class BCifDensityReader extends MapFileReader
Modifier and Type | Field and Description |
---|---|
(package private) float |
checkSum |
java.util.Map<java.lang.String,java.lang.Object> |
cifData |
private boolean |
isDiff |
private int |
pt |
java.util.Map<java.lang.String,java.lang.Object> |
thisData |
protected float[] |
values |
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
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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
Constructor and Description |
---|
BCifDensityReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
closeReader() |
protected void |
getCifData(java.lang.String fileName,
java.lang.Object data) |
protected float |
getCifFloat(java.lang.String key) |
protected java.util.Map<java.lang.String,java.lang.Object> |
getCifMap(java.lang.String type) |
protected java.lang.String |
getCifString(java.lang.String key) |
private float |
getXYZ(javajs.util.P3 a,
float x) |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
protected float |
nextVoxel() |
protected float[] |
readCifFloats(java.lang.String key,
float[] values) |
protected javajs.util.P3 |
readCifP3(java.lang.String key,
javajs.util.P3 p3) |
protected void |
readParameters() |
protected void |
skipData(int nPoints) |
checkInsideOut, getVectorsAndOrigin, init2MFR, setCutoffAutomatic
checkAtomLine, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
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
private int pt
float checkSum
protected float[] values
public java.util.Map<java.lang.String,java.lang.Object> cifData
public java.util.Map<java.lang.String,java.lang.Object> thisData
private boolean isDiff
protected void getCifData(java.lang.String fileName, java.lang.Object data)
protected javajs.util.P3 readCifP3(java.lang.String key, javajs.util.P3 p3)
protected java.util.Map<java.lang.String,java.lang.Object> getCifMap(java.lang.String type)
protected java.lang.String getCifString(java.lang.String key)
protected float getCifFloat(java.lang.String key)
protected float[] readCifFloats(java.lang.String key, float[] values)
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2
in class MapFileReader
protected void readParameters() throws java.lang.Exception
readParameters
in class VolumeFileReader
java.lang.Exception
private float getXYZ(javajs.util.P3 a, float x)
protected float nextVoxel() throws java.lang.Exception
nextVoxel
in class VolumeFileReader
java.lang.Exception
protected void skipData(int nPoints) throws java.lang.Exception
skipData
in class VolumeFileReader
java.lang.Exception
protected void closeReader()
closeReader
in class VolumeFileReader