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 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 static java.lang.String
GC_LIST
private static java.lang.String
GS_LIST
private static java.lang.String
HC_LIST
private static java.lang.String
HS_LIST
private static java.lang.String
IC_LIST
private static java.lang.String
IS_LIST
private boolean
is47File
private boolean
isOpenShell
private boolean
isOutputFile
private int
nAOs
(package private) NBOParser
nboParser
private java.lang.String
nboType
private int
nNOs
private int
nOrbitals0
private int
nStructures
private static java.lang.String
P_LIST
private static java.lang.String
PS_LIST
private static java.lang.String
SP_LIST
private static java.lang.String
SPS_LIST
private java.lang.String
topoType
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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
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
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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, filterCased, 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, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, 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 Constructor Description GenNBOReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description private static void
addAuxFile(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String fileName, java.util.Map<java.lang.String,java.lang.Object> htParams)
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 java.lang.String
getFileData(java.lang.String ext)
private int[]
getIntData()
private static java.lang.String
getLabelKey(java.lang.String labelKey)
private static void
getNBOOccupanciesStatic(javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals, int nAOs, int pt, java.lang.String data, int len, int[] next)
private javajs.util.Lst<java.lang.Object>
getStructureList()
private void
getStructures(java.lang.String type)
protected void
initializeReader()
private boolean
readData31(java.lang.String line1)
private java.util.Map<java.lang.String,java.lang.String[]>
readData46(java.lang.String labelKey)
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(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String nboType, Viewer vwr)
Called by setNBOType in IsoExt when use issues NBO TYPE xxxprivate java.util.Map<java.lang.String,java.lang.String[]>
readOutputProperties(java.lang.String data)
private boolean
resetDF()
private void
setLabels(java.util.Map<java.lang.String,java.lang.String[]> map, java.lang.String key, java.lang.String line)
private void
setMap(java.util.Map<java.lang.String,java.lang.String[]> map, java.lang.String labelKey, int nNOs, boolean doAll)
static void
setNboLabels(java.lang.String[] tokens, int nLabels, javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals, int nOrbitals0, java.lang.String moType)
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, addSlaterBasis, 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, 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 Detail
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isOutputFile
private boolean isOutputFile
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nboType
private java.lang.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 java.lang.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 java.lang.String P_LIST
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PS_LIST
private static java.lang.String PS_LIST
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SP_LIST
private static java.lang.String SP_LIST
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SPS_LIST
private static java.lang.String SPS_LIST
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DS_LIST
private static java.lang.String DS_LIST
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DC_LIST
private static java.lang.String DC_LIST
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FS_LIST
private static java.lang.String FS_LIST
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FC_LIST
private static java.lang.String FC_LIST
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GS_LIST
private static java.lang.String GS_LIST
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GC_LIST
private static java.lang.String GC_LIST
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HS_LIST
private static java.lang.String HS_LIST
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HC_LIST
private static java.lang.String HC_LIST
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IS_LIST
private static java.lang.String IS_LIST
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IC_LIST
private static java.lang.String IC_LIST
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classMOReader
- Throws:
java.lang.Exception
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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getStructures
private void getStructures(java.lang.String type) throws java.lang.Exception
- Throws:
java.lang.Exception
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getStructureList
private javajs.util.Lst<java.lang.Object> getStructureList()
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getFileData
private java.lang.String getFileData(java.lang.String ext) throws java.lang.Exception
- Throws:
java.lang.Exception
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getFile31
private boolean getFile31() throws java.lang.Exception
- Throws:
java.lang.Exception
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getFile46
private void getFile46()
read the labels from xxxx.46
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readOutputProperties
private java.util.Map<java.lang.String,java.lang.String[]> readOutputProperties(java.lang.String data)
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setLabels
private void setLabels(java.util.Map<java.lang.String,java.lang.String[]> map, java.lang.String key, java.lang.String line)
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readData47
private void readData47() throws java.lang.Exception
- Throws:
java.lang.Exception
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getIntData
private int[] getIntData() throws java.lang.Exception
- Throws:
java.lang.Exception
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fillSlater
private boolean fillSlater(int[] slater, int n, int pt, int ng)
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resetDF
private boolean resetDF()
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getAlphasAndExponents
private void getAlphasAndExponents() throws java.lang.Exception
- Throws:
java.lang.Exception
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readData31
private boolean readData31(java.lang.String line1) throws java.lang.Exception
- Throws:
java.lang.Exception
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readData46
private java.util.Map<java.lang.String,java.lang.String[]> readData46(java.lang.String labelKey) throws java.lang.Exception
read labels and not proper number of NOs, nNOs, for this nboType- Returns:
- Throws:
java.lang.Exception
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setMap
private void setMap(java.util.Map<java.lang.String,java.lang.String[]> map, java.lang.String labelKey, int nNOs, boolean doAll)
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getLabelKey
private static java.lang.String getLabelKey(java.lang.String labelKey)
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readNBOCoefficients
public static boolean readNBOCoefficients(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.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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addAuxFile
private static void addAuxFile(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String fileName, java.util.Map<java.lang.String,java.lang.Object> htParams)
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getNBOOccupanciesStatic
private static void getNBOOccupanciesStatic(javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals, int nAOs, int pt, java.lang.String data, int len, int[] next)
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readMOs
private void readMOs() throws java.lang.Exception
- Throws:
java.lang.Exception
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readNBO37Occupancies
private void readNBO37Occupancies(int pt) throws java.lang.Exception
Read occupancies from .37 file. Called by readMOs.- Parameters:
pt
-- Throws:
java.lang.Exception
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setNboLabels
public static void setNboLabels(java.lang.String[] tokens, int nLabels, javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals, int nOrbitals0, java.lang.String moType)
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