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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 <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/loop/fragger.hh>
using namespace promod3;
using namespace promod3::loop;
using namespace boost::python;
namespace{
BackboneList& wrap_GetItem(Fragger& fragger, uint index){
if(index >= fragger.size()){
throw promod3::Error("Invalid Index observed!");
}
return fragger[index];
}
FragmentInfo wrap_GetFragmentInfo(Fragger& fragger, uint index){
if(index >= fragger.size()){
throw promod3::Error("Invalid Index observed!");
}
return fragger.GetFragmentInfo(index);
}
Real wrap_GetScore(Fragger& fragger, uint index){
if(index >= fragger.size()){
throw promod3::Error("Invalid Index observed!");
}
return fragger.GetScore(index);
}
Real wrap_GetSingleParameterScore(Fragger& fragger, uint parameter_index, uint index){
if(parameter_index >= fragger.parameter_size()){
std::stringstream ss;
ss << "Provided "<<parameter_index<<" as parameter index for a Fragger with ";
ss << fragger.parameter_size()<<" parameters!";
throw promod3::Error(ss.str());
}
if(index >= fragger.size()){
throw promod3::Error("Invalid Index observed!");
}
return fragger.GetScore(parameter_index,index);
}
void WrapTorsionSingle(Fragger& fragger, Real w,
TorsionSamplerPtr t_s, const String& before,
const String& after){
fragger.AddTorsionProbabilityParameters(w,t_s,before,after);
}
void WrapTorsionList(Fragger& fragger, Real w,
const boost::python::list& t_s, const String& before,
const String& after){
TorsionSamplerList v_t_s;
core::ConvertListToVector(t_s, v_t_s);
fragger.AddTorsionProbabilityParameters(w,v_t_s,before,after);
}
FraggerPtr fm_getitem(FraggerMap& fm, int i) { return fm[i]; }
void fm_setitem(FraggerMap& fm, int i, FraggerPtr item) { fm[i] = item; }
}
void export_Fragger() {
class_<Fragger, FraggerPtr>("Fragger", init<String>())
.def("AddSeqIDParameters",&Fragger::AddSeqIDParameters,(arg("weight")))
.def("AddSeqSimParameters",&Fragger::AddSeqSimParameters,(arg("weight"),arg("subst_matrix")))
.def("AddSSAgreeParameters",&Fragger::AddSSAgreeParameters,(arg("weight"),arg("psipred_prediction")))
.def("AddTorsionProbabilityParameters",&WrapTorsionSingle,(arg("weight"),arg("torsion_sampler"),arg("aa_before")="ALA",arg("aa_after")="ALA"))
.def("AddTorsionProbabilityParameters",&WrapTorsionList,(arg("weight"),arg("torsion_sampler_list"),arg("aa_before")="ALA",arg("aa_after")="ALA"))
.def("AddSequenceProfileParameters",&Fragger::AddSequenceProfileParameters,(arg("weight"),arg("prof")))
.def("AddStructureProfileParameters",&Fragger::AddStructureProfileParameters,(arg("weight"),arg("prof")))
.def("Fill",&Fragger::Fill,(arg("structure_db"),arg("max_rmsd"),arg("num_fragments")))
.def("__len__", &Fragger::size)
.def("__getitem__", &wrap_GetItem,return_value_policy<reference_existing_object>())
.def("GetFragmentInfo",&wrap_GetFragmentInfo,(arg("index")))
.def("GetScore",&wrap_GetScore,(arg("index")))
.def("GetScore",&wrap_GetSingleParameterScore,(arg("parameter_index"),arg("index")))
;
class_<FraggerMap, FraggerMapPtr>("FraggerMap", init<>())
.def("Load", &FraggerMap::Load, (arg("filename"), arg("db")))
.staticmethod("Load")
.def("Save", &FraggerMap::Save, (arg("filename")))
.def("LoadBB", &FraggerMap::LoadBB, (arg("filename")))
.staticmethod("LoadBB")
.def("SaveBB", &FraggerMap::SaveBB, (arg("filename")))
.def("Contains", &FraggerMap::Contains, (arg("id")))
.def("__getitem__", &fm_getitem, (arg("id")))
.def("__setitem__", &fm_setitem, (arg("id"), arg("fragger")))
;
class_<FraggerList>("FraggerList", no_init)
.def(vector_indexing_suite<FraggerList>())
;
}
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