org.jmol.jvxl.readers

Class AtomDataReader

class AtomDataReader extends VolumeDataReader

Field Summary
protected intatomCount
protected AtomDataatomData
protected AtomDataServeratomDataServer
protected int[]atomIndex
protected int[]atomNo
protected float[]atomProp
protected float[]atomRadius
protected Point3f[]atomXyz
protected BitSetbsMyIgnored
protected BitSetbsMySelected
protected booleandoAddHydrogens
protected booleandoUseIterator
protected booleandoUsePlane
protected StringfileDotModel
protected StringfileName
protected intfirstNearbyAtom
protected intmodelIndex
protected intmyAtomCount
protected int[]myIndex
protected intnearbyAtomCount
Point3fxyzMax
Point3fxyzMin
Constructor Summary
AtomDataReader(SurfaceGenerator sg)
Method Summary
protected booleanfixTitleLine(int iLine)
protected voidgetAtoms(float marginAtoms, boolean doGetAllAtoms, boolean addNearbyAtoms)
floatgetWorkingRadius(int i, float marginAtoms)
protected voidsetHeader(String calcType, String line2)
protected voidsetRangesAndAddAtoms(float ptsPerAngstrom, int maxGrid, int nWritten)
protected voidsetup()

Field Detail

atomCount

protected int atomCount

atomData

protected AtomData atomData

atomDataServer

protected AtomDataServer atomDataServer

atomIndex

protected int[] atomIndex

atomNo

protected int[] atomNo

atomProp

protected float[] atomProp

atomRadius

protected float[] atomRadius

atomXyz

protected Point3f[] atomXyz

bsMyIgnored

protected BitSet bsMyIgnored

bsMySelected

protected BitSet bsMySelected

doAddHydrogens

protected boolean doAddHydrogens

doUseIterator

protected boolean doUseIterator

doUsePlane

protected boolean doUsePlane

fileDotModel

protected String fileDotModel

fileName

protected String fileName

firstNearbyAtom

protected int firstNearbyAtom

modelIndex

protected int modelIndex

myAtomCount

protected int myAtomCount

myIndex

protected int[] myIndex

nearbyAtomCount

protected int nearbyAtomCount

xyzMax

private Point3f xyzMax

xyzMin

private Point3f xyzMin

Constructor Detail

AtomDataReader

AtomDataReader(SurfaceGenerator sg)

Method Detail

fixTitleLine

protected boolean fixTitleLine(int iLine)

getAtoms

protected void getAtoms(float marginAtoms, boolean doGetAllAtoms, boolean addNearbyAtoms)

getWorkingRadius

private float getWorkingRadius(int i, float marginAtoms)

setHeader

protected void setHeader(String calcType, String line2)

setRangesAndAddAtoms

protected void setRangesAndAddAtoms(float ptsPerAngstrom, int maxGrid, int nWritten)

setup

protected void setup()