org.jmol.adapter.readers.quantum
public class GenNBOReader extends MOReader
Modifier and Type | Field and Description |
---|---|
private static String |
DC_LIST |
private static String |
DS_LIST |
private static String |
FC_LIST |
private static String |
FS_LIST |
private boolean |
isOutputFile |
private String |
moType |
private int |
nOrbitals0 |
private static String |
P_LIST |
private static String |
SP_LIST |
energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
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 and Description |
---|
GenNBOReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private String |
getFileData(String ext) |
protected void |
initializeReader() |
private boolean |
readData31(String line1,
String line2) |
private boolean |
readData46() |
private boolean |
readFile31() |
private void |
readFile46() |
private void |
readMOs() |
private void |
readOrbitalData(boolean isMO) |
addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData, setMOType
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
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
private boolean isOutputFile
private String moType
private int nOrbitals0
private static String P_LIST
private static String SP_LIST
private static String DS_LIST
private static String DC_LIST
private static String FS_LIST
private static String FC_LIST
protected void initializeReader() throws Exception
initializeReader
in class MOReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private boolean readData31(String line1, String line2) throws Exception
Exception