RDKit
Open-source cheminformatics and machine learning.
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Classes | |
class | AtomPairArguments |
class that holds atom-pair fingerprint specific arguments More... | |
class | AtomPairAtomEnv |
class that holds atom-environment data needed for atom-pair fingerprint generation More... | |
class | AtomPairAtomInvGenerator |
class | AtomPairEnvGenerator |
class that generates atom-environments for atom-pair fingerprint More... | |
Functions | |
template<typename OutputType > | |
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 | |
template<typename OutputType > | |
FingerprintGenerator< OutputType > * | getAtomPairGenerator (const AtomPairArguments &args, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool ownsAtomInvGen=false) |
overload | |
FingerprintGenerator< OutputType > * RDKit::AtomPair::getAtomPairGenerator | ( | const AtomPairArguments & | args, |
AtomInvariantsGenerator * | atomInvariantsGenerator = nullptr , |
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const bool | ownsAtomInvGen = false |
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overload
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::AtomPair::getAtomPairGenerator | ( | const unsigned int | minDistance = 1 , |
const unsigned int | maxDistance = maxPathLen - 1 , |
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const bool | includeChirality = false , |
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const bool | use2D = true , |
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AtomInvariantsGenerator * | atomInvariantsGenerator = nullptr , |
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const bool | useCountSimulation = true , |
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const std::uint32_t | fpSize = 2048 , |
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const std::vector< std::uint32_t > | countBounds = {1, 2, 4, 8} , |
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const bool | ownsAtomInvGen = false |
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) |
helper function that generates a /c FingerprintGenerator that generates atom-pair fingerprints
OutputType | determines the size of the bitIds and the result, can be 32 or 64 bit unsigned integer |
minDistance | minimum distance between atoms to be considered in a pair, default is 1 bond |
maxDistance | maximum distance between atoms to be considered in a pair, default is maxPathLen-1 bonds |
includeChirality | if set, chirality will be used in the atom invariants, this is ignored if atomInvariantsGenerator is provided |
use2D | if set, the 2D (topological) distance matrix will be used |
atomInvariantsGenerator | atom invariants to be used during fingerprint generation |
useCountSimulation | if set, use count simulation while generating the fingerprint |
countBounds | boundaries for count simulation, corresponding bit will be set if the count is higher than the number provided for that spot |
fpSize | size of the generated fingerprint, does not affect the sparse versions |
ownsAtomInvGen | if set atom invariants generator is destroyed with the fingerprint generator |
This generator supports the following AdditionalOutput
types:
atomToBits
: which bits each atom is involved inatomCounts
: how many bits each atom setsbitInfoMap
: map from bitId to (atomId1, atomId2) pairs