PeriodicBoundaries.h

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#ifndef INCLUDE_MOLASSEMBLER_PERIODIC_BOUNDARIES_H
#define INCLUDE_MOLASSEMBLER_PERIODIC_BOUNDARIES_H

#include "Molassembler/Types.h"

#include <vector>
#include <unordered_set>
#include <unordered_map>

namespace Scine {
namespace Molassembler {

class Graph;

struct PeriodicBoundaryDuplicates {
  std::unordered_set<AtomIndex> uninterestingAtoms;
  std::unordered_map<AtomIndex, AtomIndex> ghostAtomMap;
};

struct SubstitutionsGenerator {
  using SubstitutionList = std::vector<std::pair<AtomIndex, AtomIndex>>;

  using SubstitutionMap = std::unordered_map<AtomIndex, SubstitutionList>;

  static SubstitutionMap removeGhosts(
    Graph& graph,
    const PeriodicBoundaryDuplicates& periodics
  );
};

} // namespace Molassembler
} // namespace Scine

#endif