org.jmol.jvxl.readers
Class AtomPropertyMapper

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.VolumeDataReader
          extended by org.jmol.jvxl.readers.AtomDataReader
              extended by org.jmol.jvxl.readers.AtomPropertyMapper
All Implemented Interfaces:
VertexDataServer

 class AtomPropertyMapper
extends AtomDataReader


Field Summary
private  int calcType
           
private  boolean doSmoothProperty
           
private  int iAtomSurface
           
private  AtomIndexIterator iter
           
private  MepCalculationInterface mepCalc
           
private  java.lang.String mepType
           
private  float smoothingPower
           
 
Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
atomCount, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, havePlane, margin, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptXyzTemp, ptY0, ptZ0, thisAtomSet, thisPlane, thisX, validSpheres, voxelSource
 
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, atomDataServer, 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, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, 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
AtomPropertyMapper(SurfaceGenerator sg, java.lang.String mepType)
           
 
Method Summary
protected  void finalizeMapping()
           
protected  void generateCube()
           
 int getSurfaceAtomIndex()
           
 float getValueAtPoint(javax.vecmath.Point3f pt)
           
protected  void initializeMapping()
           
protected  void setup(boolean isMapData)
           
protected  void setVolumeData()
           
 
Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeForPlane, setVoxel, unsetVoxelData
 
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

mepCalc

private MepCalculationInterface mepCalc

mepType

private java.lang.String mepType

calcType

private int calcType

doSmoothProperty

private boolean doSmoothProperty

iter

private AtomIndexIterator iter

smoothingPower

private float smoothingPower

iAtomSurface

private int iAtomSurface
Constructor Detail

AtomPropertyMapper

AtomPropertyMapper(SurfaceGenerator sg,
                   java.lang.String mepType)
Method Detail

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(javax.vecmath.Point3f pt)
Overrides:
getValueAtPoint in class SurfaceReader
Returns:
value