Package org.jmol.jvxl.readers
Class PyMOLMeshReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.VolumeFileReader
org.jmol.jvxl.readers.MapFileReader
org.jmol.jvxl.readers.PyMOLMeshReader
- All Implemented Interfaces:
VertexDataServer
PyMOL surface/mesh reader.
PyMOL "mesh": Describes a cutoff and "carving" distance around a set of points
PyMOL "map": Volume data used by mesh (HupA_2) or direct visualization (HupA_LC)
- Author:
- Bob Hanson
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Field Summary
FieldsModifier and TypeFieldDescription(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
private javajs.util.Lst
<Object> private boolean
(package private) static final int
(package private) static final int
private int
private int
private String
private javajs.util.Lst
<Object> Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, n0, n1, n2, na, nb, nc, origin, p3, vectors, xIndex, xyzStart, yIndex, zIndex
Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlCutoffRange, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate float
private float
private static javajs.util.Lst
<Object> (package private) void
init2
(SurfaceGenerator sg, BufferedReader brNull) protected float
protected void
protected void
protected void
skipData
(int nPoints) Methods inherited from class org.jmol.jvxl.readers.MapFileReader
checkInsideOut, getVectorsAndOrigin, init2MFR
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getJVXLCutoff, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Details
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data
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voxelList
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surfaceName
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pymolType
private int pymolType -
isMesh
private boolean isMesh -
cMapSourceCrystallographic
static final int cMapSourceCrystallographic- See Also:
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cMapSourceCCP4
static final int cMapSourceCCP4- See Also:
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cMapSourceGeneralPurpose
static final int cMapSourceGeneralPurpose- See Also:
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cMapSourceDesc
static final int cMapSourceDesc- See Also:
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cMapSourceFLD
static final int cMapSourceFLD- See Also:
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cMapSourceBRIX
static final int cMapSourceBRIX- See Also:
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cMapSourceGRD
static final int cMapSourceGRD- See Also:
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cMapSourceChempyBrick
static final int cMapSourceChempyBrick- See Also:
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cMapSourceVMDPlugin
static final int cMapSourceVMDPlugin- See Also:
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cMapSourceObsolete
static final int cMapSourceObsolete- See Also:
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OBJECT_MAPDATA
static final int OBJECT_MAPDATA- See Also:
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OBJECT_MAPMESH
static final int OBJECT_MAPMESH- See Also:
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pt
private int pt
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Constructor Details
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PyMOLMeshReader
PyMOLMeshReader()
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Method Details
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init2
- Overrides:
init2
in classMapFileReader
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getList
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readParameters
- Specified by:
readParameters
in classVolumeFileReader
- Throws:
Exception
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nextVoxel
- Overrides:
nextVoxel
in classVolumeFileReader
- Throws:
Exception
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getFloat
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skipData
- Overrides:
skipData
in classVolumeFileReader
- Throws:
Exception
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setCutoffAutomatic
protected void setCutoffAutomatic()- Overrides:
setCutoffAutomatic
in classMapFileReader
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calculateCutoff
private float calculateCutoff()
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