org.jmol.jvxl.readers

Class IsoSolventReader

class IsoSolventReader extends AtomDataReader

Field Summary
floatcavityRadius
booleandoCalculateTroughs
booleandoSmoothProperty
floatenvelopeRadius
booleanisCavity
booleanisPocket
booleanisProperty
Point3fptS
Point3fptXyzTemp
floatsolventRadius
Constructor Summary
IsoSolventReader(SurfaceGenerator sg)
Method Summary
floatcheckSpecialVoxel(Point3f ptA, float rAS, Point3f ptB, float rBS, float dAB, Point3f ptV)
protected voidgenerateCube()
voidgenerateSolventCavity()
voidgenerateSolventCube(boolean isFirstPass)
voidselectPocket(boolean doExclude)
voidsetGridLimitsForAtom(Point3f ptA, float rA, Point3i pt0, Point3i pt1)
protected voidsetup()
floatsolventDistance(Point3f ptV, Point3f ptA, Point3f ptB, float rAS, float rBS, float dAB, float dAV, float dBV)
booleanvoxelIsInTrough(float dVS, float rAS2, float rBS, float dAB, float dAV, float dBV)

Field Detail

cavityRadius

private float cavityRadius

doCalculateTroughs

private boolean doCalculateTroughs

doSmoothProperty

private boolean doSmoothProperty

envelopeRadius

private float envelopeRadius

isCavity

private boolean isCavity

isPocket

private boolean isPocket

isProperty

private boolean isProperty

ptS

final Point3f ptS

ptXyzTemp

final Point3f ptXyzTemp

solventRadius

private float solventRadius

Constructor Detail

IsoSolventReader

IsoSolventReader(SurfaceGenerator sg)

Method Detail

checkSpecialVoxel

float checkSpecialVoxel(Point3f ptA, float rAS, Point3f ptB, float rBS, float dAB, Point3f ptV)

generateCube

protected void generateCube()

generateSolventCavity

private void generateSolventCavity()

generateSolventCube

void generateSolventCube(boolean isFirstPass)

selectPocket

public void selectPocket(boolean doExclude)

setGridLimitsForAtom

void setGridLimitsForAtom(Point3f ptA, float rA, Point3i pt0, Point3i pt1)

setup

protected void setup()

solventDistance

float solventDistance(Point3f ptV, Point3f ptA, Point3f ptB, float rAS, float rBS, float dAB, float dAV, float dBV)

voxelIsInTrough

boolean voxelIsInTrough(float dVS, float rAS2, float rBS, float dAB, float dAV, float dBV)