org.biojava.bio.structure.domain
Class LocalProteinDomainParser

java.lang.Object
  extended by org.biojava.bio.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
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