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josemduartejosemduarte
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New test
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‎biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java‎

Lines changed: 93 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -30,10 +30,14 @@
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import org.biojava.nbio.structure.AminoAcidImpl;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.AtomImpl;
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import org.biojava.nbio.structure.Chain;
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import org.biojava.nbio.structure.ChainImpl;
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import org.biojava.nbio.structure.EntityInfo;
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import org.biojava.nbio.structure.Group;
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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.StructureImpl;
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import org.biojava.nbio.structure.StructureTools;
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import org.junit.Test;
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@@ -85,6 +89,47 @@ public void testMergeIdentical() {
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}
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@Test
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public void testMergeIdenticalByEntityId() {
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// Create 2 Atom Arrays, with same entity id
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Atom[] reprAtoms1 = mockAtomArray("A", 1, 10, "ALA", -1, null);
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Structure structure1 = reprAtoms1[0].getGroup().getChain().getStructure();
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Atom[] reprAtoms2 = mockAtomArray("B", 1, 10, "PRO", -1, null);
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Structure structure2 = reprAtoms2[0].getGroup().getChain().getStructure();
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// Create two SubunitCluster with same entity id
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SubunitCluster sc1 = new SubunitCluster(new Subunit(reprAtoms1,
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"A", null, structure1));
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SubunitCluster sc2 = new SubunitCluster(new Subunit(reprAtoms2,
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"B", null, structure2));
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boolean merged = sc1.mergeIdenticalByEntityId(sc2);
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// Merged have to be true, and the merged SubunitCluster is sc1
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assertTrue(merged);
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assertEquals(2, sc1.size());
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assertEquals(1, sc2.size());
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assertEquals(10, sc1.length());
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// Create an Atom Array of poly-glycine with a different entity id
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Atom[] reprAtoms3 = mockAtomArray("A", 2, 10, "GLY", -1, null);
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Structure structure3 = reprAtoms2[0].getGroup().getChain().getStructure();
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SubunitCluster sc3 = new SubunitCluster(new Subunit(reprAtoms3,
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"A", null, structure3));
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merged = sc1.mergeIdenticalByEntityId(sc3);
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// Merged have to be false, and Clusters result unmodified
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assertFalse(merged);
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assertEquals(2, sc1.size());
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assertEquals(1, sc2.size());
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assertEquals(10, sc1.length());
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}
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/**
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* Test {@link SubunitCluster#mergeSequence(SubunitCluster, SubunitClustererParameters)}
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*
@@ -232,18 +277,64 @@ public void testDivideInternally() throws StructureException, IOException {
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}
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/**
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* Create a mock atom array, with size1 residues of type1, followed by size2 residues of type2
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* Create a mock atom array, with size1 residues of type1, followed by size2 residues of type2.
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*
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* @param size1 the number of residues of type1 to add
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* @param type1 the 3 letter code of residue
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* @param size2 the number of residues of type2 to add, if -1 none are added
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* @param type2 the 3 letter code of residue, if null none are added
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* @return the mock atom array
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*/
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private Atom[] mockAtomArray(int size1, String type1, int size2, String type2) {
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List<Atom> atoms = new ArrayList<>(size1 + size2);
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for (int i = 0; i < size1; i++) {
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Group g = new AminoAcidImpl();
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g.setPDBName(type1);
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Atom a = new AtomImpl();
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a.setName(StructureTools.CA_ATOM_NAME);
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g.addAtom(a);
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atoms.add(a);
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}
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if (size2 >= 0 && type2 !=null) {
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for (int i = 0; i < size2; i++) {
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Group g = new AminoAcidImpl();
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g.setPDBName(type2);
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Atom a = new AtomImpl();
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a.setName(StructureTools.CA_ATOM_NAME);
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g.addAtom(a);
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atoms.add(a);
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}
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}
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return atoms.toArray(new Atom[0]);
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}
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/**
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* Create a mock atom array, with size1 residues of type1, followed by size2 residues of type2.
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*
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* @param chainId a chain with this chain id will be set as parent of groups
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* @param entityId an entity with this id will be set as parent of chain
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* @param size1 the number of residues of type1 to add
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* @param type1 the 3 letter code of residue
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* @param size2 the number of residues of type2 to add, if -1 none are added
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* @param type2 the 3 letter code of residue, if null none are added
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* @return the mock atom array
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*/
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private Atom[] mockAtomArray(String chainId, int entityId, int size1, String type1, int size2, String type2) {
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Chain chain = new ChainImpl();
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Structure structure = new StructureImpl();
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chain.setId(chainId);
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structure.addChain(chain);
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EntityInfo entityInfo = new EntityInfo();
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entityInfo.setMolId(entityId);
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chain.setEntityInfo(entityInfo);
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List<Atom> atoms = new ArrayList<>(size1 + size2);
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for (int i = 0; i < size1; i++) {
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Group g = new AminoAcidImpl();
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g.setPDBName(type1);
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chain.addGroup(g);
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Atom a = new AtomImpl();
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a.setName(StructureTools.CA_ATOM_NAME);
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g.addAtom(a);
@@ -254,6 +345,7 @@ private Atom[] mockAtomArray(int size1, String type1, int size2, String type2) {
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for (int i = 0; i < size2; i++) {
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Group g = new AminoAcidImpl();
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g.setPDBName(type2);
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chain.addGroup(g);
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Atom a = new AtomImpl();
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a.setName(StructureTools.CA_ATOM_NAME);
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g.addAtom(a);

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