improve GuessAtomElement

It seems, just looking at the number of atoms is not enough,
we also have to look at the hetatm flag. The whole element
guessing code is still quite shaky and should be improved.

modules/conop/src/heuristic.cc

@@ -37,7 +37,7 @@ void HeuristicProcessor::ProcessUnkResidue(DiagnosticsPtr diags,
        i = atoms.begin(), e = atoms.end(); i != e; ++i) {
     mol::AtomHandle a = *i;
     if (!Conopology::Instance().IsValidElement(a.GetElement()))
-      a.SetElement(GuessAtomElement(a.GetName(), atoms.size()));
+      a.SetElement(GuessAtomElement(a.GetName(), a.IsHetAtom(), atoms.size()));
   }
 
   res.SetChemClass(GuessChemClass(res));

modules/conop/src/processor.cc

@@ -133,7 +133,7 @@ mol::ChemClass GuessChemClass(mol::ResidueHandle res)
   return mol::ChemClass();
 }
 
-String GuessAtomElement(const String& aname, int atom_count)
+String GuessAtomElement(const String& aname, bool hetatm, int atom_count)
 {
   static String l1[] = {
     "H","C","N","O","P","S","K"
@@ -158,7 +158,7 @@ String GuessAtomElement(const String& aname, int atom_count)
   if(ele[0]=='H') {
     return "H";
   }
-  if (atom_count > 1) {
+  if (!hetatm || atom_count > 1) {
     if (ele=="CA" || ele=="CB") {
       return "C";
     }

modules/conop/src/processor.hh

@@ -126,7 +126,8 @@ String DLLEXPORT_OST_CONOP StringFromConopAction(ConopAction action);
 
 
 /// \brief guess element of atom based on name and hetatm flag
-String DLLEXPORT_OST_CONOP GuessAtomElement(const String& atom_name, int atom_count);
+String DLLEXPORT_OST_CONOP GuessAtomElement(const String& atom_name, bool hetatm,
+                                            int atom_count);
 
 /// \brief guess chemclass based on atoms of residue
 mol::ChemClass DLLEXPORT_OST_CONOP GuessChemClass(mol::ResidueHandle res);

modules/conop/src/rule_based.cc

@@ -102,7 +102,7 @@ void RuleBasedProcessor::ProcessUnkResidue(DiagnosticsPtr diags,
          e = atoms.end(); i !=e; ++i) {
       remaining_atoms.push_back(*i);
       if (!Conopology::Instance().IsValidElement(i->GetElement()))
-        i->SetElement(GuessAtomElement(i->GetName(), atoms.size()));
+        i->SetElement(GuessAtomElement(i->GetName(), i->IsHetAtom(), atoms.size()));
     }
   }
   // Don't do anything if treatment is set to SILENT
@@ -139,7 +139,7 @@ void RuleBasedProcessor::ProcessUnkAtoms(DiagnosticsPtr diags,
          e = unks.end(); i !=e; ++i) {
       remaining_atoms.push_back(*i);
       if (!Conopology::Instance().IsValidElement(i->GetElement()))
-        i->SetElement(GuessAtomElement(i->GetName(), res.GetAtomCount()));
+        i->SetElement(GuessAtomElement(i->GetName(), i->IsHetAtom(), res.GetAtomCount()));
     }
   }