org.jmol.adapter.readers.more
Class CubeReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.CubeReader

public class CubeReader
extends AtomSetCollectionReader

Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files. Miguel 2005 07 17 a negative atom count means that it is molecular orbital (MO) data with MO data, the extra line contains the number of orbitals and the orbital number these orbitals are interspersed -- all orbital values are given together for each coordinate point. also used for JVXL and JVXL+ file format


Field Summary
(package private)  int atomCount
           
(package private)  boolean isAngstroms
           
(package private)  boolean negativeAtomCount
           
(package private)  float[] origin
           
(package private)  int[] voxelCounts
           
(package private)  float[][] voxelVectors
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
CubeReader()
           
 
Method Summary
(package private)  void readAtomCountAndOrigin()
           
(package private)  void readAtoms()
           
 void readAtomSetCollection(java.io.BufferedReader br)
           
(package private)  void readExtraLine()
           
(package private)  void readTitleLines()
           
(package private)  void readVoxelVector(int voxelVectorIndex)
           
(package private)  void readVoxelVectors()
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

negativeAtomCount

boolean negativeAtomCount

atomCount

int atomCount

isAngstroms

boolean isAngstroms

voxelCounts

final int[] voxelCounts

origin

final float[] origin

voxelVectors

final float[][] voxelVectors
Constructor Detail

CubeReader

public CubeReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader br)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

readTitleLines

void readTitleLines()
              throws java.lang.Exception
Throws:
java.lang.Exception

readAtomCountAndOrigin

void readAtomCountAndOrigin()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readVoxelVectors

void readVoxelVectors()
                throws java.lang.Exception
Throws:
java.lang.Exception

readVoxelVector

void readVoxelVector(int voxelVectorIndex)
               throws java.lang.Exception
Throws:
java.lang.Exception

readAtoms

void readAtoms()
         throws java.lang.Exception
Throws:
java.lang.Exception

readExtraLine

void readExtraLine()
             throws java.lang.Exception
Throws:
java.lang.Exception