org.biojava.nbio.structure

Class SubstructureIdentifier

java.lang.Object

org.biojava.nbio.structure.SubstructureIdentifier

All Implemented Interfaces:

StructureIdentifier

public class SubstructureIdentifier
extends java.lang.Object
implements StructureIdentifier

An arbitrary collection of residues in a Structure.

Author:

dmyersturnbull

Constructor Summary

Constructors

Constructor and Description
SubstructureIdentifier(java.lang.String id, AtomCache cache)
SubstructureIdentifier(java.lang.String pdbId, java.util.List<ResidueRange> ranges)

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 StructureIdentifier.getIdentifier().
java.util.List<? extends ResidueRange>	getResidueRanges() Returns the list of ResidueRanges that this StructureIdentifier defines.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SubstructureIdentifier

public SubstructureIdentifier(java.lang.String pdbId,
                      java.util.List<ResidueRange> ranges)

SubstructureIdentifier

public SubstructureIdentifier(java.lang.String id,
                      AtomCache cache)
                       throws java.io.IOException,
                              StructureException

Throws:

java.io.IOException

StructureException

Method Detail

getIdentifier

public java.lang.String getIdentifier()

Description copied from interface: StructureIdentifier

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.

Specified by:

getIdentifier in interface StructureIdentifier

getPdbId

public java.lang.String getPdbId()

Description copied from interface: StructureIdentifier

Returns the PDB identifier associated with this StructureIdentifier.

Specified by:

getPdbId in interface StructureIdentifier

getResidueRanges

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

Description copied from interface: StructureIdentifier

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

Specified by:

getResidueRanges in interface StructureIdentifier

getRanges

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

Description copied from interface: StructureIdentifier

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

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

This is a unique representation.

Specified by:

getRanges in interface StructureIdentifier

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object