TitrationHelper.h

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#ifndef PDBPREPARATION_TITRATIONHELPER_H
#define PDBPREPARATION_TITRATIONHELPER_H

#include <Eigen/Dense>
#include <memory>
#include <string>
#include <vector>

namespace Scine {
namespace Utils {
class Atom;
class Settings;
class AtomCollection;
} // namespace Utils

namespace Core {
struct Log;
}

namespace StructurePreparation {
struct TitrableSite;
} // namespace StructurePreparation

namespace MMParametrization {
struct TrainingData;
struct TitrationResults;

// TODO: divide this class to protonator and protonation helper

class TitrationHelper {
 public:
  TitrationHelper(std::shared_ptr<Utils::Settings>& settings);
  Utils::AtomCollection changeProtonationState(const Utils::AtomCollection& refStructure, std::string residueName,
                                               bool isBase, int indexOfCriticalAtom, std::vector<int> superfluousHydrogens);
  // Collects tr
  void collectTrainingData(TitrationResults& results);
  static void calculateFreeEnergiesOfDeprotonation(TitrationResults& results);

  double getModelPka(const std::string& residueName);

 private:
  double getPkaOfTrainingMolecule(std::string dataDirectory);
  double getEnergyOfDeprotonationForTrainingMolecule(std::string dataDirectory);

  // The settings
  std::shared_ptr<Utils::Settings>& settings_;

  const std::vector<std::string> availableFunctionalGroups_ = {"Phenol", "Alcohol", "NH3", "SH", "Imidazole", "COOH"};
};
} // namespace MMParametrization
} // namespace Scine

#endif // PDBPREPARATION_TITRATIONHELPER_H