make rigidity of stem residues optional in BackboneRelaxer

loop/pymod/export_loop_closure.cc

@@ -90,6 +90,16 @@ boost::python::list KIC_VecList(const promod3::loop::BackboneList& bb_list, cons
   return return_list;
 }
 
+//wrapper for BackboneRelaxer constructor
+//promod3::loop::BackboneRelaxerPtr BBRelaxerWrapper(const promod3::loop::BackboneList& bb_list,
+//                                                  const ost::mol::mm::MMSettingsPtr settings,
+//                                                  bool fix_nterm, bool fix_cterm){
+//  promod3::loop::BackboneRelaxerPtr 
+//  p(new promod3::loop::BackboneRelaxer(bb_list,settings,
+//                                       fix_nterm,fix_cterm));
+//  return p;
+//}
+
 }
 
 void export_LoopClosure(){
@@ -107,7 +117,8 @@ void export_LoopClosure(){
   def("KIC",&KIC_ResidueHandle,(arg("n_stem"),arg("c_stem"),arg("pivot_one"),arg("pivot_two"),arg("pivot_three")));
   def("KIC",&KIC_VecList,(arg("n_stem_positions"),arg("c_stem_positions"),arg("pivot_one"),arg("pivot_two"),arg("pivot_three")));
   
-  class_<BackboneRelaxer> ("BackboneRelaxer", init<const BackboneList&, ost::mol::mm::MMSettingsPtr>())
+  class_<BackboneRelaxer> ("BackboneRelaxer", init<const BackboneList&, ost::mol::mm::MMSettingsPtr,optional<bool,bool> >())
+    //.def("__init__",make_constructor(&BBRelaxerWrapper))
     .def("Run",&BackboneRelaxer::Run,(arg("bb_list"),arg("steps")=100,arg("stop_criterion")=0.01))
   ;
 

loop/src/backbone_relaxer.cc

@@ -8,7 +8,8 @@ namespace promod3 { namespace loop {
 
 
 BackboneRelaxer::BackboneRelaxer(const BackboneList& bb_list, 
-                                 ost::mol::mm::MMSettingsPtr settings){
+                                 ost::mol::mm::MMSettingsPtr settings,
+                                 bool fix_nterm, bool fix_cterm){
 
   if(bb_list.size() < 2){
     throw promod3::Error("bb_list must be at least of length 2 for BackboneRelaxer!");
@@ -23,7 +24,8 @@ BackboneRelaxer::BackboneRelaxer(const BackboneList& bb_list,
   }
 
   
-  ost::mol::mm::TopologyPtr top = CreateBBListTop(bb_list,settings->forcefield);
+  ost::mol::mm::TopologyPtr top = CreateBBListTop(bb_list,settings->forcefield,
+                                                  fix_nterm, fix_cterm);
 
   positions_.resize(top->GetNumParticles());
 
@@ -154,7 +156,8 @@ void BackboneRelaxer::ExtractSimulationPositions(BackboneList& bb_list){
 
 
 ost::mol::mm::TopologyPtr BackboneRelaxer::CreateBBListTop(const BackboneList& bb_list, 
-                                                           ost::mol::mm::ForcefieldPtr ff){
+                                                           ost::mol::mm::ForcefieldPtr ff,
+                                                           bool fix_nterm, bool fix_cterm){
 
   std::vector<String> atom_types;
   std::vector<Real> masses;
@@ -223,16 +226,20 @@ ost::mol::mm::TopologyPtr BackboneRelaxer::CreateBBListTop(const BackboneList& b
     charges.push_back(0.0); //let's neglect electrostatic interactions
   }
 
+  if(fix_nterm){
     //set nterm rigid but let the c and o atoms move...
     masses[0] = 0.0;
     masses[1] = 0.0;
     if(bb_list[0].aa != ost::conop::GLY) masses[2] = 0.0;
+  }
 
+  if(fix_cterm){
     //set cterm rigid but let the n atom move
     masses[masses.size()-1] = 0.0;
     masses[masses.size()-2] = 0.0;
     masses[masses.size()-3] = 0.0;
     if(bb_list.back().aa != ost::conop::GLY) masses[masses.size()-4] = 0.0;
+  }
 
   //initialize mm-topology
   ost::mol::mm::TopologyPtr top(new ost::mol::mm::Topology(masses));

loop/src/backbone_relaxer.hh

@@ -16,7 +16,8 @@ struct BackboneRelaxer;
 typedef boost::shared_ptr<BackboneRelaxer> BackboneRelaxerPtr;
 
 struct  BackboneRelaxer {
-  BackboneRelaxer(const BackboneList& bb, ost::mol::mm::MMSettingsPtr settings);
+  BackboneRelaxer(const BackboneList& bb, ost::mol::mm::MMSettingsPtr settings,
+                  bool fix_nterm = true, bool fix_c_term = true);
   
   Real Run(BackboneList& bb_list, int steps = 100, Real stop_criterion = 0.01);
 private:
@@ -30,7 +31,8 @@ private:
   void ExtractSimulationPositions(BackboneList& bb_list);
 
   ost::mol::mm::TopologyPtr CreateBBListTop(const BackboneList& bb_list,
-                                            ost::mol::mm::ForcefieldPtr ff);
+                                            ost::mol::mm::ForcefieldPtr ff,
+                                            bool fix_nterm, bool fix_cterm);
   
   std::vector<ost::conop::AminoAcid> s_;
   ost::mol::mm::SimulationPtr simulation_;