Class SubstructureIdentifier

  • All Implemented Interfaces:
    Serializable, StructureIdentifier

    public class SubstructureIdentifier
    extends Object
    implements StructureIdentifier
    This is the canonical way to identify a part of a structure.

    The current syntax allows the specification of a set of residues from the first model of a structure. Future versions may be extended to represent additional properties.

    Identifiers should adhere to the following specification, although some additional forms may be tolerated where unambiguous for backwards compatibility.

                    name          := pdbID
                                   | pdbID '.' chainID
                                   | pdbID '.' range
                    range         := range (',' range)?
                                   | chainID
                                   | chainID '_' resNum '-' resNum
                    pdbID         := [0-9][a-zA-Z0-9]{3}
                    chainID       := [a-zA-Z0-9]+
                    resNum        := [-+]?[0-9]+[A-Za-z]?
    For example:
                    1TIM                            #whole structure
                    1tim                            #same as above
                    4HHB.C                          #single chain
                    3AA0.A,B                        #two chains
                    4GCR.A_1-40                     #substructure
          3iek.A_17-28,A_56-294,A_320-377 #substructure of 3 disjoint parts
    More options may be added to the specification at a future time.
    dmyersturnbull, Spencer Bliven
    See Also:
    Serialized Form