fix rule-based conop with strict_hydrogens=false

modules/conop/src/processor.cc

@@ -290,15 +290,6 @@ void Processor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
                                       CompoundPtr compound,
                                       bool strict_hydrogens) const
 {
-
-  //if (!compound) {
-  //  dist_connect(this, rh.GetAtomList());
-  //  return;
-  //}
-  //if (unknown_atoms_) {
-  //  dist_connect(this, rh.GetAtomList());
-  //  return;
-  //}
   mol::XCSEditor e=rh.GetEntity().EditXCS(mol::BUFFERED_EDIT);
   BondSpecList::const_iterator j=compound->GetBondSpecs().begin();
   mol::AtomHandleList atoms=rh.GetAtomList();
@@ -307,18 +298,16 @@ void Processor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
       mol::AtomHandle a1=this->LocateAtom(atoms, bond.atom_one);
       mol::AtomHandle a2=this->LocateAtom(atoms, bond.atom_two);
       if (a1.IsValid() && a2.IsValid()) { 
+        if (!strict_hydrogens && (a1.GetElement()=="H" ||
+                                  a1.GetElement()=="D" ||
+                                  a2.GetElement()=="H" ||
+                                  a2.GetElement()=="D")) {
+          continue;
+        }
         if (!this->GetCheckBondFeasibility()) {
-          if (strict_hydrogens && (a1.GetElement()=="H" || 
-                                   a2.GetElement()=="D")) {
-            continue;
-          }
           e.Connect(a1, a2, bond.order);
         } else { 
           if (IsBondFeasible(a1, a2)) {
-            if (strict_hydrogens && (a1.GetElement()=="H" || 
-                                     a2.GetElement()=="D")) {
-              continue;
-            }
             e.Connect(a1, a2, bond.order);
           }
         }
@@ -405,8 +394,8 @@ void Processor::DistanceBasedConnect(mol::AtomHandle atom) const
        e=alist.end();it!=e;++it) {
     if (*it!=atom) {
       if (IsBondFeasible(atom, *it)) {
-        if (Processor::AreResiduesConsecutive(res_a, it->GetResidue()) || 
-            it->GetResidue()==res_a) {                      
+        if (it->GetResidue()==res_a ||
+            Processor::AreResiduesConsecutive(res_a, it->GetResidue())) {
             editor.Connect(*it, atom);
         }
       }

modules/conop/src/rule_based.cc

@@ -47,7 +47,7 @@ void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
       mol::ResidueHandle residue = *j;
       mol::AtomHandleList atoms_to_connect;
       CompoundPtr compound = lib_->FindCompound(residue.GetName(), Compound::PDB);
-      if (!compound) {
+      if (!compound && this->GetConnect()) {
         // process unknown residue...
         this->ProcessUnkResidue(diags, residue, atoms_to_connect);
         for (mol::AtomHandleList::iterator k = atoms_to_connect.begin(),
@@ -79,6 +79,16 @@ void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
              e3=atoms_to_connect.end(); k!= e3; ++k) {
           this->DistanceBasedConnect(*k);
         }
+        if (!this->GetStrictHydrogens()) {
+          mol::AtomHandleList atoms = residue.GetAtomList();
+          for (mol::AtomHandleList::iterator k = atoms.begin(),
+               e3 = atoms.end(); k != e3; ++k) {
+            const String& ele = k->GetElement();
+            if ((ele == "D" || ele == "H") && k->GetBondCount() == 0) {
+              this->DistanceBasedConnect(*k);
+            }
+          }
+        }
       }
       prev = residue;
     }