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https://github.com/rdkit/rdkit.git
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ac54eb3209
* reionizer and uncharger and normalizer can now operate in place * add removeUnmatchedAtoms argument to in-place version of runReactant When set to false atoms which are not explicitly removed by the reaction are preserved * Fix a case where transforms were incorrectly updating atomic numbers * add more inplace operations to MolStandardize * support those in the Python layer * support inplace for the rest of the python wrappers * move a few more functions over to the inplace code
107 lines
3.4 KiB
C++
107 lines
3.4 KiB
C++
//
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// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
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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 Normalize.h
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\brief Defines the Normalizer class.
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*/
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#include <RDGeneral/export.h>
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#ifndef RD_NORMALIZE_H
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#define RD_NORMALIZE_H
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#include <Catalogs/Catalog.h>
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#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h>
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#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
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#include <GraphMol/MolStandardize/MolStandardize.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<TransformCatalogEntry,
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TransformCatalogParams, int>
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TransformCatalog;
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typedef std::pair<std::string, ROMOL_SPTR> SmilesMolPair;
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//! The Normalizer class for applying Normalization transforms.
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/*!
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<b>Notes:</b>
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- This class is typically used to apply a series of Normalization transforms
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to correct functional groups and recombine charges.
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- Each transform is repeatedly applied until no further changes
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occur.
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*/
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class RDKIT_MOLSTANDARDIZE_EXPORT Normalizer {
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public:
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Normalizer();
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//! Construct a Normalizer with a particular normalizeFile and maxRestarts
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Normalizer(const std::string normalizeFile, const unsigned int maxRestarts);
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//! Construct a Normalizer with a particular stream (with parameters) and
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//! maxRestarts
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Normalizer(std::istream &normalizeStream, const unsigned int maxRestarts);
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//! Construct a Normalizer with a set of data and maxRestarts
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Normalizer(
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const std::vector<std::pair<std::string, std::string>> &normalizations,
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const unsigned int maxRestarts);
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//! making Normalizer objects non-copyable
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Normalizer(const Normalizer &other) = delete;
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Normalizer &operator=(Normalizer const &) = delete;
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~Normalizer();
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//! Apply a series of Normalization transforms to correct functional groups
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//! and recombine charges.
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/*!
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<b>Notes:</b>
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- A series of transforms are applied to the molecule. For each
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Normalization, the transform is applied repeatedly until no further changes
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occur.
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- If any changes occurred, we go back and start from the first
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Normalization again, in case the changes mean an earlier transform is now
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applicable.
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- The molecule is returned once the entire series of
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Normalizations cause no further changes or if max_restarts (default 200) is
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reached.
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*/
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ROMol *normalize(const ROMol &mol);
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void normalizeInPlace(RWMol &mol);
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private:
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const TransformCatalog *d_tcat;
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unsigned int MAX_RESTARTS;
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ROMOL_SPTR normalizeFragment(
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const ROMol &mol,
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const std::vector<std::shared_ptr<ChemicalReaction>> &transforms) const;
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SmilesMolPair applyTransform(const ROMOL_SPTR &mol,
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ChemicalReaction &rule) const;
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}; // Normalizer class
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// caller owns the returned pointer
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inline Normalizer *normalizerFromParams(const CleanupParameters ¶ms) {
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if (params.normalizationData.empty()) {
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return new Normalizer(params.normalizations, params.maxRestarts);
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} else {
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return new Normalizer(params.normalizationData, params.maxRestarts);
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}
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}
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} // namespace MolStandardize
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} // namespace RDKit
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#endif
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