Package org.biojava.nbio.structure

Interface StructureIdentifier

All Known Implementing Classes:
BioAssemblyIdentifier, CathDomain, EcodDomain, PassthroughIdentifier, PDPDomain, ScopDomain, StructureName, SubstructureIdentifier, URLIdentifier
public interface StructureIdentifier
An identifier that uniquely identifies a whole Structure or arbitrary substructure. Common examples would be reducing a structure to a single chain, domain, or residue range. StructureIdentifiers are represented by unique strings. The getId() and fromId() methods convert to and from the string representation. Implementations should provide a constructor which takes a String. A static fromId(String) method is also recommended.
Author:
dmyersturnbull, Spencer Bliven

  • Method Details

    • getIdentifier

      String getIdentifier()
      Get the String form of this identifier. It is recommended that the #toString() method also return the identifier, for consistency during serialization.
      Returns:
      The String form of this identifier

    • loadStructure

      Structure loadStructure(AtomCache cache) throws StructureException, IOException
      Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to reduce(Structure). It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.
      Parameters:
      AtomCache - A potential sources of structures
      Returns:
      A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
      Throws:
      StructureException - For errors loading and parsing the structure
      IOException - Errors reading the structure from disk

    • toCanonical

      SubstructureIdentifier toCanonical() throws StructureException
      Convert to a canonical SubstructureIdentifier.

      This allows all domains to be converted to a standard format String.

      Returns:
      A SubstructureIdentifier equivalent to this
      Throws:
      StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.

    • reduce

      Structure reduce(Structure input) throws StructureException
      Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

      The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

      Parameters:
      input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
      Returns:
      Throws:
      StructureException
      See Also: