From 87688908bf22d7d62996e59820dd4687c1674097 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 27 Oct 2014 19:11:33 +0100
Subject: [PATCH] removed some functionality to get rid of settings object in
simulation object
---
modules/mol/mm/src/simulation.cc | 14 ++------------
modules/mol/mm/src/simulation.hh | 3 ---
2 files changed, 2 insertions(+), 15 deletions(-)
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
index 410c9bc41..6a0d2762f 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 5712b6d5c..627e61934 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_;
--
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