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7ffd863c9b
* Fixes #2602 * Fixes #2605 * Remove vestigial isEarlyAtom() definition in Kekulize.cpp * Fixes #2606 * Fixes #2607 adds allowed valence 2 for Sn and Pb * Fixes #2610 * update in response to review
127 lines
3.6 KiB
C++
127 lines
3.6 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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/*! \file Charge.h
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\brief Defines the Reionizer class and Uncharger class.
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*/
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#include <RDGeneral/export.h>
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#ifndef RD_CHARGE_H
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#define RD_CHARGE_H
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#include "MolStandardize.h"
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#include <Catalogs/Catalog.h>
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#include <GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h>
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#include <GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h>
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namespace RDKit {
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class RWMol;
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class ROMol;
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namespace MolStandardize {
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RDKIT_MOLSTANDARDIZE_EXPORT extern const CleanupParameters
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defaultCleanupParameters;
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typedef RDCatalog::HierarchCatalog<AcidBaseCatalogEntry, AcidBaseCatalogParams,
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int>
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AcidBaseCatalog;
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struct RDKIT_MOLSTANDARDIZE_EXPORT ChargeCorrection {
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std::string Name;
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std::string Smarts;
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int Charge;
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ChargeCorrection(std::string name, std::string smarts, int charge)
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: Name(name), Smarts(smarts), Charge(charge) {}
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};
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// The default list of ChargeCorrections.
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RDKIT_MOLSTANDARDIZE_EXPORT extern std::vector<ChargeCorrection>
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CHARGE_CORRECTIONS;
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//! The reionizer class to fix charges and reionize a molecule such that the
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// strongest acids ionize first.
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/*!
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<b>Notes:</b>
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-
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*/
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class RDKIT_MOLSTANDARDIZE_EXPORT Reionizer {
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public:
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Reionizer();
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//! construct a Reionizer with a particular acidbaseFile
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Reionizer(const std::string acidbaseFile);
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//! construct a Reionizer with a particular acidbaseFile and charge
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// corrections
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Reionizer(const std::string acidbaseFile,
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const std::vector<ChargeCorrection> ccs);
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//! construct a Reionizer with a particular acidbaseFile and charge
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// corrections
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Reionizer(std::istream &acidbaseStream,
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const std::vector<ChargeCorrection> ccs);
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//! making Reionizer objects non-copyable
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Reionizer(const Reionizer &other) = delete;
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Reionizer &operator=(Reionizer const &) = delete;
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~Reionizer();
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//! Enforce charges on certain atoms, then perform competitive reionization.
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ROMol *reionize(const ROMol &mol);
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private:
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AcidBaseCatalog *d_abcat;
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std::vector<ChargeCorrection> d_ccs;
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std::pair<unsigned int, std::vector<unsigned int>> *strongestProtonated(
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const ROMol &mol,
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const std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> &abpairs);
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std::pair<unsigned int, std::vector<unsigned int>> *weakestIonized(
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const ROMol &mol,
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const std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR>> &abpairs);
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}; // Reionizer class
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//! The Uncharger class for neutralizing ionized acids and bases.
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/*!
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<b>Notes:</b>
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- This class uncharges molecules by adding and/or removing hydrogens.
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- For zwitterions, hydrogens are moved to eliminate charges where
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possible.
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- In cases where there is a positive charge that is not neutralizable,
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an attempt is made to also preserve the corresponding
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negative charge.
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*/
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class RDKIT_MOLSTANDARDIZE_EXPORT Uncharger {
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public:
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Uncharger();
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Uncharger(bool canonicalOrdering) : Uncharger() {
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df_canonicalOrdering = canonicalOrdering;
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};
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Uncharger(const Uncharger &other);
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~Uncharger();
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ROMol *uncharge(const ROMol &mol);
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private:
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bool df_canonicalOrdering = true;
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std::shared_ptr<ROMol> pos_h;
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std::shared_ptr<ROMol> pos_noh;
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std::shared_ptr<ROMol> neg;
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std::shared_ptr<ROMol> neg_acid;
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}; // Uncharger class
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} // namespace MolStandardize
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} // namespace RDKit
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#endif
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