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Merge pull request biojava#571 from lafita/quatalign
Quaternary Structural Alignment Algorithm (QsAlign)
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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java‎

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package org.biojava.nbio.structure.test.align.qsalign;
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import static org.junit.Assert.*;
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import java.io.IOException;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.align.quaternary.QsAlign;
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import org.biojava.nbio.structure.align.quaternary.QsAlignParameters;
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import org.biojava.nbio.structure.align.quaternary.QsAlignResult;
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import org.biojava.nbio.structure.align.quaternary.QsRelation;
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import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
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import org.junit.Test;
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/**
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* Test the correctness of the {@link QsAlign} algorithm with some examples of
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* different levels of quaternary structure similarity.
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*
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* @author Aleix Lafita
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* @since 5.0.0
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*
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*/
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public class TestQsAlignExamples {
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/**
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* Identity: test hemoglobin (4HHB) against itself.
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*/
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@Test
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public void testIdentity() throws StructureException, IOException {
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Structure s1 = StructureIO.getStructure("4hhb");
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Structure s2 = s1;
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QsAlignParameters alignParams = new QsAlignParameters();
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QsAlignResult result = QsAlign
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.align(s1, s2, clusterParams, alignParams);
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assertEquals(result.length(), 4);
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assertEquals(result.getRelation(), QsRelation.EQUIVALENT);
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assertEquals(result.getRmsd(), 0.0, 0.01);
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}
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/**
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* Different: test two completely different proteins (4HHB, 3IFV).
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*/
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@Test
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public void testDifferent() throws StructureException, IOException {
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Structure s1 = StructureIO.getStructure("4hhb");
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Structure s2 = StructureIO.getStructure("3ifv");
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QsAlignParameters alignParams = new QsAlignParameters();
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QsAlignResult result = QsAlign
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.align(s1, s2, clusterParams, alignParams);
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assertEquals(result.length(), 0);
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assertEquals(result.getRelation(), QsRelation.DIFFERENT);
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}
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/**
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* Proliferating cell nuclear antigens (3IFV, 3HI8) are structurally
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* equivalent C3 homotrimers.
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*/
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@Test
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public void testHomoEquivalent() throws StructureException, IOException {
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Structure s1 = StructureIO.getStructure("3ifv");
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Structure s2 = StructureIO.getStructure("BIO:3hi8:1");
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QsAlignParameters alignParams = new QsAlignParameters();
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QsAlignResult result = QsAlign
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.align(s1, s2, clusterParams, alignParams);
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assertEquals(result.length(), 3);
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assertEquals(result.getRelation(), QsRelation.EQUIVALENT);
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assertTrue(result.getRmsd() < 10.0);
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}
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/**
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* Phycocyanins (2VML, 2BV8) are equivalent D3 heterododecamers with A6B6
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* stoichiometry.
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*/
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@Test
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public void testHeteroEquivalent() throws StructureException, IOException {
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Structure s1 = StructureIO.getStructure("2vml");
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Structure s2 = StructureIO.getStructure("2bv8");
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QsAlignParameters alignParams = new QsAlignParameters();
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QsAlignResult result = QsAlign
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.align(s1, s2, clusterParams, alignParams);
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assertEquals(result.length(), 12);
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assertEquals(result.getRelation(), QsRelation.EQUIVALENT);
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assertTrue(result.getRmsd() < 10.0);
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}
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/**
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* Hydratases (2B3M dimer, 1Q6W hexamer). The C2 dimer is
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* triplicated into a D3 assembly.
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*/
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@Test
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public void testPartialComplete() throws StructureException,
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IOException {
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Structure s1 = StructureIO.getStructure("BIO:2b3m:1");
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Structure s2 = StructureIO.getStructure("BIO:1Q6W:7");
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QsAlignParameters alignParams = new QsAlignParameters();
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QsAlignResult result = QsAlign
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.align(s1, s2, clusterParams, alignParams);
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assertEquals(result.length(), 2);
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assertEquals(result.getRelation(), QsRelation.PARTIAL_COMPLETE);
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assertTrue(result.getRmsd() < 10.0);
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}
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/**
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* Cytochrome bc1 complexes (1BCC, 1KB9) have some equivalent Chains and
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* some unmatched.
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*/
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@Test
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public void testPartialIncomplete() throws StructureException,
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IOException {
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Structure s1 = StructureIO.getStructure("1bcc");
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Structure s2 = StructureIO.getStructure("1kb9");
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QsAlignParameters alignParams = new QsAlignParameters();
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QsAlignResult result = QsAlign
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.align(s1, s2, clusterParams, alignParams);
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assertEquals(result.length(), 8);
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assertEquals(result.getRelation(), QsRelation.PARTIAL_INCOMPLETE);
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assertTrue(result.getRmsd() < 10.0);
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}
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}

biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitClusterer.java renamed to biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java

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@@ -18,7 +18,7 @@
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* http://www.biojava.org/
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*
2020
*/
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package org.biojava.nbio.structure.cluster;
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package org.biojava.nbio.structure.test.cluster;
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import static org.junit.Assert.*;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.cluster.SubunitCluster;
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import org.biojava.nbio.structure.cluster.SubunitClusterer;
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import org.biojava.nbio.structure.cluster.SubunitClustererMethod;
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import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
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import org.junit.Test;
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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 TestSubunitClusterer {
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public class TestSubunitClustererExamples {
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/**
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* Test modified residues: 1HIV
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assertEquals(clusters.get(0).getClustererMethod(),
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SubunitClustererMethod.IDENTITY);
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params.setClustererMethod(SubunitClustererMethod.INTERNAL_SYMMETRY);
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params.setClustererMethod(SubunitClustererMethod.STRUCTURE);
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params.setInternalSymmetry(true);
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params.setRmsdThreshold(3.0);
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clusters = SubunitClusterer.cluster(s, params);
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assertEquals(clusters.get(0).size(), 6);
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assertTrue(clusters.get(0).length() < 177);
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assertEquals(clusters.get(0).getClustererMethod(),
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SubunitClustererMethod.INTERNAL_SYMMETRY);
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SubunitClustererMethod.STRUCTURE);
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}
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}

biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/core/TestQuatSymmetryDetector.java renamed to biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java

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* http://www.biojava.org/
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*
2020
*/
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package org.biojava.nbio.structure.symmetry.core;
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package org.biojava.nbio.structure.test.symmetry;
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import static org.junit.Assert.*;
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import org.junit.Test;
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/**
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* Test the algorithm for symmetry detection on a variety of structures with
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* different symmetries.
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* Test the {@link QuatSymmetryDetector} algorithm for symmetry detection on a
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* variety of structures with different symmetries.
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*
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* @author Peter Rose
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* @author Aleix Lafita
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*
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*/
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public class TestQuatSymmetryDetector {
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public class TestQuatSymmetryDetectorExamples {
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/**
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* An NMR multi-model entry: 1B4C
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public void testNMR() throws IOException, StructureException {
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Structure pdb = StructureIO.getStructure("BIO:1b4c:1");
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SubunitClustererParameters clusterParams = new SubunitClustererParameters();
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QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
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QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
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pdb, symmParams, clusterParams);
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// C2 symmetry non pseudosymmetric
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assertEquals("C2", symmetry.getSymmetry());
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assertEquals("A2", symmetry.getSubunits().getStoichiometry());
68-
assertFalse(symmetry.getSubunits().isPseudoStoichiometric());
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assertEquals("A2", symmetry.getStoichiometry());
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assertFalse(symmetry.isPseudoStoichiometric());
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7070
}
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// C2 symmetry
9191
assertEquals("C2", symmetry.getSymmetry());
92-
assertEquals("A2B2", symmetry.getSubunits().getStoichiometry());
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assertEquals("A2B2", symmetry.getStoichiometry());
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// Use pseudosymmetry (structural clustering)
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clusterParams.setClustererMethod(SubunitClustererMethod.STRUCTURE);
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// D2 pseudo-symmetry
100100
assertEquals("D2", symmetry.getSymmetry());
101-
assertEquals("A4", symmetry.getSubunits().getStoichiometry());
101+
assertEquals("A4", symmetry.getStoichiometry());
102102
}
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104104
/**
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// C1 global symmetry
122122
assertEquals("C1", symmetry.getSymmetry());
123-
assertEquals("A5B5C", symmetry.getSubunits().getStoichiometry());
123+
assertEquals("A5B5C", symmetry.getStoichiometry());
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125125
// Local symmetry
126126
List<QuatSymmetryResults> localSymm = QuatSymmetryDetector
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133133
assertEquals("C5", localSymm.get(2).getSymmetry());
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135135
// Two A5 and one A5B5 stoichiometries as local symmetry
136-
List<String> stoich = localSymm.stream().map(
137-
t -> t.getSubunits().getStoichiometry()).collect(Collectors.toList());
136+
List<String> stoich = localSymm.stream().map(t -> t.getStoichiometry())
137+
.collect(Collectors.toList());
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139139
assertTrue(stoich.contains("A5"));
140140
assertTrue(stoich.contains("A5B5"));
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152152
Structure pdb = StructureIO.getStructure("BIO:4e3e:1");
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154-
// Internal symmetry analysis
154+
// Internal symmetry analysis, use structural clustering
155155
SubunitClustererParameters cp = new SubunitClustererParameters();
156-
cp.setClustererMethod(SubunitClustererMethod.INTERNAL_SYMMETRY);
157-
cp.setCoverageThreshold(0.8); // Lower coverage for internal symm
156+
cp.setClustererMethod(SubunitClustererMethod.STRUCTURE);
157+
cp.setInternalSymmetry(true);
158+
cp.setCoverageThreshold(0.75); // Lower coverage for internal symm
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159160
QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
160161
QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
161162
pdb, symmParams, cp);
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163164
// D2 combined internal and quaternary symmetry
164165
assertEquals("D3", symmetry.getSymmetry());
165-
assertEquals("A6", symmetry.getSubunits().getStoichiometry());
166+
assertEquals("A6", symmetry.getStoichiometry());
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167168
}
168-
169+
169170
/**
170171
* A structure with helical symmetry: 1B47
171172
*
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184185

185186
// H symmetry A3 stoichiometry
186187
assertEquals("H", symmetry.getSymmetry());
187-
assertEquals("A3", symmetry.getSubunits().getStoichiometry());
188+
assertEquals("A3", symmetry.getStoichiometry());
189+
190+
}
191+
192+
/**
193+
* A structure with local helical symmetry: 5JLF
194+
*
195+
* @throws IOException
196+
* @throws StructureException
197+
*/
198+
@Test
199+
public void testHelicalLocal() throws IOException, StructureException {
200+
201+
Structure pdb = StructureIO.getStructure("BIO:5JLF:1");
202+
203+
SubunitClustererParameters cp = new SubunitClustererParameters();
204+
QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
205+
List<QuatSymmetryResults> results = QuatSymmetryDetector
206+
.calcLocalSymmetries(pdb, symmParams, cp);
207+
208+
// H symmetry A5 stoichiometry
209+
assertEquals("H", results.get(0).getSymmetry());
210+
assertEquals("A5", results.get(0).getStoichiometry());
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189212
}
190213
}

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

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6161
public static void main(String[] args) throws IOException,
6262
StructureException {
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64-
String name = "4hhb";
64+
String name = "1VYM";
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6666
// Download the biological assembly
6767
AtomCache cache = new AtomCache();
@@ -92,10 +92,10 @@ public static void main(String[] args) throws IOException,
9292
private static void showResults(Structure s, String name,
9393
QuatSymmetryResults results) {
9494

95-
String title = name + ": " + results.getSubunits().getStoichiometry()
95+
String title = name + ": " + results.getStoichiometry()
9696
+ ", " + results.getSymmetry();
9797

98-
if (results.getSubunits().isPseudoSymmetric())
98+
if (results.isPseudosymmetric())
9999
title += ", pseudosymmetric";
100100

101101
if (results.isLocal())

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