org.jmol.adapter.readers.quantum.CsfReader

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 <hansonr@stolaf.edu>

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
Field Summary

Fields

Modifier and Type

Field

Description

private static final byte

ANUM

private static final byte[]

atomFieldMap

private static final String[]

atomFields

private static final byte

BFXN_ANGL

private static final byte[]

bondFieldMap

private static final String[]

bondFields

private static final byte

BTYPE

private static final byte

CHRG

private static final byte

COEF_INDICES

private static final byte[]

connectorFieldMap

private static final String[]

connectorFields

private Map<String,String[]>

connectors

private static final byte

CONTRACTIONS

private static final byte

DIPOLE

private static final byte

EIG_VAL

private static final byte

EIG_VEC

private static final byte

EIG_VEC_COMPRESSED

private int

fieldCount

private final int[]

fieldTypes

private static final byte

GTO_EXP

private Map<String,Bond>

htBonds

private static final byte

ID

private static final byte

MO_OCC

private static final byte[]

moFieldMap

private static final String[]

moFields

private int

nAtoms

private int

nGaussians

private static final byte

NORMAL_MODE

private int

nSlaters

private int

nVibrations

private static final byte

objCls1

private static final byte

objCls2

private static final byte

objID1

private static final byte

objID2

private static final byte

PCHRG

private Map<String,Integer>

propertyItemCounts

private static final byte

SHELL

private static final byte

STO_EXP

private String

strAtomicNumbers

private static final byte

SYM

private static final byte

VIB_ENERGY

private static final byte[]

vibFieldMap

private static final String[]

vibFields

private static final byte

XYZ

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, 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
Constructor Summary

Constructors

Constructor

Description

CsfReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

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

processAtomObject()

private void

processBasisObject(String sto_gto)

private void

processBondObject()

private void

processConnectorObject()

private void

processLocalTransform()

private void

processMolecularOrbitalObject()

private void

processVibrationObject()

private void

setBond(Bond bond, String[] connect)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- nAtoms
  
  private int nAtoms
- strAtomicNumbers
  
  private String strAtomicNumbers
- fieldCount
  
  private int fieldCount
- nVibrations
  
  private int nVibrations
- nGaussians
  
  private int nGaussians
- nSlaters
  
  private int nSlaters
- htBonds
  
  private Map<String,Bond> htBonds
- propertyItemCounts
  
  private Map<String,Integer> propertyItemCounts
- fieldTypes
  
  private final int[] fieldTypes
- objCls1
  
  private static final byte objCls1
  See Also:
  
  Constant Field Values
- objID1
  
  private static final byte objID1
  See Also:
  
  Constant Field Values
- objCls2
  
  private static final byte objCls2
  See Also:
  
  Constant Field Values
- objID2
  
  private static final byte objID2
  See Also:
  
  Constant Field Values
- connectorFields
  
  private static final String[] connectorFields
- connectorFieldMap
  
  private static final byte[] connectorFieldMap
- connectors
  
  private Map<String,String[]> connectors
- ID
  
  private static final byte ID
  See Also:
  
  Constant Field Values
- SYM
  
  private static final byte SYM
  See Also:
  
  Constant Field Values
- ANUM
  
  private static final byte ANUM
  See Also:
  
  Constant Field Values
- CHRG
  
  private static final byte CHRG
  See Also:
  
  Constant Field Values
- XYZ
  
  private static final byte XYZ
  See Also:
  
  Constant Field Values
- PCHRG
  
  private static final byte PCHRG
  See Also:
  
  Constant Field Values
- atomFields
  
  private static final String[] atomFields
- atomFieldMap
  
  private static final byte[] atomFieldMap
- BTYPE
  
  private static final byte BTYPE
  See Also:
  
  Constant Field Values
- bondFields
  
  private static final String[] bondFields
- bondFieldMap
  
  private static final byte[] bondFieldMap
- NORMAL_MODE
  
  private static final byte NORMAL_MODE
  See Also:
  
  Constant Field Values
- VIB_ENERGY
  
  private static final byte VIB_ENERGY
  See Also:
  
  Constant Field Values
- DIPOLE
  
  private static final byte DIPOLE
  See Also:
  
  Constant Field Values
- vibFields
  
  private static final String[] vibFields
- vibFieldMap
  
  private static final byte[] vibFieldMap
- EIG_VAL
  
  private static final byte EIG_VAL
  See Also:
  
  Constant Field Values
- MO_OCC
  
  private static final byte MO_OCC
  See Also:
  
  Constant Field Values
- EIG_VEC
  
  private static final byte EIG_VEC
  See Also:
  
  Constant Field Values
- EIG_VEC_COMPRESSED
  
  private static final byte EIG_VEC_COMPRESSED
  See Also:
  
  Constant Field Values
- COEF_INDICES
  
  private static final byte COEF_INDICES
  See Also:
  
  Constant Field Values
- BFXN_ANGL
  
  private static final byte BFXN_ANGL
  See Also:
  
  Constant Field Values
- STO_EXP
  
  private static final byte STO_EXP
  See Also:
  
  Constant Field Values
- CONTRACTIONS
  
  private static final byte CONTRACTIONS
  See Also:
  
  Constant Field Values
- GTO_EXP
  
  private static final byte GTO_EXP
  See Also:
  
  Constant Field Values
- SHELL
  
  private static final byte SHELL
  See Also:
  
  Constant Field Values
- moFields
  
  private static final String[] moFields
- moFieldMap
  
  private static final byte[] moFieldMap
Constructor Details
- CsfReader
  
  public CsfReader()
Method Details
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- processLocalTransform
  
  private void processLocalTransform() throws Exception
  
  Throws:
  
  Exception
- getPropertyCount
  
  private int getPropertyCount(String what)
- parseLineParameters
  
  private int parseLineParameters(String[] fields, byte[] fieldMap) throws Exception
  
  Throws:
  
  Exception
- fillCsfArray
  
  private void fillCsfArray(String property, String[] tokens, int i0, Object f, boolean isInteger) throws Exception
  
  Throws:
  
  Exception
- processConnectorObject
  
  private void processConnectorObject() throws Exception
  
  Throws:
  
  Exception
- setBond
  
  private void setBond(Bond bond, String[] connect)
- processAtomObject
  
  private void processAtomObject() throws Exception
  
  Throws:
  
  Exception
- processBondObject
  
  private void processBondObject() throws Exception
  
  Throws:
  
  Exception
- processVibrationObject
  
  private void processVibrationObject() throws Exception
  
  Throws:
  
  Exception
- processMolecularOrbitalObject
  
  private void processMolecularOrbitalObject() throws Exception
  
  Throws:
  
  Exception
- processBasisObject
  
  private void processBasisObject(String sto_gto) throws Exception
  
  Throws:
  
  Exception

Class CsfReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader

Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader

Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

nAtoms

strAtomicNumbers

fieldCount

nVibrations

nGaussians

nSlaters

htBonds

propertyItemCounts

fieldTypes

objCls1

objID1

objCls2

objID2

connectorFields

connectorFieldMap

connectors

ID

SYM

ANUM

CHRG

XYZ

PCHRG

atomFields

atomFieldMap

BTYPE

bondFields

bondFieldMap

NORMAL_MODE

VIB_ENERGY

DIPOLE

vibFields

vibFieldMap

EIG_VAL

MO_OCC

EIG_VEC

EIG_VEC_COMPRESSED

COEF_INDICES

BFXN_ANGL

STO_EXP

CONTRACTIONS

GTO_EXP

SHELL

moFields

moFieldMap

Constructor Details

CsfReader

Method Details

checkLine

processLocalTransform

getPropertyCount

parseLineParameters

fillCsfArray

processConnectorObject

setBond

processAtomObject

processBondObject

processVibrationObject

processMolecularOrbitalObject

processBasisObject