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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/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/model.hh>
#include <promod3/core/export_helper.hh>
using namespace boost::python;
using namespace promod3::modelling;
namespace {
ModellingHandle WrapMHandleFromAln(const ost::seq::AlignmentList& aln,
const boost::python::list& chain_names,
bool include_ligands,
bool spdbv_style) {
std::vector<String> v_chain_names;
promod3::core::ConvertListToVector(chain_names, v_chain_names);
return MHandleFromAln(aln, v_chain_names, include_ligands, spdbv_style);
}
int WrapCountEnclosedGaps(ModellingHandle& mhandle, const StructuralGap& gap) {
return CountEnclosedGaps(mhandle, gap, false);
}
int WrapCountEnclosedIns(ModellingHandle& mhandle, const StructuralGap& gap) {
return CountEnclosedGaps(mhandle, gap, true);
}
promod3::scoring::BackboneOverallScorerPtr
WrapGetBackboneScorer(ModellingHandle& mhandle) {
if (!mhandle.backbone_scorer) {
throw promod3::Error("The backbone_scorer must be properly initialized "
"before it can be used!");
}
return mhandle.backbone_scorer;
}
void WrapSetBackboneScorer(ModellingHandle& mhandle,
promod3::scoring::BackboneOverallScorerPtr scorer) {
mhandle.backbone_scorer = scorer;
}
promod3::scoring::BackboneScoreEnvPtr
WrapGetBackboneScorerEnv(ModellingHandle& mhandle) {
if (!mhandle.backbone_scorer_env) {
throw promod3::Error("The backbone_scorer_env must be properly initialized "
"before it can be used!");
}
return mhandle.backbone_scorer_env;
}
void WrapSetBackboneScorerEnv(ModellingHandle& mhandle,
promod3::scoring::BackboneScoreEnvPtr env) {
mhandle.backbone_scorer_env = env;
}
promod3::scoring::AllAtomOverallScorerPtr
WrapGetAllAtomScorer(ModellingHandle& mhandle) {
if (!mhandle.all_atom_scorer) {
throw promod3::Error("The all_atom_scorer must be properly initialized "
"before it can be used!");
}
return mhandle.all_atom_scorer;
}
void WrapSetAllAtomScorer(ModellingHandle& mhandle,
promod3::scoring::AllAtomOverallScorerPtr scorer) {
mhandle.all_atom_scorer = scorer;
}
promod3::loop::AllAtomEnvPtr
WrapGetAllAtomScorerEnv(ModellingHandle& mhandle) {
if (!mhandle.all_atom_scorer_env) {
throw promod3::Error("The all_atom_scorer_env must be properly initialized "
"before it can be used!");
}
return mhandle.all_atom_scorer_env;
}
void WrapSetAllAtomScorerEnv(ModellingHandle& mhandle,
promod3::loop::AllAtomEnvPtr env) {
mhandle.all_atom_scorer_env = env;
}
promod3::loop::AllAtomEnvPtr
WrapGetAllAtomSidechainEnv(ModellingHandle& mhandle) {
if (!mhandle.all_atom_sidechain_env) {
throw promod3::Error("The all_atom_sidechain_env must be properly "
"initialized before it can be used!");
}
return mhandle.all_atom_sidechain_env;
}
void WrapSetAllAtomSidechainEnv(ModellingHandle& mhandle,
promod3::loop::AllAtomEnvPtr env) {
mhandle.all_atom_sidechain_env = env;
}
promod3::modelling::SidechainReconstructorPtr
WrapGetSidechainRec(ModellingHandle& mhandle) {
if (!mhandle.sidechain_reconstructor) {
throw promod3::Error("The sidechain_reconstructor must be properly "
"initialized before it can be used!");
}
return mhandle.sidechain_reconstructor;
}
void WrapSetSidechainRec(ModellingHandle& mhandle,
promod3::modelling::SidechainReconstructorPtr sc_rec) {
mhandle.sidechain_reconstructor = sc_rec;
}
void WrapSetSequenceProfiles(ModellingHandle& mhandle,
const boost::python::list& profiles){
ost::seq::ProfileHandleList v_profiles;
promod3::core::ConvertListToVector(profiles, v_profiles);
SetSequenceProfiles(mhandle, v_profiles);
}
void WrapSetPsipredPredictions(ModellingHandle& mhandle,
const boost::python::list& predictions){
promod3::loop::PsipredPredictionList v_predictions;
promod3::core::ConvertListToVector(predictions, v_predictions);
SetPsipredPredictions(mhandle, v_predictions);
}
boost::python::list WrapPsipredPredictionAccess(ModellingHandle& mhandle){
boost::python::list return_list;
promod3::core::AppendVectorToList(mhandle.psipred_predictions, return_list);
return return_list;
}
boost::python::list WrapProfileAccess(ModellingHandle& mhandle){
boost::python::list return_list;
promod3::core::AppendVectorToList(mhandle.profiles, return_list);
return return_list;
}
} // anon ns
void export_model()
{
class_<ModellingHandle>("ModellingHandle", init<>())
.def("Copy", &ModellingHandle::Copy)
.def_readwrite("model", &ModellingHandle::model)
.def_readwrite("gaps", &ModellingHandle::gaps)
.add_property("seqres", &ModellingHandle::seqres)
.add_property("psipred_predictions", &WrapPsipredPredictionAccess)
.add_property("profiles", &WrapProfileAccess)
.add_property("backbone_scorer", &WrapGetBackboneScorer,
&WrapSetBackboneScorer)
.add_property("backbone_scorer_env", &WrapGetBackboneScorerEnv,
&WrapSetBackboneScorerEnv)
.add_property("all_atom_scorer", &WrapGetAllAtomScorer,
&WrapSetAllAtomScorer)
.add_property("all_atom_scorer_env", &WrapGetAllAtomScorerEnv,
&WrapSetAllAtomScorerEnv)
.add_property("all_atom_sidechain_env", &WrapGetAllAtomSidechainEnv,
&WrapSetAllAtomSidechainEnv)
.add_property("sidechain_reconstructor", &WrapGetSidechainRec,
&WrapSetSidechainRec)
;
def("ClearGaps", ClearGaps, (arg("mhandle"), arg("gap")));
def("CountEnclosedGaps", WrapCountEnclosedGaps, (arg("mhandle"),
arg("gap")));
def("CountEnclosedInsertions", WrapCountEnclosedIns, (arg("mhandle"),
arg("gap")));
def("MergeGaps", MergeGaps, (arg("mhandle"),arg("index")));
def("RemoveTerminalGaps", RemoveTerminalGaps, (arg("mhandle")));
def("ReorderGaps", &ReorderGaps, (arg("mhandle")));
def("SetupDefaultBackboneScoring", &SetupDefaultBackboneScoring,
(arg("mhandle")));
def("IsBackboneScoringSetUp", &IsBackboneScoringSetUp, (arg("mhandle")));
def("SetupDefaultAllAtomScoring", &SetupDefaultAllAtomScoring,
(arg("mhandle")));
def("IsAllAtomScoringSetUp", &IsAllAtomScoringSetUp, (arg("mhandle")));
def("SetSequenceProfiles", &WrapSetSequenceProfiles,
(arg("mhandle"), arg("profiles")));
def("SetPsipredPredictions", &WrapSetPsipredPredictions,
(arg("mhandle"), arg("psipred_predictions")));
def("MergeMHandle", &MergeMHandle, (arg("source_mhandle"),
arg("target_mhandle"),
arg("source_chain_idx"),
arg("target_chain_idx"),
arg("start_resnum"),
arg("end_resnum"),
arg("transform")));
def("InsertLoop", InsertLoop,
(arg("mhandle"), arg("bb_list"), arg("start_resnum"), arg("chain_idx")));
def("InsertLoopClearGaps", InsertLoopClearGaps,
(arg("mhandle"), arg("bb_list"), arg("gap")));
def("MHandleFromAln", &WrapMHandleFromAln, (arg("aln"), arg("chain_names"),
arg("include_ligands")=false,
arg("spdbv_style")=false));
}
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