RDKit
Open-source cheminformatics and machine learning.
SubgraphUtils.h
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1 //
2 // Copyright (C) 2003-2009 Greg Landrum and Rational Discovery LLC
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 #include <RDGeneral/export.h>
11 #ifndef _RD_SUBGRAPHUTILS_H_
12 #define _RD_SUBGRAPHUTILS_H_
13 
14 #include "Subgraphs.h"
16 #include <boost/tuple/tuple.hpp>
18 
19 #include <cstdint>
20 
21 namespace RDKit {
22 class ROMol;
23 
24 namespace Subgraphs {
25 //! used to return path discriminators (three unsigned ints):
26 typedef boost::tuples::tuple<std::uint32_t, std::uint32_t, std::uint32_t>
28 
30  const ROMol &mol, const PATH_TYPE &path, bool useBO = true,
31  std::vector<std::uint32_t> *extraInvars = nullptr);
33  const PATH_LIST &allPathsb,
34  bool useBO = true);
35 
36 // Return the list of bond that connect a list of atoms
37 // ASSUMPTION: the atoms specified in the list are connected
39  const PATH_TYPE &atomIds);
40 
41 // create a new molecule object from a part of molecule "mol". The part of
42 // of the molecule is specified as a list of bonds in "path".
43 // the optional argument "useQuery" will set all the bond and atoms in the
44 // the new molecule to "QueryAtoms" and "QueryBonds" instead of regular Atoms
45 // and Bonds
46 // atomIdxMap provides a mapping between the atomsIds in mol to the atomIds in
47 // the newly created sub-molecule (the molecule that is returned)
49  const PATH_TYPE &path, bool useQuery,
50  std::map<int, int> &atomIdxMap);
52  const PATH_TYPE &path,
53  bool useQuery = false);
54 } // end of namespace Subgraphs
55 } // namespace RDKit
56 
57 #endif
functionality for finding subgraphs and paths in molecules
#define RDKIT_SUBGRAPHS_EXPORT
Definition: export.h:457
RDKIT_SUBGRAPHS_EXPORT PATH_LIST uniquifyPaths(const ROMol &mol, const PATH_LIST &allPathsb, bool useBO=true)
RDKIT_SUBGRAPHS_EXPORT DiscrimTuple calcPathDiscriminators(const ROMol &mol, const PATH_TYPE &path, bool useBO=true, std::vector< std::uint32_t > *extraInvars=nullptr)
RDKIT_SUBGRAPHS_EXPORT ROMol * pathToSubmol(const ROMol &mol, const PATH_TYPE &path, bool useQuery, std::map< int, int > &atomIdxMap)
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE bondListFromAtomList(const ROMol &mol, const PATH_TYPE &atomIds)
boost::tuples::tuple< std::uint32_t, std::uint32_t, std::uint32_t > DiscrimTuple
used to return path discriminators (three unsigned ints):
Definition: SubgraphUtils.h:27
Std stuff.
Definition: Abbreviations.h:18
std::list< PATH_TYPE > PATH_LIST
Definition: Subgraphs.h:42
std::vector< int > PATH_TYPE
Definition: Subgraphs.h:37