Package org.jmol.adapter.readers.xtal

Class ShelxReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.ShelxReader

All Implemented Interfaces:

javajs.api.GenericLineReader

public class ShelxReader
extends AtomSetCollectionReader

A reader for SHELX output (RES) files. It does not read all information. The list of fields that is read: TITL, REM, END, CELL, SPGR, SFAC Atom positions and thermal ellipsoids are read.

A reader for SHELX files. It currently supports SHELXL.

The SHELX format is described on the net: http://www.msg.ucsf.edu/local/programs/shelxl/ch_07.html. modified by Bob Hanson 2006/04 to allow variant CrystalMaker .cmdf file reading -- but by 2/2010 looks like these ASCII CrystalMaker files aren't used anymore by CrystalMaker, and instead it uses a binary format. CrystalMaker2.2.3 seems to attempt to read the files, but actually cannot. At least not for the file given at http://www.ch.ic.ac.uk/chemime/

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	isCmdf
private String[]	sfacElementSymbols
private static String[]	supportedRecordTypes
(package private) String[]	tokens
private static String	unsupportedRecordTypes

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
ShelxReader()

Method Summary

Modifier and Type	Method	Description
private void	assumeAtomRecord()
private void	cell()
protected boolean	checkLine()
private String	getSymbol(String sym)
void	initializeReader()
static boolean	isValidElementSymbolNoCaseSecondChar(String str)
private void	parseLattRecord()
private void	parseSfacCoefficients(String[] sfacTokens)
private void	parseSfacElementSymbols(String[] sfacTokens)
private void	parseSfacRecord()
private void	parseSymmRecord()
private void	processCmdfAtoms()
private void	processSupportedRecord(int recordIndex)

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, discardPreviousAtoms, 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, 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

sfacElementSymbols

private String[] sfacElementSymbols

isCmdf

private boolean isCmdf

tokens

String[] tokens

unsupportedRecordTypes

private static final String unsupportedRecordTypes

See Also:

Constant Field Values

supportedRecordTypes

private static final String[] supportedRecordTypes

Constructor Detail

ShelxReader

public ShelxReader()

Method Detail

initializeReader

public void initializeReader()

Overrides:

initializeReader in class AtomSetCollectionReader

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

processSupportedRecord

private void processSupportedRecord(int recordIndex)
                             throws Exception

Throws:

Exception

parseLattRecord

private void parseLattRecord()
                      throws Exception

Throws:

Exception

parseSymmRecord

private void parseSymmRecord()
                      throws Exception

Throws:

Exception

cell

private void cell()
           throws Exception

Throws:

Exception

parseSfacRecord

private void parseSfacRecord()

parseSfacElementSymbols

private void parseSfacElementSymbols(String[] sfacTokens)

parseSfacCoefficients

private void parseSfacCoefficients(String[] sfacTokens)

assumeAtomRecord

private void assumeAtomRecord()
                       throws Exception

Throws:

Exception

processCmdfAtoms

private void processCmdfAtoms()
                       throws Exception

Throws:

Exception

getSymbol

private String getSymbol(String sym)

isValidElementSymbolNoCaseSecondChar

public static boolean isValidElementSymbolNoCaseSecondChar(String str)