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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);
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 ¶ms) {
if (params.normalizationData.empty()) {
return new Normalizer(params.normalizations, params.maxRestarts);
} else {
return new Normalizer(params.normalizationData, params.maxRestarts);
}
}
} // namespace MolStandardize
} // namespace RDKit
#endif
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