public class ShelxReader extends AtomSetCollectionReader
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/
Modifier and Type | Field and Description |
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private boolean |
isCmdf |
private String[] |
sfacElementSymbols |
private static String[] |
supportedRecordTypes |
(package private) String[] |
tokens |
private static String |
unsupportedRecordTypes |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, 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, viewer
Constructor and Description |
---|
ShelxReader() |
Modifier and Type | Method and Description |
---|---|
private void |
assumeAtomRecord() |
private void |
cell() |
protected boolean |
checkLine() |
private String |
getSymbol(String sym) |
void |
initializeReader() |
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) |
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, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
private String[] sfacElementSymbols
private boolean isCmdf
String[] tokens
private static final String unsupportedRecordTypes
private static final String[] supportedRecordTypes
public void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private void processSupportedRecord(int recordIndex) throws Exception
Exception
private void parseSfacRecord()
private void parseSfacElementSymbols(String[] sfacTokens)
private void parseSfacCoefficients(String[] sfacTokens)