RDKit
Open-source cheminformatics and machine learning.
Metal.h
Go to the documentation of this file.
1 //
2 // Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 /*! \file Metal.h
11 
12  \brief Defines the MetalDisconnector class.
13 
14 */
15 #include <RDGeneral/export.h>
16 #ifndef RD_METAL_H
17 #define RD_METAL_H
18 
19 #include <GraphMol/ROMol.h>
20 
21 namespace RDKit {
22 class RWMol;
23 class ROMol;
24 
25 namespace MolStandardize {
26 //! The MetalDisconnector class contains tools for disconnecting metal atoms
27 //! that are defined as covalently bonded to non-metals.
28 /*!
29 
30  <b>Notes:</b>
31  -
32 */
33 
35  public:
39 
40  ROMol *getMetalNof(); // {return metal_nof;}
41  ROMol *getMetalNon(); // {return metal_non;}
42  void setMetalNof(const ROMol &mol);
43  void setMetalNon(const ROMol &mol);
44 
45  //! Break covalent bonds between metals and organic atoms under certain
46  //! conditions.
47  /*!
48  <b>Notes:</b>
49  The algorithm works as follows:
50 - Disconnect N, O, F from any metal.
51 - Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge,
52 In, Sn, As, Tl, Pb, Bi, Po).
53  - For every bond broken, adjust the charges of the begin and end atoms
54 accordingly.
55  */
56  ROMol *disconnect(const ROMol &mol);
57  //! overload
58  /// modifies the molecule in place
59  void disconnect(RWMol &mol);
60 
61  private:
62  struct NonMetal {
63  int cutBonds{0};
64  std::vector<int> boundMetalIndices;
65  };
66  int chargeAdjustment(const Atom *a, int order);
67  ROMOL_SPTR metal_nof;
68  ROMOL_SPTR metal_non;
69 
70 }; // class Metal
71 } // namespace MolStandardize
72 } // namespace RDKit
73 #endif
Defines the primary molecule class ROMol as well as associated typedefs.
The class for representing atoms.
Definition: Atom.h:68
ROMol * disconnect(const ROMol &mol)
MetalDisconnector(const MetalDisconnector &other)
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_MOLSTANDARDIZE_EXPORT
Definition: export.h:313
Std stuff.
Definition: Abbreviations.h:18
boost::shared_ptr< ROMol > ROMOL_SPTR