12 #ifndef RD_ATOMPAIRGEN_H_2018_06 13 #define RD_ATOMPAIRGEN_H_2018_06 20 using namespace AtomPairs;
24 const bool df_includeChirality;
25 const bool df_topologicalTorsionCorrection;
37 bool topologicalTorsionCorrection =
false);
39 std::vector<std::uint32_t> *getAtomInvariants(
const ROMol &mol)
const;
41 std::string infoString()
const;
49 template <
typename OutputType>
58 OutputType getResultSize()
const;
60 std::string infoString()
const;
83 const bool includeChirality =
false,
84 const bool use2D =
true,
const unsigned int minDistance = 1,
85 const unsigned int maxDistance = (
maxPathLen - 1),
86 const std::vector<std::uint32_t> countBounds = {1, 2, 4, 8},
87 const std::uint32_t fpSize = 2048);
95 template <
typename OutputType>
98 const unsigned int d_atomIdFirst;
99 const unsigned int d_atomIdSecond;
100 const unsigned int d_distance;
104 const std::vector<std::uint32_t> *atomInvariants,
105 const std::vector<std::uint32_t> *bondInvariants,
107 const bool hashResults =
false)
const;
117 const unsigned int atomIdSecond,
const unsigned int distance);
124 template <
typename OutputType>
128 std::vector<AtomEnvironment<OutputType> *> getEnvironments(
130 const std::vector<std::uint32_t> *fromAtoms,
131 const std::vector<std::uint32_t> *ignoreAtoms,
const int confId,
133 const std::vector<std::uint32_t> *atomInvariants,
134 const std::vector<std::uint32_t> *bondInvariants,
135 const bool hashResults =
false)
const;
137 std::string infoString()
const;
166 template <
typename OutputType>
169 const unsigned int minDistance = 1,
170 const unsigned int maxDistance =
maxPathLen - 1,
171 const bool includeChirality =
false,
const bool use2D =
true,
173 const bool useCountSimulation =
true,
const std::uint32_t fpSize = 2048,
174 const std::vector<std::uint32_t> countBounds = {1, 2, 4, 8},
175 const bool ownsAtomInvGen =
false);
abstract base class that holds atom-environments that will be hashed to generate the fingerprint ...
const unsigned int d_maxDistance
const unsigned int maxPathLen
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * getAtomPairGenerator(const unsigned int minDistance=1, const unsigned int maxDistance=maxPathLen - 1, const bool includeChirality=false, const bool use2D=true, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool useCountSimulation=true, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false)
helper function that generates a /c FingerprintGenerator that generates atom-pair fingerprints ...
abstract base class for atom invariants generators
class that generates atom-environments for atom-pair fingerprint
class that holds atom-environment data needed for atom-pair fingerprint generation ...
abstract base class that generates atom-environments from a molecule
const bool df_includeChirality
#define RDKIT_FINGERPRINTS_EXPORT
class that holds atom-pair fingerprint specific arguments
const unsigned int d_minDistance
class that generates same fingerprint style for different output formats
Abstract base class that holds molecule independent arguments that are common amongst all fingerprint...