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) 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 |
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
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 |
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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, unsetVoxelData2
closeReader, initVDR, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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
private java.util.Random random
private final float[] vDist
private javajs.util.P3[] points
private javajs.util.V3 vTemp
javajs.util.Lst<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
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
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(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