Package org.jmol.jvxl.readers
Class BCifDensityReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.VolumeFileReader
org.jmol.jvxl.readers.MapFileReader
org.jmol.jvxl.readers.BCifDensityReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
CifDensityReader
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.
-
Field Summary
FieldsModifier and TypeFieldDescription(package private) float
private String
private boolean
private int
protected float[]
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
Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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, jvxlCutoffRange, 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected void
protected void
getCifData
(String fileName, Object data) protected float
getCifFloat
(String key) private float
getXYZ
(javajs.util.P3 a, float x) (package private) void
init2
(SurfaceGenerator sg, BufferedReader br) protected float
protected float[]
readCifFloats
(String key, float[] values) protected javajs.util.P3
protected void
protected void
skipData
(int nPoints) Methods inherited from class org.jmol.jvxl.readers.MapFileReader
checkInsideOut, getVectorsAndOrigin, init2MFR, setCutoffAutomatic
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, getJVXLCutoff, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ
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
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
-
Field Details
-
header
-
pt
private int pt -
checkSum
float checkSum -
values
protected float[] values -
cifData
-
thisData
-
isDiff
private boolean isDiff
-
-
Constructor Details
-
BCifDensityReader
BCifDensityReader()
-
-
Method Details
-
getCifData
-
readCifP3
-
getCifMap
-
getCifFloat
-
readCifFloats
-
init2
- Overrides:
init2
in classMapFileReader
-
readParameters
- Specified by:
readParameters
in classVolumeFileReader
- Throws:
Exception
-
getXYZ
private float getXYZ(javajs.util.P3 a, float x) -
nextVoxel
- Overrides:
nextVoxel
in classVolumeFileReader
- Throws:
Exception
-
skipData
- Overrides:
skipData
in classVolumeFileReader
- Throws:
Exception
-
closeReader
protected void closeReader()- Overrides:
closeReader
in classVolumeFileReader
-