Class BioAssemblyIdentifier

    • Field Detail

      • BIO_NAME_PATTERN

        public static final java.util.regex.Pattern BIO_NAME_PATTERN
    • Constructor Detail

      • BioAssemblyIdentifier

        public BioAssemblyIdentifier​(java.lang.String name)
      • BioAssemblyIdentifier

        public BioAssemblyIdentifier​(java.lang.String pdbCode,
                                     int biolNr)
    • Method Detail

      • getIdentifier

        public java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • loadStructure

        public Structure loadStructure​(AtomCache cache)
                                throws StructureException,
                                       java.io.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
        java.io.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.