SCHWED-1560: bugfixes for all atom pipeline

modelling/pymod/_closegaps.py

@@ -149,11 +149,15 @@ def _GetBestLC(mhandle, loop_candidates, start_resnum, chain_idx,
         # extract relevant loop candidates and scores
         aa_loop_candidates = loop_candidates.Extract(min_indices)
         for key in all_scores:
-            all_scores[key] = all_scores[key][min_indices]
-        # score them w/o relaxation
+            all_scores[key] = [all_scores[key][i] for i in min_indices]
+        # keep backup of loop of interest
         loop_length = len(loop_candidates[0])
         loop_backup = aa_sc_env.GetEnvironment(start_resnum, loop_length,
                                                chain_idx)
+        # setup empty lists for AA results
+        for key in _GetAaScoringKeys():
+            all_scores[key] = list()
+        # score them w/o relaxation
         for lc_bb_list in aa_loop_candidates:
             # setup sc env. and reconstruct
             aa_sc_env.SetEnvironment(lc_bb_list, start_resnum, chain_idx)
@@ -161,9 +165,9 @@ def _GetBestLC(mhandle, loop_candidates, start_resnum, chain_idx,
             # fix env. for scoring (always contains full loop too!)
             aa_score_env.SetEnvironment(sc_result.env_pos)
             for key in _GetAaScoringKeys():
-                scores = aa_scorer[key].CalculateScore(start_resnum,
+                score = aa_scorer[key].CalculateScore(start_resnum,
                                                       loop_length, chain_idx)
-                all_scores[key] = scores
+                all_scores[key].append(score)
         # reset aa_sc_env
         aa_sc_env.SetEnvironment(loop_backup)
         # NOTE: we leave the aa_score_env in a modified state
@@ -284,6 +288,9 @@ def _CloseLoopFrame(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
         # update score env.
         mhandle.backbone_scorer_env.SetEnvironment(bb_list, start_resnum,
                                                    actual_chain_idx)
+        if all_atom:
+            mhandle.all_atom_sidechain_env.SetEnvironment(bb_list, start_resnum,
+                                                          actual_chain_idx)
         ost.LogInfo("Resolved %s by filling %s (%d candidates)" % \
                     (str(gap_orig),
                      str(actual_extended_gaps[idx_a]),