org.jmol.adapter.readers.quantum
Class GenNBOReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.MOReader
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
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 |
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 |
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
GenNBOReader
public GenNBOReader()
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