SCHWED-679: updated pipeline in BuildFromRawModel

modelling/pymod/_pipeline.py

@@ -141,6 +141,11 @@ def BuildFromRawModel(mhandle):
     # iteratively merge gaps of distance i and fill loops by database
     for distance in range(merge_distance):
         MergeGapsByDistance(mhandle, distance)
+        FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
+                            torsion_sampler, min_loops_required=-1,
+                            max_res_extension=6)
+    FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
+                        torsion_sampler, min_loops_required=-1)
     FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
                         torsion_sampler)