RDKit
Open-source cheminformatics and machine learning.
MMPA.h
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1 //
2 // Copyright (C) 2015 Novartis Institutes for BioMedical Research
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 #pragma once
11 #include <vector>
12 #include <string>
13 #include <stdexcept>
14 #include "../RDKitBase.h"
15 
16 namespace RDKit {
17 
18 namespace MMPA {
19 //! fragments a Molecule for processing with the Matched Molecular Pairs
20 //! MMPA algorithm (Hussain et al)
21 /*!
22  \param mol Molecule to fragment
23  \param result Vector of Core and Sidechain results from the various
24  cuts
25  \param maxCuts Maximum number of times to cut the molecule to generate
26  fragments. A max cut of 3 will fragment with 1,2 and 3
27  cuts.
28  \param maxCutBonds Set the bond limit for determining which molecules
29  to analyze. If a molecule has more than
30  this number of cutabble bonds, ignore.
31 
32  \return true if the molecule was fragmented, false otherwise.
33 */
34 
35 bool fragmentMol(const ROMol& mol,
36  std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& result,
37  unsigned int maxCuts = 3, unsigned int maxCutBonds = 20,
38  const std::string& pattern = "[#6+0;!$(*=,#[!#6])]!@!=!#[*]");
39 
40 //! fragments a Molecule for processing with the Matched Molecular Pairs
41 //! MMPA algorithm (Hussain et al)
42 /*!
43  \param mol Molecule to fragment
44  \param result Vector of Core and Sidechain results from the various
45  cuts
46  \param minCuts Minimum number of times to cut the molecule to generate
47  fragments.
48  \param maxCuts Maximum number of times to cut the molecule to generate
49  fragments.
50  \param maxCutBonds Set the bond limit for determining which molecules
51  to analyze. If a molecule has more than
52  this number of cutabble bonds, ignore.
53 
54  \return true if the molecule was fragmented, false otherwise.
55 */
56 bool fragmentMol(const ROMol& mol,
57  std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& result,
58  unsigned int minCuts,
59  unsigned int maxCuts,
60  unsigned int maxCutBonds,
61  const std::string& pattern = "[#6+0;!$(*=,#[!#6])]!@!=!#[*]");
62 
63 //! fragments a Molecule for processing with the Matched Molecular Pairs
64 //! MMPA algorithm (Hussain et al)
65 /*!
66  \param mol Molecule to fragment
67  \param result Vector of Core and Sidechain results from the various
68  cuts
69  \param bondsToCut Vector of bond indices to use as cut points
70  \param minCuts Minimum number of times to cut the molecule to generate
71  fragments.
72  \param maxCuts Maximum number of times to cut the molecule to generate
73  fragments.
74  \return true if the molecule was fragmented, false otherwise.
75 */
76 bool fragmentMol(const ROMol& mol,
77  std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& result,
78  const std::vector<unsigned int>& bondsToCut,
79  unsigned int minCuts = 1,
80  unsigned int maxCuts = 3);
81 
82 }
83 } // namespace RDKit
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:106
bool fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]")
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29