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

P

paint(Graphics) - Method in class org.simtk.moleculargraphics.BufferedCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.SequenceCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.SequencePane

paint(Graphics) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

paint(Graphics) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

paint(Graphics) - Method in class org.simtk.pdb.JLinkLabel

paint(Graphics) - Method in class org.simtk.splashscreen.SplashWindow

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

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

pickActor(int, int) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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(Matrix) - Method in class Jama.Matrix

C = A + B

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(Matrix) - Method in class Jama.Matrix

A = A + B

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

position1 - Variable in class org.simtk.toon.secstruct.BasePairPosition

position2 - Variable in class org.simtk.toon.secstruct.BasePairPosition

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

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

POWDER_BLUE - Static variable in class org.simtk.util.ColorName

prepareNutation(double) - Method in class org.simtk.moleculargraphics.StructureCanvas

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

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

Print the matrix to stdout.

print(PrintWriter, int, int) - Method in class Jama.Matrix

Print the matrix to the output stream.

print(NumberFormat, int) - Method in class Jama.Matrix

Print the matrix to stdout.

print(PrintWriter, NumberFormat, int) - Method in class Jama.Matrix

Print the matrix to the output stream.

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, Component, 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

ProteinCoil - Class in org.simtk.moleculargraphics.cartoon

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

ProteinHelix - Class in org.simtk.moleculargraphics.cartoon

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

ProteinRibbon - Class in org.simtk.moleculargraphics.cartoon

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

ProteinRibbonSegment - Class in org.simtk.moleculargraphics.cartoon

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

ProteinRibbonSphereTest - Class in org.simtk.moleculargraphics.cartoon

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

PublicNativeVtkPanel - Class in org.simtk.moleculargraphics

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

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