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"
15 #include <boost/tuple/tuple.hpp>
16 #include <cstdint>
17 
18 namespace RDKit {
19 class ROMol;
20 
21 namespace Subgraphs {
22 //! used to return path discriminators (three unsigned ints):
23 typedef boost::tuples::tuple<std::uint32_t, std::uint32_t, std::uint32_t>
25 
27  const ROMol &mol, const PATH_TYPE &path, bool useBO = true,
28  std::vector<std::uint32_t> *extraInvars = 0);
30  const PATH_LIST &allPathsb,
31  bool useBO = true);
32 
33 // Return the list of bond that connect a list of atoms
34 // ASSUMPTION: the atoms specified in the list are connected
36  const PATH_TYPE &atomIds);
37 
38 // create a new molecule object from a part of molecule "mol". The part of
39 // of the molecule is specified as a list of bonds in "path".
40 // the optional argument "useQuery" will set all the bond and atoms in the
41 // the new molecule to "QueryAtoms" and "QueryBonds" instead of regular Atoms
42 // and Bonds
43 // atomIdxMap provides a mapping between the atomsIds in mol to the atomIds in
44 // the newly created sub-molecule (the molecule that is returned)
46  const PATH_TYPE &path, bool useQuery,
47  std::map<int, int> &atomIdxMap);
49  const PATH_TYPE &path,
50  bool useQuery = false);
51 } // end of namespace Subgraphs
52 } // namespace RDKit
53 
54 #endif
RDKIT_SUBGRAPHS_EXPORT
#define RDKIT_SUBGRAPHS_EXPORT
Definition: export.h:658
RDKit::Subgraphs::uniquifyPaths
RDKIT_SUBGRAPHS_EXPORT PATH_LIST uniquifyPaths(const ROMol &mol, const PATH_LIST &allPathsb, bool useBO=true)
RDKit::Subgraphs::DiscrimTuple
boost::tuples::tuple< std::uint32_t, std::uint32_t, std::uint32_t > DiscrimTuple
used to return path discriminators (three unsigned ints):
Definition: SubgraphUtils.h:24
RDKit::ROMol
Definition: ROMol.h:171
RDKit::Subgraphs::bondListFromAtomList
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE bondListFromAtomList(const ROMol &mol, const PATH_TYPE &atomIds)
RDKit::Subgraphs::calcPathDiscriminators
RDKIT_SUBGRAPHS_EXPORT DiscrimTuple calcPathDiscriminators(const ROMol &mol, const PATH_TYPE &path, bool useBO=true, std::vector< std::uint32_t > *extraInvars=0)
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::PATH_LIST
std::list< PATH_TYPE > PATH_LIST
Definition: Subgraphs.h:42
RDKit::Subgraphs::pathToSubmol
RDKIT_SUBGRAPHS_EXPORT ROMol * pathToSubmol(const ROMol &mol, const PATH_TYPE &path, bool useQuery, std::map< int, int > &atomIdxMap)
Subgraphs.h
functionality for finding subgraphs and paths in molecules
RDKit::PATH_TYPE
std::vector< int > PATH_TYPE
Definition: Subgraphs.h:37
export.h