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);
64 const ROMol &mol)
const override;
70 template <
typename OutputType>
73 const OutputType d_bitId;
74 const boost::dynamic_bitset<> d_atomsInPath;
79 const std::vector<std::uint32_t> *atomInvariants,
80 const std::vector<std::uint32_t> *bondInvariants,
82 bool hashResults =
false,
83 const std::uint64_t fpSize = 0)
const override;
96 d_atomsInPath(std::move(atomsInPath)),
97 d_bondPath(std::move(bondPath)) {}
100 template <
typename OutputType>
106 const std::vector<std::uint32_t> *fromAtoms,
107 const std::vector<std::uint32_t> *ignoreAtoms,
int confId,
109 const std::vector<std::uint32_t> *atomInvariants,
110 const std::vector<std::uint32_t> *bondInvariants,
111 bool hashResults =
false)
const override;
149 template <
typename OutputType>
151 unsigned int minPath = 1,
unsigned int maxPath = 7,
bool useHs =
true,
152 bool branchedPaths =
true,
bool useBondOrder =
true,
154 bool countSimulation =
false,
155 const std::vector<std::uint32_t> countBounds = {1, 2, 4, 8},
156 std::uint32_t fpSize = 2048, std::uint32_t numBitsPerFeature = 2,
157 bool ownsAtomInvGen =
false);
abstract base class that generates atom-environments from a molecule
abstract base class that holds atom-environments that will be hashed to generate the fingerprint
abstract base class for atom invariants generators
Abstract base class that holds molecule independent arguments that are common amongst all fingerprint...
class that generates same fingerprint style for different output formats
std::string infoString() const override
method that returns information string about the fingerprint specific argument set and the arguments ...
const unsigned int d_minPath
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.
OutputType getResultSize() const override
Returns the size of the fingerprint based on arguments.
const bool df_useBondOrder
const bool df_branchedPaths
const unsigned int d_maxPath
RDKitFPAtomEnv(const OutputType bitId, boost::dynamic_bitset<> atomsInPath, INT_VECT bondPath)
Construct a new RDKitFPAtomEnv object.
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 std::uint64_t fpSize=0) const override
calculates and returns the bit id to be set for this atom-environment
RDKitFPAtomInvGenerator * clone() const override
std::vector< std::uint32_t > * getAtomInvariants(const ROMol &mol) const override
get atom invariants from a molecule
std::string infoString() const override
method that returns information about this /c AtomInvariantsGenerator and its arguments
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 override
generate and return all atom-envorinments from a molecule
std::string infoString() const override
method that returns information about this /c AtomEnvironmentGenerator and its arguments if any
#define RDKIT_FINGERPRINTS_EXPORT
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< int > INT_VECT