Package org.biojava.nbio.structure.io

Class PDBFileReader

  • All Implemented Interfaces:
    StructureIOFile, StructureProvider
    public class PDBFileReader
extends LocalPDBDirectory

    The wrapper class for parsing a PDB file.

    Several flags can be set for this class

    Example

    Q: How can I get a Structure object from a PDB file?

    A: 

     public Structure loadStructure(String pathToPDBFile){
        PDBFileReader pdbreader = new PDBFileReader();

        Structure structure = null;
        try{
                structure = pdbreader.getStructure(pathToPDBFile);
                System.out.println(structure);
        } catch (IOException e) {
                e.printStackTrace();
        }
        return structure;
 }
    Access PDB files from a directory, take care of compressed PDB files 
     public Structure loadStructureById() {
        String path = "/path/to/PDB/directory/";

        PDBFileReader pdbreader = new PDBFileReader();
        pdbreader.setPath(path);
        Structure structure = null;
        try {
                structure = pdbreader.getStructureById("5pti");
        } catch (IOException e){
                e.printStackTrace();
        }
        return structure;

 }
    Author:
    Andreas Prlic

    • Field Detail

      • PDB_SPLIT_DIR

        public static final String[] PDB_SPLIT_DIR

      • PDB_OBSOLETE_DIR

        public static final String[] PDB_OBSOLETE_DIR

    • Constructor Detail

      • PDBFileReader

        public PDBFileReader()
        Constructs a new PDBFileReader, 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

      • PDBFileReader

        public PDBFileReader​(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.

        If path is null, initialize using the system property/environment variable UserConfiguration.PDB_DIR.

        Parameters:
        path - Path to the PDB file directory

    • 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