FragmentationHelper.h

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#ifndef SWOOSEUTILITIES_FRAGMENTATIONHELPER_H
#define SWOOSEUTILITIES_FRAGMENTATIONHELPER_H

#include <Utils/Geometry/ElementTypes.h>
#include <deque>
#include <list>
#include <memory>
#include <random>
#include <vector>

namespace Scine {

namespace Core {
struct Log;
} // namespace Core

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

namespace SwooseUtilities {

// The index given to saturating atoms in the atomIndexMapping object
static constexpr int indexForSaturatingAtoms = -1;
// Minimum size of a subsystem
static constexpr int minimumSubsystemSize_ = 20;

namespace FragmentationHelper {
void addAtomsUpToReasonableCut(Utils::AtomCollection& atomsToAdd, std::vector<int>& alreadyAddedAtoms,
                               std::deque<bool>& isSaturatingAtom, int atomInside, int atomOutside,
                               const Utils::AtomCollection& fullStructure, const std::vector<std::list<int>>& listsOfNeighbors,
                               double probabilityToDivide, std::shared_ptr<std::mt19937> randomEngine);
void addMoreAtomsToSubsystem(const Utils::AtomCollection& atomsToAdd, Utils::AtomCollection& subsystem,
                             const std::deque<bool>& isSaturatingAtom, bool addSaturatingAtoms);
void checkSizeOfSubsystem(int size, double& additionToRadius, bool& unsuccessfulFragmentation, int fragmentIndex,
                          int fullStructureSize, int maximumSubsystemSize, Core::Log& log);
void updateInformationForIndexMapping(const Utils::AtomCollection& subsystem,
                                      const Utils::AtomCollection& fullStructure, std::vector<int>& atomIndexMapping);
std::vector<int> calculateSubgraphSizes(const Utils::AtomCollection& fullStructure, const Utils::BondOrderCollection& bondOrders);

bool atomIsCloseToExistingAtom(const Utils::Atom& atom, const Utils::AtomCollection& existingAtoms);

bool isDivisibleAtBond(int atomInside, int atomOutside, const Utils::AtomCollection& fullStructure,
                       const std::vector<std::list<int>>& listsOfNeighbors, double probabilityToDivide,
                       std::shared_ptr<std::mt19937> randomEngine);
Utils::AtomCollection mergeSubsystems(std::vector<int>& atomIndexMapping, std::vector<Utils::AtomCollection> subsystems,
                                      std::vector<std::vector<int>> atomIndexMappings);

} // namespace FragmentationHelper
} // namespace SwooseUtilities
} // namespace Scine

#endif // SWOOSEUTILITIES_FRAGMENTATIONHELPER_H