org.jmol.jvxl.readers

Class CastepDensityReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.VolumeFileReader

org.jmol.jvxl.readers.CastepDensityReader

All Implemented Interfaces:

VertexDataServer

class CastepDensityReader
extends VolumeFileReader

Field Summary

Fields

Modifier and Type	Field and Description
private int	nFilePoints
private int	nSkip

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

atomCount, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

binarydoc, br, line, next, out

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, 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

Constructor Summary

Constructors

Constructor and Description
CastepDensityReader()

Method Summary

Modifier and Type	Method and Description
protected void	gotoData(int n, int nPoints)
(package private) void	init2(SurfaceGenerator sg, BufferedReader br)
protected void	readParameters()
protected void	readSurfaceData(boolean isMapData)
private void	skipPoints(int n)

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, readLine, setOutputChannel, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane2, getSpanningVectors, 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nFilePoints

private int nFilePoints

nSkip

private int nSkip

Constructor Detail

CastepDensityReader

CastepDensityReader()

Method Detail

init2

void init2(SurfaceGenerator sg,
           BufferedReader br)

Overrides:

init2 in class VolumeFileReader

readParameters

protected void readParameters()
                       throws Exception

Specified by:

readParameters in class VolumeFileReader

Throws:

Exception

gotoData

protected void gotoData(int n,
                        int nPoints)
                 throws Exception

Overrides:

gotoData in class VolumeFileReader

Throws:

Exception

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws Exception

Overrides:

readSurfaceData in class VolumeFileReader

Throws:

Exception

skipPoints

private void skipPoints(int n)