Remove the useMmcif from test

Fix the bug and clean up the logic of adding seq res groups biojava#517
abradle · Jul 15, 2016 · 1dce7cb · 1dce7cb
1 parent c007868
commit 1dce7cb
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -480,21 +480,18 @@ public static void addSeqRes(Chain modelChain, String sequence) {
 		GroupType chainType = getChainType(modelChain.getAtomGroups());
 		for(int i=0; i<sequence.length(); i++){
 			char singleLetterCode = sequence.charAt(i);
-			Group group;
+			Group group = null;
 			if(seqResGroups.size()<=i){
-				group=null;
 			}
 			else{
 				group=seqResGroups.get(i);
 			}
 			if(group!=null){
-				group=null;
 				continue;
 			}
 			group = getSeqResGroup(modelChain, singleLetterCode, chainType);
 			addGroupAtId(seqResGroups, group, i);
 			seqResGroups.set(i, group);
-			group=null;
 		}
 	}
 
@@ -514,7 +511,7 @@ private static <T> void addGroupAtId(List<T> seqResGroups, T group, int sequence
 		while(seqResGroups.size()<=sequenceIndexId){
 			seqResGroups.add(null);
 		}
-		if(sequenceIndexId>0){
+		if(sequenceIndexId>=0){
 			seqResGroups.set(sequenceIndexId, group);
 		}		
 	}

diff --git a/...ture/src/test/java/org/biojava/nbio/structure/symmetry/core/TestQuatSymmetryDetector.java b/...ture/src/test/java/org/biojava/nbio/structure/symmetry/core/TestQuatSymmetryDetector.java
@@ -55,14 +55,11 @@ public class TestQuatSymmetryDetector {
 	public void testNMR() throws IOException, StructureException {
 
 		AtomCache cache = new AtomCache();
-		cache.setUseMmCif(true);
 		Structure pdb = cache.getStructure("BIO:1b4c:1");
-
 		SubunitClustererParameters clusterParams = new SubunitClustererParameters();
 		QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
 		QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
 				pdb, symmParams, clusterParams);
-
 		// C2 symmetry non pseudosymmetric
 		assertEquals("C2", symmetry.getSymmetry());
 		assertEquals("A2", symmetry.getSubunits().getStoichiometry());