Fix contiguous helices in SSE counting

lafita · sbliven · commit 3fea9a97a4a2 · 2016-06-02T15:13:56.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -29,6 +29,7 @@
 import javax.vecmath.Matrix4d;
 
 import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.multiple.Block;
@@ -341,11 +342,27 @@ private static int countHelixStrandSSE(Atom[] atoms) {
 		List<SecStrucElement> sses = SecStrucTools
 				.getSecStrucElements(SymmetryTools.getGroups(atoms));
 		int count = 0;
+
+		//keep track of different helix types
+		boolean helix = false;
+		int hEnd = 0;
+
 		for (SecStrucElement sse : sses) {
 			SecStrucType t = sse.getType();
-			if (t.isBetaStrand() || t.isHelixType()) {
+			if (t.isBetaStrand()) {
+				helix = false;
 				count++;
-			}
+			} else if (t.isHelixType()){
+				if (helix){
+					// If this helix is contiguous to the previous
+					if (sse.getRange().getStart().getSeqNum() + 1 == hEnd)
+						hEnd = sse.getRange().getEnd().getSeqNum();
+					else
+						count++;
+				} else
+					count++;
+			} else
+				helix = false;
 		}
 		return count;
 	}
