Editing.h

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#ifndef INCLUDE_MOLASSEMBLER_EDITING_H
#define INCLUDE_MOLASSEMBLER_EDITING_H

#include "Molassembler/Types.h"
#include <tuple>
#include <vector>

namespace Scine {
namespace Molassembler {

class Molecule;

struct MASM_EXPORT Editing {
  static std::pair<Molecule, Molecule> cleave(const Molecule& a, BondIndex bridge);

  static Molecule insert(
    Molecule log,
    const Molecule& wedge,
    BondIndex logBond,
    AtomIndex firstWedgeAtom,
    AtomIndex secondWedgeAtom
  );

  static Molecule superpose(
    Molecule top,
    const Molecule& bottom,
    AtomIndex topAtom,
    AtomIndex bottomAtom
  );

  static Molecule substitute(
    const Molecule& left,
    const Molecule& right,
    BondIndex leftBond,
    BondIndex rightBond
  );

  static Molecule connect(
    Molecule a,
    const Molecule& b,
    AtomIndex aConnectAtom,
    AtomIndex bConnectAtom,
    BondType bondType
  );

  static Molecule addLigand(
    Molecule a,
    const Molecule& ligand,
    AtomIndex complexatingAtom,
    const std::vector<AtomIndex>& ligandBindingAtoms
  );
};

} // namespace Molassembler
} // namespace Scine

#endif