org.jmol.jvxl.readers
Class IsoSolventReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
org.jmol.jvxl.readers.AtomDataReader
org.jmol.jvxl.readers.IsoSolventReader
- All Implemented Interfaces:
- VertexDataServer
class IsoSolventReader
- extends AtomDataReader
Fields inherited from class org.jmol.jvxl.readers.AtomDataReader |
atomCount, atomData, atomDataServer, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, doAddHydrogens, doUseIterator, doUsePlane, fileDotModel, fileName, firstNearbyAtom, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount |
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, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin |
Method Summary |
(package private) float |
checkSpecialVoxel(Point3f ptA,
float rAS,
Point3f ptB,
float rBS,
float dAB,
Point3f ptV)
|
protected void |
generateCube()
|
private void |
generateSolventCavity()
|
(package private) void |
generateSolventCube(boolean isFirstPass)
|
void |
selectPocket(boolean doExclude)
|
(package private) void |
setGridLimitsForAtom(Point3f ptA,
float rA,
Point3i pt0,
Point3i pt1)
|
protected void |
setup()
|
private float |
solventDistance(float rAS,
float rBS,
float dAB,
float dAV,
float dBV)
|
private boolean |
voxelIsInTrough(float dVS,
float rAS2,
float rBS,
float dAB,
float dAV)
|
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, setBoundingBox, setMappingPlane, 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 |
cavityRadius
private float cavityRadius
envelopeRadius
private float envelopeRadius
dots
private Point3f[] dots
doCalculateTroughs
private boolean doCalculateTroughs
isCavity
private boolean isCavity
isPocket
private boolean isPocket
solventRadius
private float solventRadius
ptXyzTemp
final Point3f ptXyzTemp
ptS
final Point3f ptS
IsoSolventReader
IsoSolventReader(SurfaceGenerator sg)
setup
protected void setup()
- Overrides:
setup
in class AtomDataReader
selectPocket
public void selectPocket(boolean doExclude)
- Overrides:
selectPocket
in class SurfaceReader
generateCube
protected void generateCube()
- Overrides:
generateCube
in class VolumeDataReader
generateSolventCavity
private void generateSolventCavity()
generateSolventCube
void generateSolventCube(boolean isFirstPass)
setGridLimitsForAtom
void setGridLimitsForAtom(Point3f ptA,
float rA,
Point3i pt0,
Point3i pt1)
checkSpecialVoxel
float checkSpecialVoxel(Point3f ptA,
float rAS,
Point3f ptB,
float rBS,
float dAB,
Point3f ptV)
voxelIsInTrough
private boolean voxelIsInTrough(float dVS,
float rAS2,
float rBS,
float dAB,
float dAV)
solventDistance
private float solventDistance(float rAS,
float rBS,
float dAB,
float dAV,
float dBV)