Fixing issue in cloning: was adding same group several times

josemduarte · josemduarte · commit 72317d93be62 · 2016-03-09T17:10:02.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -700,7 +700,14 @@ public static final Atom[] cloneAtomArray(Atom[] ca) {
 			Group parentN = (Group) parentG.clone();
 
 			newCA[apos] = parentN.getAtom(a.getName());
-			newChain.addGroup(parentN);
+			try {
+				// if the group doesn't exist yet, this produces a StructureException
+				newChain.getGroupByPDB(parentN.getResidueNumber()); 
+			} catch (StructureException e) {
+				// the group doesn't exist yet in the newChain, let's add it
+				newChain.addGroup(parentN);	
+			}
+			
 		}
 		return newCA;
 	}
