.util.ColorName
 
YELLOW_GREEN - Static variable in class org.simtk.util.ColorName
 

Z

z() - Method in interface org.simtk.geometry3d.Vector3D
 
z() - Method in class org.simtk.geometry3d.Vector3DClass
 
Z_AXIS - Static variable in class org.simtk.geometry3d.Vector3DClass
 
ZINC - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass
 
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