org.jmol.jvxl.readers.CifDensityReader

All Implemented Interfaces:: VertexDataServer

class CifDensityReader extends BCifDensityReader

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=cif Extends BCifDensityReader just enough to handle nonbinary CIF data.

Field Summary

Fields inherited from class org.jmol.jvxl.readers.BCifDensityReader
checkSum, cifData, thisData, 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

CifDensityReader()
Method Summary

Modifier and Type

Method

Description

protected void

getCifData(String fileName, Object data)

protected float

getCifFloat(String key)

protected Map<String,Object>

getCifMap(String type)

protected float[]

readCifFloats(String key, float[] values)

protected javajs.util.P3

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

Methods inherited from class org.jmol.jvxl.readers.BCifDensityReader
closeReader, init2, nextVoxel, readParameters, skipData

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

Constructor Details
- CifDensityReader
  
  CifDensityReader()
Method Details
- getCifData
  
  protected void getCifData(String fileName, Object data)
  
  Overrides:
  
  getCifData in class BCifDensityReader
- readCifP3
  
  protected javajs.util.P3 readCifP3(String key, javajs.util.P3 p3)
  
  Overrides:
  
  readCifP3 in class BCifDensityReader
- getCifMap
  
  protected Map<String,Object> getCifMap(String type)
  
  Overrides:
  
  getCifMap in class BCifDensityReader
- getCifFloat
  
  protected float getCifFloat(String key)
  
  Overrides:
  
  getCifFloat in class BCifDensityReader
- readCifFloats
  
  protected float[] readCifFloats(String key, float[] values)
  
  Overrides:
  
  readCifFloats in class BCifDensityReader

Class CifDensityReader

Field Summary

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

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.BCifDensityReader

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

Constructor Details

CifDensityReader

Method Details

getCifData

readCifP3

getCifMap

getCifFloat

readCifFloats