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#ifndef RD_REACTION_RUNNER_H
#define RD_REACTION_RUNNER_H

#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ROMol.h>

namespace RDKit {
//! Runs the reaction on a set of reactants
/*!
  \param rxn:       the template reaction we are interested
  \param reactants: the reactants to be used. The length of this must be equal
  to
                    rxn->getNumReactantTemplates()
                    Caution: The order of the reactant templates determines the
  order of the reactants!

  \return a vector of vectors of products. Each subvector will be
          rxn->getNumProductTemplates() long.

  We return a vector of vectors of products because each individual template may
  map multiple times onto its reactant. This leads to multiple possible result
  sets.
*/
std::vector<MOL_SPTR_VECT> run_Reactants(const ChemicalReaction& rxn,
                                         const MOL_SPTR_VECT& reactants);

//! Runs a single reactant against a single reactant template
/*!
  \param reactant The single reactant to use

  \param reactantTemplateIdx the reactant template to target in the reaction

  \return a vector of vectors of products. Each subvector will be
          rxn->getNumProductTemplates() long.

  We return a vector of vectors of products because each individual template may
  map multiple times onto its reactant. This leads to multiple possible result
  sets.

*/

std::vector<MOL_SPTR_VECT> run_Reactant(const ChemicalReaction& rxn,
                                        const ROMOL_SPTR& reactant,
                                        unsigned int reactantIdx);

//! Reduce the product generated by run_Reactants or run_Reactant to 
// the sidechains that come from the reagents
//
//  n.b. molecules that might be a product of the given reaction
//       but were not generated by run_Reactant(s) currently
//       produce no sidechains.
/*!
  \param addDummyAtoms If true, add dummy atoms to the sidechains for the
      non-reagent parts of the sidechain.  Dummy atoms are annotated with
      the atom maps from the reaction.
      If False, then any sidechain atom where a bond was cleaved is annotated with:
         _rgroupAtomMaps property which indicates the scaffold atommaps that where bonded
         _rgroupBonds property which indicates the bondtype for each atommap bonded
*/

ROMol* reduceProductToSideChains(const ROMOL_SPTR& product,
                                 bool addDummyAtoms = true);

namespace ReactionRunnerUtils {
MOL_SPTR_VECT generateOneProductSet(
    const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants,
    const std::vector<MatchVectType> &reactantsMatch);

RWMOL_SPTR convertTemplateToMol(const ROMOL_SPTR prodTemplateSptr);
}

}  // end of RDKit namespace

#endif
