org.jmol.adapter.readers.more
Class MOReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MOReader
- Direct Known Subclasses:
- GamessReader, GaussianReader, JaguarReader, NWChemReader, PsiReader, QchemReader
abstract class MOReader
- extends AtomSetCollectionReader
General methods for reading molecular orbital data,
including embedded output from the NBO program.
In particular, when the AONBO keyword is included.
requires the following sort of construct:
public AtomSetCollection readAtomSetCollection(BufferedReader reader) {
readAtomSetCollection(reader, "some type");
}
protected boolean checkLine() {
if (line.indexOf(...)) {
doThis();
return true/false;
}
if (line.indexOf(...)) {
doThat();
return true/false;
}
return checkNboLine();
}
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 |
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 |
shellCount
protected int shellCount
gaussianCount
protected int gaussianCount
moData
protected java.util.Hashtable moData
shells
protected java.util.Vector shells
gaussians
protected float[][] gaussians
orbitals
protected java.util.Vector orbitals
energyUnits
protected java.lang.String energyUnits
moTypes
protected java.util.Vector moTypes
getNBOs
private boolean getNBOs
getNBOCharges
private boolean getNBOCharges
haveNboCharges
protected boolean haveNboCharges
filterTokens
private java.lang.String[] filterTokens
filterIsNot
private boolean filterIsNot
iHaveAtoms
protected boolean iHaveAtoms
continuing
protected boolean continuing
ignoreMOs
protected boolean ignoreMOs
alphaBeta
protected java.lang.String alphaBeta
HEADER_GAMESS_UK_MO
protected final int HEADER_GAMESS_UK_MO
- See Also:
- Constant Field Values
HEADER_GAMESS_OCCUPANCIES
protected final int HEADER_GAMESS_OCCUPANCIES
- See Also:
- Constant Field Values
HEADER_GAMESS_ORIGINAL
protected final int HEADER_GAMESS_ORIGINAL
- See Also:
- Constant Field Values
HEADER_NONE
protected final int HEADER_NONE
- See Also:
- Constant Field Values
MOReader
MOReader()
readAtomSetCollection
public abstract void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
checkLine
protected abstract boolean checkLine()
throws java.lang.Exception
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader,
java.lang.String type)
finalizeMoReader
protected void finalizeMoReader()
initializeMoReader
private void initializeMoReader(java.io.BufferedReader reader,
java.lang.String type)
filterMO
protected boolean filterMO()
checkNboLine
protected boolean checkNboLine()
throws java.lang.Exception
- Returns:
- true if need to read line
- Throws:
java.lang.Exception
getNboCharges
private void getNboCharges()
throws java.lang.Exception
- Throws:
java.lang.Exception
getNboTypes
protected void getNboTypes()
throws java.lang.Exception
- Throws:
java.lang.Exception
readMolecularOrbitals
protected void readMolecularOrbitals(int headerType)
throws java.lang.Exception
- Throws:
java.lang.Exception
getMOHeader
protected void getMOHeader(int headerType,
java.lang.String[] tokens,
java.util.Hashtable[] mos,
int nThisLine)
throws java.lang.Exception
- Throws:
java.lang.Exception
addMOData
protected void addMOData(int nColumns,
java.util.Vector[] data,
java.util.Hashtable[] mos)
setMOData
protected void setMOData(boolean clearOrbitals)