added chain property to atom handle and view py export; fixed...

added chain property to atom handle and view py export; fixed CreateViewFromAtomList python export to accept actual python lists

modules/mol/base/pymod/export_atom.cc

@@ -28,6 +28,14 @@ using namespace ost::mol;
 
 #include <ost/export_helper/generic_property_def.hh>
 #include <ost/export_helper/vector.hh>
+
+namespace {
+  ChainHandle get_chain(AtomHandle& a)
+  {
+    return a.GetResidue().GetChain();
+  }
+}
+
 void export_Atom()
 {
   class_<AtomBase> atom_base("AtomBase", no_init);
@@ -81,6 +89,8 @@ void export_Atom()
   class_<AtomHandle, bases<AtomBase> >("AtomHandle", init<>())
     .def("GetResidue",&AtomHandle::GetResidue)
     .add_property("residue",&AtomHandle::GetResidue)
+    .def("GetChain",get_chain)
+    .add_property("chain",get_chain)
     .def("GetBondList", &AtomHandle::GetBondList)
     .def("GetBondCount", &AtomHandle::GetBondCount)
     .def("GetEntity", &AtomHandle::GetEntity)

modules/mol/base/pymod/export_atom_view.cc

@@ -26,12 +26,21 @@ using namespace boost::python;
 using namespace ost;
 using namespace ost::mol;
 
+namespace {
+  ChainView get_chain(AtomView& a)
+  {
+    return a.GetResidue().GetChain();
+  }
+}
+
 void export_AtomView()
 {
 
   class_<AtomView, bases<AtomBase> >("AtomView", init<>())
     .def("GetResidue",&AtomView::GetResidue)
     .add_property("residue",&AtomView::GetResidue)
+    .def("GetChain",get_chain)
+    .add_property("chain",get_chain)
     .def(self==self)
     .def(self!=self)
     .add_property("handle", &AtomView::GetHandle)

modules/mol/base/pymod/export_entity_view.cc

@@ -30,6 +30,17 @@ using namespace ost::mol;
 
 namespace {
 
+template<class T>
+std::vector<T> from_list(const list& seq)
+{
+  std::vector<T> nrvo;
+  for (int i = 0; i < len(seq); ++i) {
+    nrvo.push_back(extract<T>(seq[i]));
+  }
+  return nrvo;
+}
+
+
 typedef ChainView (EntityView::*StringMethod)(const String&) const;
 typedef ChainView (EntityView::*StringMethod)(const String&) const;
 typedef EntityView (EntityView::*QueryMethod)(const Query&, uint) const;
@@ -45,8 +56,21 @@ StringMethod find_chain_str=&EntityView::FindChain;
 QSMethod select_string=&EntityView::Select;
 QueryMethod  select_query=&EntityView::Select;
 
-EntityView (*create_view_1)(const AtomHandleList&)=&CreateViewFromAtomList;
-EntityView (*create_view_2)(const AtomViewList&)=&CreateViewFromAtomList;
+EntityView create_view(const list& seq)
+{
+  if(len(seq)==0) return EntityView();
+  extract<AtomHandle> get_handle(seq[0]);
+  if(get_handle.check()) {
+    return CreateViewFromAtomList(from_list<AtomHandle>(seq));
+  }
+  extract<AtomView> get_view(seq[0]);
+  if(get_view.check()) {
+    return CreateViewFromAtomList(from_list<AtomView>(seq));
+  }
+  throw Error("expected sequence of atom handles or atom views");
+  return EntityView();
+}
+
 ResidueView (EntityView::*add_res_a)(const ResidueHandle&, 
                                      ViewAddFlags)=&EntityView::AddResidue;
 ResidueView (EntityView::*add_res_b)(const ResidueView&, 
@@ -164,8 +188,7 @@ void export_EntityView()
   def("Difference", &Difference);
   def("Intersection", &Intersection);
 
-  def("CreateViewFromAtoms", create_view_1);
-  def("CreateViewFromAtoms", create_view_2);
+  def("CreateViewFromAtoms", create_view);
   
   def("CreateEntityFromView", &CreateEntityFromView, 
       arg("handle")=EntityHandle());

modules/mol/base/src/view_op.cc

@@ -250,6 +250,7 @@ mol::EntityView assemble_view(const std::vector<T>& l, mol::EntityView v)
 {
   typedef typename std::vector<T>::const_iterator Iter;
   for (Iter i=l.begin(), e=l.end(); i!=e; ++i) {
+    if(!i->IsValid()) continue;
     if (!belongs_to_same_ent(*i, v))
       throw IntegrityError(combining_not_allowed);
     v.AddAtom(to_handle(*i), mol::ViewAddFlag::CHECK_DUPLICATES);