class IsoMOReader extends AtomDataReader
Modifier and Type | Field and Description |
---|---|
private float[] |
coef |
private float[][] |
coefs |
private int[][] |
dfCoefMaps |
private boolean |
isElectronDensityCalc |
private boolean |
isNci |
private float[] |
linearCombination |
private javajs.util.Lst<Map<String,Object>> |
mos |
private javajs.util.P3[] |
points |
private QuantumCalculation |
q |
private boolean |
qSetupDone |
private Random |
random |
private float[] |
vDist |
private javajs.util.V3 |
vTemp |
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
allowMapData, 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, 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 and Description |
---|
IsoMOReader() |
Modifier and Type | Method and 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() |
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeData, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2
closeReader, initVDR, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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
private Random random
private javajs.util.P3[] points
private javajs.util.V3 vTemp
private QuantumCalculation q
private boolean isNci
private float[] coef
private int[][] dfCoefMaps
private float[] linearCombination
private float[][] coefs
private boolean isElectronDensityCalc
private final float[] vDist
private boolean qSetupDone
void init(SurfaceGenerator sg)
SurfaceReader
init
in class VolumeDataReader
protected void setup(boolean isMapData)
setup
in class AtomDataReader
protected boolean readVolumeParameters(boolean isMapData)
readVolumeParameters
in class VolumeDataReader
protected void readSurfaceData(boolean isMapData) throws Exception
readSurfaceData
in class VolumeDataReader
Exception
protected void postProcessVertices()
postProcessVertices
in class SurfaceReader
private void getValues()
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
getValueAtPoint
in class SurfaceReader
getSource
- TODOprivate 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, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)
getSurfacePointAndFraction
in class SurfaceReader