Package org.jmol.jvxl.readers
Class BCifDensityReader
- 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.BCifDensityReader
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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
CifDensityReader
class BCifDensityReader extends MapFileReader
Binary CIF density reader. See https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box, for example: https://www.ebi.ac.uk/pdbe/densities/x-ray/1eve/box/-4.413,55.607,64.124/-0.4130001,59.607,68.124?space=cartesian&encoding=bcif Reads a MessagePack file and extracts either 2Fo-Fc or Fo-Fc.
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Field Summary
Fields Modifier and Type Field Description (package private) float
checkSum
java.util.Map<java.lang.String,java.lang.Object>
cifData
private java.lang.String
header
private boolean
isDiff
private int
pt
java.util.Map<java.lang.String,java.lang.Object>
thisData
protected float[]
values
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Fields inherited from class org.jmol.jvxl.readers.MapFileReader
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
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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, readerClosed
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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 BCifDensityReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Methods inherited from class org.jmol.jvxl.readers.MapFileReader
checkInsideOut, getVectorsAndOrigin, init2MFR, setCutoffAutomatic
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Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, 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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header
private java.lang.String header
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pt
private int pt
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checkSum
float checkSum
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values
protected float[] values
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cifData
public java.util.Map<java.lang.String,java.lang.Object> cifData
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thisData
public java.util.Map<java.lang.String,java.lang.Object> thisData
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isDiff
private boolean isDiff
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Method Detail
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getCifData
protected void getCifData(java.lang.String fileName, java.lang.Object data)
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readCifP3
protected javajs.util.P3 readCifP3(java.lang.String key, javajs.util.P3 p3)
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getCifMap
protected java.util.Map<java.lang.String,java.lang.Object> getCifMap(java.lang.String type)
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getCifString
protected java.lang.String getCifString(java.lang.String key)
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getCifFloat
protected float getCifFloat(java.lang.String key)
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readCifFloats
protected float[] readCifFloats(java.lang.String key, float[] values)
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
- Overrides:
init2
in classMapFileReader
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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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getXYZ
private float getXYZ(javajs.util.P3 a, float x)
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nextVoxel
protected float nextVoxel() throws java.lang.Exception
- Overrides:
nextVoxel
in classVolumeFileReader
- Throws:
java.lang.Exception
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skipData
protected void skipData(int nPoints) throws java.lang.Exception
- Overrides:
skipData
in classVolumeFileReader
- Throws:
java.lang.Exception
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closeReader
protected void closeReader()
- Overrides:
closeReader
in classVolumeFileReader
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