Normalize.h

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//
//  Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
/*! \file Normalize.h
 
        \brief Defines the Normalizer class.
 
*/
#include <RDGeneral/export.h>
#ifndef RD_NORMALIZE_H
#define RD_NORMALIZE_H
 
#include <Catalogs/Catalog.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
 
namespace RDKit {
class RWMol;
class ROMol;
 
namespace MolStandardize {
RDKIT_MOLSTANDARDIZE_EXPORT extern const CleanupParameters
    defaultCleanupParameters;
 
typedef RDCatalog::HierarchCatalog<TransformCatalogEntry,
                                   TransformCatalogParams, int>
    TransformCatalog;
typedef std::pair<std::string, ROMOL_SPTR> SmilesMolPair;
 
//! The Normalizer class for applying Normalization transforms.
/*!
 
  <b>Notes:</b>
    - This class is typically used to apply a series of Normalization transforms
  to correct functional groups and recombine charges.
    - Each transform is repeatedly applied until no further changes
  occur.
*/
 
class RDKIT_MOLSTANDARDIZE_EXPORT Normalizer {
 public:
  Normalizer();
  //! Construct a Normalizer with a particular normalizeFile and maxRestarts
  Normalizer(const std::string normalizeFile, const unsigned int maxRestarts);
  //! Construct a Normalizer with a particular stream (with parameters) and
  //! maxRestarts
  Normalizer(std::istream &normalizeStream, const unsigned int maxRestarts);
  //! Construct a Normalizer with a set of data and maxRestarts
  Normalizer(
      const std::vector<std::pair<std::string, std::string>> &normalizations,
      const unsigned int maxRestarts);
  //! making Normalizer objects non-copyable
  Normalizer(const Normalizer &other) = delete;
  Normalizer &operator=(Normalizer const &) = delete;
  ~Normalizer();
 
  //! Apply a series of Normalization transforms to correct functional groups
  //! and recombine charges.
  /*!
    <b>Notes:</b>
      - A series of transforms are applied to the molecule. For each
    Normalization, the transform is applied repeatedly until no further changes
    occur.
      - If any changes occurred, we go back and start from the first
    Normalization again, in case the changes mean an earlier transform is now
    applicable.
      - The molecule is returned once the entire series of
    Normalizations cause no further changes or if max_restarts (default 200) is
    reached.
  */
  ROMol *normalize(const ROMol &mol);
 
  void normalizeInPlace(RWMol &mol);
 
 private:
  const TransformCatalog *d_tcat;
  unsigned int MAX_RESTARTS;
 
  ROMOL_SPTR normalizeFragment(
      const ROMol &mol,
      const std::vector<std::shared_ptr<ChemicalReaction>> &transforms) const;
  SmilesMolPair applyTransform(const ROMOL_SPTR &mol,
                               ChemicalReaction &rule) const;
 
};  // Normalizer class
 
// caller owns the returned pointer
inline Normalizer *normalizerFromParams(const CleanupParameters &params) {
  if (params.normalizationData.empty()) {
    return new Normalizer(params.normalizations, params.maxRestarts);
  } else {
    return new Normalizer(params.normalizationData, params.maxRestarts);
  }
}
 
}  // namespace MolStandardize
}  // namespace RDKit
 
#endif