Merge pull request #573 from josemduarte/issue572

Solving #572
biojava · Sep 15, 2016 · 359dce8 · 359dce8
2 parents 89f710c + b696eac
commit 359dce8
Show file tree

Hide file tree

Showing 4 changed files with 19 additions and 34 deletions.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -71,7 +71,7 @@ public class AtomCache {
 	 * The default output bioassembly style: if true the bioassemblies are multimodel,
 	 * if false the bioassemblies are flat with renamed chains for symmetry-partners.
 	 */
-	public static final boolean DEFAULT_BIOASSEMBLY_STYLE = true;
+	public static final boolean DEFAULT_BIOASSEMBLY_STYLE = false;
 
 	public static final String BIOL_ASSEMBLY_IDENTIFIER = "BIO:";
 	public static final String CHAIN_NR_SYMBOL = ":";

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
@@ -68,31 +68,24 @@ public static List<Subunit> extractSubunits(Structure structure,
 		// The extracted subunit container
 		List<Subunit> subunits = new ArrayList<Subunit>();
 
-		// Biological assemblies require all models
-		int models = 1;
-		if (structure.isBiologicalAssembly())
-			models = structure.nrModels();
+
+		for (Chain c : structure.getChains()) {
 
-		logger.info("Protein models used in calculation: " + models);
+			// Only take protein chains
+			if (c.isProtein()) {
+				Atom[] ca = StructureTools.getRepresentativeAtomArray(c);
+				logger.debug("Chain " + c.getId() + "; CA Atoms: "
+						+ ca.length + "; SEQRES: " + c.getSeqResSequence());
+				subunits.add(new Subunit(ca, c.getName(), null, structure));
 
-		for (int i = 0; i < models; i++) {
-			for (Chain c : structure.getChains(i)) {
-
-				// Only take protein chains
-				if (StructureTools.isProtein(c)) {
-					Atom[] ca = StructureTools.getRepresentativeAtomArray(c);
-					logger.info("Chain " + c.getId() + "; CA Atoms: "
-							+ ca.length + "; SEQRES: " + c.getSeqResSequence());
-					subunits.add(new Subunit(ca, c.getName(), null, structure));
-
-				}
 			}
 		}
+
 
 		// Calculate the minimum length of a Subunit
 		int adjustedMinLen = calcAdjustedMinimumSequenceLength(subunits,
 				absMinLen, fraction, minLen);
-		logger.info("Adjusted minimum sequence length: " + adjustedMinLen);
+		logger.debug("Adjusted minimum sequence length: " + adjustedMinLen);
 
 		// Filter out short Subunits
 		for (int s = subunits.size() - 1; s >= 0; s--) {

diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java
@@ -40,13 +40,13 @@ public void test() throws IOException, StructureException {
 		// first assembly
 		id = new BioAssemblyIdentifier("BIO:2ehz:1");
 		s = cache.getStructure(id);
-		assertEquals("Number of models",8, s.nrModels());
-		assertEquals("Number of chains per model",11, s.getChains(0).size());
+		assertEquals("Number of models",1, s.nrModels());
+		assertEquals("Number of chains",88, s.getChains().size());
 		// equivalent
 		id = new BioAssemblyIdentifier("BIO:2ehz");
 		s = cache.getStructure(id);
-		assertEquals("Number of models",8, s.nrModels());
-		assertEquals("Number of chains per model",1,s.getPolyChains(0).size());
+		assertEquals("Number of models",1, s.nrModels());
+		assertEquals("Number of chains",8,s.getPolyChains().size());
 		// No second
 		id = new BioAssemblyIdentifier("BIO:2ehz:2");
 		try {

diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java
@@ -63,18 +63,12 @@ public void test4A1I() throws IOException, StructureException {
 
 		//System.out.println(bioAssembly.toPDB());
 
-		assertEquals(bioAssembly.nrModels(), 2);
+		assertEquals(1, bioAssembly.nrModels());
 
-		assertTrue(bioAssembly.getChains().size() > 0);
+		assertEquals(2, bioAssembly.getPolyChains().size());
 
-		// Check that one model has Chain B and the other has chain G
-		Chain g = bioAssembly.getPolyChainByPDB("G", 0);
-		Chain b = bioAssembly.getPolyChainByPDB("B", 1);
-		// Anthony Bradley - I think the model numbering here is arbitrary???
-		if(g==null){
-			g = bioAssembly.getPolyChainByPDB("G", 1);
-			b = bioAssembly.getPolyChainByPDB("B", 0);
-		}
+		Chain g = bioAssembly.getPolyChainByPDB("G_1");
+		Chain b = bioAssembly.getPolyChainByPDB("B_2");
 
 		assertNotNull(g);
 
@@ -84,8 +78,6 @@ public void test4A1I() throws IOException, StructureException {
 
 		assertFalse(bioAssembly.hasChain("H"));
 
-		assertEquals(1,bioAssembly.getPolyChains(0).size());
-		assertEquals(1,bioAssembly.getPolyChains(1).size());
 
 
 	}