SfamParameters.h

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#ifndef MOLECULARMECHANICS_SFAMPARAMETERS_H
#define MOLECULARMECHANICS_SFAMPARAMETERS_H

#include "../MMParameters.h"
#include "../Parameters/AngleParameters.h"
#include "../Parameters/BondParameters.h"
#include "../Parameters/DihedralParameters.h"
#include "../Parameters/ImproperDihedralParameters.h"
#include "../Topology/AngleType.h"
#include "../Topology/BondType.h"
#include "../Topology/DihedralType.h"
#include "../Topology/ImproperDihedralType.h"
#include <Eigen/Core>
#include <map>
#include <vector>

namespace Scine {

namespace Utils {
class AtomCollection;
} // namespace Utils

namespace MolecularMechanics {
class AtomTypesHolder;
class SfamParameters final : public MMParameters {
 public:
  bool sanityCheck(const AtomTypesHolder& atomTypes) const;
  std::vector<double> getChargesForEachAtom(const AtomTypesHolder& atomTypes) const;
  void prepareC6Matrix(const AtomTypesHolder& atomTypes);
  float getC6(int indexOfAtomTypeA, int indexOfAtomTypeB) const;
  float getC6(const std::string& a, const std::string& b) const;
  std::vector<double> getNonCovalentParameters() const;
  void setC6(int indexOfAtomTypeA, int indexOfAtomTypeB, float c6);
  void setC6(const std::string& a, const std::string& b, float c6);
  void resetC6Matrix();
  void setNonCovalentParameters(std::vector<double> nonCovalentParameters);
  std::vector<Dihedral> getMMDihedrals(std::string t1, std::string t2, std::string t3, std::string t4) const;
  ImproperDihedral getMMImproperDihedral(std::string central, std::string t2, std::string t3, std::string t4) const;
  const std::map<std::string, int>& getC6IndicesMap() const;

  // These functions add certain parameters of the MM model
  void addCharge(std::string atomType, double charge);
  void addDihedral(DihedralType dihedralType, DihedralParameters dihedralParameters);
  void addImproperDihedral(ImproperDihedralType improperDihedralType, ImproperDihedralParameters improperDihedralParameters);

  int evaluateNumDistinctAtomTypes(const AtomTypesHolder& atomTypes) const;

  // These functions return all parameters of a certain type by reference
  std::map<BondType, BondParameters>& getBonds();
  std::map<AngleType, AngleParameters>& getAngles();
  std::map<DihedralType, DihedralParameters>& getDihedrals();
  std::map<ImproperDihedralType, ImproperDihedralParameters>& getImproperDihedrals();
  std::map<std::string, double>& getCharges();

  // These functions return all parameters of a certain type by const. reference
  const std::map<BondType, BondParameters>& getBonds() const;
  const std::map<AngleType, AngleParameters>& getAngles() const;
  const std::map<DihedralType, DihedralParameters>& getDihedrals() const;
  const std::map<ImproperDihedralType, ImproperDihedralParameters>& getImproperDihedrals() const;
  const std::map<std::string, double>& getCharges() const;

 private:
  std::map<std::string, double> charges_;
  Eigen::MatrixXf c6Matrix_; // store as floats for efficiency
  std::map<std::string, int> c6IndicesMap_;
  std::vector<double> nonCovalentParameters_;
  std::map<DihedralType, DihedralParameters> dihedrals_;
  std::map<ImproperDihedralType, ImproperDihedralParameters> improperDihedrals_;
};

} // namespace MolecularMechanics
} // namespace Scine

#endif // MOLECULARMECHANICS_SFAMPARAMETERS_H