Editing.h

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#ifndef INCLUDE_MOLASSEMBLER_EDITING_H
#define INCLUDE_MOLASSEMBLER_EDITING_H
 
#include "Molassembler/Molecule.h"
#include "Molassembler/RankingInformation.h"
#include <tuple>
 
namespace Scine {
namespace Molassembler {
 
class Molecule;
 
namespace Editing {
 
using AtomSitePair = std::pair<AtomIndex, SiteIndex>;
 
struct Cleaved {
  Molecule first;
  Molecule second;
  std::vector<std::pair<unsigned, AtomIndex>> componentMap;
};
 
Cleaved cleave(const Molecule& a, BondIndex bridge);
 
Cleaved cleave(const Molecule& a, AtomSitePair hapticSite);
 
Molecule insert(
  Molecule log,
  const Molecule& wedge,
  BondIndex logBond,
  AtomIndex firstWedgeAtom,
  AtomIndex secondWedgeAtom);
 
Molecule superpose(Molecule top, const Molecule& bottom, AtomIndex topAtom, AtomIndex bottomAtom);
 
Molecule
substitute(const Molecule& left, const Molecule& right, BondIndex leftBond, BondIndex rightBond);
 
Molecule substitute(
  const Molecule& left,
  const Molecule& right,
  BondIndex leftBond,
  BondIndex rightBond,
  AtomIndex leftSubstituteIndex,
  AtomIndex rightSubstituteIndex);
 
Molecule
connect(Molecule a, const Molecule& b, AtomIndex aConnectAtom, AtomIndex bConnectAtom, BondType bondType);
 
Molecule addLigand(
  Molecule a,
  const Molecule& ligand,
  AtomIndex complexatingAtom,
  const std::vector<AtomIndex>& ligandBindingAtoms);
 
} // namespace Editing
} // namespace Molassembler
} // namespace Scine
 
#endif