Package 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

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 byte	ANUM
private static byte[]	atomFieldMap
private static String[]	atomFields
private static byte	BFXN_ANGL
private static byte[]	bondFieldMap
private static String[]	bondFields
private static byte	BTYPE
private static byte	CHRG
private static byte	COEF_INDICES
private static byte[]	connectorFieldMap
private static String[]	connectorFields
private Map<String,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 Map<String,Bond>	htBonds
private static byte	ID
private static byte	MO_OCC
private static byte[]	moFieldMap
private static 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 Map<String,Integer>	propertyItemCounts
private static byte	SHELL
private static byte	STO_EXP
private String	strAtomicNumbers
private static byte	SYM
private static byte	VIB_ENERGY
private static byte[]	vibFieldMap
private static String[]	vibFields
private static byte	XYZ

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, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells

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

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, 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

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, 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, 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, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, 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 Detail

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 Detail

CsfReader

public CsfReader()

Method Detail

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