Fragment.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_FRAGMENT_REMOVER_H
#define RD_FRAGMENT_REMOVER_H
#include <Catalogs/Catalog.h>
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h>
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
namespace RDKit {
class ROMol;
namespace MolStandardize {
RDKIT_MOLSTANDARDIZE_EXPORT extern const CleanupParameters
defaultCleanupParameters;
typedef RDCatalog::HierarchCatalog<FragmentCatalogEntry, FragmentCatalogParams,
int>
FragmentCatalog;
class RDKIT_MOLSTANDARDIZE_EXPORT FragmentRemover {
public:
FragmentRemover();
FragmentRemover(const std::string fragmentFile, bool leave_last,
bool skip_if_all_match = false);
FragmentRemover(std::istream &fragmentStream, bool leave_last,
bool skip_if_all_match = false);
FragmentRemover(const std::vector<std::pair<std::string, std::string>> &data,
bool leave_last, bool skip_if_all_match = false);
~FragmentRemover();
//! making FragmentRemover objects non-copyable
FragmentRemover(const FragmentRemover &other) = delete;
FragmentRemover &operator=(FragmentRemover const &) = delete;
ROMol *remove(const ROMol &mol);
private:
// Setting leave_last to True will ensure at least one fragment
// is left in the molecule, even if it is matched by a
// FragmentPattern
bool LEAVE_LAST;
// If set, this causes the original molecule to be returned
// if every fragment in it matches the salt list
bool SKIP_IF_ALL_MATCH;
FragmentCatalog *d_fcat;
}; // class FragmentRemover
// caller owns the returned pointer
inline FragmentRemover *fragmentRemoverFromParams(
const CleanupParameters &params, bool leave_last = true,
bool skip_if_all_match = false) {
if (params.fragmentData.empty()) {
return new FragmentRemover(params.fragmentFile, leave_last,
skip_if_all_match);
} else {
return new FragmentRemover(params.fragmentData, leave_last,
skip_if_all_match);
}
}
class RDKIT_MOLSTANDARDIZE_EXPORT LargestFragmentChooser {
public:
// LargestFragmentChooser() {}
LargestFragmentChooser(bool prefer_organic = false)
: PREFER_ORGANIC(prefer_organic) {}
LargestFragmentChooser(const LargestFragmentChooser &other);
~LargestFragmentChooser() = default;
ROMol *choose(const ROMol &mol);
struct Largest {
Largest();
Largest(std::string &smiles, boost::shared_ptr<ROMol> fragment,
unsigned int &numatoms, double &weight, bool &organic);
std::string Smiles;
boost::shared_ptr<ROMol> Fragment;
unsigned int NumAtoms{0};
double Weight{0};
bool Organic{false};
};
private:
bool PREFER_ORGANIC;
}; // class LargestFragmentChooser
} // namespace MolStandardize
} // namespace RDKit
#endif
Catalog.h
FragmentCatalogEntry.h
FragmentCatalogParams.h
MolStandardize.h
RDCatalog::HierarchCatalog
A Catalog with a hierarchical structure.
Definition: Catalog.h:135
RDKit::MolStandardize::FragmentCatalogEntry
Definition: FragmentCatalogEntry.h:24
RDKit::MolStandardize::FragmentCatalogParams
Definition: FragmentCatalogParams.h:26
RDKit::MolStandardize::FragmentRemover
Definition: Fragment.h:31
RDKit::MolStandardize::FragmentRemover::FragmentRemover
FragmentRemover(std::istream &fragmentStream, bool leave_last, bool skip_if_all_match=false)
RDKit::MolStandardize::FragmentRemover::FragmentRemover
FragmentRemover(const std::string fragmentFile, bool leave_last, bool skip_if_all_match=false)
RDKit::MolStandardize::FragmentRemover::operator=
FragmentRemover & operator=(FragmentRemover const &)=delete
RDKit::MolStandardize::FragmentRemover::FragmentRemover
FragmentRemover()
RDKit::MolStandardize::FragmentRemover::FragmentRemover
FragmentRemover(const FragmentRemover &other)=delete
making FragmentRemover objects non-copyable
RDKit::MolStandardize::FragmentRemover::FragmentRemover
FragmentRemover(const std::vector< std::pair< std::string, std::string >> &data, bool leave_last, bool skip_if_all_match=false)
RDKit::MolStandardize::FragmentRemover::remove
ROMol * remove(const ROMol &mol)
RDKit::MolStandardize::FragmentRemover::~FragmentRemover
~FragmentRemover()
RDKit::MolStandardize::LargestFragmentChooser
Definition: Fragment.h:73
RDKit::MolStandardize::LargestFragmentChooser::~LargestFragmentChooser
~LargestFragmentChooser()=default
RDKit::MolStandardize::LargestFragmentChooser::choose
ROMol * choose(const ROMol &mol)
RDKit::MolStandardize::LargestFragmentChooser::LargestFragmentChooser
LargestFragmentChooser(const LargestFragmentChooser &other)
RDKit::MolStandardize::LargestFragmentChooser::LargestFragmentChooser
LargestFragmentChooser(bool prefer_organic=false)
Definition: Fragment.h:76
RDKit::ROMol
Definition: ROMol.h:178
export.h
RDKIT_MOLSTANDARDIZE_EXPORT
#define RDKIT_MOLSTANDARDIZE_EXPORT
Definition: export.h:305
RDKit::MolStandardize::defaultCleanupParameters
RDKIT_MOLSTANDARDIZE_EXPORT const CleanupParameters defaultCleanupParameters
Definition: Fragment.h:25
RDKit::MolStandardize::fragmentRemoverFromParams
FragmentRemover * fragmentRemoverFromParams(const CleanupParameters &params, bool leave_last=true, bool skip_if_all_match=false)
Definition: Fragment.h:61
RDKit::MolStandardize::FragmentCatalog
RDCatalog::HierarchCatalog< FragmentCatalogEntry, FragmentCatalogParams, int > FragmentCatalog
Definition: Fragment.h:29
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::MolStandardize::CleanupParameters
Definition: MolStandardize.h:40
RDKit::MolStandardize::CleanupParameters::fragmentFile
std::string fragmentFile
Definition: MolStandardize.h:49
RDKit::MolStandardize::CleanupParameters::fragmentData
std::vector< std::pair< std::string, std::string > > fragmentData
Definition: MolStandardize.h:74
RDKit::MolStandardize::LargestFragmentChooser::Largest
Definition: Fragment.h:82
RDKit::MolStandardize::LargestFragmentChooser::Largest::Largest
Largest()
RDKit::MolStandardize::LargestFragmentChooser::Largest::Largest
Largest(std::string &smiles, boost::shared_ptr< ROMol > fragment, unsigned int &numatoms, double &weight, bool &organic)
RDKit::MolStandardize::LargestFragmentChooser::Largest::Smiles
std::string Smiles
Definition: Fragment.h:86
RDKit::MolStandardize::LargestFragmentChooser::Largest::Fragment
boost::shared_ptr< ROMol > Fragment
Definition: Fragment.h:87