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
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/
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate boolean
private String[]
private static final String[]
(package private) String[]
private static final String
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, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
private void
cell()
protected boolean
private String
void
static boolean
private void
private void
parseSfacCoefficients
(String[] sfacTokens) private void
parseSfacElementSymbols
(String[] sfacTokens) private void
private void
private void
private void
processSupportedRecord
(int recordIndex) 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, discardPreviousAtoms, 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
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Field Details
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sfacElementSymbols
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isCmdf
private boolean isCmdf -
tokens
String[] tokens -
unsupportedRecordTypes
- See Also:
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supportedRecordTypes
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Constructor Details
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ShelxReader
public ShelxReader()
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Method Details
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initializeReader
public void initializeReader()- Overrides:
initializeReader
in classAtomSetCollectionReader
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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processSupportedRecord
- Throws:
Exception
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parseLattRecord
- Throws:
Exception
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parseSymmRecord
- Throws:
Exception
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cell
- Throws:
Exception
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parseSfacRecord
private void parseSfacRecord() -
parseSfacElementSymbols
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parseSfacCoefficients
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assumeAtomRecord
- Throws:
Exception
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processCmdfAtoms
- Throws:
Exception
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getSymbol
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isValidElementSymbolNoCaseSecondChar
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