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 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         := [1-9][a-zA-Z0-9]{3}
                               | PDB_[a-zA-Z0-9]{8}
                chainID       := [a-zA-Z0-9]+
                resNum        := [-+]?[0-9]+[A-Za-z]?
 

For example:

                1TIM                                    #whole structure (short format)
                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
                PDB_00001TIM                            #whole structure (extended format)
                pdb_00001tim                            #same as above
                PDB_00004HHB.C                          #single chain
                PDB_00003AA0.A,B                        #two chains
                PDB_00004GCR.A_1-40                     #substructure
      pdb_00003iek.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	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.
SubstructureIdentifier(PdbId pdbId, List<ResidueRange> ranges)	Create a new identifier based on a set of ranges.

Method Summary

Modifier and Type	Method	Description
protected static void	copyLigandsByProximity(Structure full, Structure reduced)	Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
protected static void	copyLigandsByProximity(Structure full, Structure reduced, double cutoff, int fromModel, int toModel)	Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
String	getIdentifier()	Get the String form of this identifier.
PdbId	getPdbId()	Get the PDB identifier part of the SubstructureIdentifier
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 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 - a pdb id, can't be null

ranges - the ranges

SubstructureIdentifier

public SubstructureIdentifier(PdbId 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 PdbId getPdbId()

Get the PDB identifier part of the SubstructureIdentifier

Returns:

the PDB ID

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.

Ligands are handled in a special way. If a full chain is selected (e.g. '1ABC.A') then any waters and ligands with matching chain name are included. If a residue range is present ('1ABC.A:1-100') then any ligands (technically non-water non-polymer atoms) within StructureTools.DEFAULT_LIGAND_PROXIMITY_CUTOFF of the selected range are included, regardless of chain.

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().

Returns:

Throws:

StructureException

loadStructure

public Structure loadStructure(AtomCache cache)
                        throws IOException,
StructureException

Loads the complete structure based on getPdbId().

Specified by:

loadStructure in interface StructureIdentifier

Parameters:

cache - 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

copyLigandsByProximity

protected static void copyLigandsByProximity(Structure full,
 Structure reduced)

Supplements the reduced structure with ligands from the full structure based on a distance cutoff. Ligand groups are moved (destructively) from full to reduced if they fall within the cutoff of any atom in the reduced structure. The default cutoff is used.

Parameters:

full - Structure containing all ligands

reduced - Structure with a subset of the polymer groups from full

See Also:

• StructureTools.getLigandsByProximity(java.util.Collection, Atom[], double)

copyLigandsByProximity

protected static void copyLigandsByProximity(Structure full,
 Structure reduced,
 double cutoff,
 int fromModel,
 int toModel)

Supplements the reduced structure with ligands from the full structure based on a distance cutoff. Ligand groups are moved (destructively) from full to reduced if they fall within the cutoff of any atom in the reduced structure.

Parameters:

full - Structure containing all ligands

reduced - Structure with a subset of the polymer groups from full

cutoff - Distance cutoff (Å)

fromModel - source model in full

toModel - destination model in reduced

See Also:

• StructureTools.getLigandsByProximity(java.util.Collection, Atom[], double)