org.jmol.jvxl.readers
Class IsoMOReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
org.jmol.jvxl.readers.AtomDataReader
org.jmol.jvxl.readers.IsoMOReader
- All Implemented Interfaces:
- VertexDataServer
class IsoMOReader
- extends AtomDataReader
Fields inherited from class org.jmol.jvxl.readers.AtomDataReader |
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 |
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader |
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, 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 |
Method Summary |
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()
|
Methods inherited from class org.jmol.jvxl.readers.AtomDataReader |
fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeData, setVolumeForPlane, setVoxel, unsetVoxelData |
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
addTriangleCheck, 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, updateTriangles |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
random
private java.util.Random random
vDist
private final float[] vDist
points
private javax.vecmath.Point3f[] points
vTemp
private javax.vecmath.Vector3f vTemp
q
QuantumCalculationInterface q
mos
java.util.List<java.util.Map<java.lang.String,java.lang.Object>> mos
isNci
boolean isNci
coef
float[] coef
dfCoefMaps
int[][] dfCoefMaps
linearCombination
float[] linearCombination
coefs
float[][] coefs
isElectronDensityCalc
private boolean isElectronDensityCalc
qSetupDone
private boolean qSetupDone
IsoMOReader
IsoMOReader(SurfaceGenerator sg)
setup
protected void setup(boolean isMapData)
- Overrides:
setup
in class AtomDataReader
readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Overrides:
readVolumeParameters
in class VolumeDataReader
fixTitleLine
private void fixTitleLine(int iLine,
java.util.Map<java.lang.String,java.lang.Object> mo)
readSurfaceData
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
- Overrides:
readSurfaceData
in class VolumeDataReader
- Throws:
java.lang.Exception
postProcessVertices
protected void postProcessVertices()
- Overrides:
postProcessVertices
in class SurfaceReader
getValues
private void getValues()
getValueAtPoint
public float getValueAtPoint(javax.vecmath.Point3f pt)
- Overrides:
getValueAtPoint
in class SurfaceReader
- Returns:
- value
getRnd
private float getRnd(float f)
generateCube
protected void generateCube()
- Overrides:
generateCube
in class VolumeDataReader
createOrbital
protected void createOrbital()
getPlane
public float[] getPlane(int x)
- Specified by:
getPlane
in interface VertexDataServer
- Overrides:
getPlane
in class SurfaceReader
setupCalculation
private boolean setupCalculation()
getSurfacePointAndFraction
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)
- Overrides:
getSurfacePointAndFraction
in class SurfaceReader
x
- TODOy
- TODOz
- TODO
- Returns:
- fractional distance from A to B