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>
#include <iostream>
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;
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
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:121
RDKit::MolStandardize::TransformCatalogParams
Definition: TransformCatalogParams.h:27
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::TransformCatalogParams
TransformCatalogParams(const TransformCatalogParams &other)
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:29
RDKit::MolStandardize::TransformCatalogParams::toStream
void toStream(std::ostream &) const override
serializes (pickles) to a stream
RDKit::MolStandardize::TransformCatalogParams::getTransformation
const ChemicalReaction * getTransformation(unsigned int fid) const
RDKit::MolStandardize::TransformCatalogParams::getNumTransformations
unsigned int getNumTransformations() const
Definition: TransformCatalogParams.h:44
RDKit::MolStandardize::TransformCatalogParams::~TransformCatalogParams
~TransformCatalogParams() override
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams(std::istream &transformStream)
RDKit::MolStandardize::TransformCatalogParams::TransformCatalogParams
TransformCatalogParams(const std::string &transformFile)
RDKit::MolStandardize::TransformCatalogParams::getTransformations
const std::vector< std::shared_ptr< ChemicalReaction > > & getTransformations() const
export.h
RDKIT_MOLSTANDARDIZE_EXPORT
#define RDKIT_MOLSTANDARDIZE_EXPORT
Definition: export.h:305
RDKit
Std stuff.
Definition: Abbreviations.h:18