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RDKit
Open-source cheminformatics and machine learning.
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12 #ifndef RD_RDFINGERPRINTGEN_H_2018_07
13 #define RD_RDFINGERPRINTGEN_H_2018_07
20 template <
typename OutputType>
55 bool branchedPaths,
bool useBondOrder,
bool countSimulation,
56 const std::vector<std::uint32_t> countBounds,
57 std::uint32_t fpSize, std::uint32_t numBitsPerFeature);
69 template <
typename OutputType>
72 const OutputType d_bitId;
73 const boost::dynamic_bitset<> d_atomsInPath;
77 const std::vector<std::uint32_t> *atomInvariants,
78 const std::vector<std::uint32_t> *bondInvariants,
80 bool hashResults =
false)
const;
92 template <
typename OutputType>
98 const std::vector<std::uint32_t> *fromAtoms,
99 const std::vector<std::uint32_t> *ignoreAtoms,
int confId,
101 const std::vector<std::uint32_t> *atomInvariants,
102 const std::vector<std::uint32_t> *bondInvariants,
103 bool hashResults =
false)
const;
134 template <
typename OutputType>
136 unsigned int minPath = 1,
unsigned int maxPath = 7,
bool useHs =
true,
137 bool branchedPaths =
true,
bool useBondOrder =
true,
139 bool countSimulation =
false,
140 const std::vector<std::uint32_t> countBounds = {1, 2, 4, 8},
141 std::uint32_t fpSize = 2048, std::uint32_t numBitsPerFeature = 2,
142 bool ownsAtomInvGen =
false);
RDKitFPAtomInvGenerator * clone() const
class that generates same fingerprint style for different output formats
const bool df_useBondOrder
const bool df_branchedPaths
RDKitFPAtomEnv(const OutputType bitId, boost::dynamic_bitset<> atomsInPath)
Construct a new RDKitFPAtomEnv object.
std::vector< AtomEnvironment< OutputType > * > getEnvironments(const ROMol &mol, FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *fromAtoms, const std::vector< std::uint32_t > *ignoreAtoms, int confId, const AdditionalOutput *additionalOutput, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, bool hashResults=false) const
generate and return all atom-envorinments from a molecule
abstract base class for atom invariants generators
const unsigned int d_maxPath
const unsigned int d_minPath
std::string infoString() const
method that returns information string about the fingerprint specific argument set and the arguments ...
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * getRDKitFPGenerator(unsigned int minPath=1, unsigned int maxPath=7, bool useHs=true, bool branchedPaths=true, bool useBondOrder=true, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=false, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, std::uint32_t fpSize=2048, std::uint32_t numBitsPerFeature=2, bool ownsAtomInvGen=false)
Get a RDKit fingerprint generator with given parameters.
std::vector< std::uint32_t > * getAtomInvariants(const ROMol &mol) const
get atom invariants from a molecule
abstract base class that holds atom-environments that will be hashed to generate the fingerprint
abstract base class that generates atom-environments from a molecule
std::string infoString() const
method that returns information about this /c AtomInvariantsGenerator and its arguments
OutputType getResultSize() const
Returns the size of the fingerprint based on arguments.
#define RDKIT_FINGERPRINTS_EXPORT
RDKitFPArguments(unsigned int minPath, unsigned int maxPath, bool useHs, bool branchedPaths, bool useBondOrder, bool countSimulation, const std::vector< std::uint32_t > countBounds, std::uint32_t fpSize, std::uint32_t numBitsPerFeature)
Construct a new RDKitFPArguments object.
std::string infoString() const
method that returns information about this /c AtomEnvironmentGenerator and its arguments if any
OutputType getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *additionalOutput, bool hashResults=false) const
calculates and returns the bit id to be set for this atom-environment
Abstract base class that holds molecule independent arguments that are common amongst all fingerprint...