removed some functionality to get rid of settings object in simulation

object

modules/mol/mm/src/simulation.cc

@@ -3,8 +3,7 @@
 namespace ost{ namespace mol{ namespace mm{
 
 Simulation::Simulation(const ost::mol::EntityHandle& handle, 
-                       const MMSettingsPtr settings): 
-                                         settings_(settings){
+                       const MMSettingsPtr settings){
 
   //note, that ent_ will be "completed" inside this function!
   //(hydrogens and shit)
@@ -14,8 +13,7 @@ Simulation::Simulation(const ost::mol::EntityHandle& handle,
 }
 
 Simulation::Simulation(const TopologyPtr top,
-                       const MMSettingsPtr settings): 
-                                         settings_(settings){
+                       const MMSettingsPtr settings){
 
   this->Init(top);
 }
@@ -81,14 +79,6 @@ void Simulation::Init(const TopologyPtr top){
   }
 }
 
-ost::mol::EntityHandle Simulation::GetEntityStandardNaming(){
-  ost::mol::EntityHandle ent = top_->GetEntity();
-  ent = ent.Copy();
-  settings_->forcefield->AssignFFSpecificNames(ent,true);
-  MMModeller::AssignPDBNaming(ent);
-  return ent;
-}
-
 geom::Vec3List Simulation::GetPositions(bool enforce_periodic_box, bool in_angstrom){
   geom::Vec3List return_vec;
   StateExtractor::ExtractPositions(context_,return_vec, enforce_periodic_box, in_angstrom);

modules/mol/mm/src/simulation.hh

@@ -50,8 +50,6 @@ public:
 
   ost::mol::EntityHandle GetEntity() { return top_->GetEntity(); }
 
-  ost::mol::EntityHandle GetEntityStandardNaming();
-
   geom::Vec3List GetPositions(bool enforce_periodic_box = false, bool in_angstrom = true);
 
   geom::Vec3List GetVelocities();
@@ -125,7 +123,6 @@ private:
   SystemPtr system_;
   IntegratorPtr integrator_;
   ContextPtr context_;
-  MMSettingsPtr settings_;
   TopologyPtr top_;
   std::vector<MMObserverPtr> observers_;
   std::vector<int> time_to_notify_;