Package org.jmol.adapter.readers.quantum
Class MOReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.MOReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
GaussianReader
,GenNBOReader
,JaguarReader
,NWChemReader
,OrcaReader
,PsiReader
,QchemReader
,SlaterReader
General methods for reading molecular orbital data, including embedded output
from the NBO program. In particular, when the AONBO keyword is included.
requires the following sort of construct:
public AtomSetCollection readAtomSetCollection(BufferedReader reader) {
readAtomSetCollection(reader, "some type");
}
protected boolean checkLine() {
if (line.indexOf(...)) {
doThis();
return true/false;
}
if (line.indexOf(...)) {
doThat();
return true/false;
}
return checkNboLine();
}
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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 TypeFieldDescriptionprotected boolean
private static final String
private static final String
protected String
private static String
protected boolean
private static final String
int
float[][]
private boolean
private boolean
private boolean
protected boolean
protected boolean
protected final int
protected final int
protected final int
protected final int
private int
protected javajs.util.Lst<String>
protected boolean
private static final String
int
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 TypeMethodDescriptionvoid
protected void
protected void
See MopacSlaterReaderprotected boolean
protected void
getMOHeader
(int headerType, String[] tokens, Map<String, Object>[] mos, int nThisLine) private void
protected void
protected void
protected void
readMolecularOrbitals
(int headerType) private void
void
setMOData
(boolean clearOrbitals) 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, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, 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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shellCount
public int shellCount -
gaussianCount
public int gaussianCount -
gaussians
public float[][] gaussians -
energyUnits
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moTypes
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getNBOs
private boolean getNBOs -
getNBOCharges
private boolean getNBOCharges -
haveNboCharges
protected boolean haveNboCharges -
haveNboOrbitals
protected boolean haveNboOrbitals -
orbitalsRead
protected boolean orbitalsRead -
lastMoData
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allowNoOrbitals
protected boolean allowNoOrbitals -
forceMOPAC
protected boolean forceMOPAC -
HEADER_GAMESS_UK_MO
protected final int HEADER_GAMESS_UK_MO- See Also:
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HEADER_GAMESS_OCCUPANCIES
protected final int HEADER_GAMESS_OCCUPANCIES- See Also:
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HEADER_GAMESS_ORIGINAL
protected final int HEADER_GAMESS_ORIGINAL- See Also:
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HEADER_NONE
protected final int HEADER_NONE- See Also:
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haveCoeffMap
private boolean haveCoeffMap -
P_LIST
- See Also:
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DS_LIST
- See Also:
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DC_LIST
- See Also:
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FS_LIST
- See Also:
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FC_LIST
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iMo0
private int iMo0
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Constructor Details
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MOReader
public MOReader()
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Method Details
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initializeReader
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
Exception
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checkNboLine
- Returns:
- true if need to read line
- Throws:
Exception
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getNboCharges
- Throws:
Exception
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getNboTypes
- Throws:
Exception
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readMolecularOrbitals
- Throws:
Exception
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addSlaterBasis
protected void addSlaterBasis()See MopacSlaterReader -
addCoef
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getMOHeader
protected void getMOHeader(int headerType, String[] tokens, Map<String, Object>[] mos, int nThisLine) throws Exception- Throws:
Exception
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addMOData
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setMOData
public void setMOData(boolean clearOrbitals) -
readSecondOrderData
- Throws:
Exception
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