org.jmol.adapter.readers.quantum
Class MOReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.MOReader
- Direct Known Subclasses:
- GamessReader, GaussianReader, GenNBOReader, JaguarReader, PsiReader, QchemReader
public abstract class MOReader
- extends BasisFunctionReader
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.readers.quantum.BasisFunctionReader |
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, 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
gaussians
protected float[][] gaussians
energyUnits
protected java.lang.String energyUnits
moTypes
protected java.util.List moTypes
getNBOs
private boolean getNBOs
getNBOCharges
private boolean getNBOCharges
haveNboCharges
protected boolean haveNboCharges
haveNboOrbitals
protected boolean haveNboOrbitals
orbitalsRead
protected boolean orbitalsRead
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
haveCoeffMap
private boolean haveCoeffMap
P_LIST
private static final java.lang.String P_LIST
- See Also:
- Constant Field Values
DS_LIST
private static final java.lang.String DS_LIST
- See Also:
- Constant Field Values
DC_LIST
private static final java.lang.String DC_LIST
- See Also:
- Constant Field Values
FS_LIST
private static final java.lang.String FS_LIST
- See Also:
- Constant Field Values
FC_LIST
private static java.lang.String FC_LIST
MOReader
public MOReader()
initializeReader
protected void initializeReader()
throws java.lang.Exception
- Overrides:
initializeReader
in class AtomSetCollectionReader
- Throws:
java.lang.Exception
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
setMOType
protected int setMOType(java.util.Hashtable mo,
int i)
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.List[] data,
java.util.Hashtable[] mos)
setMOData
protected void setMOData(boolean clearOrbitals)