Updated violation analysis if clusters

ariaec/analysis.py

@@ -454,9 +454,13 @@ class EnsembleAnalysis(object):
         # ens_getdists = ensemble.getDistances
 
         LOG.info("Violation analysis")
-        out_file = os.path.join(out_path, 'violations.csv')
-        self.violation_analysis(project, iteration_id, restraints, bestensemble,
-                                out_file, dists_ref=dists_ref)
+        for clustidx, clustensemble in clustensembles:
+            out_file = os.path.join(
+                out_path,
+                'violations.csv' if len(clustensembles) == 1 else
+                'violations-clust%d.csv' % clustidx)
+            self.violation_analysis(project, iteration_id, restraints,
+                                    clustensemble, out_file, dists_ref=dists_ref)
 
         # For the plotting part, we need a StructureEnsemble instance with all
         # pdb files from the iteration