diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc index 410c9bc41c268ee366ea91e938a61b6539fde092..6a0d2762f460489e4b3eb2e6d073effd05590c95 100644 --- a/modules/mol/mm/src/simulation.cc +++ b/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); diff --git a/modules/mol/mm/src/simulation.hh b/modules/mol/mm/src/simulation.hh index 5712b6d5cfab786e65265d9a5a6dfd6b861d1bf3..627e6193481d5479ec59437c60dd2b2dbefc1dc9 100644 --- a/modules/mol/mm/src/simulation.hh +++ b/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_;