org.jmol.adapter.readers.xtal
Class ShelxReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.ShelxReader
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/
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
sfacElementSymbols
private java.lang.String[] sfacElementSymbols
isCmdf
private boolean isCmdf
tokens
java.lang.String[] tokens
unsupportedRecordTypes
private static final java.lang.String unsupportedRecordTypes
- See Also:
- Constant Field Values
supportedRecordTypes
private static final java.lang.String[] supportedRecordTypes
ShelxReader
public ShelxReader()
initializeReader
public void initializeReader()
- Overrides:
initializeReader
in class AtomSetCollectionReader
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
processSupportedRecord
private void processSupportedRecord(int recordIndex)
throws java.lang.Exception
- Throws:
java.lang.Exception
parseLattRecord
private void parseLattRecord()
throws java.lang.Exception
- Throws:
java.lang.Exception
parseSymmRecord
private void parseSymmRecord()
throws java.lang.Exception
- Throws:
java.lang.Exception
cell
private void cell()
throws java.lang.Exception
- Throws:
java.lang.Exception
parseSfacRecord
private void parseSfacRecord()
parseSfacElementSymbols
private void parseSfacElementSymbols(java.lang.String[] sfacTokens)
parseSfacCoefficients
private void parseSfacCoefficients(java.lang.String[] sfacTokens)
assumeAtomRecord
private void assumeAtomRecord()
throws java.lang.Exception
- Throws:
java.lang.Exception
processCmdfAtoms
private void processCmdfAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
getSymbol
private java.lang.String getSymbol(java.lang.String sym)