Package org.biojava.nbio.structure.cluster

Class Subunit

java.lang.Object

org.biojava.nbio.structure.cluster.Subunit

public class Subunit
extends Object

A Subunit consists of a set of residues from a Structure, which may correspond to an entire Chain, a Domain, or any subset or combination of residues from them. All the residues of a Subunit are of the same type.

The Subunit object can contain additional fields for identification and annotation.

Since:

5.0.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
Subunit(Atom[] reprAtoms, String name, StructureIdentifier identifier, Structure structure)	A Subunit is solely defined by the coordinates of the representative Atoms of its residues.

Method Summary

Modifier and Type	Method	Description
StructureIdentifier	getIdentifier()	The standard identifier of the Subunit.
String	getName()	The Name of a Subunit is a free-text field, user defined.
ProteinSequence	getProteinSequence()	Get the protein sequence of the Subunit.
String	getProteinSequenceString()	Get the protein sequence of the Subunit as String.
Atom[]	getRepresentativeAtoms()	Get all the representative Atoms of the Subunit.
Structure	getStructure()	The parent Structure from which the Subunit atoms were obtained.
void	setName(String name)	The Name of a Subunit is a free-text field, user defined.
int	size()	The size of a Subunit is the number of residues it contains.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Subunit

public Subunit(Atom[] reprAtoms,
               String name,
               StructureIdentifier identifier,
               Structure structure)

A Subunit is solely defined by the coordinates of the representative Atoms of its residues. It can be identified with a StructureIdentifier and/or a name and stores a reference to the Structure from which the Atoms were obtained.

Parameters:

reprAtoms - representative Atoms. It cannot be null or empty

name - String field that identifies the Subunit. It can be null

identifier - StructureIdentifier. It can be null

structure - parent Structure object. It can be null

Method Detail

getRepresentativeAtoms

public Atom[] getRepresentativeAtoms()

Get all the representative Atoms of the Subunit. These Atoms are used for clustering and displaying the Subunit.

Returns:

representative Atom[]

size

public int size()

The size of a Subunit is the number of residues it contains.

Returns:

the size of the Subunit

getProteinSequenceString

public String getProteinSequenceString()

Get the protein sequence of the Subunit as String.

Returns:

protein sequence String

getProteinSequence

public ProteinSequence getProteinSequence()
                                   throws CompoundNotFoundException

Get the protein sequence of the Subunit.

Returns:

sequence ProteinSequence

Throws:

CompoundNotFoundException

getName

public String getName()

The Name of a Subunit is a free-text field, user defined.

Returns:

the Subunit name

setName

public void setName(String name)

The Name of a Subunit is a free-text field, user defined.

Parameters:

name - of the Subunit

getStructure

public Structure getStructure()

The parent Structure from which the Subunit atoms were obtained.

Returns:

Structure object

getIdentifier

public StructureIdentifier getIdentifier()

The standard identifier of the Subunit.

Returns:

StructureIdentifier object

toString

public String toString()

Overrides:

toString in class Object