org.biojava.nbio.structure

Interface StructureIdentifier

All Known Subinterfaces:

Structure

All Known Implementing Classes:

CathDomain, ScopDomain, StructureImpl, SubstructureIdentifier

public interface StructureIdentifier

An identifier that uniquely identifies a whole Structure or arbitrary substructure, including whole chains, ScopDomains, and CathDomains.

Author:

dmyersturnbull

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getIdentifier() The unique identifier, using the following formal specification:
java.lang.String	getPdbId() Returns the PDB identifier associated with this StructureIdentifier.
java.util.List<java.lang.String>	getRanges() Returns a list of ranges of the form described in getIdentifier().
java.util.List<? extends ResidueRange>	getResidueRanges() Returns the list of ResidueRanges that this StructureIdentifier defines.

Method Detail

getIdentifier

java.lang.String getIdentifier()

The unique identifier, using the following formal specification:

                name     := pdbID
                               | pdbID '.' chainID
                               | pdbID '.' range
                               | scopID
                range         := '('? range (',' range)? ')'?
                               | chainID
                               | chainID '_' resNum '-' resNum
                pdbID         := [0-9][a-zA-Z0-9]{3}
                chainID       := [a-zA-Z0-9]
                scopID        := 'd' pdbID [a-z_][0-9_]
                cathID        := pdbID [A-Z][0-9]{2}
                resNum        := [-+]?[0-9]+[A-Za-z]?
 

For example:

                1TIM                            #whole structure
                1tim                            #same as above
                4HHB.C                          #single chain
                3AA0.A,B                        #two chains
                d2bq6a1                         #SCOP domain
      1cukA01                         #CATH domain
                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.

getPdbId

java.lang.String getPdbId()

Returns the PDB identifier associated with this StructureIdentifier.

getResidueRanges

java.util.List<? extends ResidueRange> getResidueRanges()

Returns the list of ResidueRanges that this StructureIdentifier defines. This is a unique representation.

getRanges

java.util.List<java.lang.String> getRanges()

Returns a list of ranges of the form described in getIdentifier(). For example:

 getRanges().get(0): 'A'
 getRanges().get(1): 'B_5-100'
 

This is a unique representation.