org.jmol.jvxl.readers
Class AtomDataReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.VolumeDataReader
          extended by org.jmol.jvxl.readers.AtomDataReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
AtomPropertyMapper, IsoFxyReader, IsoIntersectReader, IsoMepReader, IsoMOReader, IsoPlaneReader, IsoSolventReader

abstract class AtomDataReader
extends VolumeDataReader


Field Summary
protected  int atomCount
           
protected  AtomData atomData
           
protected  int[] atomIndex
           
protected  int[] atomNo
           
protected  float[] atomProp
           
protected  float[] atomRadius
           
protected  javax.vecmath.Point3f[] atomXyz
           
protected  java.util.BitSet bsMyIgnored
           
protected  java.util.BitSet bsMySelected
           
protected  java.util.BitSet bsNearby
           
protected  java.util.BitSet bsSurfaceVoxels
           
protected  ContactPair contactPair
           
protected  boolean doAddHydrogens
           
protected  boolean doUseIterator
           
protected  java.lang.String fileDotModel
           
protected  java.lang.String fileName
           
protected  int firstNearbyAtom
           
protected  boolean havePlane
           
protected  float margin
           
protected  float maxDistance
           
protected  int modelIndex
           
protected  int myAtomCount
           
protected  int[] myIndex
           
protected  int nearbyAtomCount
           
protected  java.util.BitSet noFaceSpheres
           
protected  javax.vecmath.Point3i pt0
           
protected  javax.vecmath.Point3i pt1
           
protected  javax.vecmath.Point3f ptXyzTemp
           
protected  javax.vecmath.Point3f ptY0
           
protected  javax.vecmath.Point3f ptZ0
           
protected  java.util.BitSet thisAtomSet
           
protected  float[] thisPlane
           
protected  int thisX
           
protected  java.util.BitSet validSpheres
           
protected  int[] voxelSource
           
 
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, atomDataServer, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
 
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, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes
 
Constructor Summary
AtomDataReader(SurfaceGenerator sg)
           
 
Method Summary
protected  boolean fixTitleLine(int iLine)
           
protected  void getAtomMinMax(java.util.BitSet bs, java.util.BitSet[] bsAtomMinMax)
           
protected  void getAtoms(java.util.BitSet bsSelected, boolean doAddHydrogens, boolean getRadii, boolean getMolecules, boolean getAllModels, boolean addNearbyAtoms, boolean getAtomMinMax, float marginAtoms)
           
private  float getVoxel(int i, int j, int k, int ipt)
           
private  float getWorkingRadius(int i, float marginAtoms)
           
protected  void markPlaneVoxels(javax.vecmath.Point3f p, float r)
           
protected  void markSphereVoxels(float r0, float distance)
           
protected  void resetPlane(float value)
           
protected  void resetVoxelData(float value)
           
protected  void setGridLimitsForAtom(javax.vecmath.Point3f ptA, float rA, javax.vecmath.Point3i pt0, javax.vecmath.Point3i pt1)
           
protected  void setHeader(java.lang.String calcType, java.lang.String line2)
           
protected  void setRanges(float ptsPerAngstrom, int maxGrid)
           
protected  void setup(boolean isMapData)
           
protected  void setVertexSource()
           
protected  void setVolumeData()
           
protected  void setVolumeForPlane()
           
protected  void setVoxel(int i, int j, int k, int ipt, float value)
           
protected  void unsetVoxelData()
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, 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

maxDistance

protected float maxDistance

contactPair

protected ContactPair contactPair

fileName

protected java.lang.String fileName

fileDotModel

protected java.lang.String fileDotModel

modelIndex

protected int modelIndex

atomData

protected AtomData atomData

atomXyz

protected javax.vecmath.Point3f[] atomXyz

atomRadius

protected float[] atomRadius

atomProp

protected float[] atomProp

atomNo

protected int[] atomNo

atomIndex

protected int[] atomIndex

myIndex

protected int[] myIndex

atomCount

protected int atomCount

myAtomCount

protected int myAtomCount

nearbyAtomCount

protected int nearbyAtomCount

firstNearbyAtom

protected int firstNearbyAtom

bsMySelected

protected java.util.BitSet bsMySelected

bsMyIgnored

protected java.util.BitSet bsMyIgnored

bsNearby

protected java.util.BitSet bsNearby

doAddHydrogens

protected boolean doAddHydrogens

havePlane

protected boolean havePlane

doUseIterator

protected boolean doUseIterator

thisPlane

protected float[] thisPlane

thisAtomSet

protected java.util.BitSet thisAtomSet

thisX

protected int thisX

margin

protected float margin

bsSurfaceVoxels

protected java.util.BitSet bsSurfaceVoxels

validSpheres

protected java.util.BitSet validSpheres

noFaceSpheres

protected java.util.BitSet noFaceSpheres

voxelSource

protected int[] voxelSource

ptY0

protected final javax.vecmath.Point3f ptY0

ptZ0

protected final javax.vecmath.Point3f ptZ0

pt0

protected final javax.vecmath.Point3i pt0

pt1

protected final javax.vecmath.Point3i pt1

ptXyzTemp

protected final javax.vecmath.Point3f ptXyzTemp
Constructor Detail

AtomDataReader

AtomDataReader(SurfaceGenerator sg)
Method Detail

setup

protected void setup(boolean isMapData)
Overrides:
setup in class VolumeDataReader

markPlaneVoxels

protected void markPlaneVoxels(javax.vecmath.Point3f p,
                               float r)

setVolumeForPlane

protected void setVolumeForPlane()

getAtoms

protected void getAtoms(java.util.BitSet bsSelected,
                        boolean doAddHydrogens,
                        boolean getRadii,
                        boolean getMolecules,
                        boolean getAllModels,
                        boolean addNearbyAtoms,
                        boolean getAtomMinMax,
                        float marginAtoms)
Parameters:
bsSelected - TODO
doAddHydrogens - TODO
getRadii - TODO
getMolecules - TODO
getAllModels - TODO
addNearbyAtoms -
getAtomMinMax - TODO
marginAtoms -

getWorkingRadius

private float getWorkingRadius(int i,
                               float marginAtoms)

setHeader

protected void setHeader(java.lang.String calcType,
                         java.lang.String line2)

setRanges

protected void setRanges(float ptsPerAngstrom,
                         int maxGrid)

setVolumeData

protected void setVolumeData()
Overrides:
setVolumeData in class VolumeDataReader

fixTitleLine

protected boolean fixTitleLine(int iLine)

setVertexSource

protected void setVertexSource()

resetPlane

protected void resetPlane(float value)

resetVoxelData

protected void resetVoxelData(float value)

getVoxel

private float getVoxel(int i,
                       int j,
                       int k,
                       int ipt)

unsetVoxelData

protected void unsetVoxelData()

setGridLimitsForAtom

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

getAtomMinMax

protected void getAtomMinMax(java.util.BitSet bs,
                             java.util.BitSet[] bsAtomMinMax)

markSphereVoxels

protected void markSphereVoxels(float r0,
                                float distance)

setVoxel

protected void setVoxel(int i,
                        int j,
                        int k,
                        int ipt,
                        float value)