org.jmol.shapebio

Class Trace

java.lang.Object

org.jmol.shape.Shape

org.jmol.shapebio.BioShapeCollection

org.jmol.shapebio.Trace

public class Trace
extends BioShapeCollection

Field Summary

Fields

Modifier and Type	Field and Description
private static int	PUTTY_AbsoluteLinear
private static int	PUTTY_AbsoluteNonlinear
private static int	PUTTY_ImpliedRMS
private static int	PUTTY_NormalizedLinear
private static int	PUTTY_NormalizedNonlinear
private static int	PUTTY_RelativeLinear
private static int	PUTTY_RelativeNonlinear
private static int	PUTTY_ScaledLinear
private static int	PUTTY_ScaledNonlinear

Fields inherited from class org.jmol.shapebio.BioShapeCollection

atoms, bioShapes, isActive, madDnaRna, madHelixSheet, madOn, madTurnRandom

Fields inherited from class org.jmol.shape.Shape

bsColixSet, bsSizeSet, gdata, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer

Constructor Summary

Constructors

Constructor and Description
Trace()

Method Summary

Methods

Modifier and Type	Method and Description
void	initShape()
void	setProperty(java.lang.String propertyName, java.lang.Object value, BS bsSelected) may come from any source -- executed AFTER a shape's own setProperty method
private void	setPutty(float[] info, BS bsAtoms) PyMOL-based "putty"

Methods inherited from class org.jmol.shapebio.BioShapeCollection

findNearestAtomIndex, getBioShape, getMpsShapeCount, getShapeState, getSizeG, initialize, initModelSet, setModelClickability, setPropBSC, setShapeSizeRD, setVisibilityFlags

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getIndexFromName, getProperty, getPropertyData, getShapeDetail, getSize, getTranslucentLabel, getViewer, initializeShape, merge, setModelSet, setPropS, setSize, setSizeRD, wasClicked

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PUTTY_NormalizedNonlinear

private static final int PUTTY_NormalizedNonlinear

See Also:

Constant Field Values

PUTTY_RelativeNonlinear

private static final int PUTTY_RelativeNonlinear

See Also:

Constant Field Values

PUTTY_ScaledNonlinear

private static final int PUTTY_ScaledNonlinear

See Also:

Constant Field Values

PUTTY_AbsoluteNonlinear

private static final int PUTTY_AbsoluteNonlinear

See Also:

Constant Field Values

PUTTY_NormalizedLinear

private static final int PUTTY_NormalizedLinear

See Also:

Constant Field Values

PUTTY_RelativeLinear

private static final int PUTTY_RelativeLinear

See Also:

Constant Field Values

PUTTY_ScaledLinear

private static final int PUTTY_ScaledLinear

See Also:

Constant Field Values

PUTTY_AbsoluteLinear

private static final int PUTTY_AbsoluteLinear

See Also:

Constant Field Values

PUTTY_ImpliedRMS

private static final int PUTTY_ImpliedRMS

See Also:

Constant Field Values

Constructor Detail

Trace

public Trace()

Method Detail

initShape

public void initShape()

Overrides:

initShape in class Shape

setProperty

public void setProperty(java.lang.String propertyName,
               java.lang.Object value,
               BS bsSelected)

Description copied from class: Shape

may come from any source -- executed AFTER a shape's own setProperty method

Overrides:

setProperty in class BioShapeCollection

setPutty

private void setPutty(float[] info,
            BS bsAtoms)

PyMOL-based "putty"

Parameters:

info - [quality,radius,range,scale_min,scale_max,scale_power,transform]

bsAtoms -