org.jmol.shape

Class AtomShape

java.lang.Object

org.jmol.shape.Shape

org.jmol.shape.AtomShape

Direct Known Subclasses:

Balls, BioShape, Dots, Halos, Labels, Measures, Polyhedra, Stars, Vectors

public abstract class AtomShape
extends Shape

Field Summary

Fields

Modifier and Type	Field and Description
int	ac
Atom[]	atoms
BS	bsSizeDefault
short[]	colixes
boolean	isActive
short	mad
short[]	mads
int	monomerCount
byte[]	paletteIDs
private RadiusData	rd

Fields inherited from class org.jmol.shape.Shape

bsColixSet, bsSizeSet, isBioShape, ms, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr

Constructor Summary

Constructors

Constructor and Description
AtomShape()

Method Summary

Modifier and Type	Method and Description
java.lang.String	getInfoAsString(int i)
Group[]	getMonomers()
java.lang.String	getShapeState()
int	getSize(int atomIndex) overridden in Dots, CGOMesh, and AtomShape
protected void	initModelSet()
void	setAtomClickability()
protected void	setColixAndPalette(short colix, byte paletteID, int atomIndex)
protected void	setPropAS(java.lang.String propertyName, java.lang.Object value, BS bs)
protected void	setSize(int size, BS bsSelected)
protected void	setSize2(int size, BS bsSelected)
protected void	setSizeRD(RadiusData rd, BS bsSelected)
protected void	setSizeRD2(int i, RadiusData rd, boolean isVisible)

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getIndexFromName, getProperty, getPropertyData, getShapeDetail, getSizeG, getTranslucentLabel, initializeShape, initShape, merge, setModelSet, setModelVisibilityFlags, setProperty, setPropS, setShapeSizeRD, setShapeVisibility, wasClicked

Methods inherited from class java.lang.Object

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

Field Detail

mad

public short mad

mads

public short[] mads

colixes

public short[] colixes

paletteIDs

public byte[] paletteIDs

ac

public int ac

atoms

public Atom[] atoms

isActive

public boolean isActive

monomerCount

public int monomerCount

bsSizeDefault

public BS bsSizeDefault

rd

private RadiusData rd

Constructor Detail

AtomShape

public AtomShape()

Method Detail

getMonomers

public Group[] getMonomers()

initModelSet

protected void initModelSet()

Overrides:

initModelSet in class Shape

getSize

public int getSize(int atomIndex)

Description copied from class: Shape

overridden in Dots, CGOMesh, and AtomShape

Overrides:

getSize in class Shape

Returns:

size

setSize

protected void setSize(int size,
                       BS bsSelected)

Overrides:

setSize in class Shape

setSize2

protected void setSize2(int size,
                        BS bsSelected)

setSizeRD

protected void setSizeRD(RadiusData rd,
                         BS bsSelected)

Overrides:

setSizeRD in class Shape

setSizeRD2

protected void setSizeRD2(int i,
                          RadiusData rd,
                          boolean isVisible)

setPropAS

protected void setPropAS(java.lang.String propertyName,
                         java.lang.Object value,
                         BS bs)

setColixAndPalette

protected void setColixAndPalette(short colix,
                                  byte paletteID,
                                  int atomIndex)

setAtomClickability

public void setAtomClickability()

Overrides:

setAtomClickability in class Shape

getShapeState

public java.lang.String getShapeState()

Specified by:

getShapeState in class Shape

getInfoAsString

public java.lang.String getInfoAsString(int i)

Parameters:

i -

Returns:

script, but only for Measures