Package org.jmol.adapter.readers.quantum
Class MOReader
- 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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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
GamessReader
,GaussianReader
,GenNBOReader
,JaguarReader
,NWChemReader
,PsiReader
,QchemReader
public class MOReader extends BasisFunctionReader
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
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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 protected boolean
allowNoOrbitals
private static String
DC_LIST
private static String
DS_LIST
protected String
energyUnits
private static String
FC_LIST
private static String
FS_LIST
int
gaussianCount
float[][]
gaussians
private boolean
getNBOCharges
private boolean
getNBOs
private boolean
haveCoeffMap
protected boolean
haveNboCharges
protected boolean
haveNboOrbitals
protected int
HEADER_GAMESS_OCCUPANCIES
protected int
HEADER_GAMESS_ORIGINAL
protected int
HEADER_GAMESS_UK_MO
protected int
HEADER_NONE
private int
iMo0
private Map<String,Object>
lastMoData
protected javajs.util.Lst<String>
moTypes
protected boolean
orbitalsRead
private static String
P_LIST
int
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 MOReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCoef(Map<String,Object> mo, float[] coefs, String type, float energy, float occ, int moCount)
protected void
addMOData(int nColumns, javajs.util.Lst<String>[] data, Map<String,Object>[] mos)
boolean
checkAndRemoveFilterKey(String key)
Prior to filterMO all extraneous filter keys must be removed.protected boolean
checkNboLine()
protected void
getMOHeader(int headerType, String[] tokens, Map<String,Object>[] mos, int nThisLine)
private void
getNboCharges()
protected void
getNboTypes()
protected void
initializeReader()
protected void
readMolecularOrbitals(int headerType)
private void
readSecondOrderData()
void
setMOData(boolean clearOrbitals)
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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, 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, 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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shellCount
public int shellCount
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gaussianCount
public int gaussianCount
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gaussians
public float[][] gaussians
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energyUnits
protected String energyUnits
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moTypes
protected javajs.util.Lst<String> moTypes
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getNBOs
private boolean getNBOs
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getNBOCharges
private boolean getNBOCharges
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haveNboCharges
protected boolean haveNboCharges
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haveNboOrbitals
protected boolean haveNboOrbitals
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orbitalsRead
protected boolean orbitalsRead
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allowNoOrbitals
protected boolean allowNoOrbitals
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HEADER_GAMESS_UK_MO
protected final int HEADER_GAMESS_UK_MO
- See Also:
- Constant Field Values
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HEADER_GAMESS_OCCUPANCIES
protected final int HEADER_GAMESS_OCCUPANCIES
- See Also:
- Constant Field Values
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HEADER_GAMESS_ORIGINAL
protected final int HEADER_GAMESS_ORIGINAL
- See Also:
- Constant Field Values
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HEADER_NONE
protected final int HEADER_NONE
- See Also:
- Constant Field Values
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haveCoeffMap
private boolean haveCoeffMap
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P_LIST
private static final String P_LIST
- See Also:
- Constant Field Values
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DS_LIST
private static final String DS_LIST
- See Also:
- Constant Field Values
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DC_LIST
private static final String DC_LIST
- See Also:
- Constant Field Values
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FS_LIST
private static final String FS_LIST
- See Also:
- Constant Field Values
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FC_LIST
private static String FC_LIST
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iMo0
private int iMo0
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Method Detail
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initializeReader
protected void initializeReader() throws Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
Exception
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checkAndRemoveFilterKey
public boolean checkAndRemoveFilterKey(String key)
Prior to filterMO all extraneous filter keys must be removed.- Parameters:
key
-- Returns:
- true if the key existed; filter is set null if this is the only key
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checkNboLine
protected boolean checkNboLine() throws Exception
- Returns:
- true if need to read line
- Throws:
Exception
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readMolecularOrbitals
protected void readMolecularOrbitals(int headerType) throws Exception
- Throws:
Exception
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addCoef
public void addCoef(Map<String,Object> mo, float[] coefs, String type, float energy, float occ, int moCount)
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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
protected void addMOData(int nColumns, javajs.util.Lst<String>[] data, Map<String,Object>[] mos)
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setMOData
public void setMOData(boolean clearOrbitals)
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