org.jmol.adapter.readers.quantum
Class GamessUSReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.quantum.BasisFunctionReader
          extended by org.jmol.adapter.readers.quantum.MOReader
              extended by org.jmol.adapter.readers.quantum.GamessReader
                  extended by org.jmol.adapter.readers.quantum.GamessUSReader

public class GamessUSReader
extends GamessReader


Field Summary
private  boolean lowdenCharges
           
 
Fields inherited from class org.jmol.adapter.readers.quantum.GamessReader
atomNames
 
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
 
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, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
 
Constructor Summary
GamessUSReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  java.lang.String fixShellTag(java.lang.String tag)
           
protected  void initializeReader()
           
private  void readAtomsInAngstromCoordinates()
           
protected  void readAtomsInBohrCoordinates()
           
(package private)  void readDipoleMoment()
           
protected  void readEFPInBohrCoordinates()
           
protected  void readMolecularOrbitals(int headerType)
           
(package private)  void readPartialCharges()
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.GamessReader
fixBasisLine, readBasisInfo, readControlInfo, readFrequencies, readGaussianBasis, setCalculationType
 
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addMOData, checkNboLine, getMOHeader, getNboTypes, setMOData, setMOType
 
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

lowdenCharges

private boolean lowdenCharges
Constructor Detail

GamessUSReader

public GamessUSReader()
Method Detail

initializeReader

protected void initializeReader()
Overrides:
initializeReader in class MOReader

checkLine

protected boolean checkLine()
                     throws java.lang.Exception
Overrides:
checkLine in class AtomSetCollectionReader
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