/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package demo;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.ArrayList;
import java.util.concurrent.ExecutionException;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.SubstructureIdentifier;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain;
import org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters;
import org.biojava.nbio.structure.align.util.AtomCache;
/**
* Demo for running the CEMC Algorithm on a protein family and
* visualizing the results.
* Choose the family by commenting out the protein family names.
*
* @author Aleix Lafita
*
*/
public class DemoMultipleMC {
public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
//ASP-proteinases (CEMC paper)
//List<String> names = Arrays.asList("3app", "4ape", "2apr", "5pep", "1psn", "4cms", "1bbs.A", "1smr.A", "2jxr.A", "1mpp", "2asi", "1am5");
//Protein Kinases (CEMC paper)
//List<String> names = Arrays.asList("1cdk.A", "1cja.A", "1csn", "1b6c.B", "1ir3.A", "1fgk.A", "1byg.A", "1hck", "1blx.A", "3erk", "1bmk.A", "1kob.A", "1tki.A", "1phk", "1a06");
//DHFR (Gerstein 1998 paper)
List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
//Beta-propeller (MATT paper)
//List<String> names = Arrays.asList("d1nr0a1", "d1nr0a2", "d1p22a2", "d1tbga_");
//Beta-helix (MATT paper)
//List<String> names = Arrays.asList("d1hm9a1", "d1kk6a_", "d1krra_", "d1lxaa_", "d1ocxa_", "d1qrea_", "d1xata_", "d3tdta_");
//TIM barrels (MUSTA paper)
//List<String> names = Arrays.asList("1tim.A", "1vzw", "1nsj", "3tha.A", "4enl", "2mnr", "7tim.A", "1tml", "1btc", "a1piia1", "6xia", "5rub.A", "2taa.B");
//Calcium Binding (MUSTA paper)
//List<String> names = Arrays.asList("4cpv", "2scp.A", "2sas", "1top", "1scm.B", "3icb");
//Serine Rich Proteins SERP (MUSTA paper)
//List<String> names = Arrays.asList("7api.A", "8api.A", "1hle.A", "1ova.A", "2ach.A", "9api.A", "1psi", "1atu", "1kct", "1ath.A", "1att.A");
//Serine Proteases (MUSTA paper)
//List<String> names = Arrays.asList("1cse.E", "1sbn.E", "1pek.E", "3prk", "3tec.E");
//GPCRs
//List<String> names = Arrays.asList("2z73.A", "1u19.A", "4ug2.A", "4xt3", "4or2.A", "3odu.A");
//Immunoglobulins (MAMMOTH paper)
//List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
//Globins (MAMMOTH, POSA, Gerstein&Levitt and MUSTA papers)
//List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.A", "1ith.A", "1idr.A", "1dlw", "1kr7.A", "1ew6.A", "1it2.A", "1eco", "3sdh.A", "1cg5.B", "1fhj.B", "1ird.A", "1mba", "2gdm", "1b0b", "1h97.A", "1ash.A", "1jl7.A");
//Rossman-Fold (POSA paper)
//List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
//Circular Permutations (Bliven CECP paper) - dynamin GTP-ase with CP G-domain
//List<String> names = Arrays.asList("d1u0la2", "d1jwyb_");
//Circular Permutations (Bliven CECP paper) - Legume lectins
//List<String> names = Arrays.asList("2pel.A", "2eig.A", "1uzy.A", "1lec.A", "3cna.A", "4i30.A", "4z8b.A", "2d3p.A");
//Circular Permutations: SAND and MFPT domains
//List<String> names = Arrays.asList("d2bjqa1", "d1h5pa_", "d1ufna_"); //"d1oqja"
//Flexible domain family of proteins (FatCat paper?)
//List<String> names = Arrays.asList();
//Amonium Transporters (Aleix Bachelor's Thesis)
//List<String> names = Arrays.asList("1xqf.A","2b2f.A", "3b9w.A","3hd6.A");
//Cytochrome C Oxidases (Aleix Bachelor's Thesis)
//List<String> names = Arrays.asList("2dyr.A","2gsm.A","2yev.A","3hb3.A","3omn.A","1fft.A","1xme.A","3o0r.B","3ayf.A");
//List<String> names = Arrays.asList("2dyr.A","2gsm.A","1fft.A","1xme.A","3o0r.B","3ayf.A");
//Cation Transporting ATPases (Aleix Bachelor's Thesis)
//List<String> names = Arrays.asList("3b8e.A","2zxe.A", "3tlm.A","1iwo.A");
//Ankyrin Repeats
//List<String> names = Arrays.asList("d1n0ra_", "3ehq.A", "1awc.B"); //ankyrin
//Load the CA atoms of the structures
AtomCache cache = new AtomCache();
List<StructureIdentifier> identifiers = new ArrayList<StructureIdentifier>();
List<Atom[]> atomArrays = new ArrayList<Atom[]>();
for (String name:names) {
atomArrays.add(cache.getAtoms(name));
identifiers.add(new SubstructureIdentifier(name));
}
//Here the multiple structural alignment algorithm comes in place to generate the alignment object
//StructureAlignment pairwise = new FatCatFlexible();
StructureAlignment pairwise = new CeMain();
MultipleMcMain algorithm = new MultipleMcMain(pairwise);
MultipleMcParameters params = (MultipleMcParameters) algorithm.getParameters();
params.setMinBlockLen(10);
params.setGapExtension(20.0);
MultipleAlignment result = algorithm.align(atomArrays);
result.getEnsemble().setStructureIdentifiers(identifiers);
//Information about the alignment
result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
result.getEnsemble().setVersion(algorithm.getVersion());
MultipleAlignmentJmolDisplay.display(result);
}
}