ParametrizationData.h

Go to the documentation of this file.

#ifndef MMPARAMETRIZATION_DATAMANAGER_H
#define MMPARAMETRIZATION_DATAMANAGER_H

#include <Swoose/MolecularMechanics/AtomTypesHolder.h>
#include <Swoose/MolecularMechanics/SFAM/SfamParameters.h>
#include <Swoose/MolecularMechanics/Topology/IndexedStructuralTopology.h>
#include <Swoose/StructurePreparation/Protonation/TitrationData.h>
#include <Utils/Bonds/BondOrderCollection.h>
#include <Utils/Geometry/AtomCollection.h>
#include <Utils/Typenames.h>
#include <Eigen/Dense>
#include <Eigen/Sparse>
#include <list>
#include <memory>

namespace Scine {
namespace MMParametrization {
struct ParametrizationData {
  Utils::AtomCollection fullStructure;
  int numberOfAtoms{0};
  Eigen::SparseMatrix<double> fullHessian;
  std::vector<std::unique_ptr<Utils::HessianMatrix>> vectorOfHessians;
  std::vector<std::unique_ptr<Utils::AtomCollection>> vectorOfStructures;
  std::vector<std::unique_ptr<Utils::AtomCollection>> vectorOfOptimizedStructures;
  std::vector<std::pair<int, int>> vectorOfChargesAndMultiplicities;
  std::vector<std::unique_ptr<Utils::BondOrderCollection>> vectorOfBondOrderCollections;
  std::vector<double> atomicCharges;
  std::vector<std::vector<double>> atomicChargesForEachFragment;
  std::vector<std::list<int>> listsOfNeighbors;
  MolecularMechanics::IndexedStructuralTopology topology;
  MolecularMechanics::SfamParameters parameters;
  MolecularMechanics::AtomTypesHolder atomTypes;
  std::vector<std::pair<int, int>> vectorOfHessianSubmatrixIndices;
  std::vector<std::string> vectorOfAtomTypesForParameter;
  Utils::BondOrderCollection bondOrders;
  std::map<int, int> formalCharges;
  std::map<int, int> unpairedElectrons;
  std::map<int, std::string> pHSensitiveSites;
  std::vector<bool> siteIspHSensitive;
  std::vector<std::vector<int>> atomIndexMapping;
  std::vector<std::vector<int>> constrainedAtoms;
  std::vector<int> superfluousFragments;
};

struct TrainingData {
  std::string groupType;
  std::vector<double> eneryOfDeprotonation;
  std::vector<double> pKas;
};

// This struct holds all results from titration calculations
struct TitrationResults {
  std::vector<std::string> requiredFunctionalGroups;
  std::map<int, std::unique_ptr<Utils::AtomCollection>> vectorOfOptimizedNonRefStructures;
  std::map<int, std::unique_ptr<Utils::HessianMatrix>> vectorOfHessiansForNonRefStates;
  std::vector<StructurePreparation::TitrableSite> sites;
  std::map<int, std::pair<double, double>> electronicEnergies;

  std::vector<TrainingData> trainingData;
};

} // namespace MMParametrization
} // namespace Scine

#endif // MMPARAMETRIZATION_DATAMANAGER_H