org.jmol.adapter.readers.more
Class ShelxReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by 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() applySymmetry()


Field Summary
(package private)  boolean iHaveAtomSet
           
(package private)  boolean isCmdf
           
(package private)  java.lang.String[] sfacElementSymbols
           
(package private) static java.lang.String[] supportedRecordTypes
           
(package private) static java.lang.String[] unsupportedRecordTypes
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup
 
Constructor Summary
ShelxReader()
           
 
Method Summary
(package private)  void assumeAtomRecord()
           
(package private)  void cell()
           
(package private)  java.lang.String getSymbol(java.lang.String sym)
           
(package private)  void parseLattRecord()
           
(package private)  void parseSfacCoefficients(java.lang.String[] sfacTokens)
           
(package private)  void parseSfacElementSymbols(java.lang.String[] sfacTokens)
           
(package private)  void parseSfacRecord()
           
(package private)  void parseSymmRecord()
           
(package private)  void processCmdfAtoms()
           
(package private)  void processSupportedRecord(int recordIndex)
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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
Constructor Detail

ShelxReader

public ShelxReader()
Method Detail

readAtomSetCollection

public AtomSetCollection 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)