added RuleBasedBuilder::GetUnknownAtoms

modules/conop/doc/connectivity.rst

@@ -250,4 +250,11 @@ The RuleBasedBuilder class
       
       :param atom: The missing atom's name
       :type  atom: string
+    
+   .. method:: GetUnknownAtoms(residue)
+   
+     Returns the unknown atoms of this residue, that is all atoms that 
+     are not part of the compound lib definition.
+     
+     :rtype: list of :class:`~ost.mol.AtomHandle` instances
 

modules/conop/pymod/export_builder.cc

@@ -55,5 +55,6 @@ void export_Builder() {
   class_<RuleBasedBuilder, bases<Builder> >("RuleBasedBuilder", 
                                             init<const CompoundLibPtr&>())
      .add_property("compound_lib", &RuleBasedBuilder::GetCompoundLib)
+     .def("GetUnknownAtoms", &RuleBasedBuilder::GetUnknownAtoms)
   ;
 }

modules/conop/src/chemdict_tool.cc

@@ -80,7 +80,9 @@ int main(int argc, char const *argv[])
     PrintUsage();
     return 0;
   }
-
+  if (!compound_lib) {
+    return 0;
+  }
   assert(compound_lib);
   conop::CompoundLibPtr in_mem_lib=compound_lib->Copy(":memory:");  
   compound_lib.reset();  

modules/conop/src/rule_based_builder.cc

@@ -82,6 +82,30 @@ bool RuleBasedBuilder::HasUnknownAtoms(mol::ResidueHandle res)
   return false;
 }
 
+mol::AtomHandleList RuleBasedBuilder::GetUnknownAtoms(mol::ResidueHandle res)
+{
+  mol::AtomHandleList unknown;
+  this->LookupCompound(res);
+  if (!last_compound_) {
+    return unknown;
+  }
+  this->ReorderAtoms(res, last_compound_);
+  AtomSpecList::const_iterator j=last_compound_->GetAtomSpecs().begin();
+  mol::AtomHandleList atoms=res.GetAtomList();
+  mol::AtomHandleList::iterator i=atoms.begin();
+  for (mol::AtomHandleList::iterator 
+       i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
+    if ((*i).Impl()->GetState()==std::numeric_limits<unsigned int>::max()) {
+      if (((*i).GetElement()=="H" || (*i).GetElement()=="D") && 
+          this->GetStrictHydrogenMode()==false) {
+        continue;
+      }
+      unknown.push_back(*i);
+    }
+  }
+  return unknown;
+}
+
 void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec) 
 {
   Conopology& conop_inst=Conopology::Instance();

modules/conop/src/rule_based_builder.hh

@@ -117,7 +117,10 @@ public:
   virtual void FillResidueProps(mol::ResidueHandle residue);
 
   /// \brief whether the residue has unknown atoms
-  bool HasUnknownAtoms(mol::ResidueHandle res);                              
+  bool HasUnknownAtoms(mol::ResidueHandle res);
+  
+  mol::AtomHandleList GetUnknownAtoms(mol::ResidueHandle res);
+  
   /// \brief Check whether the residue has all required atoms. This does not
   ///        include hydrogens and leaving atoms such as the terminal OXT.
   virtual bool IsResidueComplete(const mol::ResidueHandle& residue);