Charge.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 Charge.h
 
        \brief Defines the Reionizer class and Uncharger class.
 
*/
#include <RDGeneral/export.h>
#ifndef RD_CHARGE_H
#define RD_CHARGE_H
#include <utility>
 
#include "MolStandardize.h"
#include <Catalogs/Catalog.h>
#include <GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h>
#include <GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h>
 
namespace RDKit {
class RWMol;
class ROMol;
 
namespace MolStandardize {
 
RDKIT_MOLSTANDARDIZE_EXPORT extern const CleanupParameters
    defaultCleanupParameters;
 
typedef RDCatalog::HierarchCatalog<AcidBaseCatalogEntry, AcidBaseCatalogParams,
                                   int>
    AcidBaseCatalog;
 
struct RDKIT_MOLSTANDARDIZE_EXPORT ChargeCorrection {
  std::string Name;
  std::string Smarts;
  int Charge;
 
  ChargeCorrection(std::string name, std::string smarts, int charge)
      : Name(std::move(name)), Smarts(std::move(smarts)), Charge(charge) {}
};
 
// The default list of ChargeCorrections.
RDKIT_MOLSTANDARDIZE_EXPORT extern std::vector<ChargeCorrection>
    CHARGE_CORRECTIONS;
 
//! The reionizer class to fix charges and reionize a molecule such that the
/// strongest acids ionize first.
/*!
 
  <b>Notes:</b>
    -
*/
 
class RDKIT_MOLSTANDARDIZE_EXPORT Reionizer {
 public:
  Reionizer();
  //! construct a Reionizer with a particular acidbaseFile
  Reionizer(const std::string acidbaseFile);
  //! construct a Reionizer with parameter data
  Reionizer(const std::vector<std::tuple<std::string, std::string, std::string>>
                &data);
  //! construct a Reionizer with a particular acidbaseFile and charge
  /// corrections
  Reionizer(const std::string acidbaseFile,
            const std::vector<ChargeCorrection> ccs);
  //! construct a Reionizer with a particular acidbaseFile and charge
  /// corrections
  Reionizer(std::istream &acidbaseStream,
            const std::vector<ChargeCorrection> ccs);
 
  //! construct a Reionizer with parameter data and charge corrections
  Reionizer(const std::vector<std::tuple<std::string, std::string, std::string>>
                &data,
            const std::vector<ChargeCorrection> ccs);
 
  //! making Reionizer objects non-copyable
  Reionizer(const Reionizer &other) = delete;
  Reionizer &operator=(Reionizer const &) = delete;
  ~Reionizer();
 
  //! Enforce charges on certain atoms, then perform competitive reionization.
  ROMol *reionize(const ROMol &mol);
  //! Enforce charges on certain atoms, then perform competitive reionization,
  //! modifies molecule in place
  void reionizeInPlace(RWMol &mol);
 
 private:
  AcidBaseCatalog *d_abcat;
  std::vector<ChargeCorrection> d_ccs;
 
  std::pair<unsigned int, std::vector<unsigned int>> *strongestProtonated(
      const ROMol &mol,
      const std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> &abpairs);
  std::pair<unsigned int, std::vector<unsigned int>> *weakestIonized(
      const ROMol &mol,
      const std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> &abpairs);
 
};  // Reionizer class
 
// caller owns the returned pointer
inline Reionizer *reionizerFromParams(const CleanupParameters &params) {
  if (params.acidbaseData.empty()) {
    return new Reionizer(params.acidbaseFile);
  } else {
    return new Reionizer(params.acidbaseData);
  }
}
 
//! The Uncharger class for neutralizing ionized acids and bases.
/*!
 
  <b>Notes:</b>
    - This class uncharges molecules by adding and/or removing hydrogens.
          - For zwitterions, hydrogens are moved to eliminate charges where
            possible.
          - By default, in cases where there is a positive charge that is not
            neutralizable, an attempt is made to also preserve the corresponding
            negative charge.
          - When the `force` option is set, all neutralizable sites are
            uncharged, also when not-neutralizable positive charges are present
            and the resulting overall charge is therefore not null.
 
*/
 
class RDKIT_MOLSTANDARDIZE_EXPORT Uncharger {
 public:
  Uncharger();
  Uncharger(bool canonicalOrdering) : Uncharger() {
    df_canonicalOrdering = canonicalOrdering;
  }
  Uncharger(bool canonicalOrdering, bool force) : Uncharger() {
    df_canonicalOrdering = canonicalOrdering;
    df_force = force;
  }
  Uncharger(const Uncharger &) = default;
  ~Uncharger() = default;
  
  ROMol *uncharge(const ROMol &mol);
  void unchargeInPlace(RWMol &mol);
 
 private:
  bool df_canonicalOrdering = true;
  bool df_force = false;
  std::shared_ptr<ROMol> pos_h;
  std::shared_ptr<ROMol> pos_noh;
  std::shared_ptr<ROMol> neg;
  std::shared_ptr<ROMol> neg_acid;
};  // Uncharger class
 
}  // namespace MolStandardize
}  // namespace RDKit
#endif