org.jmol.adapter.readers.more
Class GamessReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.GamessReader
- Direct Known Subclasses:
- GamessUKReader, GamessUSReader
public abstract class GamessReader
- extends AtomSetCollectionReader
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 |
atomCount
protected int atomCount
shellCount
protected int shellCount
gaussianCount
protected int gaussianCount
calculationType
protected java.lang.String calculationType
moData
protected java.util.Hashtable moData
orbitals
protected java.util.Vector orbitals
atomNames
protected java.util.Vector atomNames
GamessReader
public GamessReader()
readAtomSetCollection
public abstract AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
readAtomsInBohrCoordinates
protected abstract void readAtomsInBohrCoordinates()
throws java.lang.Exception
- Throws:
java.lang.Exception
readGaussianBasis
protected void readGaussianBasis(java.lang.String initiator,
java.lang.String terminator)
throws java.lang.Exception
- Throws:
java.lang.Exception
fixShellTag
protected abstract java.lang.String fixShellTag(java.lang.String tag)
readMolecularOrbitals
protected void readMolecularOrbitals()
throws java.lang.Exception
- Throws:
java.lang.Exception
getMOHeader
protected abstract void getMOHeader(java.lang.String[] tokens,
java.util.Hashtable[] mos,
int nThisLine)
throws java.lang.Exception
- Throws:
java.lang.Exception
readFrequencies
protected void readFrequencies()
throws java.lang.Exception
- Throws:
java.lang.Exception
readComponents
private void readComponents(int count,
float[] components)
fixBasisLine
protected static java.lang.String fixBasisLine(java.lang.String line)