TopologyUtils.h

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#ifndef SWOOSEUTILITIES_TOPOLOGYUTILS_H
#define SWOOSEUTILITIES_TOPOLOGYUTILS_H

#include <Utils/Typenames.h>
#include <list>
#include <vector>

namespace Scine {

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

namespace SwooseUtilities {

class TopologyUtils {
 public:
  static std::vector<std::list<int>>
  generateListsOfNeighborsFromBondOrderMatrix(int nAtoms, const Utils::BondOrderCollection& bondOrderMatrix,
                                              double minimalBondOrderToConsider);
  static Utils::BondOrderCollection generateBondOrderMatrixFromListsOfNeighbors(const std::vector<std::list<int>>& listsOfNeighbors);
  static std::vector<int> divideStructureAtBond(int a1, int a2, const Utils::BondOrderCollection& bondOrderMatrix, bool& ok);
  static int countNeighborsOfElementType(int atomType, const std::vector<std::list<int>>& listsOfNeighbors,
                                         Utils::ElementType elementType,
                                         const Utils::ElementTypeCollection& elementTypeCollection);
  static void calculateNumberOfNeighbors(int nAtoms, std::vector<std::list<int>> listsOfNeighbors, std::vector<int>& nNeighbors);
};

} // namespace SwooseUtilities
} // namespace Scine

#endif // SWOOSEUTILITIES_TOPOLOGYUTILS_H