org.biojava.nbio.structure.domain

Class LocalProteinDomainParser

java.lang.Object

org.biojava.nbio.structure.domain.LocalProteinDomainParser

public class LocalProteinDomainParser
extends Object

Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures. Since domains in proteins are difficult to define, results detected by automated algorithms have to be taken with a grain of salt. see

J Mol Biol. 2004 Jun 4;339(3):647-78.

Toward consistent assignment of structural domains in proteins.

Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN.

This implementation is based on a Java port of the PDP algorithm, as described in:

Since:

3.0.2

Author:

Andreas Prlic

Method Summary

Modifier and Type	Method and Description
static List<Domain>	suggestDomains(Atom[] ca) Suggest domains for a set of Calpha atoms
static List<Domain>	suggestDomains(Structure s) Suggest domains for a protein structure

Methods inherited from class java.lang.Object

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

Method Detail

suggestDomains

public static List<Domain> suggestDomains(Structure s)
                                   throws StructureException

Suggest domains for a protein structure

Parameters:

s - the protein structure

Returns:

a list of possible domains

Throws:

StructureException

suggestDomains

public static List<Domain> suggestDomains(Atom[] ca)
                                   throws StructureException

Suggest domains for a set of Calpha atoms

Parameters:

ca - an array of Calpha atoms

Returns:

a list of possible domains

Throws:

StructureException