GaffPotentialTermsGenerator.h

Go to the documentation of this file.

#ifndef MOLECULARMECHANICS_GAFFPOTENTIALTERMSGENERATOR_H
#define MOLECULARMECHANICS_GAFFPOTENTIALTERMSGENERATOR_H

#include "../Interactions/AngleTerm.h"
#include "../Interactions/BondedTerm.h"
#include "../Interactions/DihedralTerm.h"
#include "../Interactions/ElectrostaticTerm.h"
#include "../Interactions/ImproperDihedralTerm.h"
#include "../Interactions/LennardJonesTerm.h"
#include <vector>

namespace Scine {

namespace Core {
class Log;
} // namespace Core

namespace MolecularMechanics {
class IndexedStructuralTopology;
class AtomTypesHolder;
class GaffParameters;

class GaffPotentialTermsGenerator {
 public:
  GaffPotentialTermsGenerator(int nAtoms, const AtomTypesHolder& atomTypes, const IndexedStructuralTopology& topology,
                              const GaffParameters& parameters, const Utils::PositionCollection& positions,
                              const double& nonCovalentCutoffRadius, Core::Log& log);

  std::vector<BondedTerm> getBondedTerms();
  std::vector<AngleTerm> getAngleTerms();
  std::vector<DihedralTerm> getDihedralTerms();
  std::vector<DihedralTerm> getImproperDihedralTerms();
  std::vector<LennardJonesTerm> getLennardJonesTerms(bool applyCutoff);
  std::vector<ElectrostaticTerm> getElectrostaticTerms(bool applyCutoff);

 private:
  int nAtoms_;
  const AtomTypesHolder& atomTypesHolder_;
  const IndexedStructuralTopology& topology_;
  const GaffParameters& parameters_;
  const Utils::PositionCollection& positions_;
  /*
   * @brief The cutoff radius for the non-covalent interactions.
   *
   *        It is a pointer so that it is updated with the settings.
   *        This is important since it is passed on from here to the actual DispersionTerms, etc.
   *        A reference does not work because then the assignment operator of DispersionTerms, etc. vanishes.
   */
  std::shared_ptr<double> cutoff_;
  // The logger
  Core::Log& log_;

  static constexpr double scalingFactorForElectrostaticOneFourTerms_ = 0.5;
  static constexpr double scalingFactorForLennardJonesOneFourTerms_ = 0.5;
};

} // namespace MolecularMechanics
} // namespace Scine

#endif // MOLECULARMECHANICS_GAFFPOTENTIALTERMSGENERATOR_H