org.jmol.adapter.readers.quantum
Class GenNBOReader

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.GenNBOReader

public class GenNBOReader
extends MOReader

NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold

Author:
hansonr

Field Summary
private static java.lang.String DC_LIST
           
private static java.lang.String DS_LIST
           
private static java.lang.String FC_LIST
           
private static java.lang.String FS_LIST
           
private  boolean isOutputFile
           
private  java.lang.String moType
           
private  int nOrbitals0
           
private static java.lang.String P_LIST
           
private static java.lang.String SP_LIST
           
 
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
GenNBOReader()
           
 
Method Summary
protected  boolean checkLine()
           
private  java.lang.String getFileData(java.lang.String ext)
           
protected  void initializeReader()
           
private  boolean readData31(java.lang.String line1, java.lang.String line2)
           
private  boolean readData46()
           
private  boolean readFile31()
           
private  void readFile46()
           
private  void readMOs()
           
private  void readOrbitalData(boolean isMO)
           
 
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, 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

isOutputFile

private boolean isOutputFile

moType

private java.lang.String moType

nOrbitals0

private int nOrbitals0

P_LIST

private static java.lang.String P_LIST

SP_LIST

private static java.lang.String SP_LIST

DS_LIST

private static java.lang.String DS_LIST

DC_LIST

private static java.lang.String DC_LIST

FS_LIST

private static java.lang.String FS_LIST

FC_LIST

private static java.lang.String FC_LIST
Constructor Detail

GenNBOReader

public GenNBOReader()
Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception
Overrides:
initializeReader in class MOReader
Throws:
java.lang.Exception

readMOs

private void readMOs()
              throws java.lang.Exception
Throws:
java.lang.Exception

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

getFileData

private java.lang.String getFileData(java.lang.String ext)
                              throws java.lang.Exception
Throws:
java.lang.Exception

readFile31

private boolean readFile31()
                    throws java.lang.Exception
Throws:
java.lang.Exception

readFile46

private void readFile46()
                 throws java.lang.Exception
Throws:
java.lang.Exception

readData31

private boolean readData31(java.lang.String line1,
                           java.lang.String line2)
                    throws java.lang.Exception
Throws:
java.lang.Exception

readData46

private boolean readData46()
                    throws java.lang.Exception
Throws:
java.lang.Exception

readOrbitalData

private void readOrbitalData(boolean isMO)
                      throws java.lang.Exception
Throws:
java.lang.Exception