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// Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
// Biozentrum - University of Basel
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/loop/mm_system_creator.hh>
using namespace promod3;
using namespace promod3::loop;
using namespace boost::python;
// WRAPPERS
namespace {
boost::python::list
WrapGetDisulfidBridges(const MmSystemCreator& mm_sys,
const AllAtomPositions& all_pos,
const boost::python::list& res_idx_list) {
// get indices
std::vector<uint> res_indices;
core::ConvertListToVector(res_idx_list, res_indices);
// get bridges and convert into list
MmSystemCreator::DisulfidBridgeVector bridges
= mm_sys.GetDisulfidBridges(all_pos, res_indices);
boost::python::list return_list;
core::AppendVectorToList(bridges, return_list);
return return_list;
}
void ConvertBridges(const boost::python::list& bridge_list,
MmSystemCreator::DisulfidBridgeVector& bridges) {
// special conversion for bridges (list of tuples)
const uint num_bridges = boost::python::len(bridge_list);
bridges.resize(num_bridges);
for (uint i = 0; i < num_bridges; ++i) {
boost::python::extract<boost::python::tuple> extract_tuple(bridge_list[i]);
if (!extract_tuple.check()) {
throw promod3::Error("Invalid bridge list: Must contain tuples!");
}
if (boost::python::len(bridge_list[i]) != uint(2)) {
throw promod3::Error("Invalid bridge list: Tuples must contain two "
"elements!");
}
bridges[i].first = boost::python::extract<uint>(bridge_list[i][0]);
bridges[i].second = boost::python::extract<uint>(bridge_list[i][1]);
}
}
void WrapSetupSystem(MmSystemCreator& mm_sys,
const AllAtomPositions& all_pos,
const boost::python::list& res_idx_list,
uint loop_length, const boost::python::list& is_n_ter_list,
const boost::python::list& is_c_ter_list,
const boost::python::list& bridge_list) {
// get vectors
std::vector<uint> res_indices;
std::vector<bool> is_n_ter;
std::vector<bool> is_c_ter;
MmSystemCreator::DisulfidBridgeVector bridges;
core::ConvertListToVector(res_idx_list, res_indices);
core::ConvertListToVector(is_n_ter_list, is_n_ter);
core::ConvertListToVector(is_c_ter_list, is_c_ter);
ConvertBridges(bridge_list, bridges);
// finally setup system
mm_sys.SetupSystem(all_pos, res_indices, loop_length, is_n_ter, is_c_ter,
bridges);
}
void WrapSetupSystemMulti(MmSystemCreator& mm_sys,
const AllAtomPositions& all_pos,
const boost::python::list& res_idx_list,
const boost::python::list& loop_start_indices_list,
const boost::python::list& loop_lengths_list,
const boost::python::list& is_n_ter_list,
const boost::python::list& is_c_ter_list,
const boost::python::list& bridge_list) {
// get vectors
std::vector<uint> res_indices;
std::vector<uint> loop_start_indices;
std::vector<uint> loop_lengths;
std::vector<bool> is_n_ter;
std::vector<bool> is_c_ter;
MmSystemCreator::DisulfidBridgeVector bridges;
core::ConvertListToVector(res_idx_list, res_indices);
core::ConvertListToVector(loop_start_indices_list, loop_start_indices);
core::ConvertListToVector(loop_lengths_list, loop_lengths);
core::ConvertListToVector(is_n_ter_list, is_n_ter);
core::ConvertListToVector(is_c_ter_list, is_c_ter);
ConvertBridges(bridge_list, bridges);
// finally setup system
mm_sys.SetupSystem(all_pos, res_indices, loop_start_indices, loop_lengths,
is_n_ter, is_c_ter, bridges);
}
void WrapUpdatePositions(MmSystemCreator& mm_sys,
const AllAtomPositions& all_pos,
const boost::python::list& res_idx_list) {
// get indices
std::vector<uint> res_indices;
core::ConvertListToVector(res_idx_list, res_indices);
// update positions
mm_sys.UpdatePositions(all_pos, res_indices);
}
void WrapExtractLoopPositions(MmSystemCreator& mm_sys,
AllAtomPositions& loop_pos) {
mm_sys.ExtractLoopPositions(loop_pos);
}
void WrapExtractLoopPositionsIndexed(MmSystemCreator& mm_sys,
AllAtomPositions& out_pos,
const boost::python::list& res_idx_list) {
// get indices
std::vector<uint> res_indices;
core::ConvertListToVector(res_idx_list, res_indices);
// update positions
mm_sys.ExtractLoopPositions(out_pos, res_indices);
}
boost::python::list WrapGetLoopStartIndices(const MmSystemCreator& mm_sys) {
// convert into list
boost::python::list return_list;
core::AppendVectorToList(mm_sys.GetLoopStartIndices(), return_list);
return return_list;
}
boost::python::list WrapGetLoopLengths(const MmSystemCreator& mm_sys) {
// convert into list
boost::python::list return_list;
core::AppendVectorToList(mm_sys.GetLoopLengths(), return_list);
return return_list;
}
boost::python::list WrapGetFfAa(const MmSystemCreator& mm_sys) {
// convert into list
boost::python::list return_list;
core::AppendVectorToList(mm_sys.GetForcefieldAminoAcids(), return_list);
return return_list;
}
boost::python::list WrapGetIndexing(const MmSystemCreator& mm_sys) {
// convert into list
boost::python::list return_list;
core::AppendVectorToList(mm_sys.GetIndexing(), return_list);
return return_list;
}
} // anon wrapper ns
void export_MmSystemCreator() {
class_<MmSystemCreator, MmSystemCreatorPtr>("MmSystemCreator", no_init)
.def(init<ForcefieldLookupPtr, bool, bool, Real, bool>(
(arg("ff_lookup"), arg("fix_surrounding_hydrogens")=true,
arg("kill_electrostatics")=false, arg("nonbonded_cutoff")=8,
arg("inaccurate_pot_energy")=false)))
.def("GetDisulfidBridges", WrapGetDisulfidBridges,
(arg("all_pos"), arg("res_indices")))
.def("SetupSystem", WrapSetupSystem,
(arg("all_pos"), arg("res_indices"), arg("loop_length"),
arg("is_n_ter"), arg("is_c_ter"), arg("disulfid_bridges")))
.def("SetupSystem", WrapSetupSystemMulti,
(arg("all_pos"), arg("res_indices"), arg("loop_start_indices"),
arg("loop_lengths"), arg("is_n_ter"), arg("is_c_ter"),
arg("disulfid_bridges")))
.def("UpdatePositions", WrapUpdatePositions,
(arg("all_pos"), arg("res_indices")))
.def("ExtractLoopPositions", WrapExtractLoopPositions, (arg("loop_pos")))
.def("ExtractLoopPositions", WrapExtractLoopPositionsIndexed,
(arg("out_pos"), arg("res_indices")))
.def("GetSimulation", &MmSystemCreator::GetSimulation)
.def("GetNumResidues", &MmSystemCreator::GetNumResidues)
.def("GetNumLoopResidues", &MmSystemCreator::GetNumLoopResidues)
.def("GetLoopStartIndices", WrapGetLoopStartIndices)
.def("GetLoopLengths", WrapGetLoopLengths)
.def("GetForcefieldAminoAcids", WrapGetFfAa)
.def("GetIndexing", WrapGetIndexing)
.def("GetCpuPlatformSupport", &MmSystemCreator::GetCpuPlatformSupport)
.def("SetCpuPlatformSupport", &MmSystemCreator::SetCpuPlatformSupport,
(arg("cpu_platform_support")))
;
}
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