Use all repeats to calculate hierarchical axes in internal symmetry

lafita · lafita · commit a07102d79663 · 2016-06-14T12:55:23.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
@@ -581,14 +581,11 @@ private int getNumRepeats(int level) {
 	 */
 	public List<Integer> getFirstRepeats(int level) {
 		List<Integer> firstRepeats = new ArrayList<Integer>();
-		if (level == 0)
-			firstRepeats.add(0); // No top level present
-		else {
-			int m = getNumRepeats(level);//size of the level
-			int d = axes.get(level).getOrder(); // degree of this node
-			for (int firstRepeat = 0; firstRepeat < m*d; firstRepeat+=d)
-				firstRepeats.add(firstRepeat);
-		}
+		int m = getNumRepeats(level+1); //size of the level
+		int d = axes.get(level).getOrder(); //degree of this level
+		int n = m*d; // number of repeats included in each axis
+		for (int firstRepeat = 0; firstRepeat < getNumRepeats(); firstRepeat+=n)
+			firstRepeats.add(firstRepeat);
 		return firstRepeats;
 	}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -902,8 +902,6 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 
 		List<List<Integer>> block = msa.getBlocks().get(0).getAlignRes();
 		int length = block.get(0).size();
-		Atom[] atoms = StructureTools.cloneAtomArray(msa.getEnsemble()
-				.getAtomArrays().get(0));
 
 		if (axes != null) {
 			for (int level = 0; level < axes.getNumLevels(); level++) {
@@ -913,7 +911,7 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 				List<Atom> list2 = new ArrayList<Atom>();
 
 				for (int firstRepeat : axes.getFirstRepeats(level)) {
-
+						
 					Matrix4d transform = axes.getRepeatTransform(firstRepeat);
 
 					List<List<Integer>> relation = axes.getRepeatRelation(
@@ -927,10 +925,12 @@ public static void updateSymmetryTransformation(SymmetryAxes axes,
 							Integer pos1 = block.get(p1).get(k);
 							Integer pos2 = block.get(p2).get(k);
 							if (pos1 != null && pos2 != null) {
-								Calc.transform(atoms[pos1], transform);
-								Calc.transform(atoms[pos2], transform);
-								list1.add(atoms[pos1]);
-								list2.add(atoms[pos2]);
+								Atom a = (Atom) msa.getAtomArrays().get(p1)[pos1].clone();
+								Atom b = (Atom) msa.getAtomArrays().get(p2)[pos2].clone();
+								Calc.transform(a, transform);
+								Calc.transform(b, transform);
+								list1.add(a);
+								list2.add(b);
 							}
 						}
 					}
