Package org.biojava.nbio.structure

Class SubstructureIdentifier

java.lang.Object
org.biojava.nbio.structure.SubstructureIdentifier
All Implemented Interfaces:
Serializable, StructureIdentifier
public class SubstructureIdentifier extends Object implements Serializable, 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.
Author:
dmyersturnbull, Spencer Bliven
See Also:

  • Constructor Details

    • SubstructureIdentifier

      public SubstructureIdentifier(String id)
      Create a new identifier from a string.
      Parameters:
      id -

    • SubstructureIdentifier

      public SubstructureIdentifier(String pdbId, List<ResidueRange> ranges)
      Create a new identifier based on a set of ranges. If ranges is empty, includes all residues.
      Parameters:
      pdbId -
      ranges -

  • Method Details