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/*! \internal \file
 * \brief
 * Implements nblib Molecule
 *
 * \author Victor Holanda <victor.holanda@cscs.ch>
 * \author Joe Jordan <ejjordan@kth.se>
 * \author Prashanth Kanduri <kanduri@cscs.ch>
 * \author Sebastian Keller <keller@cscs.ch>
 * \author Artem Zhmurov <zhmurov@gmail.com>
 */
#include "nblib/molecules.h"

#include <algorithm>
#include <tuple>

#include "nblib/exception.h"
#include "nblib/particletype.h"

namespace nblib
{

Molecule::Molecule(MoleculeName moleculeName) : name_(std::move(moleculeName)) {}

MoleculeName Molecule::name() const
{
    return name_;
}

Molecule& Molecule::addParticle(const ParticleName& particleName,
                                const ResidueName&  residueName,
                                const Charge&       charge,
                                ParticleType const& particleType)
{
    auto found = particleTypes_.find(particleType.name());
    if (found == particleTypes_.end())
    {
        particleTypes_.insert(std::make_pair(particleType.name(), particleType));
    }
    else
    {
        if (!(found->second == particleType))
        {
            throw InputException(
                    "Differing ParticleTypes with identical names encountered in the same "
                    "molecule.");
        }
    }

    particles_.emplace_back(ParticleData{ particleName, residueName, particleType.name(), charge });

    // Add self exclusion. We just added the particle, so we know its index and that the exclusion doesn't exist yet
    std::size_t id = particles_.size() - 1;
    exclusions_.emplace_back(id, id);

    return *this;
}

Molecule& Molecule::addParticle(const ParticleName& particleName,
                                const ResidueName&  residueName,
                                ParticleType const& particleType)
{
    addParticle(particleName, residueName, Charge(0), particleType);

    return *this;
}

Molecule& Molecule::addParticle(const ParticleName& particleName,
                                const Charge&       charge,
                                ParticleType const& particleType)
{
    addParticle(particleName, ResidueName(name_), charge, particleType);

    return *this;
}

Molecule& Molecule::addParticle(const ParticleName& particleName, const ParticleType& particleType)
{
    addParticle(particleName, ResidueName(name_), Charge(0), particleType);

    return *this;
}

ResidueName Molecule::residueName(const ParticleIdentifier& particleIdentifier)
{
    return (particleIdentifier.residueName() == ResidueName{}) ? ResidueName(name_)
                                                               : particleIdentifier.residueName();
}

template<class ListedVariant, class... ParticleIdentifiers>
void Molecule::addInteractionImpl(const ListedVariant& interaction, const ParticleIdentifiers&... particles)
{
    auto storeInteraction = [&](const auto& interaction_) {
        using Interaction = std::decay_t<decltype(interaction_)>;

        auto& interactionContainer = pickType<Interaction>(interactionData_);
        interactionContainer.interactions_.emplace_back(particles...);
        interactionContainer.interactionTypes_.push_back(interaction_);
    };

    // add the interaction to the correct location in interactionData_
    std::visit(storeInteraction, interaction);
}

void Molecule::addInteraction(const ParticleIdentifier&   particleI,
                              const ParticleIdentifier&   particleJ,
                              const TwoCenterInteraction& interaction)
{
    if (particleI == particleJ)
    {
        throw InputException(std::string("Cannot add interaction of particle ")
                             + particleI.particleName().value() + " with itself in molecule "
                             + name_.value());
    }

    addInteractionImpl(interaction,
                       particleI.particleName(),
                       residueName(particleI),
                       particleJ.particleName(),
                       residueName(particleJ));
}

void Molecule::addInteraction(const ParticleIdentifier&     particleI,
                              const ParticleIdentifier&     particleJ,
                              const ParticleIdentifier&     particleK,
                              const ThreeCenterInteraction& interaction)
{
    if (particleI == particleJ and particleJ == particleK)
    {
        throw InputException(std::string("Cannot add interaction of particle ")
                             + particleI.particleName().value() + " with itself in molecule "
                             + name_.value());
    }

    addInteractionImpl(interaction,
                       particleI.particleName(),
                       residueName(particleI),
                       particleJ.particleName(),
                       residueName(particleJ),
                       particleK.particleName(),
                       residueName(particleK));
}

void Molecule::addInteraction(const ParticleIdentifier&    particleI,
                              const ParticleIdentifier&    particleJ,
                              const ParticleIdentifier&    particleK,
                              const ParticleIdentifier&    particleL,
                              const FourCenterInteraction& interaction)
{
    if (particleI == particleJ and particleJ == particleK and particleK == particleL)
    {
        throw InputException(std::string("Cannot add interaction of particle ")
                             + particleI.particleName().value() + " with itself in molecule "
                             + name_.value());
    }

    addInteractionImpl(interaction,
                       particleI.particleName(),
                       residueName(particleI),
                       particleJ.particleName(),
                       residueName(particleJ),
                       particleK.particleName(),
                       residueName(particleK),
                       particleL.particleName(),
                       residueName(particleL));
}

void Molecule::addInteraction(const ParticleIdentifier&    particleI,
                              const ParticleIdentifier&    particleJ,
                              const ParticleIdentifier&    particleK,
                              const ParticleIdentifier&    particleL,
                              const ParticleIdentifier&    particleM,
                              const FiveCenterInteraction& interaction)
{
    if (particleI == particleJ and particleJ == particleK and particleK == particleL and particleL == particleM)
    {
        throw InputException(std::string("Cannot add interaction of particle ")
                             + particleI.particleName().value() + " with itself in molecule "
                             + name_.value());
    }

    addInteractionImpl(interaction,
                       particleI.particleName(),
                       residueName(particleI),
                       particleJ.particleName(),
                       residueName(particleJ),
                       particleK.particleName(),
                       residueName(particleK),
                       particleL.particleName(),
                       residueName(particleL),
                       particleM.particleName(),
                       residueName(particleM));
}


int Molecule::numParticlesInMolecule() const
{
    return particles_.size();
}

void Molecule::addExclusion(const ParticleIdentifier& particle, const ParticleIdentifier& particleToExclude)
{
    if (particle == particleToExclude)
    {
        return;
    }

    // duplication for the swapped pair happens in getExclusions()
    exclusionsByName_.emplace_back(std::make_tuple(particle.particleName(),
                                                   residueName(particle),
                                                   particleToExclude.particleName(),
                                                   residueName(particleToExclude)));
}

const Molecule::InteractionTuple& Molecule::interactionData() const
{
    return interactionData_;
}

const ParticleType& Molecule::at(const std::string& particleTypeName) const
{
    return particleTypes_.at(particleTypeName);
}

ParticleName Molecule::particleName(int i) const
{
    return ParticleName(particles_[i].particleName_);
}

ResidueName Molecule::residueName(int i) const
{
    return ResidueName(particles_[i].residueName_);
}

std::vector<std::tuple<int, int>> Molecule::getExclusions() const
{
    // tuples of (particleName, residueName, index)
    std::vector<std::tuple<std::string, std::string, int>> indexKey;
    indexKey.reserve(numParticlesInMolecule());

    for (int i = 0; i < numParticlesInMolecule(); ++i)
    {
        indexKey.emplace_back(particles_[i].particleName_, particles_[i].residueName_, i);
    }

    std::sort(std::begin(indexKey), std::end(indexKey));

    std::vector<std::tuple<int, int>> ret = exclusions_;
    ret.reserve(exclusions_.size() + exclusionsByName_.size());

    // normal operator<, except ignore third element
    auto sortKey = [](const auto& tup1, const auto& tup2) {
        if (std::get<0>(tup1) < std::get<0>(tup2))
        {
            return true;
        }
        else
        {
            return std::get<1>(tup1) < std::get<1>(tup2);
        }
    };

    // convert exclusions given by names to indices and append
    for (auto& tup : exclusionsByName_)
    {
        const std::string& particleName1 = std::get<0>(tup);
        const std::string& residueName1  = std::get<1>(tup);
        const std::string& particleName2 = std::get<2>(tup);
        const std::string& residueName2  = std::get<3>(tup);

        // look up first index (binary search)
        auto it1 = std::lower_bound(std::begin(indexKey),
                                    std::end(indexKey),
                                    std::make_tuple(particleName1, residueName2, 0),
                                    sortKey);

        // make sure we have the (particleName,residueName) combo
        if (it1 == std::end(indexKey) or std::get<0>(*it1) != particleName1 or std::get<1>(*it1) != residueName1)
        {
            throw std::runtime_error(
                    (std::string("Particle ") += particleName1 + std::string(" in residue ") +=
                     residueName1 + std::string(" not found in list of particles\n")));
        }

        int firstIndex = std::get<2>(*it1);

        // look up second index (binary search)
        auto it2 = std::lower_bound(std::begin(indexKey),
                                    std::end(indexKey),
                                    std::make_tuple(particleName2, residueName2, 0),
                                    sortKey);

        // make sure we have the (particleName,residueName) combo
        if (it2 == std::end(indexKey) or std::get<0>(*it2) != particleName2 or std::get<1>(*it2) != residueName2)
        {
            throw std::runtime_error(
                    (std::string("Particle ") += particleName2 + std::string(" in residue ") +=
                     residueName2 + std::string(" not found in list of particles\n")));
        }

        int secondIndex = std::get<2>(*it2);

        ret.emplace_back(firstIndex, secondIndex);
        ret.emplace_back(secondIndex, firstIndex);
    }

    std::sort(std::begin(ret), std::end(ret));

    auto uniqueEnd = std::unique(std::begin(ret), std::end(ret));
    if (uniqueEnd != std::end(ret))
    {
        printf("[nblib] Warning: exclusionList for molecule %s contained duplicates",
               name_.value().c_str());
    }

    ret.erase(uniqueEnd, std::end(ret));
    return ret;
}

std::unordered_map<std::string, ParticleType> Molecule::particleTypesMap() const
{
    return particleTypes_;
}

std::vector<ParticleData> Molecule::particleData() const
{
    return particles_;
}

} // namespace nblib
