Class BcifFileReader

java.lang.Object
org.biojava.nbio.structure.io.LocalPDBDirectory
org.biojava.nbio.structure.io.BcifFileReader
All Implemented Interfaces:
StructureIOFile, StructureProvider

public class BcifFileReader extends LocalPDBDirectory
Parse binary Cif files and provide capabilities to store them locally.
Since:
5.3.0
Author:
Sebastian Bittrich
  • Field Details

    • CIF_SPLIT_DIR

      public static final String[] CIF_SPLIT_DIR
    • CIF_OBSOLETE_DIR

      public static final String[] CIF_OBSOLETE_DIR
  • Constructor Details

    • BcifFileReader

      public BcifFileReader()
      Constructs a new BcifFileReader, 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
    • BcifFileReader

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

    • 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
      Parameters:
      inStream -
      Returns:
      Throws:
      IOException
    • 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
      Parameters:
      pdbId -
      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