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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/scoring/constraint_constructor.hh>
using namespace boost::python;
using namespace promod3;
using namespace promod3::scoring;
namespace{
void WrapAttachConstraintsSingle(DiscoContainerPtr p,
promod3::scoring::BackboneScoreEnv& env,
uint chain_idx, Real cluster_thresh,
Real gamma){
std::vector<uint> indices(1, chain_idx);
p->AttachConstraints(env, indices, cluster_thresh, gamma);
}
void WrapAttachConstraintsList(DiscoContainerPtr p,
promod3::scoring::BackboneScoreEnv& env,
const boost::python::list& chain_indices,
Real cluster_thresh, Real gamma){
std::vector<uint> v_chain_indices;
core::ConvertListToVector(chain_indices, v_chain_indices);
p->AttachConstraints(env, v_chain_indices, cluster_thresh, gamma);
}
void WrapAttachEvolutionaryConstraintsSingle(promod3::scoring::BackboneScoreEnv& env,
const ost::seq::AlignmentHandle& aln,
uint chain_idx,
promod3::scoring::PairwiseFunctionType ft,
Real fraction_constraints,
uint constant_function_length,
uint tail_length){
std::vector<uint> chain_indices(1, chain_idx);
promod3::scoring::AttachEvolutionaryConstraints(env, aln, chain_indices, ft,
fraction_constraints,
constant_function_length,
tail_length);
}
void WrapAttachEvolutionaryConstraintsList(promod3::scoring::BackboneScoreEnv& env,
const ost::seq::AlignmentHandle& aln,
const boost::python::list& chain_indices,
promod3::scoring::PairwiseFunctionType ft,
Real fraction_constraints,
uint constant_function_length,
uint tail_length){
std::vector<uint> v_chain_indices;
core::ConvertListToVector(chain_indices, v_chain_indices);
promod3::scoring::AttachEvolutionaryConstraints(env, aln, v_chain_indices, ft,
fraction_constraints,
constant_function_length,
tail_length);
}
}
void export_constraint_constructor()
{
class_<DiscoContainer, DiscoContainerPtr>("DiscoContainer", no_init)
.def(init<const ost::seq::SequenceHandle&, PairwiseFunctionType>(
(arg("seqres"), arg("function_type")=CA_PAIRWISE_FUNCTION)))
.def("AddStructuralInfo", &DiscoContainer::AddStructuralInfo, (arg("aln")))
.def("AttachConstraints", &WrapAttachConstraintsSingle,
(arg("environment"), arg("chain_idx"), arg("cluster_thresh")=0.50,
arg("gamma")=70.0))
.def("AttachConstraints", &WrapAttachConstraintsList,
(arg("environment"), arg("chain_indices"), arg("cluster_thresh")=0.50,
arg("gamma")=70.0))
.def("AttachEvolutionaryConstraints", &WrapAttachEvolutionaryConstraintsSingle,
(arg("environment"), arg("alignment"), arg("chain_idx")=0,
arg("function_type")=CB_PAIRWISE_FUNCTION,
arg("fraction_constraints")=0.1, arg("constant_function_length")=8,
arg("tail_length")=4))
.def("AttachEvolutionaryConstraints", &WrapAttachEvolutionaryConstraintsList,
(arg("environment"), arg("alignment"), arg("chain_indices"),
arg("function_type")=CB_PAIRWISE_FUNCTION,
arg("fraction_constraints")=0.1, arg("constant_function_length")=8,
arg("tail_length")=4))
;
}
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