Package org.jmol.jvxl.readers
Class PyMOLMeshReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.SurfaceFileReader
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- org.jmol.jvxl.readers.VolumeFileReader
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- org.jmol.jvxl.readers.MapFileReader
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- org.jmol.jvxl.readers.PyMOLMeshReader
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- All Implemented Interfaces:
VertexDataServer
class PyMOLMeshReader extends MapFileReader
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
Fields Modifier and Type Field Description (package private) static int
cMapSourceBRIX
(package private) static int
cMapSourceCCP4
(package private) static int
cMapSourceChempyBrick
(package private) static int
cMapSourceCrystallographic
(package private) static int
cMapSourceDesc
(package private) static int
cMapSourceFLD
(package private) static int
cMapSourceGeneralPurpose
(package private) static int
cMapSourceGRD
(package private) static int
cMapSourceObsolete
(package private) static int
cMapSourceVMDPlugin
private javajs.util.Lst<Object>
data
private boolean
isMesh
(package private) static int
OBJECT_MAPDATA
(package private) static int
OBJECT_MAPMESH
private int
pt
private int
pymolType
private String
surfaceName
private javajs.util.Lst<Object>
voxelList
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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
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Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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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, 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 Constructor Description PyMOLMeshReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description private float
calculateCutoff()
private float
getFloat(javajs.util.Lst<Object> list, int i)
private static javajs.util.Lst<Object>
getList(javajs.util.Lst<Object> list, int i)
(package private) void
init2(SurfaceGenerator sg, BufferedReader brNull)
protected float
nextVoxel()
protected void
readParameters()
protected void
setCutoffAutomatic()
protected void
skipData(int nPoints)
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Methods inherited from class org.jmol.jvxl.readers.MapFileReader
checkInsideOut, getVectorsAndOrigin, init2MFR
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Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ
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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
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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 Detail
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data
private javajs.util.Lst<Object> data
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voxelList
private javajs.util.Lst<Object> voxelList
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surfaceName
private String surfaceName
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pymolType
private int pymolType
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isMesh
private boolean isMesh
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cMapSourceCrystallographic
static final int cMapSourceCrystallographic
- See Also:
- Constant Field Values
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cMapSourceCCP4
static final int cMapSourceCCP4
- See Also:
- Constant Field Values
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cMapSourceGeneralPurpose
static final int cMapSourceGeneralPurpose
- See Also:
- Constant Field Values
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cMapSourceDesc
static final int cMapSourceDesc
- See Also:
- Constant Field Values
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cMapSourceFLD
static final int cMapSourceFLD
- See Also:
- Constant Field Values
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cMapSourceBRIX
static final int cMapSourceBRIX
- See Also:
- Constant Field Values
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cMapSourceGRD
static final int cMapSourceGRD
- See Also:
- Constant Field Values
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cMapSourceChempyBrick
static final int cMapSourceChempyBrick
- See Also:
- Constant Field Values
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cMapSourceVMDPlugin
static final int cMapSourceVMDPlugin
- See Also:
- Constant Field Values
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cMapSourceObsolete
static final int cMapSourceObsolete
- See Also:
- Constant Field Values
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OBJECT_MAPDATA
static final int OBJECT_MAPDATA
- See Also:
- Constant Field Values
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OBJECT_MAPMESH
static final int OBJECT_MAPMESH
- See Also:
- Constant Field Values
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pt
private int pt
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Method Detail
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init2
void init2(SurfaceGenerator sg, BufferedReader brNull)
- Overrides:
init2
in classMapFileReader
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readParameters
protected void readParameters() throws Exception
- Specified by:
readParameters
in classVolumeFileReader
- Throws:
Exception
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nextVoxel
protected float nextVoxel() throws Exception
- Overrides:
nextVoxel
in classVolumeFileReader
- Throws:
Exception
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getFloat
private float getFloat(javajs.util.Lst<Object> list, int i)
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skipData
protected void skipData(int nPoints) throws Exception
- 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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