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);
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
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.
std::string infoString() const
method that returns information string about the fingerprint specific argument set and the arguments ...
const bool df_useBondOrder
const bool df_branchedPaths
OutputType getResultSize() const
Returns the size of the fingerprint based on arguments.
const unsigned int d_maxPath
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
RDKitFPAtomEnv(const OutputType bitId, boost::dynamic_bitset<> atomsInPath)
Construct a new RDKitFPAtomEnv object.
std::string infoString() const
method that returns information about this /c AtomInvariantsGenerator and its arguments
std::vector< std::uint32_t > * getAtomInvariants(const ROMol &mol) const
get atom invariants from a molecule
RDKitFPAtomInvGenerator * clone() const
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
std::string infoString() const
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.