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

M

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

MAGENTA1 - Static variable in class org.simtk.util.ColorName

MAGENTA2 - Static variable in class org.simtk.util.ColorName

MAGENTA3 - Static variable in class org.simtk.util.ColorName

MAGENTA4 - Static variable in class org.simtk.util.ColorName

magic(int) - Static method in class Jama.examples.MagicSquareExample

Generate magic square test matrix.

MagicSquareExample - Class in Jama.examples

Example of use of Matrix Class, featuring magic squares.

MagicSquareExample() - Constructor for class Jama.examples.MagicSquareExample

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

main(String[]) - Static method in class Jama.examples.MagicSquareExample

main(String[]) - Static method in class Jama.test.TestMatrix

main(String[]) - Static method in class org.simtk.geometry3d.TestKabschSuperposition

main(String[]) - Static method in class org.simtk.geometry3d.TestSuperposition

main(String[]) - Static method in class org.simtk.geometry3d.TestVector3DClass

main(String[]) - Static method in class org.simtk.moleculargraphics.CameraPanel

Main method for testing the CameraPanel

main(String[]) - Static method in class org.simtk.moleculargraphics.CylinderPanel

main(String[]) - Static method in class org.simtk.moleculargraphics.EthaneDemo

main(String[]) - Static method in class org.simtk.moleculargraphics.TestArrowRibbon

main(String[]) - Static method in class org.simtk.moleculargraphics.TestMenu

main(String[]) - Static method in class org.simtk.moleculargraphics.Tornado

main(String[]) - Static method in class org.simtk.splashscreen.EthaneSplasher

main(String[]) - Static method in class org.simtk.splashscreen.TornadoSplasher

main(String[]) - Static method in class org.simtk.toon.secstruct.TestSecondaryStructureCanvas

main(String[]) - Static method in class org.simtk.util.UncompressInputStream

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

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

makeBasePair(Residue, Residue, String) - Static method in class org.simtk.molecularstructure.nucleicacid.BasePair

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

mapper - Variable in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

mapper - Variable in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

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

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

MAROON1 - Static variable in class org.simtk.util.ColorName

MAROON2 - Static variable in class org.simtk.util.ColorName

MAROON3 - Static variable in class org.simtk.util.ColorName

MAROON4 - Static variable in class org.simtk.util.ColorName

MassBody - Interface in org.simtk.geometry3d

MassBodyClass - Class in org.simtk.geometry3d

MassBodyClass() - Constructor for class org.simtk.geometry3d.MassBodyClass

matchesPdbLine(String) - Method in class org.simtk.molecularstructure.ResidueClass

MathMatrix - Interface in org.simtk.geometry3d

MathMatrixClass - Class in org.simtk.geometry3d

MathMatrixClass(int, int) - Constructor for class org.simtk.geometry3d.MathMatrixClass

MathMatrixClass(int, int, double) - Constructor for class org.simtk.geometry3d.MathMatrixClass

MathMatrixClass(MathMatrix) - Constructor for class org.simtk.geometry3d.MathMatrixClass

Maths - Class in Jama.util

Maths() - Constructor for class Jama.util.Maths

MathVector - Interface in org.simtk.geometry3d

MathVectorClass - Class in org.simtk.geometry3d

MathVectorClass(int) - Constructor for class org.simtk.geometry3d.MathVectorClass

Matrix - Class in Jama

Jama = Java Matrix class.

Matrix(int, int) - Constructor for class Jama.Matrix

Construct an m-by-n matrix of zeros.

Matrix(int, int, double) - Constructor for class Jama.Matrix

Construct an m-by-n constant matrix.

Matrix(double[][]) - Constructor for class Jama.Matrix

Construct a matrix from a 2-D array.

Matrix(double[][], int, int) - Constructor for class Jama.Matrix

Construct a matrix quickly without checking arguments.

Matrix(double[], int) - Constructor for class Jama.Matrix

Construct a matrix from a one-dimensional packed array

Matrix3D - Interface in org.simtk.geometry3d

Matrix3DClass - Class in org.simtk.geometry3d

Matrix3DClass() - Constructor for class org.simtk.geometry3d.Matrix3DClass

Matrix3DClass(MathMatrix) - Constructor for class org.simtk.geometry3d.Matrix3DClass

Matrix3DClass(double, double, double, double, double, double, double, double, double) - Constructor for class org.simtk.geometry3d.Matrix3DClass

MatrixSizeMismatchException - Exception in org.simtk.geometry3d

mean() - Method in class org.simtk.util.DoubleRing

Compute mean value of the elements in the ring.

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

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

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

MEDIUM_ORCHID1 - Static variable in class org.simtk.util.ColorName

MEDIUM_ORCHID2 - Static variable in class org.simtk.util.ColorName

MEDIUM_ORCHID3 - Static variable in class org.simtk.util.ColorName

MEDIUM_ORCHID4 - Static variable in class org.simtk.util.ColorName

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

MEDIUM_PURPLE1 - Static variable in class org.simtk.util.ColorName

MEDIUM_PURPLE2 - Static variable in class org.simtk.util.ColorName

MEDIUM_PURPLE3 - Static variable in class org.simtk.util.ColorName

MEDIUM_PURPLE4 - Static variable in class org.simtk.util.ColorName

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

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

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

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

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

Methionine - Class in org.simtk.molecularstructure.protein

Methionine() - Constructor for class org.simtk.molecularstructure.protein.Methionine

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

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

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

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

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

minus(Matrix) - Method in class Jama.Matrix

C = A - B

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

minus(MathMatrix) - Method in interface org.simtk.geometry3d.MathMatrix

minus(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass

minus(MathVector) - Method in interface org.simtk.geometry3d.MathVector

minus(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass

minus(MathMatrix) - Method in interface org.simtk.geometry3d.Matrix3D

minus(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass

minus(MathVector) - Method in interface org.simtk.geometry3d.Vector2D

minus(MathVector) - Method in class org.simtk.geometry3d.Vector2DClass

minus(MathVector) - Method in interface org.simtk.geometry3d.Vector3D

minus(MathVector) - Method in class org.simtk.geometry3d.Vector3DClass

minusEquals(Matrix) - Method in class Jama.Matrix

A = A - B

minusEquals(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass

minusEquals(MathVector) - Method in class org.simtk.geometry3d.MathVectorClass

minusEquals(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass

minusEquals(MathMatrix) - Method in interface org.simtk.geometry3d.MutableMathMatrix

minusEquals(MathVector) - Method in interface org.simtk.geometry3d.MutableMathVector

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

MISTY_ROSE1 - Static variable in class org.simtk.util.ColorName

MISTY_ROSE2 - Static variable in class org.simtk.util.ColorName

MISTY_ROSE3 - Static variable in class org.simtk.util.ColorName

MISTY_ROSE4 - Static variable in class org.simtk.util.ColorName

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

modifiedAdenylates - Static variable in class org.simtk.molecularstructure.ResidueClass

modifiedCytidylates - Static variable in class org.simtk.molecularstructure.ResidueClass

modifiedGuanylates - Static variable in class org.simtk.molecularstructure.ResidueClass

modifiedInositates - Static variable in class org.simtk.molecularstructure.ResidueClass

modifiedThymidylates - Static variable in class org.simtk.molecularstructure.ResidueClass

modifiedUridylates - Static variable in class org.simtk.molecularstructure.ResidueClass

MolApp - Class in org.simtk.moleculargraphics

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

Molecular - Interface in org.simtk.molecularstructure

MolecularClass - Class in org.simtk.molecularstructure

MolecularClass() - Constructor for class org.simtk.molecularstructure.MolecularClass

MolecularClass(AtomSet) - Constructor for class org.simtk.molecularstructure.MolecularClass

Molecule - Interface in org.simtk.molecularstructure

MoleculeAcquisitionMethodDialog - Class in org.simtk.pdb

MoleculeAcquisitionMethodDialog(JFrame, ProgressDialog) - Constructor for class org.simtk.pdb.MoleculeAcquisitionMethodDialog

MoleculeAcquisitionMethodDialog(JFrame, ProgressDialog, String) - Constructor for class org.simtk.pdb.MoleculeAcquisitionMethodDialog

MoleculeBlobActor - Class in org.simtk.moleculargraphics.cartoon

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

MoleculeBlobs - Class in org.simtk.moleculargraphics.cartoon

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

MoleculeCartoon - Interface in org.simtk.moleculargraphics.cartoon

MoleculeCartoonClass - Class in org.simtk.moleculargraphics.cartoon

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

MoleculeClass - Class in org.simtk.molecularstructure

MoleculeClass(char) - Constructor for class org.simtk.molecularstructure.MoleculeClass

MoleculeCollection - Class in org.simtk.molecularstructure

MoleculeCollection() - Constructor for class org.simtk.molecularstructure.MoleculeCollection

MoleculeColorScheme - Class in org.simtk.moleculargraphics.cartoon

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

MoleculeMVCModel - Class in org.simtk.mvc

MoleculeMVCModel() - Constructor for class org.simtk.mvc.MoleculeMVCModel

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

MoleculeTensorActor - Class in org.simtk.moleculargraphics.cartoon

MoleculeTensorActor(Molecule) - Constructor for class org.simtk.moleculargraphics.cartoon.MoleculeTensorActor

MoleculeTensorCartoon - Class in org.simtk.moleculargraphics.cartoon

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

MonitoredProcess - Interface in org.simtk.gui

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseClicked(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.CylinderPanel

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.StructureCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseDragged(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseEntered(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseExited(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.CylinderPanel

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseMoved(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.StructureCanvas

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mousePressed(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mouseReleased(MouseEvent) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

mouseReleased(MouseEvent) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

mouseReleased(MouseEvent) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

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

mouseWheelMoved(MouseWheelEvent) - Method in class org.simtk.moleculargraphics.StructureCanvas

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

MutableHomogeneousTransform - Interface in org.simtk.geometry3d

MutableMathMatrix - Interface in org.simtk.geometry3d

MutableMathVector - Interface in org.simtk.geometry3d

MutableMatrix3D - Interface in org.simtk.geometry3d

MutableVector2D - Interface in org.simtk.geometry3d

MutableVector3D - Interface in org.simtk.geometry3d

MVCModel - Interface in org.simtk.mvc

MVCView - Interface in org.simtk.mvc

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

MyJFileFilter - Class in org.simtk.util

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