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

B

BackboneCurve - Class in org.simtk.moleculargraphics.cartoon

backboneGroup - Static variable in class org.simtk.molecularstructure.protein.AminoAcid

BackboneStick - Class in org.simtk.moleculargraphics.cartoon

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

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

BackboneStick(double, int) - Constructor for class org.simtk.moleculargraphics.cartoon.BackboneStick

BackboneTubeActor - Class in org.simtk.moleculargraphics.cartoon

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

BackboneTubeCartoon - Class in org.simtk.moleculargraphics.cartoon

BallAndStickCartoon - Class in org.simtk.moleculargraphics.cartoon

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

BaseCartoon - Interface in org.simtk.moleculargraphics.cartoon

BaseConnectorTube - Class in org.simtk.moleculargraphics.cartoon

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

BaseConnectorTubeActor - Class in org.simtk.moleculargraphics.cartoon

BaseConnectorTubeActor(Residue) - Constructor for class org.simtk.moleculargraphics.cartoon.BaseConnectorTubeActor

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

BasePairBrick - Class in org.simtk.moleculargraphics.cartoon

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

BasePairConnectorStick - Class in org.simtk.moleculargraphics.cartoon

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

BasePairOval - Class in org.simtk.moleculargraphics.cartoon

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

BasePairPosition - Class in org.simtk.toon.secstruct

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

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

BasePairRibbon - Class in org.simtk.moleculargraphics.cartoon

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

BasePairRod - Class in org.simtk.moleculargraphics.cartoon

basePairs() - Method in class org.simtk.molecularstructure.nucleicacid.BaseTriple

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

BasePosition - Class in org.simtk.toon.secstruct

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

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

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

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

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

BetaStrandRibbon - Class in org.simtk.moleculargraphics.cartoon

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

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

BondStickCartoon - Class in org.simtk.moleculargraphics.cartoon

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

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

BORON - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass

BoundingBox - Class in org.simtk.moleculargraphics.cartoon

BoundingBox(double[]) - Constructor for class org.simtk.moleculargraphics.cartoon.BoundingBox

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

BufferedCanvas - Class in org.simtk.moleculargraphics

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

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