Enumerate.h

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#include <RDGeneral/export.h>
#ifndef RDKIT_ENUMERATE_H
#define RDKIT_ENUMERATE_H
#include "EnumerateBase.h"
 
/*! \file Enumerate.h
 
\brief Contains the public API of the for the reaction enumeration engine
 
\b Note that this should be considered beta and that the API may change in
future releases.
 
*/
 
namespace RDKit {
 
//! This is a class for providing enumeration options that control
///  how enumerations are performed.
/*!
 Option
   reagentMaxMatchCount [default INT_MAX]
    This specifies how many times the reactant template can match a reagent.
 
   sanePartialProducts [default false]
    If true, forces all products of the reagent plus the product templates\n\
     pass chemical sanitization.  Note that if the product template itself\n\
     does not pass sanitization, then none of the products will.
*/
struct RDKIT_CHEMREACTIONS_EXPORT EnumerationParams {
  int reagentMaxMatchCount{INT_MAX};
  bool sanePartialProducts{false};
  EnumerationParams() {}
 
  EnumerationParams(const EnumerationParams &rhs)
      : reagentMaxMatchCount(rhs.reagentMaxMatchCount),
        sanePartialProducts(rhs.sanePartialProducts) {}
};
 
//!  Helper function, remove reagents that are incompatible
///   with the reaction.
/// rxn must be sanitized, initialized and preprocessed.
///  this happens automatically in EnumerateLibrary
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS removeNonmatchingReagents(
    const ChemicalReaction &rxn, EnumerationTypes::BBS bbs,
    const EnumerationParams &params = EnumerationParams());
 
//! This is a class for running reactions on sets of reagents.
/*!
  This class is a fully self contained reaction engine that can be
  serialized and restarted.  For example, a million products can
  be generated, the engine can be saved for later and reloaded
  to retrieve the next million products.
 
  basic usage will be something like:
  \verbatim
   ChemicalReaction rxn = ...
   BBS bbs(num_rgroups);
   ... somehow LoadRGroups(bbs[0]);
   ... somehow LoadRGroups(bbs[1]..);
   ...
   EnumerateLibrary enumerator(en, bbs);
   for(; (bool)en; ++i) {
     // This is the same as rxn.run_Reactants( reagents );
     std::vector<MOL_SPTR_VECT> products = en.next();
     ...
   }
   \endverbatim
 
   In general, reactions will enumerate to more products than desired,
   a standard use is:
 
   \verbatim
   for(int i=0;i<num_samples && (bool)en; ++i) {
     std::vector<MOL_SPTR_VECT> products = en.next();
     ...
   }
   \endverbatim
 */
 
class RDKIT_CHEMREACTIONS_EXPORT EnumerateLibrary
    : public EnumerateLibraryBase {
  EnumerationTypes::BBS m_bbs;
 
 public:
  EnumerateLibrary() : EnumerateLibraryBase(), m_bbs() {}
  EnumerateLibrary(const std::string &s) : EnumerateLibraryBase(), m_bbs() {
    initFromString(s);
  }
 
  EnumerateLibrary(const ChemicalReaction &rxn,
                   const EnumerationTypes::BBS &reagents,
                   const EnumerationParams &params = EnumerationParams());
  EnumerateLibrary(const ChemicalReaction &rxn,
                   const EnumerationTypes::BBS &reagents,
                   const EnumerationStrategyBase &enumerator,
                   const EnumerationParams &params = EnumerationParams());
  EnumerateLibrary(const EnumerateLibrary &rhs);
 
  //! Return the reagents used in the library
  const EnumerationTypes::BBS &getReagents() const { return m_bbs; }
 
  //! Get the next product set
  std::vector<MOL_SPTR_VECT> next() override;
 
  void toStream(std::ostream &ss) const override;
  void initFromStream(std::istream &ss) override;
 
 private:
#ifdef RDK_USE_BOOST_SERIALIZATION
  friend class boost::serialization::access;
  template <class Archive>
  void save(Archive &ar, const unsigned int /*version*/) const {
    ar &boost::serialization::base_object<EnumerateLibraryBase>(*this);
    size_t sz = m_bbs.size();
    ar & sz;
 
    std::string pickle;
    for (size_t i = 0; i < m_bbs.size(); ++i) {
      sz = m_bbs[i].size();
      ar & sz;
      for (size_t j = 0; j < m_bbs[i].size(); ++j) {
        MolPickler::pickleMol(*m_bbs[i][j], pickle);
        ar & pickle;
      }
    }
  }
  template <class Archive>
  void load(Archive &ar, const unsigned int /*version*/) {
    ar &boost::serialization::base_object<EnumerateLibraryBase>(*this);
 
    size_t sz;
    ar & sz;
 
    m_bbs.resize(sz);
 
    for (size_t i = 0; i < m_bbs.size(); ++i) {
      ar & sz;
      m_bbs[i].resize(sz);
      std::string pickle;
      for (size_t j = 0; j < m_bbs[i].size(); ++j) {
        ar & pickle;
        RWMol *mol = new RWMol();
        MolPickler::molFromPickle(pickle, *mol);
        m_bbs[i][j].reset(mol);
      }
    }
  }
 
  BOOST_SERIALIZATION_SPLIT_MEMBER();
#endif
};
 
RDKIT_CHEMREACTIONS_EXPORT bool EnumerateLibraryCanSerialize();
 
}  // namespace RDKit
#endif