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:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SubstructureIdentifier(String id) Create a new identifier from a string.
SubstructureIdentifier(String pdbId, List<ResidueRange> ranges) Create a new identifier based on a set of ranges.

Method Summary

Modifier and Type	Method and Description
String	getIdentifier() Get the String form of this identifier.
String	getPdbId()
List<ResidueRange>	getResidueRanges()
Structure	loadStructure(AtomCache cache) Loads the complete structure based on getPdbId().
Structure	reduce(Structure s) Takes a complete structure as input and reduces it to residues present in the specified ranges
SubstructureIdentifier	toCanonical() Return itself.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

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 Detail

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:

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:

StructureTools.getReducedStructure(Structure, String)

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