Package org.jmol.adapter.readers.quantum
Class CsfReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
CSF file reader based on CIF idea -- fluid property fields.
note that, like CIF, the order of fields is totally unpredictable
in addition, ID numbers are not sequential, requiring atomNames
first crack at this 2006/04/13
added DGAUSS, MOPAC, EHT orbital/basis reading 2007/04/09
streamlined CSF dataset reading capabilities 2007/04/09
- Author:
- hansonr <hansonr@stolaf.edu>
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final byte
private static final byte[]
private static final String[]
private static final byte
private static final byte[]
private static final String[]
private static final byte
private static final byte
private static final byte
private static final byte[]
private static final String[]
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private int
private final int[]
private static final byte
private static final byte
private static final byte
private static final byte[]
private static final String[]
private int
private int
private static final byte
private int
private int
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private String
private static final byte
private static final byte
private static final byte[]
private static final String[]
private static final byte
Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
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
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, 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
private void
fillCsfArray
(String property, String[] tokens, int i0, Object f, boolean isInteger) private int
getPropertyCount
(String what) private int
parseLineParameters
(String[] fields, byte[] fieldMap) private void
private void
processBasisObject
(String sto_gto) private void
private void
private void
private void
private void
private void
Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals
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, 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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nAtoms
private int nAtoms -
strAtomicNumbers
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fieldCount
private int fieldCount -
nVibrations
private int nVibrations -
nGaussians
private int nGaussians -
nSlaters
private int nSlaters -
htBonds
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propertyItemCounts
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fieldTypes
private final int[] fieldTypes -
objCls1
private static final byte objCls1- See Also:
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objID1
private static final byte objID1- See Also:
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objCls2
private static final byte objCls2- See Also:
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objID2
private static final byte objID2- See Also:
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connectorFields
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connectorFieldMap
private static final byte[] connectorFieldMap -
connectors
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ID
private static final byte ID- See Also:
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SYM
private static final byte SYM- See Also:
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ANUM
private static final byte ANUM- See Also:
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CHRG
private static final byte CHRG- See Also:
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XYZ
private static final byte XYZ- See Also:
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PCHRG
private static final byte PCHRG- See Also:
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atomFields
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atomFieldMap
private static final byte[] atomFieldMap -
BTYPE
private static final byte BTYPE- See Also:
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bondFields
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bondFieldMap
private static final byte[] bondFieldMap -
NORMAL_MODE
private static final byte NORMAL_MODE- See Also:
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VIB_ENERGY
private static final byte VIB_ENERGY- See Also:
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DIPOLE
private static final byte DIPOLE- See Also:
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vibFields
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vibFieldMap
private static final byte[] vibFieldMap -
EIG_VAL
private static final byte EIG_VAL- See Also:
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MO_OCC
private static final byte MO_OCC- See Also:
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EIG_VEC
private static final byte EIG_VEC- See Also:
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EIG_VEC_COMPRESSED
private static final byte EIG_VEC_COMPRESSED- See Also:
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COEF_INDICES
private static final byte COEF_INDICES- See Also:
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BFXN_ANGL
private static final byte BFXN_ANGL- See Also:
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STO_EXP
private static final byte STO_EXP- See Also:
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CONTRACTIONS
private static final byte CONTRACTIONS- See Also:
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GTO_EXP
private static final byte GTO_EXP- See Also:
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SHELL
private static final byte SHELL- See Also:
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moFields
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moFieldMap
private static final byte[] moFieldMap
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Constructor Details
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CsfReader
public CsfReader()
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Method Details
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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processLocalTransform
- Throws:
Exception
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getPropertyCount
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parseLineParameters
- Throws:
Exception
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fillCsfArray
private void fillCsfArray(String property, String[] tokens, int i0, Object f, boolean isInteger) throws Exception - Throws:
Exception
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processConnectorObject
- Throws:
Exception
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setBond
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processAtomObject
- Throws:
Exception
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processBondObject
- Throws:
Exception
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processVibrationObject
- Throws:
Exception
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processMolecularOrbitalObject
- Throws:
Exception
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processBasisObject
- Throws:
Exception
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