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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

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

CameraPanel - Class in org.simtk.moleculargraphics

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

CappedBondActor - Class in org.simtk.moleculargraphics.cartoon

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

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

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

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

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

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

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

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

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

chainDirection(Residue) - Static method in class org.simtk.moleculargraphics.cartoon.ProteinRibbonSegment

chainId - Variable in class org.simtk.molecularstructure.MoleculeClass

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

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

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

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

Set the minimum size to show the entire height

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

chemicalIndices - Variable in class org.simtk.moleculargraphics.cartoon.ToonColors

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

chol() - Method in class Jama.Matrix

Cholesky Decomposition

CholeskyDecomposition - Class in Jama

Cholesky Decomposition.

CholeskyDecomposition(Matrix) - Constructor for class Jama.CholeskyDecomposition

Cholesky algorithm for symmetric and positive definite matrix.

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

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

clear() - Method in class org.simtk.geometry3d.Hash3D

clear() - Method in class org.simtk.geometry3d.MassBodyClass

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

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

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

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

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

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

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

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

clone() - Method in class Jama.Matrix

Clone the Matrix object.

clone() - Method in class org.simtk.geometry3d.Hash3D

color - Variable in class org.simtk.moleculargraphics.cartoon.ConstantColor

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

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

colorByScalar() - Method in class org.simtk.moleculargraphics.cartoon.TensorGlyphCartoon

ColorName - Class in org.simtk.util

colorOf(Object) - Method in class org.simtk.moleculargraphics.cartoon.AtomColorScheme

colorOf(Object) - Method in interface org.simtk.moleculargraphics.cartoon.ColorScheme

colorOf(Object) - Method in class org.simtk.moleculargraphics.cartoon.ConstantColor

colorOf(Object) - Method in class org.simtk.moleculargraphics.cartoon.DefaultColorScheme

colorOf(Object) - Method in class org.simtk.moleculargraphics.cartoon.HighlightColorScheme

colorOf(Object) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeColorScheme

colorOf(Object) - Method in class org.simtk.moleculargraphics.cartoon.SequencingNucleotideColorScheme

colorScheme - Variable in class org.simtk.moleculargraphics.cartoon.BackboneStick

colorScheme - Variable in class org.simtk.moleculargraphics.cartoon.BasePairRod

ColorScheme - Interface in org.simtk.moleculargraphics.cartoon

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

colorToon(Object, ColorScheme) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

colorToon(ColorScheme) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

colorToon(Object, ColorScheme) - Method in interface org.simtk.moleculargraphics.cartoon.BaseCartoon

colorToon(ColorScheme) - Method in interface org.simtk.moleculargraphics.cartoon.BaseCartoon

colorToon(Object, ColorScheme) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

colorToon(ColorScheme) - Method in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

CommandLineInterface - Class in org.simtk.util

CommandLineInterface() - Constructor for class org.simtk.util.CommandLineInterface

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

CompositeCartoon - Class in org.simtk.moleculargraphics.cartoon

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

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

cond() - Method in class Jama.Matrix

Matrix condition (2 norm)

cond() - Method in class Jama.SingularValueDecomposition

Two norm condition number

ConstantColor - Class in org.simtk.moleculargraphics.cartoon

ConstantColor(Color) - Constructor for class org.simtk.moleculargraphics.cartoon.ConstantColor

constructWithCopy(double[][]) - Static method in class Jama.Matrix

Construct a matrix from a copy of a 2-D array.

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

copy() - Method in class Jama.Matrix

Make a deep copy of a matrix

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

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

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

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

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

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

createExtrudedRibbon(vtkPolyData, double, double, double) - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbonSegment

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.

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

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

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

CylinderCartoon - Class in org.simtk.moleculargraphics.cartoon

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

CylinderPanel - Class in org.simtk.moleculargraphics

cylinderRadius - Variable in class org.simtk.moleculargraphics.cartoon.CylinderCartoon

cylinderSource - Variable in class org.simtk.moleculargraphics.cartoon.CylinderCartoon

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