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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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 <boost/python.hpp>
#include <ost/mol/mm/simulation.hh>
using namespace boost::python;
namespace{
template<typename T>
std::vector<T> ListToVec(const boost::python::list& l){
std::vector<T> vec;
for (int i = 0; i < boost::python::len(l); ++i){
vec.push_back(boost::python::extract<T>(l[i]));
}
return vec;
}
void WrapAddPositionConstraints(ost::mol::mm::SimulationPtr p, const boost::python::list& l){
std::vector<uint> vec = ListToVec<uint>(l);
p->AddPositionConstraints(vec);
}
}
void export_Simulation()
{
class_<ost::mol::mm::Simulation>("Simulation",no_init)
.def(init<const ost::mol::EntityHandle, const ost::mol::mm::SettingsPtr>())
.def(init<const ost::mol::mm::TopologyPtr,const ost::mol::EntityHandle&,const ost::mol::mm::SettingsPtr>())
.def("Save",&ost::mol::mm::Simulation::Save,(arg("filename")))
.def("Load",&ost::mol::mm::Simulation::Load,(arg("filename")))
.staticmethod("Load")
.def("IsPlatformAvailable",&ost::mol::mm::Simulation::IsPlatformAvailable,
(arg("settings")))
.staticmethod("IsPlatformAvailable")
.def("Steps",&ost::mol::mm::Simulation::Steps,(arg("steps")))
.def("GetPositions",&ost::mol::mm::Simulation::GetPositions,(arg("enforce_periodic_box")=false, arg("in_angstrom")=true))
.def("GetVelocities",&ost::mol::mm::Simulation::GetVelocities)
.def("GetForces",&ost::mol::mm::Simulation::GetForces)
.def("SetPositions",&ost::mol::mm::Simulation::SetPositions,(arg("positions"),arg("in_angstrom")=true))
.def("SetVelocities",&ost::mol::mm::Simulation::SetVelocities)
.def("GetEntity",&ost::mol::mm::Simulation::GetEntity)
.def("ApplySD",&ost::mol::mm::Simulation::ApplySD, (arg("tolerance")=100.0,arg("max_iterations")=1000))
.def("ApplyLBFGS",&ost::mol::mm::Simulation::ApplyLBFGS,(arg("tolerance")=1.0,arg("max_iterations")=1000))
.def("GetEnergy",&ost::mol::mm::Simulation::GetEnergy)
.def("GetPotentialEnergy",&ost::mol::mm::Simulation::GetPotentialEnergy)
.def("GetKineticEnergy",&ost::mol::mm::Simulation::GetKineticEnergy)
.def("Register",&ost::mol::mm::Simulation::Register)
.def("UpdatePositions",&ost::mol::mm::Simulation::UpdatePositions, (arg("enforce_periodic_box")=false))
.def("GetTopology",&ost::mol::mm::Simulation::GetTopology)
.def("ResetHarmonicBond",&ost::mol::mm::Simulation::ResetHarmonicBond,(arg("bond_idx"),arg("bond_length"),arg("force_constant")))
.def("ResetHarmonicAngle",&ost::mol::mm::Simulation::ResetHarmonicAngle,(arg("angle_idx"),arg("angle"),arg("force_constant")))
.def("ResetUreyBradleyAngle",&ost::mol::mm::Simulation::ResetUreyBradleyAngle,(arg("angle_idx"),arg("angle"),arg("angle_force_constant"),arg("bond_length"),arg("bond_force_constant")))
.def("ResetPeriodicDihedral",&ost::mol::mm::Simulation::ResetPeriodicDihedral,(arg("dihedral_idx"),arg("multiplicity"),arg("phase"),arg("force_constant")))
.def("ResetPeriodicImproper",&ost::mol::mm::Simulation::ResetPeriodicImproper,(arg("improper_idx"),arg("multiplicity"),arg("phase"),arg("force_constant")))
.def("ResetHarmonicImproper",&ost::mol::mm::Simulation::ResetHarmonicImproper,(arg("improper_idx"),arg("phase"),arg("force_constant")))
.def("ResetLJPair",&ost::mol::mm::Simulation::ResetLJPair,(arg("ljpair_idx"),arg("sigma"),arg("epsilon")))
.def("ResetDistanceConstraint",&ost::mol::mm::Simulation::ResetDistanceConstraint,(arg("constraint_idx"),arg("length")))
.def("ResetHarmonicPositionRestraint",&ost::mol::mm::Simulation::ResetHarmonicPositionRestraint,(arg("restraint_idx"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
.def("ResetHarmonicDistanceRestraint",&ost::mol::mm::Simulation::ResetHarmonicDistanceRestraint,(arg("restraint_idx"),arg("length"),arg("force_constant")))
.def("ResetLJ",&ost::mol::mm::Simulation::ResetLJ,(arg("particle_idx"),arg("sigma"),arg("epsilon")))
.def("ResetGBSA",&ost::mol::mm::Simulation::ResetGBSA,(arg("particle_idx"),arg("radius"),arg("scaling")))
.def("ResetCharge",&ost::mol::mm::Simulation::ResetCharge,(arg("particle_idx"),arg("charge")))
.def("ResetMass",&ost::mol::mm::Simulation::ResetMass,(arg("particle_idx"),arg("mass")))
.def("AddPositionConstraint",&ost::mol::mm::Simulation::AddPositionConstraint,(arg("particle_idx")))
.def("AddPositionConstraints",&WrapAddPositionConstraints,(arg("particle_idx")))
.def("ResetPositionConstraints",&ost::mol::mm::Simulation::ResetPositionConstraints)
.def("GetPeriodicBoxExtents",&ost::mol::mm::Simulation::GetPeriodicBoxExtents)
.def("SetPeriodicBoxExtents",&ost::mol::mm::Simulation::SetPeriodicBoxExtents,(arg("extents")))
;
boost::python::register_ptr_to_python<ost::mol::mm::SimulationPtr>();
}
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