001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 * Created on May 1, 2012 021 * Created by Andreas Prlic 022 * 023 * @since 3.0.2 024 */ 025package org.biojava.nbio.structure.domain; 026 027import java.io.IOException; 028import java.util.SortedSet; 029 030import org.biojava.nbio.structure.Structure; 031import org.biojava.nbio.structure.StructureException; 032import org.biojava.nbio.structure.align.util.AtomCache; 033 034/** 035 * Decomposes a structure into representative PDP domains. 036 * 037 * Implementations will probably want to also implement {@link DomainProvider}, 038 * which provides a very similar set of methods for general structure domain 039 * decomposition. 040 * @author Andreas Prlic 041 * @since 3.0.2 042 */ 043public interface PDPProvider { 044 045 /** 046 * Get a list of all PDP domains for a given PDB entry 047 * @param pdbId PDB ID 048 * @return Set of domain names, e.g. "PDP:4HHBAa" 049 * @throws IOException 050 */ 051 public SortedSet<String> getPDPDomainNamesForPDB(String pdbId) throws IOException; 052 /** 053 * Get the structure for a particular PDP domain 054 * @param pdpDomainName PDP identifier, e.g. "PDP:4HHBAa" 055 * @param cache AtomCache, responsible for fetching and storing the coordinates 056 * @return Structure representing the PDP domain 057 * @throws IOException For IO errors, e.g. when parsing PDP information 058 * @throws StructureException For errors creating the structure 059 */ 060 public Structure getDomain(String pdpDomainName, AtomCache cache) throws IOException, StructureException; 061 /** 062 * Get a StructureIdentifier representing the specified PDP domain. 063 * 064 * @param pdpDomainName PDP domain name 065 * @return a PDPDomain representing this domain name 066 * @throws IOException 067 */ 068 public PDPDomain getPDPDomain(String pdpDomainName) throws IOException; 069}