added a io/mae profiling test

modules/conop/src/builder.cc

@@ -63,7 +63,6 @@ bool Builder::DoesPeptideBondExist(const mol::AtomHandle& n,
 bool Builder::IsBondFeasible(const mol::AtomHandle& atom_a,
                              const mol::AtomHandle& atom_b)
 {
-  Real len=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
   Real radii=0.0;
   if (atom_a.GetRadius()>0.0) {
     radii=atom_a.GetRadius();
@@ -75,9 +74,9 @@ bool Builder::IsBondFeasible(const mol::AtomHandle& atom_a,
   } else {
     return false;
   } 
-  radii*=0.5;
-  Real upper_bound=1.5*radii*radii;
-  Real lower_bound=0.25*radii*radii;
+  Real len=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
+  Real lower_bound=radii*radii*0.0625;
+  Real upper_bound=lower_bound*6.0;
   return (len<=upper_bound && len>=lower_bound);
 }
 

modules/io/src/mol/entity_io_mae_handler.cc

@@ -330,14 +330,19 @@ bool EntityIOMAEHandler::ProvidesExport(const boost::filesystem::path& loc,
 
 mol::EntityHandle LoadMAE(const String& file_name) 
 {
-  Profile profile_load("LoadMAE");
   //conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();  
   conop::BuilderP builder(new conop::HeuristicBuilder);
   MAEReader reader(file_name);
   mol::EntityHandle ent=mol::CreateEntity();
   mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
-  reader.Import(ent);
-  conop::Conopology::Instance().ConnectAll(builder,ent);    
+  {
+    Profile profile("import MAE");
+    reader.Import(ent);
+  }
+  {
+    Profile profile("connect all");
+    conop::Conopology::Instance().ConnectAll(builder,ent);    
+  }
   return ent;
 }
 

modules/io/tests/CMakeLists.txt

@@ -11,4 +11,8 @@ set(OST_IO_UNIT_TESTS
 # missing: test_star_parser.cc
 ost_unittest(io "${OST_IO_UNIT_TESTS}")
 target_link_libraries(io_tests ost_mol)
-target_link_libraries(io_tests ost_seq)
\ No newline at end of file
+target_link_libraries(io_tests ost_seq)
+
+add_executable(test_mae_standalone test_mae_standalone.cc)
+target_link_libraries(test_mae_standalone ost_mol)
+target_link_libraries(test_mae_standalone ost_io)

modules/io/tests/test_mae_standalone.cc

+#include <ost/log.hh>
+#include <ost/conop/conop.hh>
+#include <ost/io/entity_io_mae_handler.hh>
+
+using namespace ost;
+
+int main(int argc, char** argv)
+{
+  if(argc>1) {
+    mol::EntityHandle eh=io::LoadMAE(argv[1]);
+  }
+
+  return 0;
+}