org.jmol.jvxl.readers

Class IsoSolventReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.VolumeDataReader

org.jmol.jvxl.readers.AtomDataReader

org.jmol.jvxl.readers.IsoSolventReader

All Implemented Interfaces:

VertexDataServer

 class IsoSolventReader
extends AtomDataReader

Field Summary

Fields

Modifier and Type	Field and Description
private float	cavityRadius
private boolean	doCalculateTroughs
private javax.vecmath.Point3f[]	dots
private float	envelopeRadius
private boolean	isCavity
private boolean	isPocket
(package private) javax.vecmath.Point3f	ptS
(package private) javax.vecmath.Point3f	ptXyzTemp
private float	solventRadius

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader

atomCount, atomData, atomDataServer, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, doAddHydrogens, doUseIterator, doUsePlane, fileDotModel, fileName, firstNearbyAtom, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader

allowMapData, dataType, point, precalculateVoxelData

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin

Constructor Summary

Constructors

Constructor and Description
IsoSolventReader(SurfaceGenerator sg)

Method Summary

Methods

Modifier and Type	Method and Description
(package private) float	checkSpecialVoxel(javax.vecmath.Point3f ptA, float rAS, javax.vecmath.Point3f ptB, float rBS, float dAB, javax.vecmath.Point3f ptV)
protected void	generateCube()
private void	generateSolventCavity()
(package private) void	generateSolventCube(boolean isFirstPass)
void	selectPocket(boolean doExclude)
(package private) void	setGridLimitsForAtom(javax.vecmath.Point3f ptA, float rA, javax.vecmath.Point3i pt0, javax.vecmath.Point3i pt1)
protected void	setup()
private float	solventDistance(float rAS, float rBS, float dAB, float dAV, float dBV)
private boolean	voxelIsInTrough(float dVS, float rAS2, float rBS, float dAB, float dAV)

Methods inherited from class org.jmol.jvxl.readers.AtomDataReader

fixTitleLine, getAtoms, setHeader, setRangesAndAddAtoms

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader

closeReader, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, setBoundingBox, setMappingPlane, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

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

Field Detail

cavityRadius

private float cavityRadius

envelopeRadius

private float envelopeRadius

dots

private javax.vecmath.Point3f[] dots

doCalculateTroughs

private boolean doCalculateTroughs

isCavity

private boolean isCavity

isPocket

private boolean isPocket

solventRadius

private float solventRadius

ptXyzTemp

final javax.vecmath.Point3f ptXyzTemp

ptS

final javax.vecmath.Point3f ptS

Constructor Detail

IsoSolventReader

IsoSolventReader(SurfaceGenerator sg)

Method Detail

setup

protected void setup()

Overrides:

setup in class AtomDataReader

selectPocket

public void selectPocket(boolean doExclude)

Overrides:

selectPocket in class SurfaceReader

generateCube

protected void generateCube()

Overrides:

generateCube in class VolumeDataReader

generateSolventCavity

private void generateSolventCavity()

generateSolventCube

void generateSolventCube(boolean isFirstPass)

setGridLimitsForAtom

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

checkSpecialVoxel

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

voxelIsInTrough

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

solventDistance

private float solventDistance(float rAS,
                    float rBS,
                    float dAB,
                    float dAV,
                    float dBV)