Package org.biojava.nbio.structure.io

Class 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 Detail

      • MMCIF_SPLIT_DIR

        public static final String[] MMCIF_SPLIT_DIR

      • MMCIF_OBSOLETE_DIR

        public static final String[] MMCIF_OBSOLETE_DIR

    • Constructor Detail

      • 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 Detail

      • 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