diff --git a/modules/mol/mm/pymod/export_mm.cc b/modules/mol/mm/pymod/export_mm.cc
deleted file mode 100644
index 7a4e4ab5ce887f1b4dd3590a350c9562c9560202..0000000000000000000000000000000000000000
--- a/modules/mol/mm/pymod/export_mm.cc
+++ /dev/null
@@ -1,189 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <OpenMM.h>
-#include <boost/python.hpp>
-#include <boost/shared_ptr.hpp>
-#include <ost/mol/mm/force_field.hh>
-#include <ost/mol/mm/simulation.hh>
-#include <ost/mol/mm/mm_algorithms.hh>
-#include <ost/mol/residue_handle.hh>
-#include <ost/mol/mm/mm_settings.hh>
-
-using namespace boost::python;
-using namespace ost::mol::mm;
-
-namespace{
-
-std::vector<std::pair<String, ost::mol::ResNum> > list_to_vec(boost::python::list& l){
- std::vector<std::pair<String,ost::mol::ResNum> > return_vec;
- boost::python::tuple t;
- String s;
- ost::mol::ResNum rn;
- for(int i = 0; i < boost::python::len(l); ++i){
- t = boost::python::extract<boost::python::tuple>(l[0]);
- s = boost::python::extract<String>(t[0]);
- rn = boost::python::extract<ost::mol::ResNum>(t[1]);
- return_vec.push_back(std::make_pair(s,rn));
- }
- return return_vec;
-}
-
-ost::mol::mm::SimulationPtr WrapSimulationConstructor(ost::mol::EntityHandle& e, ost::mol::mm::ForcefieldPtr ff,
- ost::mol::mm::IntegratorPtr integrator, ost::mol::mm::MMSettingsPtr settings,
- list& d_protonated_his,
- list& e_protonated_his,
- list& positive_his,
- list& neutral_glutamates,
- list& neutral_aspartates){
-
- std::vector<std::pair<String,ost::mol::ResNum> > v_d_protonated_his = list_to_vec(d_protonated_his);
- std::vector<std::pair<String,ost::mol::ResNum> > v_e_protonated_his = list_to_vec(e_protonated_his);
- std::vector<std::pair<String,ost::mol::ResNum> > v_positive_his = list_to_vec(positive_his);
- std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_glutamates = list_to_vec(neutral_glutamates);
- std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_aspartates = list_to_vec(neutral_aspartates);
-
- ost::mol::mm::SimulationPtr p(new ost::mol::mm::Simulation(e,ff,integrator, settings,
- v_d_protonated_his,
- v_e_protonated_his,
- v_positive_his,
- v_neutral_glutamates,
- v_neutral_aspartates));
- return p;
-}
-
-ost::mol::mm::SimulationPtr WrapSimulationConstructorNoSettings(ost::mol::EntityHandle& e, ost::mol::mm::ForcefieldPtr ff,
- ost::mol::mm::IntegratorPtr integrator,
- list& d_protonated_his,
- list& e_protonated_his,
- list& positive_his,
- list& neutral_glutamates,
- list& neutral_aspartates){
-
- ost::mol::mm::MMSettingsPtr p(new ost::mol::mm::MMSettings);
- return WrapSimulationConstructor(e,ff,integrator,p,
- d_protonated_his,
- e_protonated_his,
- positive_his,
- neutral_glutamates,
- neutral_aspartates);
-
-
-}
-
-void WrapAssignFFSpecificNames(ost::mol::mm::ForcefieldPtr p,
- ost::mol::EntityHandle& e,
- boost::python::list& d_protonated_his,
- boost::python::list& e_protonated_his,
- boost::python::list& positive_his,
- boost::python::list& neutral_glutamates,
- boost::python::list& neutral_aspartates){
-
- std::vector<std::pair<String,ost::mol::ResNum> > v_d_protonated_his = list_to_vec(d_protonated_his);
- std::vector<std::pair<String,ost::mol::ResNum> > v_e_protonated_his = list_to_vec(e_protonated_his);
- std::vector<std::pair<String,ost::mol::ResNum> > v_positive_his = list_to_vec(positive_his);
- std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_glutamates = list_to_vec(neutral_glutamates);
- std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_aspartates = list_to_vec(neutral_aspartates);
-
- p->AssignFFSpecificNames(e,v_d_protonated_his,
- v_e_protonated_his,
- v_positive_his,
- v_neutral_glutamates,
- v_neutral_aspartates);
-
-}
-
-}
-
-
-
-void export_MM()
-{
-
- //export the settings
-
- class_<ost::mol::mm::MMSettings>("MMSettings",init<>())
- .def_readwrite("add_bonds",&ost::mol::mm::MMSettings::add_bonds)
- .def_readwrite("add_angles",&ost::mol::mm::MMSettings::add_angles)
- .def_readwrite("add_dihedrals",&ost::mol::mm::MMSettings::add_dihedrals)
- .def_readwrite("add_impropers",&ost::mol::mm::MMSettings::add_impropers)
- .def_readwrite("add_cmaps",&ost::mol::mm::MMSettings::add_cmaps)
- .def_readwrite("add_exclusions",&ost::mol::mm::MMSettings::add_exclusions)
- .def_readwrite("add_nonbonded",&ost::mol::mm::MMSettings::add_nonbonded)
- .def_readwrite("kill_electrostatics",&ost::mol::mm::MMSettings::kill_electrostatics)
- .def_readwrite("nonbonded_method",&ost::mol::mm::MMSettings::nonbonded_method)
- .def_readwrite("nonbonded_cutoff",&ost::mol::mm::MMSettings::nonbonded_cutoff)
- .def_readwrite("rigid_water",&ost::mol::mm::MMSettings::rigid_water)
- .def_readwrite("removeCMMMotion",&ost::mol::mm::MMSettings::removeCMMMotion)
- .def_readwrite("constraints",&ost::mol::mm::MMSettings::constraints)
- ;
-
- boost::python::register_ptr_to_python<ost::mol::mm::MMSettingsPtr>();
-
- //we have to tell boost, that the Integrator class is around...
- class_<OpenMM::Integrator, boost::noncopyable>("Integrator",no_init);
- //We do not export any further function for the Verlet integrator, since we want
- //to perform the steps via the simulation...
- class_<OpenMM::VerletIntegrator, bases<OpenMM::Integrator> >("VerletIntegrator", init<Real>());
- boost::python::register_ptr_to_python<ost::mol::mm::IntegratorPtr>();
- boost::python::register_ptr_to_python<ost::mol::mm::VerletIntegratorPtr>();
-
- class_<ost::mol::mm::Forcefield>("Forcefield", init<const String&>())
- .def("AssignFFSpecificNames", &WrapAssignFFSpecificNames, (arg("entity"),
- arg("d_protonated_his") = boost::python::list(),
- arg("e_protonated_his") = boost::python::list(),
- arg("positive_his") = boost::python::list(),
- arg("neutral_glutamates") = boost::python::list(),
- arg("neutral_aspartates") = boost::python::list()))
- .def("AddHydrogens", &ost::mol::mm::Forcefield::AddHydrogens)
- .def("ReadResidueDatabase", &ost::mol::mm::Forcefield::ReadResidueDatabase)
- ;
-
- class_<ost::mol::mm::Simulation>("Simulation",no_init)
- .def("__init__",boost::python::make_constructor(&WrapSimulationConstructor,default_call_policies(),
- (arg("entity"),arg("forcefield"),
- arg("integrator"),arg("settings"),
- arg("d_protonated_his") = boost::python::list(),
- arg("e_protonated_his") = boost::python::list(),
- arg("positive_his") = boost::python::list(),
- arg("neutral_glutamates") = boost::python::list(),
- arg("neutral_aspartates") = boost::python::list())))
- .def("__init__",boost::python::make_constructor(&WrapSimulationConstructorNoSettings,default_call_policies(),
- (arg("entity"),arg("forcefield"),
- arg("integrator"),
- arg("d_protonated_his") = boost::python::list(),
- arg("e_protonated_his") = boost::python::list(),
- arg("positive_his") = boost::python::list(),
- arg("neutral_glutamates") = boost::python::list(),
- arg("neutral_aspartates") = boost::python::list())))
- .def("GetEntity",&ost::mol::mm::Simulation::GetEntity)
- .def("GetMMEntity",&ost::mol::mm::Simulation::GetMMEntity)
- .def("UpdatePositions",&ost::mol::mm::Simulation::UpdatePositions)
- .def("MinimizeEnergy",&ost::mol::mm::Simulation::MinimizeEnergy, (arg("tolerance")=1.0,arg("max_iterations")=1000))
- .def("GetTimeSteps",&ost::mol::mm::Simulation::GetTimeSteps)
- .def("Steps",&ost::mol::mm::Simulation::Steps, (arg("steps")=1))
- ;
-
- boost::python::register_ptr_to_python<ost::mol::mm::SimulationPtr>();
-
- //functions from mm_algorithms
- def("Minimize",&ost::mol::mm::Minimize, (arg("ent"), arg("ff")));
-
-}
-
-