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Merge pull request biojava#278 from sbliven/multaln
Multiple Structure Alignment Datastructures
2 parents b6bb812 + 1c717b6 commit 85378c8

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‎biojava-structure-gui/src/main/java/demo/CookBook.java‎

Lines changed: 1 addition & 1 deletion
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@@ -91,7 +91,7 @@ public static void main(String[] args){
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jmol.setTitle(algorithm.getAlgorithmName() + " : " + name1 + " vs. " + name2);
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// here we open up the alignment - text panel that can interact with the 3D jmol display.
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DisplayAFP.showAlignmentImage(afpChain, ca1,ca2,jmol);
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DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);
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// we can print an XML version
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//System.out.println(AFPChainXMLConverter.toXML(afpChain, ca1, ca2));

‎biojava-structure-gui/src/main/java/demo/DemoCEMC.java‎

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package demo;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.ArrayList;
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import java.util.concurrent.ExecutionException;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.cemc.CeMcMain;
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import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.util.AtomCache;
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/**
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* Demo for running a CEMC Multiple Structure Alignment and visualizing the results.
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*
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* @author Aleix Lafita
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*
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*/
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public class DemoCEMC {
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public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
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//Specify the structures to align
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//ASP-proteinases (CEMC paper)
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//List<String> names = Arrays.asList("3app", "4ape", "2apr", "5pep", "1psn", "4cms", "1bbs.A", "1smr.A", "2jxr.A", "1mpp", "2asi", "1am5");
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//Protein Kinases (CEMC paper)
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//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");
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//DHFR (Gerstein 1998 paper)
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List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
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//TIM barrels (MUSTA paper)
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//List<String> names = Arrays.asList("1tim.A", "1vzw", "1nsj", "3tha.A", "4enl", "2mnr", "7tim.A", "1tml", "1btc", "a1piia1", "6xia", "5rub.A", "2taa.B");
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//Helix-bundle (MUSTA paper)
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//List<String> names = Arrays.asList("1bbh.A", "1aep", "1bge.B", "256b.A", "2ccy.A", "2hmz.A", "3ink.C");
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//Calcium Binding (MUSTA paper)
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//List<String> names = Arrays.asList("4cpv", "2scp.A", "2sas", "1top", "1scm.B", "3icb");
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//Serine Rich Proteins SERP (MUSTA paper)
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//List<String> names = Arrays.asList("7api.A", "8api.A", "1hle.A", "1ova.A", "2ach.A", "9api.A", "1psi", "1atu", "1kct", "1ath.A", "1att.A");
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//Serine Proteases (MUSTA paper)
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//List<String> names = Arrays.asList("1cse.E", "1sbn.E", "1pek.E", "3prk", "3tec.E");
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//GPCRs
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//List<String> names = Arrays.asList("2z73.A", "1u19.A", "4ug2.A", "4xt3", "4or2.A", "3odu.A");
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//Immunoglobulins (MAMMOTH paper)
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//List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
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//Globins (MAMMOTH and MUSTA papers)
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//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");
49+
//Rossman-Fold (POSA paper)
50+
//List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
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//Load the CA atoms of the structures
53+
AtomCache cache = new AtomCache();
54+
List<Atom[]> atomArrays = new ArrayList<Atom[]>();
55+
for (String name:names) {
56+
atomArrays.add(cache.getAtoms(name));
57+
}
58+
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//Here the multiple structural alignment algorithm comes in place to generate the alignment object
60+
CeMcMain algorithm = new CeMcMain();
61+
MultipleAlignment result = algorithm.align(atomArrays);
62+
result.getEnsemble().setStructureNames(names);
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//Information about the alignment
65+
result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
66+
result.getEnsemble().setVersion(algorithm.getVersion());
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68+
MultipleAlignmentDisplay.display(result);
69+
}
70+
}

‎biojava-structure-gui/src/main/java/demo/DemoMultipleAlignmentJmol.java‎

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package demo;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
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import org.biojava.nbio.structure.align.multiple.Block;
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import org.biojava.nbio.structure.align.multiple.BlockImpl;
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import org.biojava.nbio.structure.align.multiple.BlockSet;
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import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentScorer;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.multiple.MultipleSuperimposer;
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import org.biojava.nbio.structure.align.multiple.ReferenceSuperimposer;
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import org.biojava.nbio.structure.align.util.AtomCache;
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/**
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* Demo for visualizing the results of a Multiple Alignment, from a sample MultipleAlignment object.
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*
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* @author Aleix Lafita
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*
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*/
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public class DemoMultipleAlignmentJmol {
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public static void main(String[] args) throws IOException, StructureException {
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//Specify the structures to align
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//List<String> names = Arrays.asList("1tim.a", "1vzw", "1nsj", "3tha.a"); //TIM barrels
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List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.a", "1ith.a"); //globins
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//Load the CA atoms of the structures
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AtomCache cache = new AtomCache();
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List<Atom[]> atomArrays = new ArrayList<Atom[]>();
42+
for (String name:names) atomArrays.add(cache.getAtoms(name));
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//Here the multiple structural alignment algorithm comes in place to generate the alignment object
45+
MultipleAlignment fakeMultAln = fakeMultipleAlignment("globins", atomArrays);
46+
fakeMultAln.getEnsemble().setStructureNames(names);
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//Generate a pairwise alignment and convert it to a MultipleAlignment
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//FatCat fatcat = new FatCat();
50+
//AFPChain afpChain = fatcat.alignRigid(atomArrays.get(0),atomArrays.get(1));
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//MultipleAlignmentEnsemble ensemble = new MultipleAlignmentEnsembleImpl(afpChain, atomArrays.get(0),atomArrays.get(1));
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//MultipleAlignment pairwise = ensemble.getMultipleAlignments().get(0);
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System.out.println(MultipleAlignmentWriter.toFASTA(fakeMultAln));
55+
MultipleAlignmentDisplay.display(fakeMultAln);
56+
//StructureAlignmentDisplay.display(pairwise);
57+
//For comparison display the original AFP
58+
//StructureAlignmentDisplay.display(afpChain,atomArrays.get(0),atomArrays.get(1));
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}
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/**
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* Method that constructs a fake MultipleAlignment with two BlockSets, with two and one Blocks respectively. Used to
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* test the correctness of the DataStructure. In the future it will be in the Test packages.
64+
* @param family name of the protein family
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* @param atomArrays
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* @return MultipleAlignment
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* @throws StructureException
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* @throws StructureAlignmentException
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*/
70+
private static MultipleAlignment fakeMultipleAlignment(String family, List<Atom[]>atomArrays) throws StructureException {
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//Initialize the multiple alignment parent ensemble
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MultipleAlignmentEnsemble ensemble = new MultipleAlignmentEnsembleImpl();
74+
ensemble.setAtomArrays(atomArrays);
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ensemble.setAlgorithmName("fakeAlgorithm");
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MultipleAlignment fakeMultAln = new MultipleAlignmentImpl(ensemble);
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if (family == "globins"){
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BlockSet blockSet1 = new BlockSetImpl(fakeMultAln); //first BlockSet with 2 Blocks
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BlockSet blockSet2 = new BlockSetImpl(fakeMultAln); //second BlockSet with 1 Block
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Block block1 = new BlockImpl(blockSet1);
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Block block2 = new BlockImpl(blockSet1);
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Block block3 = new BlockImpl(blockSet2);
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//Alignment obtained from MUSTANG multiple alignment (just some of the residues, not the whole alignment)
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List<Integer> aligned11 = Arrays.asList(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21);
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List<Integer> aligned12 = Arrays.asList(29,30,31,32,33,34,35,36,38);
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List<Integer> aligned13 = Arrays.asList(123,124,125,126,127,128,129,130,131,132,133,134);
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List<Integer> aligned21 = Arrays.asList(10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,null,27,28,29,30,31);
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List<Integer> aligned22 = Arrays.asList(39,40,41,42,43,44,45,46,48);
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List<Integer> aligned23 = Arrays.asList(133,134,135,136,137,138,139,140,141,142,143,144);
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List<Integer> aligned31 = Arrays.asList(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21);
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List<Integer> aligned32 = Arrays.asList(29,30,31,32,33,34,35,36,38);
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List<Integer> aligned33 = Arrays.asList(117,118,119,120,121,122,123,124,125,126,127,128);
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List<Integer> aligned41 = Arrays.asList(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,null,17,18,19,20,21);
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List<Integer> aligned42 = Arrays.asList(30,31,32,33,34,35,36,37,39);
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List<Integer> aligned43 = Arrays.asList(121,122,123,124,125,126,127,128,129,130,131,132);
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block1.getAlignRes().add(aligned11);
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block1.getAlignRes().add(aligned21);
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block1.getAlignRes().add(aligned31);
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block1.getAlignRes().add(aligned41);
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block2.getAlignRes().add(aligned12);
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block2.getAlignRes().add(aligned22);
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block2.getAlignRes().add(aligned32);
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block2.getAlignRes().add(aligned42);
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block3.getAlignRes().add(aligned13);
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block3.getAlignRes().add(aligned23);
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block3.getAlignRes().add(aligned33);
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block3.getAlignRes().add(aligned43);
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//Calculating all information in the alignment is as easy as that line, once the residue equivalencies are set
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MultipleSuperimposer imposer = new ReferenceSuperimposer();
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imposer.superimpose(fakeMultAln);
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MultipleAlignmentScorer.calculateScores(fakeMultAln);
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}
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return fakeMultAln;
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}
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}

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java‎

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Original file line numberDiff line numberDiff line change
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title += " " + algorithm.getParameters().toString();
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jmol.setTitle(title);
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DisplayAFP.showAlignmentImage(afpChain,ca1,ca2,jmol);
109+
DisplayAFP.showAlignmentPanel(afpChain,ca1,ca2,jmol);
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System.out.println(afpChain.toCE(ca1,ca2));
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113113
} catch (StructureException e){
114114
e.printStackTrace();
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logger.warn(e.getMessage());
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}
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java‎

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//String rot = afpChain.toRotMat();
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DisplayAFP.showAlignmentImage(afpChain, ca1,ca2,jmol);
341+
DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);
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} catch (Exception e){

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