class IsoMOReader extends AtomDataReader
| 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) 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 |
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, voxelSourceallowMapData, atomDataServer, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPointsallowSigma, 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 and Description |
|---|
IsoMOReader(SurfaceGenerator sg) |
| 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,
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() |
fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeData, setVolumeForPlane, setVoxel, unsetVoxelDatacloseReader, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfoaddTriangleCheck, 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, updateTrianglesprivate java.util.Random random
private final float[] vDist
private javax.vecmath.Point3f[] points
private javax.vecmath.Vector3f vTemp
java.util.List<java.util.Map<java.lang.String,java.lang.Object>> mos
boolean isNci
float[] coef
int[][] dfCoefMaps
float[] linearCombination
float[][] coefs
private boolean isElectronDensityCalc
private boolean qSetupDone
IsoMOReader(SurfaceGenerator sg)
protected void setup(boolean isMapData)
setup in class AtomDataReaderprotected boolean readVolumeParameters(boolean isMapData)
readVolumeParameters in class VolumeDataReaderprivate void fixTitleLine(int iLine,
java.util.Map<java.lang.String,java.lang.Object> mo)
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
readSurfaceData in class VolumeDataReaderjava.lang.Exceptionprotected void postProcessVertices()
postProcessVertices in class SurfaceReaderprivate void getValues()
public float getValueAtPoint(javax.vecmath.Point3f pt)
getValueAtPoint in class SurfaceReaderprivate float getRnd(float f)
protected void generateCube()
generateCube in class VolumeDataReaderprotected void createOrbital()
public float[] getPlane(int x)
getPlane in interface VertexDataServergetPlane in class SurfaceReaderprivate boolean setupCalculation()
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)
getSurfacePointAndFraction in class SurfaceReaderx - TODOy - TODOz - TODO