Bugfixed BFT testset gen. and using new copy constructor for rotamers.

extras/scoring_weight_training/generate_bft_testset.py

 """
 GOAL: extract loop examples from structure DB
 OUT: fragments.json: list of fragment infos ([chain_idx, offset, length])
+-> fragments are linked to PM3's default structure DB
+-> each fragment has at least 50% coils and doesn't touch termini
 """
 
 import random, json
@@ -12,7 +14,7 @@ from promod3 import loop
 ###############################################################################
 min_coord_size = 50        # min. size for StructureDB entry to be considered
 terminal_res_to_skip = 2   # first and last x residues are never chosen for loop
-num_chains = 3973          # get x random chains from structure DB
+num_chains = 4000          # get x random chains from structure DB
 num_loops_per_len = 5000   # number of loops to pick for each loop length
 loop_range = range(3,13)   # range of loop lengths (uniformly distributed)
 random.seed(42)            # fixed seed for reproducibilty
@@ -88,7 +90,7 @@ for loop_length in loop_range:
   for start_idx in range(terminal_res_to_skip, range_end):
     num_coil = sum(is_coil[start_idx:start_idx+loop_length])
     to_skip = any(res_to_skip[start_idx:start_idx+loop_length])
-    if num_coil >= num_coil_thresh:
+    if num_coil >= num_coil_thresh and not to_skip:
       possible_start_indices.append(start_idx)
   # show it
   print "LOOP LEN %d: %d choices" % (loop_length, len(possible_start_indices))
@@ -96,9 +98,23 @@ for loop_length in loop_range:
   start_indices = random.sample(possible_start_indices, num_loops_per_len)
   for start_idx in start_indices:
     coord_idx = back_mapping[start_idx]
-    fragment = loop.FragmentInfo(coord_idx, start_idx - first_idx[coord_idx],
-                                 loop_length)
-    fragments.append(fragment)
+    offset = start_idx - first_idx[coord_idx]
+    fragments.append(loop.FragmentInfo(coord_idx, offset, loop_length))
+
+# check all fragments
+for fragment in fragments:
+  # check termini
+  coord_info = structure_db.GetCoordInfo(fragment.chain_index)
+  assert(fragment.offset >= terminal_res_to_skip)
+  assert(fragment.offset + fragment.length + terminal_res_to_skip\
+         <= coord_info.size)
+  # check coils
+  frag_info = loop.FragmentInfo(fragment.chain_index, 0, coord_info.size)
+  dssp_states = structure_db.GetDSSPStates(frag_info)
+  coilness = [1 if el in ['T','C','S'] else 0 for el in dssp_states]
+  assert(len(coilness) == coord_info.size)
+  num_coil = sum(coilness[fragment.offset:fragment.offset+fragment.length])
+  assert(num_coil >= round(fragment.length*0.5))
 
 # store it
 with open(out_fragments, "w") as json_file:

sidechain/src/sidechain_reconstructor.cc

@@ -261,9 +261,7 @@ void SidechainReconstructor::CollectRotamerGroups_(
       env_->GetRotamerGroup(rot_group, res_idx);
       if (rot_group) {
         // add a copy (we modify rotamer in ApplySelfEnergyThresh!)
-        RotamerGroupPtr new_group(
-          new RotamerGroup(rot_group->GetRotamers(),
-                           rot_group->GetResidueIndex()));
+        RotamerGroupPtr new_group(new RotamerGroup(*rot_group));
         rotamer_groups.push_back(new_group);
         res->rotamer_res_indices.push_back(i);
       }