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// SPDX-License-Identifier: LGPL-3.0-or-later
// Author: Kristian Lytje
#include <em/manager/SimpleProteinManager.h>
#include <hist/histogram_manager/HistogramManagerMT.h>
#include <data/Molecule.h>
#include <utility/Exceptions.h>
#include <utility/Logging.h>
#include <data/Body.h>
using namespace ausaxs;
void em::managers::SimpleProteinManager::update_protein(double cutoff) {
logging::log("SimpleProteinManager::update_protein: cutoff = " + std::to_string(cutoff));
auto atoms = generate_atoms(cutoff);
// this sorting step is principially not necessary, but required for consistency with SmartProteinManager
// otherwise we may see tiny differences in the generated hydration shells which breaks the tests
std::sort(
atoms.begin(),
atoms.end(),
[] (const data::EMAtom& atom1, const data::EMAtom& atom2) {return atom1.charge_density() < atom2.charge_density();}
);
std::vector<data::AtomFF> converted(atoms.size());
std::transform(atoms.begin(), atoms.end(), converted.begin(), [] (const data::EMAtom& atom) {return atom.get_atom_ff();});
protein = std::make_unique<data::Molecule>(std::vector{data::Body{converted}});
protein->set_histogram_manager(settings::hist::HistogramManagerChoice::HistogramManagerMT);
}
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