Class BioAssemblyIdentifier

java.lang.Object
org.biojava.nbio.structure.BioAssemblyIdentifier
All Implemented Interfaces:
Serializable, StructureIdentifier

public class BioAssemblyIdentifier extends Object implements StructureIdentifier
See Also:
  • Field Details

    • BIO_NAME_PATTERN

      public static final Pattern BIO_NAME_PATTERN
  • Constructor Details

    • BioAssemblyIdentifier

      public BioAssemblyIdentifier(String name)
    • BioAssemblyIdentifier

      public BioAssemblyIdentifier(String pdbCode, int biolNr)
      Parameters:
      pdbCode -
      biolNr -
    • BioAssemblyIdentifier

      public BioAssemblyIdentifier(PdbId pdbId, int biolNr)
      Parameters:
      pdbCode -
      biolNr -
  • 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)