StructurePreparationData.h

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#ifndef PDBPREPARATION_DATAMANAGER_H
#define PDBPREPARATION_DATAMANAGER_H

#include "ProteinStructures.h"
#include <Utils/Bonds/BondOrderCollection.h>
#include <Utils/Geometry/AtomCollection.h>
#include <Utils/IO/NativeFilenames.h>
#include <list>
#include <vector>

namespace Scine {
namespace StructurePreparation {

struct StructurePreparationData {
  Utils::AtomCollection fullStructure;
  Utils::AtomCollection proteinStructure;
  Utils::AtomCollection nonregularContainer;
  Utils::BondOrderCollection bondOrders;
  int numberOfAtoms{0};
  std::vector<int> vectorOfProteinIndices;
  std::vector<int> vectorOfNonRegContainerIndices;
  std::vector<std::list<int>> listsOfNeighbors;
  std::vector<std::vector<int>> atomIndexMapping;
  std::vector<std::vector<int>> subsystemMapping;
  std::vector<ProteinAtom> protein;
  std::vector<int> listOfBackboneAlphaCarbons;
};

// Default filenames
struct Default {
  std::string proteinFile = "rmc.pdb";
  std::string nonRegContainerFile = "nonregular_container.xyz";
  std::string protonatedProteinFile = "rmc_H.xyz";
  std::string protonatedNonRegContainerFile = "nonregular_container_H.xyz";
  std::string nonRegContainerInfoFile = "atomic_info_nonregular_container.dat";
  std::string systemFile = "system.xyz";
  std::string titrationSitesFile = "titrable_sites.dat";
};

struct StructurePreparationFiles {
  Default d;
  std::string proteinFile;
  std::string nonRegContainerFile;
  std::string protonatedProteinFile;
  std::string protonatedNonRegContainerFile;
  std::string atomicInfoFile;
  std::string nonRegContainerInfoFile;
  std::string systemFile;
  std::string connectivityFile;
  std::string preparationDataDirectory;
  std::string workingDirectory;
  std::string titrationSitesFile;
  void initialize() {
    // Define files here because they are needed in every mode
    proteinFile = Utils::NativeFilenames::combinePathSegments(workingDirectory, d.proteinFile);
    nonRegContainerFile = Utils::NativeFilenames::combinePathSegments(workingDirectory, d.nonRegContainerFile);
    protonatedProteinFile = Utils::NativeFilenames::combinePathSegments(workingDirectory, d.protonatedProteinFile);
    protonatedNonRegContainerFile =
        Utils::NativeFilenames::combinePathSegments(workingDirectory, d.protonatedNonRegContainerFile);
    systemFile = Utils::NativeFilenames::combinePathSegments(workingDirectory, d.systemFile);
    titrationSitesFile = Utils::NativeFilenames::combinePathSegments(workingDirectory, d.titrationSitesFile);
    nonRegContainerInfoFile = Utils::NativeFilenames::combinePathSegments(workingDirectory, d.nonRegContainerInfoFile);
  }
};

} // namespace StructurePreparation
} // namespace Scine

#endif // PDBPREPARATION_DATAMANAGER_H