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

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

radius - Variable in class org.simtk.moleculargraphics.cartoon.BackboneTubeCartoon

random(int, int) - Static method in class Jama.Matrix

Generate matrix with random elements

rank() - Method in class Jama.Matrix

Matrix rank

rank() - Method in class Jama.SingularValueDecomposition

Effective numerical matrix rank

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

read(BufferedReader) - Static method in class Jama.Matrix

Read a matrix from a stream.

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

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

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

removeResidueCenterListener(ResidueCenterListener) - Method in class org.simtk.moleculargraphics.ResidueCenterBroadcaster

removeResidueHighlightListener(ResidueHighlightListener) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

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

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

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

RenderCreate(vtkRenderWindow) - Method in class org.simtk.moleculargraphics.PublicNativeVtkPanel

RenderCreate(vtkRenderWindow) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

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

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

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

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

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

Residue - Interface in org.simtk.molecularstructure

ResidueCenterBroadcaster - Class in org.simtk.moleculargraphics

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

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

residueCenterBroadcaster - Variable in class org.simtk.moleculargraphics.Tornado3DCanvas

ResidueCenterListener - Interface in org.simtk.moleculargraphics

ResidueClass - Class in org.simtk.molecularstructure

ResidueClass(ResidueType) - Constructor for class org.simtk.molecularstructure.ResidueClass

ResidueClass(String) - Constructor for class org.simtk.molecularstructure.ResidueClass

ResidueHighlightBroadcaster - Class in org.simtk.moleculargraphics

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

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

residueHighlightBroadcaster - Variable in class org.simtk.moleculargraphics.Tornado3DCanvas

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

ResidueHighlightListener - Interface in org.simtk.moleculargraphics

residueName - Variable in class org.simtk.molecularstructure.ResidueTypeClass

residueNumber - Variable in class org.simtk.molecularstructure.ResidueClass

residuePositions - Variable in class org.simtk.moleculargraphics.SequenceCanvas

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

ResidueSphereActor - Class in org.simtk.moleculargraphics.cartoon

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

ResidueSpheres - Class in org.simtk.moleculargraphics.cartoon

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

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

ribbonThickness - Variable in class org.simtk.moleculargraphics.cartoon.RichardsonProteinRibbon

ribbonWidth - Variable in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

RichardsonProteinRibbon - Class in org.simtk.moleculargraphics.cartoon

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

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

RopeAndCylinder - Class in org.simtk.moleculargraphics.cartoon

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

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

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

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