Fix biojava#449 by copying SEQRES to new chains

sbliven · sbliven · commit bfb6a31f1493 · 2016-04-06T16:51:20.000+02:00
Conveniently, the reducing a chain doesn't alter the seqres so we just copy it.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -264,26 +264,27 @@ public Structure reduce(Structure s) throws StructureException {
 						groups = Arrays.asList(chain.getGroupsByPDB(pdbresnum1, pdbresnum2));
 					}
 
-					// Create new chain, if needed
 					Chain c = null;
-					if ( prevChainId == null) {
-						// first chain...
-						c = new ChainImpl();
-						c.setChainID(chain.getChainID());
-						newS.addChain(c,modelNr);
-					} else if ( prevChainId.equals(chain.getChainID())) {
+					
+					// Reuse prevChain
+					if ( prevChainId != null && prevChainId.equals(chain.getChainID())) {
 						c = newS.getChainByPDB(prevChainId,modelNr);
-
 					} else {
 						try {
 							c = newS.getChainByPDB(chain.getChainID(),modelNr);
 						} catch (StructureException e){
 							// chain not in structure yet...
-							c = new ChainImpl();
-							c.setChainID(chain.getChainID());
-							newS.addChain(c,modelNr);
 						}
 					}
+					// Create new chain
+					if ( c == null) {
+						// first chain...
+						c = new ChainImpl();
+						c.setChainID(chain.getChainID());
+						newS.addChain(c,modelNr);
+						c.setSeqResGroups(chain.getSeqResGroups());
+						c.setSeqMisMatches(chain.getSeqMisMatches());
+					} 
 
 					// add the groups to the chain:
 					for ( Group g: groups) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -245,4 +245,71 @@ public void testFetchBehavior() throws IOException, ParseException {
 
 	}
 
+	@Test
+	public void testSeqRes() throws StructureException, IOException {
+		String name;
+		StructureIdentifier id;
+		Structure full, reduced;
+		Chain chain;
+		List<Group> seqres;
+
+		// normal structure
+		name = "1hh0";
+		id = new SubstructureIdentifier(name);
+		
+		full = id.loadStructure(cache);
+		assertEquals("Wrong number of models in full "+name,1,full.nrModels());
+		assertEquals("Wrong number of chains in full "+name,1,full.getChains().size());
+		chain = full.getChain(0);
+		seqres = chain.getSeqResGroups();
+		assertEquals("Wrong seqres length in full "+name,46,seqres.size());
+		
+		reduced = id.reduce(full);
+		assertEquals("Wrong number of models in reduced "+name,1,reduced.nrModels());
+		assertEquals("Wrong number of chains in reduced "+name,1,reduced.getChains().size());
+		chain = reduced.getChain(0);
+		seqres = chain.getSeqResGroups();
+		assertEquals("Wrong seqres length in reduced "+name,46,seqres.size());
+
+		// single chain
+		name = "1hh0.A";
+		id = new SubstructureIdentifier(name);
+		
+		full = id.loadStructure(cache);
+		assertEquals("Wrong number of models in full "+name,1,full.nrModels());
+		assertEquals("Wrong number of chains in full "+name,1,full.getChains().size());
+		chain = full.getChain(0);
+		seqres = chain.getSeqResGroups();
+		assertEquals("Wrong seqres length in full "+name,46,seqres.size());
+		
+		reduced = id.reduce(full);
+		assertEquals("Wrong number of models in reduced "+name,1,reduced.nrModels());
+		assertEquals("Wrong number of chains in reduced "+name,1,reduced.getChains().size());
+		chain = reduced.getChain(0);
+		seqres = chain.getSeqResGroups();
+		assertEquals("Wrong seqres length in reduced "+name,46,seqres.size());
+
+		// subrange
+		name = "1hh0.A:10-20";
+		id = new SubstructureIdentifier(name);
+		
+		full = id.loadStructure(cache);
+		assertEquals("Wrong number of models in full "+name,1,full.nrModels());
+		assertEquals("Wrong number of chains in full "+name,1,full.getChains().size());
+		chain = full.getChain(0);
+		seqres = chain.getSeqResGroups();
+		assertEquals("Wrong seqres length in full "+name,46,seqres.size());
+		assertEquals("Wrong SeqNum at first group in full",1,(int)chain.getAtomGroup(0).getResidueNumber().getSeqNum());
+
+		reduced = id.reduce(full);
+		assertEquals("Wrong number of models in reduced "+name,1,reduced.nrModels());
+		assertEquals("Wrong number of chains in reduced "+name,1,reduced.getChains().size());
+		chain = reduced.getChain(0);
+		seqres = chain.getSeqResGroups();
+		assertEquals("Wrong seqres length in reduced "+name,46,seqres.size());
+		
+		assertEquals("Wrong SeqNum at first group in reduced",10,(int)chain.getAtomGroup(0).getResidueNumber().getSeqNum());
+
+	}
+	
 }
