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.

There are two fundamental requirements. First, the residues have to be sequential and connected in the original Structure (with the exception of missing residues or loops in between). All the residues are of the same type. These requirements are not checked when constructing the Object, but they are assumed to always hold.

Since:

5.0.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
Subunit(Atom[] reprAtoms) A Subunit is uniquely defined by the coordinates of the representative Atoms of its residues, in sequential order.

Method Summary

Modifier and Type	Method and Description
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.
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)

A Subunit is uniquely defined by the coordinates of the representative Atoms of its residues, in sequential order.

Parameters:

repAtoms - representative Atoms

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

toString

public String toString()

Overrides:

toString in class Object