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:
IsoMepReader, IsoMOReader, IsoPlaneReader, IsoSolventReader

abstract class AtomDataReader
extends VolumeDataReader


Field Summary
protected  int atomCount
           
protected  AtomData atomData
           
protected  AtomDataServer atomDataServer
           
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  boolean doAddHydrogens
           
protected  boolean doUseIterator
           
protected  boolean doUsePlane
           
protected  java.lang.String fileDotModel
           
protected  java.lang.String fileName
           
protected  int firstNearbyAtom
           
protected  int modelIndex
           
protected  int myAtomCount
           
protected  int[] myIndex
           
protected  int nearbyAtomCount
           
private  javax.vecmath.Point3f xyzMax
           
private  javax.vecmath.Point3f xyzMin
           
 
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, anisotropy, center, dataType, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, isAnisotropic, isEccentric, point, precalculateVoxelData
 
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vContours, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData
 
Constructor Summary
AtomDataReader(SurfaceGenerator sg)
           
 
Method Summary
protected  boolean fixTitleLine(int iLine)
           
protected  void getAtoms(float marginAtoms, boolean doGetAllAtoms, boolean addNearbyAtoms)
           
private  float getWorkingRadius(int i, float marginAtoms)
           
protected  void setHeader(java.lang.String calcType, java.lang.String line2)
           
protected  void setRangesAndAddAtoms(float ptsPerAngstrom, int maxGrid, int nWritten)
           
protected  void setup()
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
generateCube, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, getArgbFromPalette, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeVolumetricData, jvxlUpdateInfo, readColorData, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

atomDataServer

protected AtomDataServer atomDataServer

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

xyzMin

private javax.vecmath.Point3f xyzMin

xyzMax

private javax.vecmath.Point3f xyzMax

doAddHydrogens

protected boolean doAddHydrogens

doUsePlane

protected boolean doUsePlane

doUseIterator

protected boolean doUseIterator
Constructor Detail

AtomDataReader

AtomDataReader(SurfaceGenerator sg)
Method Detail

setup

protected void setup()
Overrides:
setup in class VolumeDataReader

getAtoms

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

getWorkingRadius

private float getWorkingRadius(int i,
                               float marginAtoms)

setHeader

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

setRangesAndAddAtoms

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

fixTitleLine

protected boolean fixTitleLine(int iLine)