Package org.biojava.nbio.structure.io

Class MMCIFFileReader

java.lang.Object
org.biojava.nbio.structure.io.LocalPDBDirectory
org.biojava.nbio.structure.io.MMCIFFileReader
All Implemented Interfaces:
StructureIOFile, StructureProvider
public class MMCIFFileReader extends LocalPDBDirectory
How to parse an mmCif file: 
public static void main(String[] args) throws Exception {
        String filename =  "/path/to/something.cif.gz" ;

        StructureIOFile reader = new MMCIFFileReader();

        Structure struc = reader.getStructure(filename);
        System.out.println(struc);
}
Since:
1.7
Author:
Andreas Prlic

  • Field Details

    • MMCIF_SPLIT_DIR

      public static final String[] MMCIF_SPLIT_DIR

    • MMCIF_OBSOLETE_DIR

      public static final String[] MMCIF_OBSOLETE_DIR

  • Constructor Details

    • MMCIFFileReader

      public MMCIFFileReader()
      Constructs a new MMCIFFileReader, initializing the extensions member variable. The path is initialized in the same way as UserConfiguration, i.e. to system property/environment variable UserConfiguration.PDB_DIR. Both autoFetch and splitDir are initialized to false

    • MMCIFFileReader

      public MMCIFFileReader(String path)
      Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized to the given path, both autoFetch and splitDir are initialized to false.

  • Method Details

    • main

      public static void main(String[] args) throws Exception
      Throws:
      Exception

    • getStructure

      public Structure getStructure(InputStream inStream) throws IOException
      Description copied from class: LocalPDBDirectory
      Handles the actual parsing of the file into a Structure object.
      Specified by:
      getStructure in class LocalPDBDirectory
      Returns:
      Throws:
      IOException

    • getMMcifConsumer

      public SimpleMMcifConsumer getMMcifConsumer()

    • getFilename

      protected String getFilename(String pdbId)
      Description copied from class: LocalPDBDirectory
      Converts a PDB ID into a filename with the proper extension
      Specified by:
      getFilename in class LocalPDBDirectory
      Returns:
      The filename, e.g. "4hhb.pdb.gz"

    • getSplitDirPath

      protected String[] getSplitDirPath()
      Description copied from class: LocalPDBDirectory
      Location of split files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.
      Specified by:
      getSplitDirPath in class LocalPDBDirectory
      Returns:
      A list of directories, relative to the /pub/pdb directory on the server

    • getObsoleteDirPath

      protected String[] getObsoleteDirPath()
      Description copied from class: LocalPDBDirectory
      Location of obsolete files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.
      Specified by:
      getObsoleteDirPath in class LocalPDBDirectory
      Returns:
      A list of directories, relative to the /pub/pdb directory on the server