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

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

BasisFunctionReader.MOEnergySorter

Field Summary

Fields

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

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, nCoef, 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, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
GenNBOReader()

Method Summary

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)

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, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR

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 String moType

nOrbitals0

private int nOrbitals0

P_LIST

private static String P_LIST

SP_LIST

private static String SP_LIST

DS_LIST

private static String DS_LIST

DC_LIST

private static String DC_LIST

FS_LIST

private static String FS_LIST

FC_LIST

private static String FC_LIST

Constructor Detail

GenNBOReader

public GenNBOReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws Exception

Overrides:

initializeReader in class MOReader

Throws:

Exception

readMOs

private void readMOs()
              throws Exception

Throws:

Exception

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

getFileData

private String getFileData(String ext)
                    throws Exception

Throws:

Exception

readFile31

private boolean readFile31()
                    throws Exception

Throws:

Exception

readFile46

private void readFile46()
                 throws Exception

Throws:

Exception

readData31

private boolean readData31(String line1,
                           String line2)
                    throws Exception

Throws:

Exception

readData46

private boolean readData46()
                    throws Exception

Throws:

Exception

readOrbitalData

private void readOrbitalData(boolean isMO)
                      throws Exception

Throws:

Exception