org.jmol.jvxl.readers
Class IsoSolventReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.VolumeDataReader
          extended by org.jmol.jvxl.readers.AtomDataReader
              extended by org.jmol.jvxl.readers.IsoSolventReader
All Implemented Interfaces:
VertexDataServer

 class IsoSolventReader
extends AtomDataReader


Field Summary
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
IsoSolventReader(SurfaceGenerator sg)
           
 
Method Summary
(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)