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TransformCatalogParams.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.
//
#include <RDGeneral/export.h>
#ifndef RD_TRANSFORM_CATALOG_PARAMS_H
#define RD_TRANSFORM_CATALOG_PARAMS_H
#include <Catalogs/CatalogParams.h>
#include "TransformCatalogUtils.h"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <string>
#include <vector>
namespace RDKit {
class ROMol;
namespace MolStandardize {
class RDKIT_MOLSTANDARDIZE_EXPORT TransformCatalogParams
: public RDCatalog::CatalogParams {
public:
TransformCatalogParams() {
d_typeStr = "Transform Catalog Parameters";
d_transformations.clear();
}
// if the string here is empty the default transforms will be used
TransformCatalogParams(const std::string &transformFile);
TransformCatalogParams(std::istream &transformStream);
TransformCatalogParams(
const std::vector<std::pair<std::string, std::string>> &data);
// copy constructor
TransformCatalogParams(const TransformCatalogParams &other);
~TransformCatalogParams() override;
unsigned int getNumTransformations() const {
return static_cast<unsigned int>(d_transformations.size());
}
const std::vector<std::shared_ptr<ChemicalReaction>> &getTransformations()
const;
const ChemicalReaction *getTransformation(unsigned int fid) const;
void toStream(std::ostream &) const override;
std::string Serialize() const override;
void initFromStream(std::istream &ss) override;
void initFromString(const std::string &text) override;
// it's a bit dirty to make this "const", but it's weakly defensible
// since the set of transformations themselves will not be changed.
void initializeTransforms() const;
private:
std::vector<std::shared_ptr<ChemicalReaction>> d_transformations;
}; // class TransformCatalogParams
} // namespace MolStandardize
} // namespace RDKit
#endif
CatalogParams.h
RDKitBase.h
pulls in the core RDKit functionality
Reaction.h
TransformCatalogUtils.h
RDCatalog::CatalogParams
abstract base class for the container used to create a catalog
Definition CatalogParams.h:18
RDCatalog::CatalogParams::d_typeStr
std::string d_typeStr
our type string
Definition CatalogParams.h:38
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:122
RDKit::MolStandardize::TransformCatalogParams::initFromString
void initFromString(const std::string &text) override
initializes from a string pickle
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams(const std::vector< std::pair< std::string, std::string > > &data)
RDKit::MolStandardize::TransformCatalogParams::initFromStream
void initFromStream(std::istream &ss) override
initializes from a stream pickle
RDKit::MolStandardize::TransformCatalogParams::getTransformation
const ChemicalReaction * getTransformation(unsigned int fid) const
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams(const TransformCatalogParams &other)
RDKit::MolStandardize::TransformCatalogParams::getTransformations
const std::vector< std::shared_ptr< ChemicalReaction > > & getTransformations() const
RDKit::MolStandardize::TransformCatalogParams::Serialize
std::string Serialize() const override
returns a string with a serialized (pickled) representation
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams()
Definition TransformCatalogParams.h:28
RDKit::MolStandardize::TransformCatalogParams::initializeTransforms
void initializeTransforms() const
RDKit::MolStandardize::TransformCatalogParams::toStream
void toStream(std::ostream &) const override
serializes (pickles) to a stream
RDKit::MolStandardize::TransformCatalogParams::getNumTransformations
unsigned int getNumTransformations() const
Definition TransformCatalogParams.h:43
RDKit::MolStandardize::TransformCatalogParams::~TransformCatalogParams
~TransformCatalogParams() override
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams(std::istream &transformStream)
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams(const std::string &transformFile)
RDKit::ROMol
Definition ROMol.h:319
export.h
RDKIT_MOLSTANDARDIZE_EXPORT
#define RDKIT_MOLSTANDARDIZE_EXPORT
Definition export.h:377
RDKit::MolStandardize
Definition AcidBaseCatalogEntry.h:22
RDKit
Std stuff.
Definition Abbreviations.h:19