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

Fields

Modifier and Type	Field and Description
(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) javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>	mos
private javajs.util.P3[]	points
(package private) MOCalculationInterface	q
private boolean	qSetupDone
private java.util.Random	random
private float[]	vDist
private javajs.util.V3	vTemp

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

ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, 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, 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 and Description
IsoMOReader()

Method Summary

Modifier and Type	Method and Description
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, 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, getPlane2, 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 Detail

random

private java.util.Random random

vDist

private final float[] vDist

points

private javajs.util.P3[] points

vTemp

private javajs.util.V3 vTemp

q

MOCalculationInterface q

mos

javajs.util.Lst<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()

Method Detail

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,
                          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(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