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
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/

  • Field Details

    • sfacElementSymbols

      private String[] sfacElementSymbols

    • isCmdf

      private boolean isCmdf

    • tokens

      String[] tokens

    • unsupportedRecordTypes

      private static final String unsupportedRecordTypes
      See Also:

    • supportedRecordTypes

      private static final String[] supportedRecordTypes

  • Constructor Details

    • ShelxReader

      public ShelxReader()

  • Method Details

    • initializeReader

      public void initializeReader()
      Overrides:
      initializeReader in class AtomSetCollectionReader

    • checkLine

      protected boolean checkLine() throws Exception
      Overrides:
      checkLine in class AtomSetCollectionReader
      Returns:
      true if need to read new line
      Throws:
      Exception

    • processSupportedRecord

      private void processSupportedRecord(int recordIndex) throws Exception
      Throws:
      Exception

    • parseLattRecord

      private void parseLattRecord() throws Exception
      Throws:
      Exception

    • parseSymmRecord

      private void parseSymmRecord() throws Exception
      Throws:
      Exception

    • cell

      private void cell() throws Exception
      Throws:
      Exception

    • parseSfacRecord

      private void parseSfacRecord()

    • parseSfacElementSymbols

      private void parseSfacElementSymbols(String[] sfacTokens)

    • parseSfacCoefficients

      private void parseSfacCoefficients(String[] sfacTokens)

    • assumeAtomRecord

      private void assumeAtomRecord() throws Exception
      Throws:
      Exception

    • processCmdfAtoms

      private void processCmdfAtoms() throws Exception
      Throws:
      Exception

    • getSymbol

      private String getSymbol(String sym)

    • isValidElementSymbolNoCaseSecondChar

      public static boolean isValidElementSymbolNoCaseSecondChar(String str)