org.jmol.jvxl.readers
Class IsoMOReader

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.IsoMOReader
All Implemented Interfaces:
VertexDataServer

 class IsoMOReader
extends AtomDataReader


Field Summary
(package private)  float[] coef
           
(package private)  float[][] coefs
           
(package private)  int[][] dfCoefMaps
           
private  boolean isElectronDensityCalc
           
(package private)  boolean isNci
           
(package private)  float[] linearCombination
           
(package private)  java.util.List<java.util.Map<java.lang.String,java.lang.Object>> mos
           
private  javax.vecmath.Point3f[] points
           
(package private)  QuantumCalculationInterface q
           
private  boolean qSetupDone
           
private  java.util.Random random
           
private  float[] vDist
           
private  javax.vecmath.Vector3f vTemp
           
 
Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
atomCount, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, havePlane, margin, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptXyzTemp, ptY0, ptZ0, thisAtomSet, thisPlane, thisX, validSpheres, 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
IsoMOReader(SurfaceGenerator sg)
           
 
Method Summary
protected  void createOrbital()
           
private  void fixTitleLine(int iLine, java.util.Map<java.lang.String,java.lang.Object> mo)
           
protected  void generateCube()
           
 float[] getPlane(int x)
           
private  float getRnd(float f)
           
protected  float getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javax.vecmath.Point3f pointA, javax.vecmath.Vector3f edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javax.vecmath.Point3f ptReturn)
           
 float getValueAtPoint(javax.vecmath.Point3f pt)
           
private  void getValues()
           
protected  void postProcessVertices()
           
protected  void readSurfaceData(boolean isMapData)
           
protected  boolean readVolumeParameters(boolean isMapData)
           
protected  void setup(boolean isMapData)
           
private  boolean setupCalculation()
           
 
Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeData, setVolumeForPlane, setVoxel, unsetVoxelData
 
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, 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

random

private java.util.Random random

vDist

private final float[] vDist

points

private javax.vecmath.Point3f[] points

vTemp

private javax.vecmath.Vector3f vTemp

q

QuantumCalculationInterface q

mos

java.util.List<java.util.Map<java.lang.String,java.lang.Object>> mos

isNci

boolean isNci

coef

float[] coef

dfCoefMaps

int[][] dfCoefMaps

linearCombination

float[] linearCombination

coefs

float[][] coefs

isElectronDensityCalc

private boolean isElectronDensityCalc

qSetupDone

private boolean qSetupDone
Constructor Detail

IsoMOReader

IsoMOReader(SurfaceGenerator sg)
Method Detail

setup

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

readVolumeParameters

protected boolean readVolumeParameters(boolean isMapData)
Overrides:
readVolumeParameters in class VolumeDataReader

fixTitleLine

private void fixTitleLine(int iLine,
                          java.util.Map<java.lang.String,java.lang.Object> mo)

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception
Overrides:
readSurfaceData in class VolumeDataReader
Throws:
java.lang.Exception

postProcessVertices

protected void postProcessVertices()
Overrides:
postProcessVertices in class SurfaceReader

getValues

private void getValues()

getValueAtPoint

public float getValueAtPoint(javax.vecmath.Point3f pt)
Overrides:
getValueAtPoint in class SurfaceReader
Returns:
value

getRnd

private float getRnd(float f)

generateCube

protected void generateCube()
Overrides:
generateCube in class VolumeDataReader

createOrbital

protected void createOrbital()

getPlane

public float[] getPlane(int x)
Specified by:
getPlane in interface VertexDataServer
Overrides:
getPlane in class SurfaceReader

setupCalculation

private boolean setupCalculation()

getSurfacePointAndFraction

protected float getSurfacePointAndFraction(float cutoff,
                                           boolean isCutoffAbsolute,
                                           float valueA,
                                           float valueB,
                                           javax.vecmath.Point3f pointA,
                                           javax.vecmath.Vector3f edgeVector,
                                           int x,
                                           int y,
                                           int z,
                                           int vA,
                                           int vB,
                                           float[] fReturn,
                                           javax.vecmath.Point3f ptReturn)
Overrides:
getSurfacePointAndFraction in class SurfaceReader
x - TODO
y - TODO
z - TODO
Returns:
fractional distance from A to B