Package org.jmol.jvxl.readers
Class CastepDensityReader
- 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.PeriodicVolumeFileReader
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- org.jmol.jvxl.readers.CastepDensityReader
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- All Implemented Interfaces:
VertexDataServer
class CastepDensityReader extends PeriodicVolumeFileReader
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Field Summary
Fields Modifier and Type Field Description private int
nFilePoints
private int
nSkip
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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 CastepDensityReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
getPeriodicVoxels()
protected void
gotoData(int n, int nPoints)
(package private) void
init2(SurfaceGenerator sg, java.io.BufferedReader br)
protected void
readParameters()
private void
skipPoints(int n)
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Methods inherited from class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readSurfaceData
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Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, 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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Method Detail
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
- Overrides:
init2
in classVolumeFileReader
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gotoData
protected void gotoData(int n, int nPoints) throws java.lang.Exception
- Overrides:
gotoData
in classVolumeFileReader
- Throws:
java.lang.Exception
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readParameters
protected void readParameters() throws java.lang.Exception
- Specified by:
readParameters
in classVolumeFileReader
- Throws:
java.lang.Exception
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getPeriodicVoxels
protected void getPeriodicVoxels() throws java.lang.Exception
- Specified by:
getPeriodicVoxels
in classPeriodicVolumeFileReader
- Throws:
java.lang.Exception
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skipPoints
private void skipPoints(int n)
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