Package org.jmol.adapter.readers.quantum
Class CsfReader
- java.lang.Object
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class CsfReader extends MopacSlaterReader
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
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
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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 byte
ANUM
private static byte[]
atomFieldMap
private static java.lang.String[]
atomFields
private static byte
BFXN_ANGL
private static byte[]
bondFieldMap
private static java.lang.String[]
bondFields
private static byte
BTYPE
private static byte
CHRG
private static byte
COEF_INDICES
private static byte[]
connectorFieldMap
private static java.lang.String[]
connectorFields
private java.util.Map<java.lang.String,java.lang.String[]>
connectors
private static byte
CONTRACTIONS
private static byte
DIPOLE
private static byte
EIG_VAL
private static byte
EIG_VEC
private static byte
EIG_VEC_COMPRESSED
private int
fieldCount
private int[]
fieldTypes
private static byte
GTO_EXP
private java.util.Map<java.lang.String,Bond>
htBonds
private static byte
ID
private static byte
MO_OCC
private static byte[]
moFieldMap
private static java.lang.String[]
moFields
private int
nAtoms
private int
nGaussians
private static byte
NORMAL_MODE
private int
nSlaters
private int
nVibrations
private static byte
objCls1
private static byte
objCls2
private static byte
objID1
private static byte
objID2
private static byte
PCHRG
private java.util.Map<java.lang.String,java.lang.Integer>
propertyItemCounts
private static byte
SHELL
private static byte
STO_EXP
private java.lang.String
strAtomicNumbers
private static byte
SYM
private static byte
VIB_ENERGY
private static byte[]
vibFieldMap
private static java.lang.String[]
vibFields
private static byte
XYZ
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Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
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Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
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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, 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 CsfReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
private void
fillCsfArray(java.lang.String property, java.lang.String[] tokens, int i0, java.lang.Object f, boolean isInteger)
private int
getPropertyCount(java.lang.String what)
private int
parseLineParameters(java.lang.String[] fields, byte[] fieldMap)
private void
processAtomObject()
private void
processBasisObject(java.lang.String sto_gto)
private void
processBondObject()
private void
processConnectorObject()
private void
processLocalTransform()
private void
processMolecularOrbitalObject()
private void
processVibrationObject()
private void
setBond(Bond bond, java.lang.String[] connect)
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Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
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Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
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Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, initializeReader, readMolecularOrbitals
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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, 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 Detail
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nAtoms
private int nAtoms
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strAtomicNumbers
private java.lang.String strAtomicNumbers
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fieldCount
private int fieldCount
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nVibrations
private int nVibrations
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nGaussians
private int nGaussians
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nSlaters
private int nSlaters
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htBonds
private java.util.Map<java.lang.String,Bond> htBonds
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propertyItemCounts
private java.util.Map<java.lang.String,java.lang.Integer> propertyItemCounts
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fieldTypes
private final int[] fieldTypes
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objCls1
private static final byte objCls1
- See Also:
- Constant Field Values
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objID1
private static final byte objID1
- See Also:
- Constant Field Values
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objCls2
private static final byte objCls2
- See Also:
- Constant Field Values
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objID2
private static final byte objID2
- See Also:
- Constant Field Values
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connectorFields
private static final java.lang.String[] connectorFields
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connectorFieldMap
private static final byte[] connectorFieldMap
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connectors
private java.util.Map<java.lang.String,java.lang.String[]> connectors
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ID
private static final byte ID
- See Also:
- Constant Field Values
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SYM
private static final byte SYM
- See Also:
- Constant Field Values
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ANUM
private static final byte ANUM
- See Also:
- Constant Field Values
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CHRG
private static final byte CHRG
- See Also:
- Constant Field Values
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XYZ
private static final byte XYZ
- See Also:
- Constant Field Values
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PCHRG
private static final byte PCHRG
- See Also:
- Constant Field Values
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atomFields
private static final java.lang.String[] atomFields
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atomFieldMap
private static final byte[] atomFieldMap
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BTYPE
private static final byte BTYPE
- See Also:
- Constant Field Values
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bondFields
private static final java.lang.String[] bondFields
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bondFieldMap
private static final byte[] bondFieldMap
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NORMAL_MODE
private static final byte NORMAL_MODE
- See Also:
- Constant Field Values
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VIB_ENERGY
private static final byte VIB_ENERGY
- See Also:
- Constant Field Values
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DIPOLE
private static final byte DIPOLE
- See Also:
- Constant Field Values
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vibFields
private static final java.lang.String[] vibFields
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vibFieldMap
private static final byte[] vibFieldMap
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EIG_VAL
private static final byte EIG_VAL
- See Also:
- Constant Field Values
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MO_OCC
private static final byte MO_OCC
- See Also:
- Constant Field Values
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EIG_VEC
private static final byte EIG_VEC
- See Also:
- Constant Field Values
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EIG_VEC_COMPRESSED
private static final byte EIG_VEC_COMPRESSED
- See Also:
- Constant Field Values
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COEF_INDICES
private static final byte COEF_INDICES
- See Also:
- Constant Field Values
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BFXN_ANGL
private static final byte BFXN_ANGL
- See Also:
- Constant Field Values
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STO_EXP
private static final byte STO_EXP
- See Also:
- Constant Field Values
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CONTRACTIONS
private static final byte CONTRACTIONS
- See Also:
- Constant Field Values
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GTO_EXP
private static final byte GTO_EXP
- See Also:
- Constant Field Values
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SHELL
private static final byte SHELL
- See Also:
- Constant Field Values
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moFields
private static final java.lang.String[] moFields
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moFieldMap
private static final byte[] moFieldMap
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Method Detail
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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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processLocalTransform
private void processLocalTransform() throws java.lang.Exception
- Throws:
java.lang.Exception
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getPropertyCount
private int getPropertyCount(java.lang.String what)
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parseLineParameters
private int parseLineParameters(java.lang.String[] fields, byte[] fieldMap) throws java.lang.Exception
- Throws:
java.lang.Exception
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fillCsfArray
private void fillCsfArray(java.lang.String property, java.lang.String[] tokens, int i0, java.lang.Object f, boolean isInteger) throws java.lang.Exception
- Throws:
java.lang.Exception
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processConnectorObject
private void processConnectorObject() throws java.lang.Exception
- Throws:
java.lang.Exception
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setBond
private void setBond(Bond bond, java.lang.String[] connect)
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processAtomObject
private void processAtomObject() throws java.lang.Exception
- Throws:
java.lang.Exception
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processBondObject
private void processBondObject() throws java.lang.Exception
- Throws:
java.lang.Exception
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processVibrationObject
private void processVibrationObject() throws java.lang.Exception
- Throws:
java.lang.Exception
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processMolecularOrbitalObject
private void processMolecularOrbitalObject() throws java.lang.Exception
- Throws:
java.lang.Exception
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processBasisObject
private void processBasisObject(java.lang.String sto_gto) throws java.lang.Exception
- Throws:
java.lang.Exception
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