PotentialTermsHelper.h

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#ifndef MOLECULARMECHANICS_POTENTIALTERMSHELPER_H
#define MOLECULARMECHANICS_POTENTIALTERMSHELPER_H

#include "Interactions/AngleTerm.h"
#include "Interactions/BondedTerm.h"
#include "Interactions/ElectrostaticTerm.h"
#include <Eigen/Dense>
#include <vector>

namespace Scine {
namespace MolecularMechanics {
class IndexedStructuralTopology;
class AtomTypesHolder;
class MMParameters;

namespace PotentialTermsHelper {

Eigen::MatrixXi getExclusionTypeMatrix(const IndexedStructuralTopology& topology, int nAtoms);

std::vector<BondedTerm> getBondedTerms(const IndexedStructuralTopology& topology, const MMParameters& parameters,
                                       const AtomTypesHolder& atomTypesHolder);

std::vector<AngleTerm> getAngleTerms(const IndexedStructuralTopology& topology, const MMParameters& parameters,
                                     const AtomTypesHolder& atomTypesHolder);

std::vector<ElectrostaticTerm>
getElectrostaticTerms(bool applyCutoff, std::shared_ptr<double> cutoffRadius, double scalingFactorForOneFourTerms,
                      const Eigen::MatrixXi& exclusionTypeMatrix, const Utils::PositionCollection& positions);

} // namespace PotentialTermsHelper
} // namespace MolecularMechanics
} // namespace Scine

#endif // MOLECULARMECHANICS_POTENTIALTERMSHELPER_H