Class BioAssemblyIdentifier

Method Details

• getIdentifier

  public String getIdentifier()

  Description copied from interface: StructureIdentifier

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

  Specified by:

  getIdentifier in interface StructureIdentifier

  Returns:

  The String form of this identifier

• toString

  public String toString()

  Overrides:

  toString in class Object

• loadStructure

  public Structure loadStructure(AtomCache cache) throws StructureException, IOException

  Description copied from interface: StructureIdentifier

  Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.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.

  Specified by:

  loadStructure in interface StructureIdentifier

  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

  public SubstructureIdentifier toCanonical() throws StructureException

  Description copied from interface: StructureIdentifier

  Convert to a canonical SubstructureIdentifier.

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

  Specified by:

  toCanonical in interface StructureIdentifier

  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

  public Structure reduce(Structure input) throws StructureException

  Description copied from interface: StructureIdentifier

  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.

  Specified by:

  reduce in interface StructureIdentifier

  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)