org.jmol.adapter.readers.more
Class CubeReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
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
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
negativeAtomCount
boolean negativeAtomCount
atomCount
int atomCount
isAngstroms
boolean isAngstroms
voxelCounts
final int[] voxelCounts
origin
final float[] origin
voxelVectors
final float[][] voxelVectors
CubeReader
public CubeReader()
readAtomSetCollection
public AtomSetCollection 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