Interface StructureIdentifier

    • Method Detail

      • 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.
        The String form of this identifier
      • loadStructure

        Structure loadStructure​(AtomCache cache)
                         throws StructureException,
        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.
        AtomCache - A potential sources of structures
        A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
        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.

        A SubstructureIdentifier equivalent to this
        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.

        input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
        See Also:
        StructureTools#getReducedStructure(Structure, String)