org.jmol.adapter.readers.more
Class ShelxReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.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
In addition atoms are read.
A reader for SHELX files. It currently supports SHELXL.
The SHELXL 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.
symmetry added by Bob Hanson:
setFractionalCoordinates()
setSpaceGroupName()
setSymmetryOperator()
setUnitCellItem()
setAtomCoord()
applySymmetryAndSetTrajectory()
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
sfacElementSymbols
java.lang.String[] sfacElementSymbols
isCmdf
boolean isCmdf
iHaveAtomSet
boolean iHaveAtomSet
supportedRecordTypes
static final java.lang.String[] supportedRecordTypes
unsupportedRecordTypes
static final java.lang.String[] unsupportedRecordTypes
ShelxReader
public ShelxReader()
readAtomSetCollection
public void readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
processSupportedRecord
void processSupportedRecord(int recordIndex)
throws java.lang.Exception
- Throws:
java.lang.Exception
parseLattRecord
void parseLattRecord()
throws java.lang.Exception
- Throws:
java.lang.Exception
parseSymmRecord
void parseSymmRecord()
throws java.lang.Exception
- Throws:
java.lang.Exception
cell
void cell()
throws java.lang.Exception
- Throws:
java.lang.Exception
parseSfacRecord
void parseSfacRecord()
parseSfacElementSymbols
void parseSfacElementSymbols(java.lang.String[] sfacTokens)
parseSfacCoefficients
void parseSfacCoefficients(java.lang.String[] sfacTokens)
assumeAtomRecord
void assumeAtomRecord()
throws java.lang.Exception
- Throws:
java.lang.Exception
processCmdfAtoms
void processCmdfAtoms()
throws java.lang.Exception
- Throws:
java.lang.Exception
getSymbol
java.lang.String getSymbol(java.lang.String sym)