Package org.biojava.nbio.structure

Class BioAssemblyIdentifier

java.lang.Object

org.biojava.nbio.structure.BioAssemblyIdentifier

All Implemented Interfaces:

Serializable, StructureIdentifier

public class BioAssemblyIdentifier
extends Object
implements StructureIdentifier

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final Pattern	BIO_NAME_PATTERN

Constructor Summary

Constructors

Constructor	Description
BioAssemblyIdentifier(String name)
BioAssemblyIdentifier(String pdbCode, int biolNr)
BioAssemblyIdentifier(PdbId pdbId, int biolNr)

Method Summary

Modifier and Type	Method	Description
String	getIdentifier()	Get the String form of this identifier.
Structure	loadStructure(AtomCache cache)	Loads a structure encompassing the structure identified.
Structure	reduce(Structure input)	Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
SubstructureIdentifier	toCanonical()	Convert to a canonical SubstructureIdentifier.
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

BIO_NAME_PATTERN

public static final Pattern BIO_NAME_PATTERN

Constructor Details

BioAssemblyIdentifier

public BioAssemblyIdentifier(String name)

BioAssemblyIdentifier

public BioAssemblyIdentifier(String pdbCode,
 int biolNr)

Parameters:

pdbCode -

biolNr -

BioAssemblyIdentifier

public BioAssemblyIdentifier(PdbId pdbId,
 int biolNr)

Parameters:

pdbId -

biolNr -

Method Details

getIdentifier

public String getIdentifier()

Description copied from interface: StructureIdentifier

Get the String form of this identifier. It is recommended that the toString() method also return the identifier, for consistency during serialization.

Specified by:

getIdentifier in interface StructureIdentifier

Returns:

The String form of this identifier

toString

public String toString()

Overrides:

toString in class Object

loadStructure

public Structure loadStructure(AtomCache cache)
                        throws StructureException,
IOException

Description copied from interface: StructureIdentifier

Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.reduce(Structure).

It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.

Specified by:

loadStructure in interface StructureIdentifier

Parameters:

cache - A potential sources of structures

Returns:

A Structure containing at least the atoms identified by this, or null if Structures are not applicable.

Throws:

StructureException - For errors loading and parsing the structure

IOException - Errors reading the structure from disk

toCanonical

public SubstructureIdentifier toCanonical()
                                   throws StructureException

Description copied from interface: StructureIdentifier

Convert to a canonical SubstructureIdentifier.

This allows all domains to be converted to a standard format String.

Specified by:

toCanonical in interface StructureIdentifier

Returns:

A SubstructureIdentifier equivalent to this

Throws:

StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.

reduce

public Structure reduce(Structure input)
                 throws StructureException

Description copied from interface: StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

The returned structure may 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(), if applicable.

Returns:

Throws:

StructureException