org.jmol.adapter.readers.quantum

Class CsfReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.SlaterReader

org.jmol.adapter.readers.quantum.MopacSlaterReader

org.jmol.adapter.readers.quantum.CsfReader

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

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 and Description
private static byte	anum
private static byte[]	atomFieldMap
private static java.lang.String[]	atomFields
private static byte	bfxn_ang
private static byte[]	bondFieldMap
private static java.lang.String[]	bondFields
private static byte	bondType
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,int[]>	connectors
private static byte	contractions
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	nBonds
private int	nGaussians
private static byte	normalMode
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	transitionDipole
private static byte	vibEnergy
private static byte[]	vibFieldMap
private static java.lang.String[]	vibFields
private static byte	xyz_coordinates

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

atomicNumbers, MIN_COEF

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

slaterArray, slaters

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

alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells

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

addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr

Constructor Summary

Constructors

Constructor and Description
CsfReader()

Method Summary

Modifier and Type	Method and 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, int[] connect)

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

createSphericalSlaterByType, scaleSlater

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

addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

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

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO

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

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nAtoms

private int nAtoms

strAtomicNumbers

private java.lang.String strAtomicNumbers

fieldCount

private int fieldCount

nVibrations

private int nVibrations

nGaussians

private int nGaussians

nSlaters

private int nSlaters

htBonds

private java.util.Map<java.lang.String,Bond> htBonds

propertyItemCounts

private java.util.Map<java.lang.String,java.lang.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 java.lang.String[] connectorFields

connectorFieldMap

private static final byte[] connectorFieldMap

connectors

private java.util.Map<java.lang.String,int[]> 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_coordinates

private static final byte xyz_coordinates

See Also:

Constant Field Values

pchrg

private static final byte pchrg

See Also:

Constant Field Values

atomFields

private static final java.lang.String[] atomFields

atomFieldMap

private static final byte[] atomFieldMap

bondType

private static final byte bondType

See Also:

Constant Field Values

bondFields

private static final java.lang.String[] bondFields

bondFieldMap

private static final byte[] bondFieldMap

nBonds

private int nBonds

normalMode

private static final byte normalMode

See Also:

Constant Field Values

vibEnergy

private static final byte vibEnergy

See Also:

Constant Field Values

transitionDipole

private static final byte transitionDipole

See Also:

Constant Field Values

vibFields

private static final java.lang.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_ang

private static final byte bfxn_ang

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 java.lang.String[] moFields

moFieldMap

private static final byte[] moFieldMap

Constructor Detail

CsfReader

public CsfReader()

Method Detail

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

processLocalTransform

private void processLocalTransform()
                            throws java.lang.Exception

Throws:

java.lang.Exception

getPropertyCount

private int getPropertyCount(java.lang.String what)

parseLineParameters

private int parseLineParameters(java.lang.String[] fields,
                                byte[] fieldMap)
                         throws java.lang.Exception

Throws:

java.lang.Exception

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

processConnectorObject

private void processConnectorObject()
                             throws java.lang.Exception

Throws:

java.lang.Exception

setBond

private void setBond(Bond bond,
                     int[] connect)

processAtomObject

private void processAtomObject()
                        throws java.lang.Exception

Throws:

java.lang.Exception

processBondObject

private void processBondObject()
                        throws java.lang.Exception

Throws:

java.lang.Exception

processVibrationObject

private void processVibrationObject()
                             throws java.lang.Exception

Throws:

java.lang.Exception

processMolecularOrbitalObject

private void processMolecularOrbitalObject()
                                    throws java.lang.Exception

Throws:

java.lang.Exception

processBasisObject

private void processBasisObject(java.lang.String sto_gto)
                         throws java.lang.Exception

Throws:

java.lang.Exception