org.jmol.adapter.readers.more
Class GamessReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.GamessReader
Direct Known Subclasses:
GamessUKReader, GamessUSReader

public abstract class GamessReader
extends AtomSetCollectionReader


Field Summary
protected  int atomCount
           
protected  java.util.Vector atomNames
           
protected  java.lang.String calculationType
           
protected  int gaussianCount
           
protected  java.util.Hashtable moData
           
protected  java.util.Vector orbitals
           
protected  int shellCount
           
 
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
 
Constructor Summary
GamessReader()
           
 
Method Summary
protected static java.lang.String fixBasisLine(java.lang.String line)
           
protected abstract  java.lang.String fixShellTag(java.lang.String tag)
           
protected abstract  void getMOHeader(java.lang.String[] tokens, java.util.Hashtable[] mos, int nThisLine)
           
abstract  AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
protected abstract  void readAtomsInBohrCoordinates()
           
private  void readComponents(int count, float[] components)
           
protected  void readFrequencies()
           
protected  void readGaussianBasis(java.lang.String initiator, java.lang.String terminator)
           
protected  void readMolecularOrbitals()
           
 
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
 

Field Detail

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
Constructor Detail

GamessReader

public GamessReader()
Method Detail

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)