SCHWED-1316: remove conflicting atoms when building raw model.

modelling/src/model.cc

@@ -46,8 +46,25 @@ bool CheckBackboneAtoms(ResidueView res)
   return true;
 }
 
+void CleanupAtomConflicts(ResidueView& res) {
+  // remove atoms which are on top of any other atoms in the tpl entity
+  EntityView tpl = res.GetEntity();
+  AtomViewList atom_views = res.GetAtomList();
+  for (uint i = 0; i < atom_views.size(); ++i) {
+    AtomViewList on_top_atoms = tpl.FindWithin(atom_views[i].GetPos(), 0.0);
+    if (on_top_atoms.size() > 1) {
+      res.RemoveAtom(atom_views[i]);
+      // report
+      std::stringstream ss;
+      ss << "residue " << res.GetQualifiedName() << " has conflicting atom "
+         << atom_views[i].GetName() << " - skipping atom.";
+      LOG_WARNING(ss.str());
+    }
+  }
 }
 
+} // anon ns
+
 int CountEnclosedGaps(ModellingHandle& mhandle, const StructuralGap& gap,
                       bool insertions_only)
 {
@@ -541,6 +558,8 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
         src_res.GetOneLetterCode() << "'";
       throw promod3::Error(ss.str());
     }
+    // remove atoms with conflicting positions (i.e. on top of each other)
+    CleanupAtomConflicts(src_res);
     // check for complete backbone, or in case of Calpha only model building,
     // if the src_res has a Calpha atom
     if(!CheckBackboneAtoms(src_res)){