StructurePreparationHelper.h

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#ifndef PDBPREPARATION_PDBPREPARATIONHELPER_H
#define PDBPREPARATION_PDBPREPARATIONHELPER_H

#include "StructurePreparationData.h"
#include "boost/filesystem.hpp"
#include <Utils/Geometry/AtomCollection.h>
#include <list>
#include <memory>
#include <string>
#include <vector>

namespace Scine {
namespace Utils {
class Settings;
enum class ElementType : unsigned;
class AtomCollection;

} // namespace Utils
namespace Core {
struct Log;
}

namespace StructurePreparation {
struct ProteinAtom;
struct TitrableSite;

namespace StructurePreparationHelper {
void performInitialCheck(const StructurePreparationFiles& files, int mode, std::shared_ptr<Utils::Settings> settings);
void performGraphAnalysisOnStructure(StructurePreparationData& data, const Utils::AtomCollection& structure);
void mergeProteinAndNonRegContainer(StructurePreparationData& data, const StructurePreparationFiles& files);
void reevaluateConnectivityForAminoAcids(StructurePreparationData& data);
void handleBoundariesBetweenProteinAndNonRegContainer(StructurePreparationData& data);
Utils::AtomCollection addSolvation(StructurePreparationData& data, std::shared_ptr<Utils::Settings> settings);
void updatePdbPreparationData(StructurePreparationData& data, Utils::AtomCollection& structure);
/*
 * @brief Updates the information regarding the nonRegContainer.
 */
void updateNonRegContainerVector(StructurePreparationData& data);
std::vector<TitrableSite> collectTitrableSites(StructurePreparationData& data);
void removeAtomsFromStructure(Utils::AtomCollection& structure, std::list<int> atomsToRemove);
void determineChargedSites(std::vector<int>& listOfNegatives, std::vector<int>& listOfPositives,
                           const StructurePreparationData& data);
/*
 * @brief This functions extracts all atoms that are part of the amino acid side chain by recursively following the
 * bonds starting from CA.
 * @param atomIndex The Index of the CA atom in the amino acid.
 * @param atomsToAdd This list is filled with all indices that belong to this amino acid.
 */
void getSideChainNeighbors(StructurePreparationData& data, int atomIndex, std::list<int>& atomsToAdd);
/*
 * @brief Detects C-Termini in the structure and moves the corresponding residue to the protein substructure.
 */
void findTermini(StructurePreparationData& data, std::list<int>& atomsToTransferToNonRegContainer);
/*
 * @brief This function maps the indices of protein and nonRegContainer to the indices in the full structure.
 */
void mapSubsystemIndicesToFullStructure(const Utils::AtomCollection& fullStructure,
                                        const Utils::AtomCollection& structure, std::vector<int>& indicesInStructure,
                                        std::vector<std::vector<int>>& subsystemMapping);
/*
 * @brief Internally transfers atoms from the protein substructure to the nonRegContainer substructure.
 */
void moveAtomsFromProteinToNonRegContainer(StructurePreparationData& data, const std::list<int>& atomsToMove);
bool compareByIndex(const ProteinAtom& a, const ProteinAtom& b);

} // namespace StructurePreparationHelper
} // namespace StructurePreparation
} // namespace Scine

#endif // PDBPREPARATION_PDBPREPARATIONHELPER_H