mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
d41752d558
* run clang-tidy with readability-braces-around-statements clang-format the results clean up all the parts that clang-tidy-8 broke * fix problem on windows
85 lines
2.5 KiB
C++
85 lines
2.5 KiB
C++
//
|
|
// Copyright (C) 2018 Susan H. Leung
|
|
//
|
|
// @@ 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();
|
|
|
|
//! 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
|
|
|
|
class RDKIT_MOLSTANDARDIZE_EXPORT LargestFragmentChooser {
|
|
public:
|
|
// LargestFragmentChooser(){};
|
|
LargestFragmentChooser(bool prefer_organic = false)
|
|
: PREFER_ORGANIC(prefer_organic){};
|
|
LargestFragmentChooser(const LargestFragmentChooser &other);
|
|
~LargestFragmentChooser(){};
|
|
|
|
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;
|
|
double Weight;
|
|
bool Organic;
|
|
};
|
|
|
|
private:
|
|
bool PREFER_ORGANIC;
|
|
}; // class LargestFragmentChooser
|
|
} // namespace MolStandardize
|
|
} // namespace RDKit
|
|
|
|
#endif
|