Package org.jmol.jvxl.readers
Class Ras3DReader
- 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.PolygonFileReader
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- org.jmol.jvxl.readers.Ras3DReader
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- All Implemented Interfaces:
VertexDataServer
class Ras3DReader extends PolygonFileReader
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Field Summary
Fields Modifier and Type Field Description private booleanasQuads(package private) java.util.Map<java.lang.String,java.lang.Integer>htVerticesprivate intnPolygonsprivate java.lang.StringpmeshErrorprivate java.lang.Stringtype-
Fields inherited from class org.jmol.jvxl.readers.PolygonFileReader
nTriangles, nVertices
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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 Ras3DReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private intgetPoint(java.lang.String[] tokens, int i)(package private) voidgetSurfaceData()(package private) voidinit2(SurfaceGenerator sg, java.io.BufferedReader br)protected voidinit2PR(SurfaceGenerator sg, java.io.BufferedReader br)private booleanreadVertices()protected booleanreadVerticesAndPolygons()protected voidsetHeader()-
Methods inherited from class org.jmol.jvxl.readers.PolygonFileReader
init2PFR, readSurfaceData, readVolumeData, readVolumeParameters
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Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReader, 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, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Method Detail
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
- Overrides:
init2in classSurfaceFileReader
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init2PR
protected void init2PR(SurfaceGenerator sg, java.io.BufferedReader br)
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setHeader
protected void setHeader()
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getSurfaceData
void getSurfaceData() throws java.lang.Exception- Specified by:
getSurfaceDatain classPolygonFileReader- Throws:
java.lang.Exception
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readVerticesAndPolygons
protected boolean readVerticesAndPolygons()
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readVertices
private boolean readVertices() throws java.lang.Exception- Throws:
java.lang.Exception
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getPoint
private int getPoint(java.lang.String[] tokens, int i)
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