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, voxelSource
allowMapData, atomDataServer, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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 and Description |
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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, unsetVoxelData
closeReader, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSpanningVectors, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
private 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 AtomDataReader
protected boolean readVolumeParameters(boolean isMapData)
readVolumeParameters
in class VolumeDataReader
private 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 VolumeDataReader
java.lang.Exception
protected void postProcessVertices()
postProcessVertices
in class SurfaceReader
private void getValues()
public float getValueAtPoint(javax.vecmath.Point3f pt)
getValueAtPoint
in class SurfaceReader
private float getRnd(float f)
protected void generateCube()
generateCube
in class VolumeDataReader
protected void createOrbital()
public float[] getPlane(int x)
getPlane
in interface VertexDataServer
getPlane
in class SurfaceReader
private 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 SurfaceReader
x
- TODOy
- TODOz
- TODO