org.jmol.jvxl.readers.IsoMOReader

All Implemented Interfaces:: VertexDataServer

class IsoMOReader extends AtomDataReader

Field Summary

Fields

Modifier and Type

Field

Description

private float[]

coef

private float[][]

coefs

private int[][]

dfCoefMaps

private boolean

isElectronDensityCalc

private boolean

isNci

private float[]

linearCombination

private Map<String,Object>

mo

private javajs.util.Lst<Map<String,Object>>

mos

private javajs.util.P3[]

points

private QuantumCalculation

q

private boolean

qSetupDone

private Random

random

private final float[]

vDist

private javajs.util.V3

vTemp

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyzTruncated, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, maxRS, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptV, ptY0, ptZ0, rs, rs2, sr, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, vl0, vl1, vl2, voxelSource

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, 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, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlCutoffRange, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, 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

Constructors

Constructor

Description

IsoMOReader()
Method Summary

Modifier and Type

Method

Description

protected void

createOrbital()

private void

fixTitleLine(int iLine, Map<String,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, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)

float

getValueAtPoint(javajs.util.T3 pt, boolean getSource)

private void

getValues()

(package private) void

init(SurfaceGenerator sg)

implemented in SurfaceFileReader and

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
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeData, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, initVDR, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue, getValue2, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- random
  
  private Random random
- points
  
  private javajs.util.P3[] points
- vTemp
  
  private javajs.util.V3 vTemp
- q
  
  private QuantumCalculation q
- mos
  
  private javajs.util.Lst<Map<String,Object>> mos
- isNci
  
  private boolean isNci
- coef
  
  private float[] coef
- dfCoefMaps
  
  private int[][] dfCoefMaps
- linearCombination
  
  private float[] linearCombination
- coefs
  
  private float[][] coefs
- isElectronDensityCalc
  
  private boolean isElectronDensityCalc
- mo
  
  private Map<String,Object> mo
- vDist
  
  private final float[] vDist
- qSetupDone
  
  private boolean qSetupDone
Constructor Details
- IsoMOReader
  
  IsoMOReader()
Method Details
- init
  
  void init(SurfaceGenerator sg)
  
  Description copied from class: SurfaceReader
  
  implemented in SurfaceFileReader and
  
  Overrides:
  
  init in class VolumeDataReader
- 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, Map<String,Object> mo)
- readSurfaceData
  
  protected void readSurfaceData(boolean isMapData) throws Exception
  
  Overrides:
  
  readSurfaceData in class VolumeDataReader
  
  Throws:
  
  Exception
- postProcessVertices
  
  protected void postProcessVertices()
  
  Overrides:
  
  postProcessVertices in class SurfaceReader
- getValues
  
  private void getValues()
- getValueAtPoint
  
  public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
  
  Overrides:
  
  getValueAtPoint in class SurfaceReader
  
  getSource - TODO
  
  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, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)
  
  Overrides:
  
  getSurfacePointAndFraction in class SurfaceReader

Class IsoMOReader

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Details

random

points

vTemp

q

mos

isNci

coef

dfCoefMaps

linearCombination

coefs

isElectronDensityCalc

mo

vDist

qSetupDone

Constructor Details

IsoMOReader

Method Details

init

setup

readVolumeParameters

fixTitleLine

readSurfaceData

postProcessVertices

getValues

getValueAtPoint

getRnd

generateCube

createOrbital

getPlane

setupCalculation

getSurfacePointAndFraction