Package org.jmol.adapter.readers.quantum
Class GenNBOReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.quantum.BasisFunctionReader
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- org.jmol.adapter.readers.quantum.MOReader
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- org.jmol.adapter.readers.quantum.GenNBOReader
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- 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 upgrade to NBO 6 allows reading of resonance structures, including base structure- Author:
- hansonr
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
Fields Modifier and Type Field Description private boolean
addBetaSet
private boolean
alphaOnly
private boolean
betaOnly
private static String
DC_LIST
private static String
DS_LIST
private static String
FC_LIST
private static String
FS_LIST
private static String
GC_LIST
private static String
GS_LIST
private static String
HC_LIST
private static String
HS_LIST
private static String
IC_LIST
private static String
IS_LIST
private boolean
is47File
private boolean
isOpenShell
private boolean
isOutputFile
private int
nAOs
(package private) NBOParser
nboParser
private String
nboType
private int
nNOs
private int
nOrbitals0
private int
nStructures
private static String
P_LIST
private static String
SP_LIST
private String
topoType
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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
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description GenNBOReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
private boolean
fillSlater(int[] slater, int n, int pt, int ng)
protected void
finalizeSubclassReader()
optional reader-specific method run first.private void
getAlphasAndExponents()
private boolean
getFile31()
private void
getFile46()
read the labels from xxxx.46private String
getFileData(String ext)
private int[]
getIntData()
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>
getStructureList()
private void
getStructures(String type)
protected void
initializeReader()
private boolean
readData31(String line1)
private void
readData46()
read labels and not proper number of NOs, nNOs, for this nboTypeprivate void
readData47()
private void
readMOs()
private void
readNBO37Occupancies(int pt)
Read occupancies from .37 file.static boolean
readNBOCoefficients(Map<String,Object> moData, String nboType, Viewer vwr)
Called by setNBOType in IsoExt when use issues NBO TYPE xxxstatic void
setNboLabels(String[] tokens, int nLabels, javajs.util.Lst<Map<String,Object>> orbitals, int nOrbitals0, String moType)
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
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Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, 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, 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 Detail
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isOutputFile
private boolean isOutputFile
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nboType
private String nboType
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nOrbitals0
private int nOrbitals0
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is47File
private boolean is47File
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isOpenShell
private boolean isOpenShell
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alphaOnly
private boolean alphaOnly
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betaOnly
private boolean betaOnly
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nAOs
private int nAOs
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nNOs
private int nNOs
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topoType
private String topoType
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nStructures
private int nStructures
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nboParser
NBOParser nboParser
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addBetaSet
private boolean addBetaSet
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P_LIST
private static String P_LIST
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SP_LIST
private static String SP_LIST
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DS_LIST
private static String DS_LIST
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DC_LIST
private static String DC_LIST
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FS_LIST
private static String FS_LIST
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FC_LIST
private static String FC_LIST
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GS_LIST
private static String GS_LIST
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GC_LIST
private static String GC_LIST
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HS_LIST
private static String HS_LIST
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HC_LIST
private static String HC_LIST
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IS_LIST
private static String IS_LIST
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IC_LIST
private static String IC_LIST
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Method Detail
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initializeReader
protected void initializeReader() throws Exception
- Overrides:
initializeReader
in classMOReader
- Throws:
Exception
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finalizeSubclassReader
protected void finalizeSubclassReader() throws Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
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checkLine
protected boolean checkLine() throws Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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getStructureList
private javajs.util.Lst<Object> getStructureList()
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fillSlater
private boolean fillSlater(int[] slater, int n, int pt, int ng)
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readData46
private void readData46() throws Exception
read labels and not proper number of NOs, nNOs, for this nboType- Throws:
Exception
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readNBOCoefficients
public static boolean readNBOCoefficients(Map<String,Object> moData, String nboType, Viewer vwr)
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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getNBOOccupanciesStatic
private static void getNBOOccupanciesStatic(javajs.util.Lst<Map<String,Object>> orbitals, int nAOs, int pt, String data, int len, int[] next)
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readNBO37Occupancies
private void readNBO37Occupancies(int pt) throws Exception
Read occupancies from .37 file. Called by readMOs.- Parameters:
pt
-- Throws:
Exception
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