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 intcMapSourceBRIX(package private) static intcMapSourceCCP4(package private) static intcMapSourceChempyBrick(package private) static intcMapSourceCrystallographic(package private) static intcMapSourceDesc(package private) static intcMapSourceFLD(package private) static intcMapSourceGeneralPurpose(package private) static intcMapSourceGRD(package private) static intcMapSourceObsolete(package private) static intcMapSourceVMDPluginprivate javajs.util.Lst<java.lang.Object>dataprivate booleanisMesh(package private) static intOBJECT_MAPDATA(package private) static intOBJECT_MAPMESHprivate intptprivate intpymolTypeprivate java.lang.StringsurfaceNameprivate javajs.util.Lst<java.lang.Object>voxelList-
Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors
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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
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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 floatcalculateCutoff()private floatgetFloat(javajs.util.Lst<java.lang.Object> list, int i)private static javajs.util.Lst<java.lang.Object>getList(javajs.util.Lst<java.lang.Object> list, int i)(package private) voidinit2(SurfaceGenerator sg, java.io.BufferedReader brNull)protected floatnextVoxel()protected voidreadParameters()protected voidsetCutoffAutomatic()protected voidskipData(int nPoints)-
Methods inherited from class org.jmol.jvxl.readers.MapFileReader
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<java.lang.Object> data
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voxelList
private javajs.util.Lst<java.lang.Object> voxelList
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surfaceName
private java.lang.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, java.io.BufferedReader brNull)
- Overrides:
init2in classMapFileReader
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getList
private static javajs.util.Lst<java.lang.Object> getList(javajs.util.Lst<java.lang.Object> list, int i)
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readParameters
protected void readParameters() throws java.lang.Exception- Specified by:
readParametersin classVolumeFileReader- Throws:
java.lang.Exception
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nextVoxel
protected float nextVoxel() throws java.lang.Exception- Overrides:
nextVoxelin classVolumeFileReader- Throws:
java.lang.Exception
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getFloat
private float getFloat(javajs.util.Lst<java.lang.Object> list, int i)
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skipData
protected void skipData(int nPoints) throws java.lang.Exception- Overrides:
skipDatain classVolumeFileReader- Throws:
java.lang.Exception
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setCutoffAutomatic
protected void setCutoffAutomatic()
- Overrides:
setCutoffAutomaticin classMapFileReader
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calculateCutoff
private float calculateCutoff()
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