Package 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
NBO file nn reader will pull in other files as necessary
acknowledgments: Grange Hermitage, Frank Weinhold
upgrade to NBO 6 allows reading of resonance structures, including base structure
- Author:
- hansonr
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate boolean
private boolean
private boolean
private static String
private static String
private static String
private static String
private static String
private static String
private static String
private static String
private static String
private static String
private boolean
private boolean
private boolean
private int
(package private) NBOParser
private String
private int
private int
private int
private static String
private static String
private static String
private static String
private String
Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate static void
protected boolean
private boolean
fillSlater
(int[] slater, int n, int pt, int ng) protected void
optional reader-specific method run first.private void
private boolean
private void
read the labels from xxxx.46private String
getFileData
(String ext) private int[]
private static String
getLabelKey
(String labelKey) private static void
getNBOOccupanciesStatic
(javajs.util.Lst<Map<String, Object>> orbitals, int nAOs, int pt, String data, int len, int[] next) private javajs.util.Lst<Object>
private void
getStructures
(String type) protected void
private boolean
readData31
(String line1) readData46
(String labelKey) read labels and not proper number of NOs, nNOs, for this nboTypeprivate void
private void
readMOs()
private void
readNBO37Occupancies
(int pt) Read occupancies from .37 file.static boolean
Called by setNBOType in IsoExt when use issues NBO TYPE xxxreadOutputProperties
(String data) private boolean
resetDF()
private void
private void
static void
setNboLabels
(String[] tokens, int nLabels, javajs.util.Lst<Map<String, Object>> orbitals, int nOrbitals0, String moType) Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, addSlaterBasis, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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, 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
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Field Details
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isOutputFile
private boolean isOutputFile -
nboType
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nOrbitals0
private int nOrbitals0 -
is47File
private boolean is47File -
isOpenShell
private boolean isOpenShell -
alphaOnly
private boolean alphaOnly -
betaOnly
private boolean betaOnly -
nAOs
private int nAOs -
nNOs
private int nNOs -
topoType
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nStructures
private int nStructures -
nboParser
NBOParser nboParser -
addBetaSet
private boolean addBetaSet -
P_LIST
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PS_LIST
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SP_LIST
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SPS_LIST
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DS_LIST
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DC_LIST
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FS_LIST
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FC_LIST
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GS_LIST
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GC_LIST
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HS_LIST
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HC_LIST
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IS_LIST
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IC_LIST
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Constructor Details
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GenNBOReader
public GenNBOReader()
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Method Details
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initializeReader
- Overrides:
initializeReader
in classMOReader
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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getStructures
- Throws:
Exception
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getStructureList
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getFileData
- Throws:
Exception
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getFile31
- Throws:
Exception
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getFile46
private void getFile46()read the labels from xxxx.46 -
readOutputProperties
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setLabels
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readData47
- Throws:
Exception
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getIntData
- Throws:
Exception
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fillSlater
private boolean fillSlater(int[] slater, int n, int pt, int ng) -
resetDF
private boolean resetDF() -
getAlphasAndExponents
- Throws:
Exception
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readData31
- Throws:
Exception
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readData46
read labels and not proper number of NOs, nNOs, for this nboType- Returns:
- Throws:
Exception
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setMap
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getLabelKey
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readNBOCoefficients
Called by setNBOType in IsoExt when use issues NBO TYPE xxx- Parameters:
moData
-nboType
-vwr
-- Returns:
- true if sucessful or false if required file is missing
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addAuxFile
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getNBOOccupanciesStatic
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readMOs
- Throws:
Exception
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readNBO37Occupancies
Read occupancies from .37 file. Called by readMOs.- Parameters:
pt
-- Throws:
Exception
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setNboLabels
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