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- 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 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
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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, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, 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 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()
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()
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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, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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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, 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 java.lang.String nboType
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nOrbitals0
private int nOrbitals0
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isArchive
private boolean isArchive
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P_LIST
private static java.lang.String P_LIST
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SP_LIST
private static java.lang.String SP_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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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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readMOs
private void readMOs() throws java.lang.Exception
- 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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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() throws java.lang.Exception
- Throws:
java.lang.Exception
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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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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 void readData46() throws java.lang.Exception
- Throws:
java.lang.Exception
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