Use pdbx_entity_branch connectivity data in DNG

modules/io/src/mol/entity_io_mmcif_handler.cc

@@ -55,6 +55,13 @@ void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
   MMCifReader reader(stream,ent,  
                      IOProfileRegistry::Instance().GetDefault());
   reader.Parse();
+  // This is a hack: the reader is not available in
+  // file_loader.cc/ FileLoader::TryLoadEntity, but this is where the Conop
+  // processor is called to establish covalent bonds. Since RequiresProcessor()
+  // always returns true, the mechanism always tries to establish bonds, so we
+  // do that here.
+  MMCifInfo info = reader.GetInfo();
+  info.ConnectBranchLinks();
 }
 
 void EntityIOMMCIFHandler::Export(const mol::EntityView& ent,
@@ -69,6 +76,13 @@ void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
   MMCifReader reader(filename, ent,  
                      IOProfileRegistry::Instance().GetDefault());
   reader.Parse();
+  // This is a hack: the reader is not available in
+  // file_loader.cc/ FileLoader::TryLoadEntity, but this is where the Conop
+  // processor is called to establish covalent bonds. Since RequiresProcessor()
+  // always returns true, the mechanism always tries to establish bonds, so we
+  // do that here.
+  MMCifInfo info = reader.GetInfo();
+  info.ConnectBranchLinks();
 }
 
 bool EntityIOMMCIFHandler::ProvidesImport(const boost::filesystem::path& loc,