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 java.util.Map<java.lang.String,java.lang.Object> |
mo |
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
mos |
private javajs.util.P3[] |
points |
private QuantumCalculation |
q |
private boolean |
qSetupDone |
private java.util.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, voxelSourceallowMapData, 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, 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,
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() |
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeData, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2closeReader, initVDR, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfoaddTriangleCheck, 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, updateTrianglesprivate java.util.Random random
private javajs.util.P3[] points
private javajs.util.V3 vTemp
private QuantumCalculation q
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> mos
private boolean isNci
private float[] coef
private int[][] dfCoefMaps
private float[] linearCombination
private float[][] coefs
private boolean isElectronDensityCalc
private java.util.Map<java.lang.String,java.lang.Object> mo
private final float[] vDist
private boolean qSetupDone
void init(SurfaceGenerator sg)
SurfaceReaderinit in class VolumeDataReaderprotected 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(javajs.util.T3 pt,
boolean getSource)
getValueAtPoint in class SurfaceReadergetSource - TODOprivate 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,
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