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

All Implemented Interfaces:

javajs.api.GenericLineReader

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 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	isArchive
private boolean	isOutputFile
private java.lang.String	nboType
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

allowNoOrbitals, 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

addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor and Description
GenNBOReader()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkLine()
private boolean	fillSlater(int[] slater, int n, int pt, int ng)
private void	getAlphasAndExponents()
private boolean	getFile31()
private void	getFile46()
private java.lang.String	getFileData(java.lang.String ext)
private int[]	getIntData()
protected void	initializeReader()
private boolean	readData31(java.lang.String line1)
private void	readData46()
private void	readData47()
private void	readMOs()

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, getNewDfCoefMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, processDSSR, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, 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

nboType

private java.lang.String nboType

nOrbitals0

private int nOrbitals0

isArchive

private boolean isArchive

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

getFile31

private boolean getFile31()
                   throws java.lang.Exception

Throws:

java.lang.Exception

getFile46

private void getFile46()
                throws java.lang.Exception

Throws:

java.lang.Exception

readData47

private void readData47()
                 throws java.lang.Exception

Throws:

java.lang.Exception

getIntData

private int[] getIntData()
                  throws java.lang.Exception

Throws:

java.lang.Exception

fillSlater

private boolean fillSlater(int[] slater,
                           int n,
                           int pt,
                           int ng)

getAlphasAndExponents

private void getAlphasAndExponents()
                            throws java.lang.Exception

Throws:

java.lang.Exception

readData31

private boolean readData31(java.lang.String line1)
                    throws java.lang.Exception

Throws:

java.lang.Exception

readData46

private void readData46()
                 throws java.lang.Exception

Throws:

java.lang.Exception