org.jmol.jvxl.readers.AtomPropertyMapper

All Implemented Interfaces:: VertexDataServer

class AtomPropertyMapper extends AtomDataReader

maps property data

Field Summary

Fields

Modifier and Type

Field

Description

private int

calcType

private boolean

doSmoothProperty

private int

iAtomSurface

private AtomIndexIterator

iter

private MepCalculation

mepCalc

private String

mepType

private float

smoothingPower

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyzTruncated, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, maxRS, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptV, ptY0, ptZ0, rs, rs2, sr, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, vl0, vl1, vl2, voxelSource

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints

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

AtomPropertyMapper()
Method Summary

Modifier and Type

Method

Description

protected void

finalizeMapping()

protected void

generateCube()

int

getSurfaceAtomIndex()

float

getValueAtPoint(javajs.util.T3 pt, boolean getSource)

(package private) void

init(SurfaceGenerator sg)

implemented in SurfaceFileReader and

protected void

initializeMapping()

protected void

setup(boolean isMapData)

protected void

setVolumeData()

Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, gotoAndReadVoxelData, gotoData, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, 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
- mepCalc
  
  private MepCalculation mepCalc
- mepType
  
  private String mepType
- calcType
  
  private int calcType
- doSmoothProperty
  
  private boolean doSmoothProperty
- iter
  
  private AtomIndexIterator iter
- smoothingPower
  
  private float smoothingPower
- iAtomSurface
  
  private int iAtomSurface
Constructor Details
- AtomPropertyMapper
  
  AtomPropertyMapper()
Method Details
- init
  
  void init(SurfaceGenerator sg)
  
  Description copied from class: SurfaceReader
  
  implemented in SurfaceFileReader and
  
  Overrides:
  
  init in class VolumeDataReader
- setup
  
  protected void setup(boolean isMapData)
  
  Overrides:
  
  setup in class AtomDataReader
- setVolumeData
  
  protected void setVolumeData()
  
  Overrides:
  
  setVolumeData in class AtomDataReader
- initializeMapping
  
  protected void initializeMapping()
  
  Overrides:
  
  initializeMapping in class SurfaceReader
- finalizeMapping
  
  protected void finalizeMapping()
  
  Overrides:
  
  finalizeMapping in class SurfaceReader
- generateCube
  
  protected void generateCube()
  
  Overrides:
  
  generateCube in class VolumeDataReader
- getSurfaceAtomIndex
  
  public int getSurfaceAtomIndex()
  
  Overrides:
  
  getSurfaceAtomIndex in class SurfaceReader
- getValueAtPoint
  
  public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
  
  Overrides:
  
  getValueAtPoint in class SurfaceReader
  
  getSource - TODO
  
  Returns:
  
  value

Class AtomPropertyMapper

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Details

mepCalc

mepType

calcType

doSmoothProperty

iter

smoothingPower

iAtomSurface

Constructor Details

AtomPropertyMapper

Method Details

init

setup

setVolumeData

initializeMapping

finalizeMapping

generateCube

getSurfaceAtomIndex

getValueAtPoint