/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "nblib/exception.h"
#include "nblib/molecules.h"
#include "nblib/particletype.h"
-#include "nblib/util/internal.h"
namespace nblib
{
-
Molecule::Molecule(MoleculeName moleculeName) : name_(std::move(moleculeName)) {}
MoleculeName Molecule::name() const
return *this;
}
-//! Two-particle interactions such as bonds and LJ1-4
-template<class Interaction>
-void Molecule::addInteraction(const ParticleName& particleNameI,
- const ResidueName& residueNameI,
- const ParticleName& particleNameJ,
- const ResidueName& residueNameJ,
- const Interaction& interaction)
+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 (particleNameI == particleNameJ and residueNameI == residueNameJ)
+ if (particleI == particleJ)
{
throw InputException(std::string("Cannot add interaction of particle ")
- + particleNameI.value() + " with itself in molecule " + name_.value());
+ + particleI.particleName().value() + " with itself in molecule "
+ + name_.value());
}
- auto& interactionContainer = pickType<Interaction>(interactionData_);
- interactionContainer.interactions_.emplace_back(particleNameI, residueNameI, particleNameJ, residueNameJ);
- interactionContainer.interactionTypes_.push_back(interaction);
+ addInteractionImpl(interaction,
+ particleI.particleName(),
+ residueName(particleI),
+ particleJ.particleName(),
+ residueName(particleJ));
}
-//! \cond DO_NOT_DOCUMENT
-#define ADD_INTERACTION_INSTANTIATE_TEMPLATE(x) \
- template void Molecule::addInteraction(const ParticleName& particleNameI, \
- const ResidueName& residueNameI, \
- const ParticleName& particleNameJ, \
- const ResidueName& residueNameJ, \
- const x& interaction);
-MAP(ADD_INTERACTION_INSTANTIATE_TEMPLATE, SUPPORTED_TWO_CENTER_TYPES)
-#undef ADD_INTERACTION_INSTANTIATE_TEMPLATE
-//! \endcond
-
-// add interactions with default residue name
-template<class Interaction>
-void Molecule::addInteraction(const ParticleName& particleNameI,
- const ParticleName& particleNameJ,
- const Interaction& interaction)
+void Molecule::addInteraction(const ParticleIdentifier& particleI,
+ const ParticleIdentifier& particleJ,
+ const ParticleIdentifier& particleK,
+ const ThreeCenterInteraction& interaction)
{
- addInteraction(particleNameI, ResidueName(name_), particleNameJ, ResidueName(name_), 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));
}
-//! \cond DO_NOT_DOCUMENT
-#define ADD_INTERACTION_INSTANTIATE_TEMPLATE(x) \
- template void Molecule::addInteraction( \
- const ParticleName& particleNameI, const ParticleName& particleNameJ, const x& interaction);
-MAP(ADD_INTERACTION_INSTANTIATE_TEMPLATE, SUPPORTED_TWO_CENTER_TYPES)
-#undef ADD_INTERACTION_INSTANTIATE_TEMPLATE
-
-//! 3-particle interactions such as angles
-template<class Interaction>
-void Molecule::addInteraction(const ParticleName& particleNameI,
- const ResidueName& residueNameI,
- const ParticleName& particleNameJ,
- const ResidueName& residueNameJ,
- const ParticleName& particleNameK,
- const ResidueName& residueNameK,
- const Interaction& interaction)
+void Molecule::addInteraction(const ParticleIdentifier& particleI,
+ const ParticleIdentifier& particleJ,
+ const ParticleIdentifier& particleK,
+ const ParticleIdentifier& particleL,
+ const FourCenterInteraction& interaction)
{
- if (particleNameI == particleNameJ and particleNameJ == particleNameK)
+ if (particleI == particleJ and particleJ == particleK and particleK == particleL)
{
throw InputException(std::string("Cannot add interaction of particle ")
- + particleNameI.value() + " with itself in molecule " + name_.value());
+ + particleI.particleName().value() + " with itself in molecule "
+ + name_.value());
}
- auto& interactionContainer = pickType<Interaction>(interactionData_);
- interactionContainer.interactions_.emplace_back(
- particleNameI, residueNameI, particleNameJ, residueNameJ, particleNameK, residueNameK);
- interactionContainer.interactionTypes_.push_back(interaction);
+ addInteractionImpl(interaction,
+ particleI.particleName(),
+ residueName(particleI),
+ particleJ.particleName(),
+ residueName(particleJ),
+ particleK.particleName(),
+ residueName(particleK),
+ particleL.particleName(),
+ residueName(particleL));
}
-#define ADD_INTERACTION_INSTANTIATE_TEMPLATE(x) \
- template void Molecule::addInteraction(const ParticleName& particleNameI, \
- const ResidueName& residueNameI, \
- const ParticleName& particleNameJ, \
- const ResidueName& residueNameJ, \
- const ParticleName& particleNameK, \
- const ResidueName& residueNameK, \
- const x& interaction);
-MAP(ADD_INTERACTION_INSTANTIATE_TEMPLATE, SUPPORTED_THREE_CENTER_TYPES)
-#undef ADD_INTERACTION_INSTANTIATE_TEMPLATE
-
-template<class Interaction>
-void Molecule::addInteraction(const ParticleName& particleNameI,
- const ParticleName& particleNameJ,
- const ParticleName& particleNameK,
- const Interaction& interaction)
+void Molecule::addInteraction(const ParticleIdentifier& particleI,
+ const ParticleIdentifier& particleJ,
+ const ParticleIdentifier& particleK,
+ const ParticleIdentifier& particleL,
+ const ParticleIdentifier& particleM,
+ const FiveCenterInteraction& interaction)
{
- addInteraction(particleNameI,
- ResidueName(name_),
- particleNameJ,
- ResidueName(name_),
- particleNameK,
- ResidueName(name_),
- 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));
}
-#define ADD_INTERACTION_INSTANTIATE_TEMPLATE(x) \
- template void Molecule::addInteraction(const ParticleName& particleNameI, \
- const ParticleName& particleNameJ, \
- const ParticleName& particleNameK, \
- const x& interaction);
-MAP(ADD_INTERACTION_INSTANTIATE_TEMPLATE, SUPPORTED_THREE_CENTER_TYPES)
-#undef ADD_INTERACTION_INSTANTIATE_TEMPLATE
-//! \endcond
int Molecule::numParticlesInMolecule() const
{
return particles_.size();
}
-void Molecule::addExclusion(const int particleIndex, const int particleIndexToExclude)
+void Molecule::addExclusion(const ParticleIdentifier& particle, const ParticleIdentifier& particleToExclude)
{
- // We do not need to add exclusion in case the particle indexes are the same
- // because self exclusion are added by addParticle
- if (particleIndex != particleIndexToExclude)
+ if (particle == particleToExclude)
{
- exclusions_.emplace_back(particleIndex, particleIndexToExclude);
- exclusions_.emplace_back(particleIndexToExclude, particleIndex);
+ return;
}
-}
-void Molecule::addExclusion(std::tuple<ParticleName, ResidueName> particle,
- std::tuple<ParticleName, ResidueName> particleToExclude)
-{
// duplication for the swapped pair happens in getExclusions()
- exclusionsByName_.emplace_back(std::make_tuple(std::get<0>(particle),
- std::get<1>(particle),
- std::get<0>(particleToExclude),
- std::get<1>(particleToExclude)));
-}
-
-void Molecule::addExclusion(const ParticleName& particleName, const ParticleName& particleNameToExclude)
-{
- addExclusion(std::make_tuple(particleName, ResidueName(name_)),
- std::make_tuple(particleNameToExclude, ResidueName(name_)));
+ exclusionsByName_.emplace_back(std::make_tuple(particle.particleName(),
+ residueName(particle),
+ particleToExclude.particleName(),
+ residueName(particleToExclude)));
}
const Molecule::InteractionTuple& Molecule::interactionData() const
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff