RDKit
Open-source cheminformatics and machine learning.
FingerprintUtil.h
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1 //
2 // Copyright (C) 2018 Boran Adas, Google Summer of Code
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 
11 #include <RDGeneral/export.h>
12 #ifndef RD_FINGERPRINTUTIL_H_2018_07
13 #define RD_FINGERPRINTUTIL_H_2018_07
14 
15 #include <GraphMol/RDKitBase.h>
17 #include <DataStructs/BitVects.h>
18 #include <cstdint>
19 #include <tuple>
20 #include <vector>
21 #include <map>
23 
25 
26 namespace RDKit {
27 namespace AtomPairs {
28 const unsigned int numTypeBits = 4;
29 const unsigned int atomNumberTypes[1 << numTypeBits] = {
30  5, 6, 7, 8, 9, 14, 15, 16, 17, 33, 34, 35, 51, 52, 43};
31 const unsigned int numPiBits = 2;
32 const unsigned int maxNumPi = (1 << numPiBits) - 1;
33 const unsigned int numBranchBits = 3;
34 const unsigned int maxNumBranches = (1 << numBranchBits) - 1;
35 const unsigned int numChiralBits = 2;
36 const unsigned int codeSize = numTypeBits + numPiBits + numBranchBits;
37 const unsigned int numPathBits = 5;
38 const unsigned int maxPathLen = (1 << numPathBits) - 1;
39 const unsigned int numAtomPairFingerprintBits =
40  numPathBits + 2 * codeSize; // note that this is only accurate if chirality
41  // is not included
42 
43 //! returns a numeric code for the atom (the atom's hash in the
44 //! atom-pair scheme)
45 /*!
46  \param atom the atom to be considered
47  \param branchSubtract (optional) a constant to subtract from
48  the number of neighbors when the hash
49  is calculated (used in the topological
50  torsions code)
51  \param includeChirality toggles the inclusions of bits indicating R/S
52  chirality
53 */
55  const Atom *atom, unsigned int branchSubtract = 0,
56  bool includeChirality = false);
57 
58 //! returns an atom pair hash based on two atom hashes and the
59 //! distance between the atoms.
60 /*!
61  \param codeI the hash for the first atom
62  \param codeJ the hash for the second atom
63  \param dist the distance (number of bonds) between the two
64  atoms
65  \param includeChirality toggles the inclusions of bits indicating R/S
66  chirality
67 */
69  std::uint32_t codeI, std::uint32_t codeJ, unsigned int dist,
70  bool includeChirality = false);
71 
72 //! returns an topological torsion hash based on the atom hashes
73 //! passed in
74 /*!
75  \param atomCodes the vector of atom hashes
76 */
78  const std::vector<std::uint32_t> &atomCodes, bool includeChirality = false);
79 
81  const std::vector<std::uint32_t> &pathCodes);
82 } // namespace AtomPairs
83 
84 namespace MorganFingerprints {
85 
87  public:
89  ss_matcher(const std::string &pattern);
90 
91  // const RDKit::ROMOL_SPTR &getMatcher() const { return m_matcher; }
92  const RDKit::ROMol *getMatcher() const;
93 
94  private:
95  RDKit::ROMOL_SPTR m_matcher;
96 };
97 
98 typedef std::tuple<boost::dynamic_bitset<>, uint32_t, unsigned int> AccumTuple;
99 
100 RDKIT_FINGERPRINTS_EXPORT extern std::vector<std::string> defaultFeatureSmarts;
101 
102 //! returns the connectivity invariants for a molecule
103 /*!
104 
105  \param mol : the molecule to be considered
106  \param invars : used to return the results
107  \param includeRingMembership : if set, whether or not the atom is in
108  a ring will be used in the invariant list.
109 */
111  const ROMol &mol, std::vector<std::uint32_t> &invars,
112  bool includeRingMembership = true);
113 const std::string morganConnectivityInvariantVersion = "1.0.0";
114 
115 //! returns the feature invariants for a molecule
116 /*!
117 
118  \param mol: the molecule to be considered
119  \param invars : used to return the results
120  \param patterns: if provided should contain the queries used to assign
121  atom-types.
122  if not provided, feature definitions adapted from reference:
123  Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998)
124  will be used for Donor, Acceptor, Aromatic, Halogen, Basic,
125  Acidic
126 
127 */
129  const ROMol &mol, std::vector<std::uint32_t> &invars,
130  std::vector<const ROMol *> *patterns = nullptr);
131 const std::string morganFeatureInvariantVersion = "0.1.0";
132 
133 } // namespace MorganFingerprints
134 
135 namespace RDKitFPUtils {
136 
138  const ROMol &mol, std::vector<std::uint32_t> &lAtomInvariants);
139 
141  const ROMol &mol, std::map<int, std::list<std::vector<int>>> &allPaths,
142  const std::vector<std::uint32_t> *fromAtoms, bool branchedPaths, bool useHs,
143  unsigned int minPath, unsigned int maxPath);
144 
146  const ROMol &mol, std::vector<const Bond *> &bondCache,
147  std::vector<short> &isQueryBond);
148 
150  const ROMol &mol, boost::dynamic_bitset<> &atomsInPath,
151  const std::vector<const Bond *> &bondCache,
152  const std::vector<short> &isQueryBond, const std::vector<int> &path,
153  bool useBondOrder, const std::vector<std::uint32_t> *atomInvariants);
154 
155 } // namespace RDKitFPUtils
156 
157 } // namespace RDKit
158 
159 #endif
Pulls in all the BitVect classes.
pulls in the core RDKit functionality
functionality for finding subgraphs and paths in molecules
The class for representing atoms.
Definition: Atom.h:68
const RDKit::ROMol * getMatcher() const
ss_matcher(const std::string &pattern)
#define RDKIT_FINGERPRINTS_EXPORT
Definition: export.h:177
const unsigned int numPiBits
RDKIT_FINGERPRINTS_EXPORT std::uint64_t getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false)
const unsigned int numPathBits
const unsigned int maxNumPi
const unsigned int numChiralBits
const unsigned int atomNumberTypes[1<< numTypeBits]
const unsigned int maxNumBranches
RDKIT_FINGERPRINTS_EXPORT std::uint32_t getAtomPairCode(std::uint32_t codeI, std::uint32_t codeJ, unsigned int dist, bool includeChirality=false)
const unsigned int codeSize
const unsigned int numTypeBits
const unsigned int numBranchBits
const unsigned int numAtomPairFingerprintBits
RDKIT_FINGERPRINTS_EXPORT std::uint32_t getTopologicalTorsionHash(const std::vector< std::uint32_t > &pathCodes)
const unsigned int maxPathLen
RDKIT_FINGERPRINTS_EXPORT std::uint32_t getAtomCode(const Atom *atom, unsigned int branchSubtract=0, bool includeChirality=false)
RDKIT_FINGERPRINTS_EXPORT std::vector< std::string > defaultFeatureSmarts
RDKIT_FINGERPRINTS_EXPORT void getFeatureInvariants(const ROMol &mol, std::vector< std::uint32_t > &invars, std::vector< const ROMol * > *patterns=nullptr)
returns the feature invariants for a molecule
const std::string morganFeatureInvariantVersion
const std::string morganConnectivityInvariantVersion
RDKIT_FINGERPRINTS_EXPORT void getConnectivityInvariants(const ROMol &mol, std::vector< std::uint32_t > &invars, bool includeRingMembership=true)
returns the connectivity invariants for a molecule
std::tuple< boost::dynamic_bitset<>, uint32_t, unsigned int > AccumTuple
RDKIT_FINGERPRINTS_EXPORT std::vector< unsigned int > generateBondHashes(const ROMol &mol, boost::dynamic_bitset<> &atomsInPath, const std::vector< const Bond * > &bondCache, const std::vector< short > &isQueryBond, const std::vector< int > &path, bool useBondOrder, const std::vector< std::uint32_t > *atomInvariants)
RDKIT_FINGERPRINTS_EXPORT void identifyQueryBonds(const ROMol &mol, std::vector< const Bond * > &bondCache, std::vector< short > &isQueryBond)
RDKIT_FINGERPRINTS_EXPORT void enumerateAllPaths(const ROMol &mol, std::map< int, std::list< std::vector< int >>> &allPaths, const std::vector< std::uint32_t > *fromAtoms, bool branchedPaths, bool useHs, unsigned int minPath, unsigned int maxPath)
RDKIT_FINGERPRINTS_EXPORT void buildDefaultRDKitFingerprintAtomInvariants(const ROMol &mol, std::vector< std::uint32_t > &lAtomInvariants)
Std stuff.
Definition: Abbreviations.h:19
boost::shared_ptr< ROMol > ROMOL_SPTR