SanitizeRxn.h

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#include <RDGeneral/export.h>
#ifndef RDKIT_SANITIZERXN_H
#define RDKIT_SANITIZERXN_H
 
#include "Reaction.h"
#include <GraphMol/MolOps.h>
#include <string>
#include <exception>
#include <utility>
 
namespace RDKit {
 
//! class for flagging sanitization errors
class RDKIT_CHEMREACTIONS_EXPORT RxnSanitizeException : public std::exception {
 public:
  RxnSanitizeException(const char *msg) : _msg(msg) {}
  RxnSanitizeException(std::string msg) : _msg(std::move(msg)) {}
  const char *what() const noexcept override { return _msg.c_str(); }
  ~RxnSanitizeException() noexcept override = default;
 
 private:
  std::string _msg;
};
 
namespace RxnOps {
//! Any dummy atom with a map but no RGroup label, should be an RGroup
//!  in RDKit's view of a reaction.
//!  See if these atoms can be salvaged into RGroups.
RDKIT_CHEMREACTIONS_EXPORT void fixRGroups(ChemicalReaction &rxn);
 
//! If atom maps are not defined on rgroups, attempt to deduce them from the
//! RGroup
//!  labels, or add new ones if possible.
RDKIT_CHEMREACTIONS_EXPORT void fixAtomMaps(ChemicalReaction &rxn);
 
//! Adjusts the reactant templates to properly match reagents
RDKIT_CHEMREACTIONS_EXPORT void adjustTemplates(
    const MOL_SPTR_VECT &templates,
    const MolOps::AdjustQueryParameters &params);
 
//! merge query Hs if appropriate
RDKIT_CHEMREACTIONS_EXPORT void fixHs(ChemicalReaction &rxn);
 
// Default adjustment parameters for matching reagents
inline const MolOps::AdjustQueryParameters DefaultRxnAdjustParams() {
  MolOps::AdjustQueryParameters params;
  params.adjustDegree = false;
  params.adjustDegreeFlags = MolOps::ADJUST_IGNOREALL;
  params.adjustRingCount = false;
  params.adjustRingCountFlags = MolOps::ADJUST_IGNOREALL;
  params.makeDummiesQueries = false;
  params.aromatizeIfPossible = true;
  return params;
}
 
// Default adjustment parameters for ChemDraw style matching of reagents
//  -- deprecated - renamed MatchOnlyAtRgroupsAdjustParams
//  -- this doesn't match sciquest style searching
inline const MolOps::AdjustQueryParameters ChemDrawRxnAdjustParams() {
  BOOST_LOG(rdWarningLog)
      << " deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead"
      << std::endl;
  MolOps::AdjustQueryParameters params;
  params.adjustDegree = true;
  params.adjustDegreeFlags = MolOps::ADJUST_IGNOREDUMMIES;
  params.adjustRingCount = false;
  params.adjustRingCountFlags = MolOps::ADJUST_IGNORENONE;
  params.makeDummiesQueries = false;
  params.aromatizeIfPossible = true;
  return params;
}
 
inline const MolOps::AdjustQueryParameters MatchOnlyAtRgroupsAdjustParams() {
  MolOps::AdjustQueryParameters params;
  params.adjustDegree = true;
  params.adjustDegreeFlags = MolOps::ADJUST_IGNOREDUMMIES;
  params.adjustRingCount = false;
  params.adjustRingCountFlags = MolOps::ADJUST_IGNORENONE;
  params.makeDummiesQueries = false;
  params.aromatizeIfPossible = true;
  return params;
}
 
typedef enum {
  SANITIZE_NONE = 0x0,
  SANITIZE_RGROUP_NAMES = 0x1,
  SANITIZE_ATOM_MAPS = 0x2,
  SANITIZE_ADJUST_REACTANTS = 0x4,
  SANITIZE_MERGEHS = 0x8,
  SANITIZE_ADJUST_PRODUCTS = 0x10,
  SANITIZE_ALL = 0xFFFFFFFF
} SanitizeRxnFlags;
 
//! \brief carries out a collection of tasks for cleaning up a reaction and
/// ensuring
//! that it makes "chemical sense" in the context of RDKit reacitons
/*!
   This functions calls the following in sequence
     -# RxnOps::fixRGroups()
     -# RxnOps::fixupAtomMaps()
     -# RxnOps::fixupTemplateAromaticity()
     -# RxnOps::mergeHs()
 
   \param rxn : the ChemicalReaction to be cleaned
 
   \param operationThatFailed : the first (if any) sanitization operation that
   fails is set here.
                                The values are taken from the \c SanitizeFlags
   enum.
                                On success, the value is  \c
   SanitizeFlags::SANITIZE_NONE
 
   \param sanitizeOps : the bits here are used to set which sanitization
   operations are carried
                        out. The elements of the \c SanitizeFlags enum define
   the operations.
 
   <b>Notes:</b>
    - This attempts to fix known issues with certain reaction drawers.
       HOWEVER, if any flag is returned in operationsPerformed,
       the reaction may still be suspect to its validity.
    - Aromaticity can be tricky when starting with Kekule structures that
      have query features, aromaticity works well for non-query rings, however
      certain structures (substitutions on Kekule rings that should really be
      aromatic) may not have enough information.
*/
 
RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxn(
    ChemicalReaction &rxn, unsigned int &operationsThatFailed,
    unsigned int sanitizeOps = SANITIZE_ALL,
    const MolOps::AdjustQueryParameters &params = DefaultRxnAdjustParams());
//! \overload
RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxn(
    ChemicalReaction &rxn,
    const MolOps::AdjustQueryParameters &params = DefaultRxnAdjustParams());
 
//! Does the usual molecular sanitization on each reactant, agent, and product
///  of the reaction
RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxnAsMols(
    ChemicalReaction &rxn,
    unsigned int sanitizeOps = MolOps::SanitizeFlags::SANITIZE_ALL);
 
}  // namespace RxnOps
}  // namespace RDKit
 
#endif