- All Superinterfaces:
- All Known Implementing Classes:
public interface StructureIdentifier extends SerializableAn identifier that uniquely identifies a whole
Structureor 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.
- dmyersturnbull, Spencer Bliven
All Methods Instance Methods Abstract Methods Modifier and Type Method Description
getIdentifier()Get the String form of this identifier.
loadStructure(AtomCache cache)Loads a structure encompassing the structure identified.
reduce(Structure input)Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
toCanonical()Convert to a canonical SubstructureIdentifier.
getIdentifierGet 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
Structure loadStructure(AtomCache cache) throws StructureException, IOExceptionLoads 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.
toCanonicalConvert 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.
Structure reduce(Structure input) throws StructureExceptionTakes 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: