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

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 Jama.Matrix

Get a single element.

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

getActor() - Method in interface org.simtk.moleculargraphics.cartoon.ActorCartoon

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

getArray() - Method in class Jama.Matrix

Access the internal two-dimensional array.

getArrayCopy() - Method in class Jama.Matrix

Copy the internal two-dimensional array.

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

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

getBackgroundColor() - Method in class org.simtk.moleculargraphics.MolApp

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

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

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

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

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

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

getChemicalFromScalar(int) - Method in interface org.simtk.moleculargraphics.cartoon.ActorCartoon

getChemicalFromScalar(int) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

getChemicalFromScalar(int) - Method in class org.simtk.moleculargraphics.cartoon.ToonColors

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

getColorIndex(Chemical) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

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

getColumnDimension() - Method in class Jama.Matrix

Get column dimension.

getColumnPackedCopy() - Method in class Jama.Matrix

Make a one-dimensional column packed copy of the internal array.

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

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

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.moleculargraphics.Tornado

getCurrentPath() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

getD() - Method in class Jama.EigenvalueDecomposition

Return the block diagonal eigenvalue matrix

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

getDoublePivot() - Method in class Jama.LUDecomposition

Return pivot permutation vector as a one-dimensional double array

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

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

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

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

getH() - Method in class Jama.QRDecomposition

Return the Householder vectors

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

getHighlightActor() - Method in interface org.simtk.moleculargraphics.cartoon.ActorCartoon

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

getHighlightColor() - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

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

getImagEigenvalues() - Method in class Jama.EigenvalueDecomposition

Return the imaginary parts of the eigenvalues

getInputStream() - Method in class org.simtk.pdb.LoadPdbUrlProcess

getInputStructureFileName() - Method in class org.simtk.molecularstructure.MoleculeCollection

getL() - Method in class Jama.CholeskyDecomposition

Return triangular factor.

getL() - Method in class Jama.LUDecomposition

Return lower triangular factor

getLabelCorner(Graphics2D, String, Vector2D, Vector2D) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

getLeftEdgePixel() - Method in class org.simtk.moleculargraphics.SequenceCanvas

getMapper() - Method in interface org.simtk.moleculargraphics.cartoon.ActorCartoon

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

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

getMatrix(int, int, int, int) - Method in class Jama.Matrix

Get a submatrix.

getMatrix(int[], int[]) - Method in class Jama.Matrix

Get a submatrix.

getMatrix(int, int, int[]) - Method in class Jama.Matrix

Get a submatrix.

getMatrix(int[], int, int) - Method in class Jama.Matrix

Get a submatrix.

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

getMaximumSize() - Method in class org.simtk.moleculargraphics.SequenceCanvas

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

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

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

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

getMidpoint() - Method in class org.simtk.geometry3d.Cylinder

getMilliseconds() - Method in class org.simtk.util.Stopwatch

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

getMinimumSize() - Method in class org.simtk.moleculargraphics.SequenceCanvas

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

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

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

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

getMolecule() - Method in class org.simtk.moleculargraphics.SequenceCanvas

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

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

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

getPivot() - Method in class Jama.LUDecomposition

Return pivot permutation vector

getPreferredSize() - Method in class org.simtk.moleculargraphics.SequenceCanvas

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

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

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

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

getQ() - Method in class Jama.QRDecomposition

Generate and return the (economy-sized) orthogonal factor

getR() - Method in class Jama.QRDecomposition

Return the upper triangular factor

getRadius() - Method in class org.simtk.geometry3d.Cylinder

getRange() - Method in class org.simtk.geometry3d.Angle

getRealEigenvalues() - Method in class Jama.EigenvalueDecomposition

Return the real parts of the eigenvalues

getRedoAction() - Method in class org.simtk.gui.UndoRedoMechanism

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

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

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

getResidue() - Method in class org.simtk.toon.secstruct.BasePosition

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

getResidueWidth() - Method in class org.simtk.moleculargraphics.SequenceCanvas

GetRibbonFilterWidth() - Method in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

GetRibbonFilterWidth() - Method in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

GetRibbonFilterWidthFactor() - Method in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

GetRibbonFilterWidthFactor() - Method in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

getRightEdgePixel() - Method in class org.simtk.moleculargraphics.SequenceCanvas

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

getRowDimension() - Method in class Jama.Matrix

Get row dimension.

getRowPackedCopy() - Method in class Jama.Matrix

Make a one-dimensional row packed copy of the internal array.

getS() - Method in class Jama.SingularValueDecomposition

Return the diagonal matrix of singular values

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

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

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

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

What is the total width in pixels of the entire sequence?

getSideChainPosition() - Method in interface org.simtk.molecularstructure.Residue

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

getSingularValues() - Method in class Jama.SingularValueDecomposition

Return the one-dimensional array of singular values

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

GetThickness() - Method in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

GetThickness() - Method in class org.simtk.moleculargraphics.cartoon.vtkPreExtrusionCenteringFilter

GetThickness() - Method in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

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

getTotalSequenceWidth() - Method in class org.simtk.moleculargraphics.SequenceCanvas

Get width of entire sequence, not just the visible canvas

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

getU() - Method in class Jama.LUDecomposition

Return upper triangular factor

getU() - Method in class Jama.SingularValueDecomposition

Return the left singular vectors

getUndoAction() - Method in class org.simtk.gui.UndoRedoMechanism

getUnits() - Method in class org.simtk.geometry3d.Angle

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

getV() - Method in class Jama.EigenvalueDecomposition

Return the eigenvector matrix

getV() - Method in class Jama.SingularValueDecomposition

Return the right singular vectors

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

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

How wide is the viewport in which the sequence is shown?

getVtkActors() - Method in class org.simtk.moleculargraphics.ScaleBar

getVtkCylinder(Cylinder, Color, int) - Static method in class org.simtk.moleculargraphics.GraphicsCylinder

getVtkCylinderFilter(Cylinder, int) - Static method in class org.simtk.moleculargraphics.GraphicsCylinder

getVtkMeshCylinder(double, double, double) - Static method in class org.simtk.moleculargraphics.cartoon.NewDuplexCylinderActor

getVtkMeshCylinder(Cylinder, double) - Static method in class org.simtk.moleculargraphics.cartoon.NewDuplexCylinderActor

getVtkMeshCylinder(Cylinder, Color, double) - Method in class org.simtk.moleculargraphics.cartoon.NewDuplexCylinderActor

getVtkProp3D() - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbon

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

getX() - Method in class org.simtk.toon.secstruct.BasePosition

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

getY() - Method in class org.simtk.toon.secstruct.BasePosition

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

GlyphCartoon - Class in org.simtk.moleculargraphics.cartoon

Cartoon consisting of a single vtkGlyph3D.

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

GraphicsCylinder - Class in org.simtk.moleculargraphics

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

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