Serialized Form

Package Jama

Class Jama.CholeskyDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

L

double[][] L

Array for internal storage of decomposition.

internal array storage.

n

int n

Row and column dimension (square matrix).

matrix dimension.

isspd

boolean isspd

Symmetric and positive definite flag.

is symmetric and positive definite flag.

Class Jama.EigenvalueDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

n

int n

Row and column dimension (square matrix).

matrix dimension.

issymmetric

boolean issymmetric

Symmetry flag.

internal symmetry flag.

d

double[] d

Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

e

double[] e

Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

V

double[][] V

Array for internal storage of eigenvectors.

internal storage of eigenvectors.

H

double[][] H

Array for internal storage of nonsymmetric Hessenberg form.

internal storage of nonsymmetric Hessenberg form.

ort

double[] ort

Working storage for nonsymmetric algorithm.

working storage for nonsymmetric algorithm.

Class Jama.LUDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

LU

double[][] LU

Array for internal storage of decomposition.

internal array storage.

m

int m

Row and column dimensions, and pivot sign.

column dimension.

n

int n

Row and column dimensions, and pivot sign.

column dimension.

pivsign

int pivsign

Row and column dimensions, and pivot sign.

column dimension.

piv

int[] piv

Internal storage of pivot vector.

pivot vector.

Class Jama.Matrix extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

A

double[][] A

Array for internal storage of elements.

internal array storage.

m

int m

Row and column dimensions.

row dimension.

n

int n

Row and column dimensions.

row dimension.

Class Jama.QRDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

QR

double[][] QR

Array for internal storage of decomposition.

internal array storage.

m

int m

Row and column dimensions.

column dimension.

n

int n

Row and column dimensions.

column dimension.

Rdiag

double[] Rdiag

Array for internal storage of diagonal of R.

diagonal of R.

Class Jama.SingularValueDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

U

double[][] U

Arrays for internal storage of U and V.

internal storage of U.

V

double[][] V

Arrays for internal storage of U and V.

internal storage of U.

s

double[] s

Array for internal storage of singular values.

internal storage of singular values.

m

int m

Row and column dimensions.

row dimension.

n

int n

Row and column dimensions.

row dimension.

Package org.simtk.geometry3d

Class org.simtk.geometry3d.Angle extends java.lang.Number implements Serializable

serialVersionUID: 1L

Serialized Fields

radianAngle

double radianAngle

angleRange

Angle.Range angleRange

angleUnits

Angle.Units angleUnits

Class org.simtk.geometry3d.Hash3D extends java.util.HashMap<Vector3D,V> implements Serializable

Serialized Fields

cubeletSize

double cubeletSize

cubelets

java.util.Map<K,V> cubelets

Class org.simtk.geometry3d.InsufficientPointsException extends java.lang.Exception implements Serializable

Class org.simtk.geometry3d.MatrixSizeMismatchException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1L

Class org.simtk.geometry3d.VectorSizeException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1L

Package org.simtk.gui

Class org.simtk.gui.ProgressDialogClass extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

progressPanel

ProgressPanel progressPanel

Class org.simtk.gui.ProgressPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

throbber

Throbber throbber

startTime

java.util.Date startTime

timeLabel

javax.swing.JLabel timeLabel

cancelButton

javax.swing.JButton cancelButton

m_isCancelled

boolean m_isCancelled

Class org.simtk.gui.Throbber extends javax.swing.JLabel implements Serializable

serialVersionUID: 1L

Serialized Fields

icons

javax.swing.Icon[] icons

iconIndex

int iconIndex

Class org.simtk.gui.UndoableDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

currentParameterState

ParameterSetModel currentParameterState

parameterHistory

java.util.Vector<E> parameterHistory

currentHistoryPosition

int currentHistoryPosition

undoButton

javax.swing.JButton undoButton

redoButton

javax.swing.JButton redoButton

closeButton

javax.swing.JButton closeButton

contentPane

javax.swing.JPanel contentPane

Package org.simtk.moleculargraphics

Class org.simtk.moleculargraphics.BufferedCanvas extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

offScreenImage

java.awt.Image offScreenImage

width

int width

height

int height

Class org.simtk.moleculargraphics.CameraPanel extends javax.swing.JPanel implements Serializable

Class org.simtk.moleculargraphics.CylinderPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

renWin

vtk.vtkCanvas renWin

exitButton

javax.swing.JButton exitButton

renderer

vtk.vtkRenderer renderer

vtkPropNames

java.util.Hashtable<K,V> vtkPropNames

vtkPropObjects

java.util.Hashtable<K,V> vtkPropObjects

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

sphereCount

int sphereCount

cylinderCount

int cylinderCount

picker

vtk.vtkPropPicker picker

Class org.simtk.moleculargraphics.EthaneDemo extends MolApp implements Serializable

Serialized Fields

userAppName

java.lang.String userAppName

ethaneTorsion

org.simtk.moleculargraphics.AtomTorsion ethaneTorsion

actorCartoon

CappedBondActor actorCartoon

ethane

Molecule ethane

Class org.simtk.moleculargraphics.MolApp extends javax.swing.JFrame implements Serializable

Serialized Fields

classLoader

java.lang.ClassLoader classLoader

canvas

StructureCanvas canvas

Class org.simtk.moleculargraphics.PublicNativeVtkPanel extends vtk.vtkPanel implements Serializable

Class org.simtk.moleculargraphics.SequenceCanvas extends BufferedCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

numberOfResidues

int numberOfResidues

minHeight

int minHeight

minWidth

int minWidth

sequenceColor

java.awt.Color sequenceColor

myGraphics

java.awt.Graphics myGraphics

parentContainer

javax.swing.JComponent parentContainer

font

java.awt.Font font

symbolWidth

double symbolWidth

symbolHeight

double symbolHeight

characterSpacing

double characterSpacing

baseLine

int baseLine

numberFont

java.awt.Font numberFont

numberHeight

int numberHeight

numberBaseLine

int numberBaseLine

leftEdgeVirtualPixel

int leftEdgeVirtualPixel

sequenceMolecule

Biopolymer sequenceMolecule

residuePositions

java.util.Map<K,V> residuePositions

positionResidues

java.util.Map<K,V> positionResidues

residueSymbols

java.util.Vector<E> residueSymbols

Class org.simtk.moleculargraphics.SequenceCartoonCanvas extends BufferedCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

sequenceCanvas

TornadoSequenceCanvas sequenceCanvas

highlightedResidues

java.util.Map<K,V> highlightedResidues

residuePositions

java.util.Map<K,V> residuePositions

positionResidues

java.util.Hashtable<K,V> positionResidues

residueCount

int residueCount

cartoonBackgroundColor

java.awt.Color cartoonBackgroundColor

cartoonVisibleColor

java.awt.Color cartoonVisibleColor

cartoonHeight

int cartoonHeight

cartoonTop

int cartoonTop

cartoonBottom

int cartoonBottom

cartoonLeft

int cartoonLeft

cartoonRight

int cartoonRight

cartoonMargin

int cartoonMargin

defaultCursor

java.awt.Cursor defaultCursor

leftRightCursor

java.awt.Cursor leftRightCursor

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

prefSize

java.awt.Dimension prefSize

mousePressedInCartoon

boolean mousePressedInCartoon

mouseMoveHighlights

boolean mouseMoveHighlights

Class org.simtk.moleculargraphics.SequencePane extends javax.swing.JScrollPane implements Serializable

serialVersionUID: 1L

Serialized Fields

currentHighlightedResidue

Residue currentHighlightedResidue

firstResidue

Residue firstResidue

finalResidue

Residue finalResidue

sequenceCanvas

TornadoSequenceCanvas sequenceCanvas

backgroundColor

java.awt.Color backgroundColor

tornado

Tornado tornado

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

contentPanel

java.awt.Panel contentPanel

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

Class org.simtk.moleculargraphics.StructureCanvas extends vtk.vtkPanel implements Serializable

Serialized Fields

actorCartoons

java.util.Map<K,V> actorCartoons

useScaleBar

boolean useScaleBar

scaleBar

ScaleBar scaleBar

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

prefSize

java.awt.Dimension prefSize

mouseDragAction

org.simtk.moleculargraphics.StructureCanvas.MouseDragAction mouseDragAction

backgroundColor

java.awt.Color backgroundColor

nutationRangeAngle

double nutationRangeAngle

currentNutationAxis

Vector3D currentNutationAxis

Class org.simtk.moleculargraphics.TestMenu extends MolApp implements Serializable

Class org.simtk.moleculargraphics.Tornado extends MolApp implements Serializable

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

activeMoleculeBroadcaster

ActiveMoleculeBroadcaster activeMoleculeBroadcaster

initialBackgroundColor

java.awt.Color initialBackgroundColor

highlightColor

java.awt.Color highlightColor

initialLoadStructurePanel

javax.swing.JPanel initialLoadStructurePanel

currentPath

java.lang.String currentPath

saveImagePath

java.lang.String saveImagePath

loadStructureDialog

org.simtk.moleculargraphics.Tornado.LoadStructureDialog loadStructureDialog

colorScheme

ColorScheme colorScheme

currentCartoon

MoleculeCartoon currentCartoon

toonRange

org.simtk.moleculargraphics.Tornado.ToonRange toonRange

selectedSourceTypes

java.util.List<E> selectedSourceTypes

undoRedoMechanism

UndoRedoMechanism undoRedoMechanism

userIsInteracting

boolean userIsInteracting

viewMenu

javax.swing.JMenu viewMenu

sequencePane

SequencePane sequencePane

sequenceCartoonCanvas

SequenceCartoonCanvas sequenceCartoonCanvas

sequencePanel

java.awt.Panel sequencePanel

messageArea

javax.swing.JLabel messageArea

currentHighlightedResidue

Residue currentHighlightedResidue

useRotationThread

boolean useRotationThread

rotationThread

InertialRotationThread rotationThread

drawSecondaryStructure

boolean drawSecondaryStructure

moleculeCollection

MoleculeCollection moleculeCollection

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

waitCursor

java.awt.Cursor waitCursor

titleBase

java.lang.String titleBase

Class org.simtk.moleculargraphics.Tornado3DCanvas extends StructureCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

highlightResidues

java.util.Map<K,V> highlightResidues

currentlyDepressedKeyboardKeys

java.util.HashSet<E> currentlyDepressedKeyboardKeys

showLogo

boolean showLogo

doFog

boolean doFog

fogLinear

boolean fogLinear

gl

net.java.games.jogl.GL gl

overlayRenderer

vtk.vtkRenderer overlayRenderer

logoImageData

vtk.vtkImageData logoImageData

logoReader

vtk.vtkPNGReader logoReader

logoActor

vtk.vtkActor2D logoActor

logoWidth

int logoWidth

logoHeight

int logoHeight

crosshairCursor

java.awt.Cursor crosshairCursor

defaultCursor

java.awt.Cursor defaultCursor

classLoader

java.lang.ClassLoader classLoader

firstPaint

boolean firstPaint

fpsStopWatch

Stopwatch fpsStopWatch

frameCount

int frameCount

fpsRing

DoubleRing fpsRing

pickIsPending

boolean pickIsPending

picker

vtk.vtkCellPicker picker

doPick

boolean doPick

Class org.simtk.moleculargraphics.TornadoSequenceCanvas extends SequenceCanvas implements Serializable

serialVersionUID: 1L

Serialized Fields

parent

SequencePane parent

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

residueCenterBroadcaster

ResidueCenterBroadcaster residueCenterBroadcaster

highlightResidue

Residue highlightResidue

highlightPosition

int highlightPosition

highlightResidues

java.util.Map<K,V> highlightResidues

defaultCursor

java.awt.Cursor defaultCursor

moveCursor

java.awt.Cursor moveCursor

handCursor

java.awt.Cursor handCursor

textCursor

java.awt.Cursor textCursor

waitCursor

java.awt.Cursor waitCursor

leftRightCursor

java.awt.Cursor leftRightCursor

crosshairCursor

java.awt.Cursor crosshairCursor

insertionResidue

Residue insertionResidue

insertionResidueRightSide

boolean insertionResidueRightSide

temporarilySelectedResidues

java.util.Set<E> temporarilySelectedResidues

highlightColor

java.awt.Color highlightColor

autoScrollThread

org.simtk.moleculargraphics.TornadoSequenceCanvas.AutoScrollThread autoScrollThread

mousePressedInSequenceArea

boolean mousePressedInSequenceArea

mousePressedInNumberArea

boolean mousePressedInNumberArea

mousePressedViewportX

int mousePressedViewportX

mousePressedBarCenter

int mousePressedBarCenter

mousePressedResidue

Residue mousePressedResidue

mousePressedResidueRightSide

boolean mousePressedResidueRightSide

previousDragResidue

Residue previousDragResidue

previousAutoscrollTime

long previousAutoscrollTime

Class org.simtk.moleculargraphics.vtkSwingPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

rw

vtk.vtkRenderWindow rw

ren

vtk.vtkRenderer ren

cam

vtk.vtkCamera cam

lgt

vtk.vtkLight lgt

lastX

int lastX

lastY

int lastY

windowset

int windowset

lightingset

int lightingset

LightFollowCamera

int LightFollowCamera

InteractionMode

int InteractionMode

rendering

boolean rendering

windowSetObservable

org.simtk.moleculargraphics.vtkSwingPanel.WindowObservable windowSetObservable

privatePanel

PublicNativeVtkPanel privatePanel

Package org.simtk.moleculargraphics.cartoon

Class org.simtk.moleculargraphics.cartoon.NoCartoonCreatedException extends java.lang.Exception implements Serializable

Class org.simtk.moleculargraphics.cartoon.UnknownObjectColorException extends java.lang.Exception implements Serializable

Package org.simtk.molecularstructure

Class org.simtk.molecularstructure.InsufficientAtomsException extends java.lang.Exception implements Serializable

Package org.simtk.molecularstructure.atom

Class org.simtk.molecularstructure.atom.AtomSet extends java.util.Vector<Atom> implements Serializable

Package org.simtk.molecularstructure.nucleicacid

Class org.simtk.molecularstructure.nucleicacid.Hairpin extends java.util.Vector implements Serializable

serialVersionUID: 1L

Package org.simtk.pdb

Class org.simtk.pdb.JLinkLabel extends javax.swing.JLabel implements Serializable

Serialized Fields

COLOR_NORMAL

java.awt.Color COLOR_NORMAL

COLOR_HOVER

java.awt.Color COLOR_HOVER

COLOR_ACTIVE

java.awt.Color COLOR_ACTIVE

COLOR_BG_NORMAL

java.awt.Color COLOR_BG_NORMAL

COLOR_BG_ACTIVE

java.awt.Color COLOR_BG_ACTIVE

mouseOutDefault

java.awt.Color mouseOutDefault

Class org.simtk.pdb.MoleculeAcquisitionMethodDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

loadFileButton

javax.swing.JButton loadFileButton

webPDBButton

javax.swing.JButton webPDBButton

cancelButton

javax.swing.JButton cancelButton

idField

javax.swing.JTextField idField

bioUnitList

javax.swing.JComboBox bioUnitList

parent

java.awt.Frame parent

moleculeFileChooser

org.simtk.pdb.MoleculeFileChooser moleculeFileChooser

defaultPdbId

java.lang.String defaultPdbId

pdbId

java.lang.String pdbId

progressDialog

ProgressDialog progressDialog

loadPDBProcess

LoadPdbUrlProcess loadPDBProcess

progressManager

ProgressManager progressManager

fileLoadObservable

SimpleObservable fileLoadObservable

currentPath

java.lang.String currentPath

waitCursor

java.awt.Cursor waitCursor

defaultCursor

java.awt.Cursor defaultCursor

Package org.simtk.splashscreen

Class org.simtk.splashscreen.SplashWindow extends java.awt.Window implements Serializable

Serialized Fields

paintCalled

boolean paintCalled

Package org.simtk.toon.secstruct

Class org.simtk.toon.secstruct.SecondaryStructureCanvas extends javax.swing.JPanel implements Serializable

Serialized Fields

residueHighlightBroadcaster

ResidueHighlightBroadcaster residueHighlightBroadcaster

characterDensity

double characterDensity

fonts

java.util.List<E> fonts

fontHeights

java.util.Map<K,V> fontHeights

fontWidths

java.util.Map<K,V> fontWidths

diagram

SecondaryStructureDiagram diagram

transform

org.simtk.toon.secstruct.SecondaryStructureCanvas.Transform2D transform

worstBasePairs

java.util.Set<E> worstBasePairs

previousHeight

double previousHeight

finiteHeightWasSeen

boolean finiteHeightWasSeen

maxSize

java.awt.Dimension maxSize

minSize

java.awt.Dimension minSize

prefSize

java.awt.Dimension prefSize

oldMouseX

int oldMouseX

oldMouseY

int oldMouseY

Package org.simtk.util

Class org.simtk.util.ProgrammerLogicProblem extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1L