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 Summary

Methods

Modifier and Type	Method and Description
String	getIdentifier() Get the String form of this identifier.
Structure	loadStructure(AtomCache cache) Loads a structure encompassing the structure identified.
Structure	reduce(Structure input) Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
SubstructureIdentifier	toCanonical() Convert to a canonical SubstructureIdentifier.

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.

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:

StructureTools.getReducedStructure(Structure, String)