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

    • toString

      public String toString()
      Overrides:
      toString in class Object
    • getIdentifier

      public String getIdentifier()
      Get the String form of this identifier. This provides the canonical form for a StructureIdentifier and has all the information needed to recreate a particular substructure. Example: 3iek.A_17-28,A_56-294
      Specified by:
      getIdentifier in interface StructureIdentifier
      Returns:
      The String form of this identifier
    • getPdbId

      public String getPdbId()
    • getResidueRanges

      public List<ResidueRange> getResidueRanges()
    • toCanonical

      public SubstructureIdentifier toCanonical()
      Return itself. SubstructureIdentifiers are canonical!
      Specified by:
      toCanonical in interface StructureIdentifier
      Returns:
      A SubstructureIdentifier equivalent to this
    • reduce

      public Structure reduce(Structure s) throws StructureException
      Takes a complete structure as input and reduces it to residues present in the specified ranges

      The returned structure will be a shallow copy of the input, with shared Chains, Residues, etc.

      Specified by:
      reduce in interface StructureIdentifier
      Parameters:
      s - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
      input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId().
      Returns:
      Throws:
      StructureException
      See Also:
    • loadStructure

      public Structure loadStructure(AtomCache cache) throws IOException, StructureException
      Loads the complete structure based on getPdbId().
      Specified by:
      loadStructure in interface StructureIdentifier
      Parameters:
      AtomCache - A source of structures
      Returns:
      A Structure containing at least the atoms identified by this, or null if no PDB ID is set
      Throws:
      StructureException - For errors loading and parsing the structure
      IOException - Errors reading the structure from disk