org.jmol.jvxl.readers
Class IsoMOReader

java.lang.Object
  org.jmol.jvxl.readers.SurfaceReader
      org.jmol.jvxl.readers.VolumeDataReader
          org.jmol.jvxl.readers.AtomDataReader
              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) List<Map<String,Object>>	mos
private Point3f[]	points
(package private) QuantumCalculationInterface	q
private boolean	qSetupDone
private Random	random
private float[]	vDist
private 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, 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

IsoMOReader(SurfaceGenerator sg)

Method Summary

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, Point3f pointA, Vector3f edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, Point3f ptReturn)
float	getValueAtPoint(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 Random random

vDist

private final float[] vDist

points

private Point3f[] points

vTemp

private Vector3f vTemp

q

QuantumCalculationInterface q

mos

List<Map<String,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,
                          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(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,
                                           Point3f pointA,
                                           Vector3f edgeVector,
                                           int x,
                                           int y,
                                           int z,
                                           int vA,
                                           int vB,
                                           float[] fReturn,
                                           Point3f ptReturn)

Overrides:

getSurfacePointAndFraction in class SurfaceReader

x - TODO

y - TODO

z - TODO

Returns:

fractional distance from A to B