class IsoSolventReader extends AtomDataReader
Modifier and Type | Field and Description |
---|---|
private float |
cavityRadius |
private boolean |
doCalculateTroughs |
private javax.vecmath.Point3f[] |
dots |
private float |
envelopeRadius |
private boolean |
isCavity |
private boolean |
isPocket |
(package private) javax.vecmath.Point3f |
ptS |
(package private) javax.vecmath.Point3f |
ptXyzTemp |
private float |
solventRadius |
atomCount, atomData, atomDataServer, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, doAddHydrogens, doUseIterator, doUsePlane, fileDotModel, fileName, firstNearbyAtom, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount
allowMapData, dataType, point, precalculateVoxelData
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
Constructor and Description |
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IsoSolventReader(SurfaceGenerator sg) |
Modifier and Type | Method and Description |
---|---|
(package private) float |
checkSpecialVoxel(javax.vecmath.Point3f ptA,
float rAS,
javax.vecmath.Point3f ptB,
float rBS,
float dAB,
javax.vecmath.Point3f ptV) |
protected void |
generateCube() |
private void |
generateSolventCavity() |
(package private) void |
generateSolventCube(boolean isFirstPass) |
void |
selectPocket(boolean doExclude) |
(package private) void |
setGridLimitsForAtom(javax.vecmath.Point3f ptA,
float rA,
javax.vecmath.Point3i pt0,
javax.vecmath.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) |
fixTitleLine, getAtoms, setHeader, setRangesAndAddAtoms
closeReader, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange
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
private float cavityRadius
private float envelopeRadius
private javax.vecmath.Point3f[] dots
private boolean doCalculateTroughs
private boolean isCavity
private boolean isPocket
private float solventRadius
final javax.vecmath.Point3f ptXyzTemp
final javax.vecmath.Point3f ptS
IsoSolventReader(SurfaceGenerator sg)
protected void setup()
setup
in class AtomDataReader
public void selectPocket(boolean doExclude)
selectPocket
in class SurfaceReader
protected void generateCube()
generateCube
in class VolumeDataReader
private void generateSolventCavity()
void generateSolventCube(boolean isFirstPass)
void setGridLimitsForAtom(javax.vecmath.Point3f ptA, float rA, javax.vecmath.Point3i pt0, javax.vecmath.Point3i pt1)
float checkSpecialVoxel(javax.vecmath.Point3f ptA, float rAS, javax.vecmath.Point3f ptB, float rBS, float dAB, javax.vecmath.Point3f ptV)
private boolean voxelIsInTrough(float dVS, float rAS2, float rBS, float dAB, float dAV)
private float solventDistance(float rAS, float rBS, float dAB, float dAV, float dBV)