RDKit
Open-source cheminformatics and machine learning.
ReducedGraphs.h
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1 //
2 // Copyright (C) 2013 Greg Landrum
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_REDUCEDGRAPHS_H_
12 #define _RD_REDUCEDGRAPHS_H_
13 
14 #include <vector>
15 #include <cstdint>
16 #include <boost/dynamic_bitset.hpp>
17 #include <Numerics/Vector.h>
18 
19 namespace RDKit {
20 class ROMol;
21 
22 namespace ReducedGraphs {
23 //! \brief Generates a reduced graph representation of a molecule
24 /*!
25 
26  \param mol: the molecule to be fingerprinted
27 
28  \return a new molecule
29 
30  <b>Notes:</b>
31  - the caller is responsible for <tt>delete</tt>ing the result
32 
33 */
35  const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = 0);
36 //! \brief Generates a ErG fingerprint vector for a molecule that's already a
37 // reduced graph
38 /*!
39 
40  \param mol: the molecule to be fingerprinted
41  \param atomTypes: [optional] contains bit vectors indicating whether each
42  atom in
43  the molecule matches each type.
44  \param fuzzIncrement: amount to be added to neighboring bins
45  \param minPath: minimum distance (in bonds) to be considered
46  \param maxPath: maximum distance (in bonds) to be considered
47 
48  \return the fingerprint, as a DoubleVector
49 
50  <b>Notes:</b>
51  - the caller is responsible for <tt>delete</tt>ing the result
52 
53 */
56  const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = 0,
57  double fuzzIncrement = 0.3, unsigned int minPath = 1,
58  unsigned int maxPath = 15);
59 
60 //! \brief Generates a ErG fingerprint vector for a molecule
61 /*!
62 
63  \param mol: the molecule to be fingerprinted
64  \param atomTypes: [optional] contains bit vectors indicating whether each
65  atom in
66  the molecule matches each type.
67  \param fuzzIncrement: amount to be added to neighboring bins
68  \param minPath: minimum distance (in bonds) to be considered
69  \param maxPath: maximum distance (in bonds) to be considered
70 
71  \return the fingerprint, as a DoubleVector
72 
73  <b>Notes:</b>
74  - the caller is responsible for <tt>delete</tt>ing the result
75 
76 */
78  const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = 0,
79  double fuzzIncrement = 0.3, unsigned int minPath = 1,
80  unsigned int maxPath = 15);
81 } // namespace ReducedGraphs
82 } // namespace RDKit
83 
84 #endif
Vector.h
RDKit::ReducedGraphs::generateErGFingerprintForReducedGraph
RDKIT_REDUCEDGRAPHS_EXPORT RDNumeric::DoubleVector * generateErGFingerprintForReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<>> *atomTypes=0, double fuzzIncrement=0.3, unsigned int minPath=1, unsigned int maxPath=15)
Generates a ErG fingerprint vector for a molecule that's already a.
RDNumeric::Vector
A class to represent vectors of numbers.
Definition: Vector.h:29
RDKit::ROMol
Definition: ROMol.h:171
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::ReducedGraphs::getErGFingerprint
RDKIT_REDUCEDGRAPHS_EXPORT RDNumeric::DoubleVector * getErGFingerprint(const ROMol &mol, std::vector< boost::dynamic_bitset<>> *atomTypes=0, double fuzzIncrement=0.3, unsigned int minPath=1, unsigned int maxPath=15)
Generates a ErG fingerprint vector for a molecule.
RDKit::ReducedGraphs::generateMolExtendedReducedGraph
RDKIT_REDUCEDGRAPHS_EXPORT ROMol * generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<>> *atomTypes=0)
Generates a reduced graph representation of a molecule.
RDKIT_REDUCEDGRAPHS_EXPORT
#define RDKIT_REDUCEDGRAPHS_EXPORT
Definition: export.h:567
export.h