org.jmol.adapter.readers.more
Class GamessUSReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MOReader
org.jmol.adapter.readers.more.GamessReader
org.jmol.adapter.readers.more.GamessUSReader
public class GamessUSReader
- extends GamessReader
Fields inherited from class org.jmol.adapter.readers.more.MOReader |
alphaBeta, continuing, energyUnits, gaussianCount, gaussians, haveNboCharges, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, ignoreMOs, iHaveAtoms, moData, moTypes, orbitals, shellCount, shells |
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 |
GamessUSReader
public GamessUSReader()
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class MOReader
checkLine
protected boolean checkLine()
throws java.lang.Exception
- Specified by:
checkLine
in class MOReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
readMolecularOrbitals
protected void readMolecularOrbitals(int headerType)
throws java.lang.Exception
- Overrides:
readMolecularOrbitals
in class MOReader
- Throws:
java.lang.Exception
readEFPInBohrCoordinates
protected void readEFPInBohrCoordinates()
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtomsInBohrCoordinates
protected void readAtomsInBohrCoordinates()
throws java.lang.Exception
- Specified by:
readAtomsInBohrCoordinates
in class GamessReader
- Throws:
java.lang.Exception
readAtomsInAngstromCoordinates
private void readAtomsInAngstromCoordinates()
throws java.lang.Exception
- Throws:
java.lang.Exception
fixShellTag
protected java.lang.String fixShellTag(java.lang.String tag)
- Specified by:
fixShellTag
in class GamessReader
readPartialCharges
void readPartialCharges()
throws java.lang.Exception
- Throws:
java.lang.Exception
readDipoleMoment
void readDipoleMoment()
throws java.lang.Exception
- Throws:
java.lang.Exception