org.jmol.jvxl.readers.BCifDensityReader

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.

Field Summary

Fields

Modifier and Type

Field

Description

(package private) float

checkSum

Map<String,Object>

cifData

private String

header

private boolean

isDiff

private int

pt

Map<String,Object>

thisData

protected float[]

values

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.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, 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

Constructor

Description

BCifDensityReader()
Method Summary

Modifier and Type

Method

Description

protected void

closeReader()

protected void

getCifData(String fileName, Object data)

protected float

getCifFloat(String key)

protected Map<String,Object>

getCifMap(String type)

private float

getXYZ(javajs.util.P3 a, float x)

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

protected float

nextVoxel()

protected float[]

readCifFloats(String key, float[] values)

protected javajs.util.P3

readCifP3(String key, javajs.util.P3 p3)

protected void

readParameters()

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- header
  
  private String header
- pt
  
  private int pt
- checkSum
  
  float checkSum
- values
  
  protected float[] values
- cifData
  
  public Map<String,Object> cifData
- thisData
  
  public Map<String,Object> thisData
- isDiff
  
  private boolean isDiff
Constructor Details
- BCifDensityReader
  
  BCifDensityReader()
Method Details
- getCifData
  
  protected void getCifData(String fileName, Object data)
- readCifP3
  
  protected javajs.util.P3 readCifP3(String key, javajs.util.P3 p3)
- getCifMap
  
  protected Map<String,Object> getCifMap(String type)
- getCifFloat
  
  protected float getCifFloat(String key)
- readCifFloats
  
  protected float[] readCifFloats(String key, float[] values)
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader br)
  
  Overrides:
  
  init2 in class MapFileReader
- readParameters
  
  protected void readParameters() throws Exception
  
  Specified by:
  
  readParameters in class VolumeFileReader
  
  Throws:
  
  Exception
- getXYZ
  
  private float getXYZ(javajs.util.P3 a, float x)
- nextVoxel
  
  protected float nextVoxel() throws Exception
  
  Overrides:
  
  nextVoxel in class VolumeFileReader
  
  Throws:
  
  Exception
- skipData
  
  protected void skipData(int nPoints) throws Exception
  
  Overrides:
  
  skipData in class VolumeFileReader
  
  Throws:
  
  Exception
- closeReader
  
  protected void closeReader()
  
  Overrides:
  
  closeReader in class VolumeFileReader

Class BCifDensityReader

Field Summary

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

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

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

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

Constructor Summary

Method Summary

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

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

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

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

Methods inherited from class java.lang.Object

Field Details

header

pt

checkSum

values

cifData

thisData

isDiff

Constructor Details

BCifDensityReader

Method Details

getCifData

readCifP3

getCifMap

getCifFloat

readCifFloats

init2

readParameters

getXYZ

nextVoxel

skipData

closeReader