RDKit
Open-source cheminformatics and machine learning.
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Classes | |
class | MorganArguments |
Class for holding Morgan fingerprint specific arguments. More... | |
class | MorganAtomEnv |
Class for holding the bit-id created from Morgan fingerprint environments and the additional data necessary extra outputs. More... | |
class | MorganAtomInvGenerator |
Default atom invariants generator for Morgan fingerprint, generates ECFP-type invariants. More... | |
class | MorganBondInvGenerator |
Bond invariants generator for Morgan fingerprint. More... | |
class | MorganEnvGenerator |
Class that generates atom environments for Morgan fingerprint. More... | |
class | MorganFeatureAtomInvGenerator |
Alternative atom invariants generator for Morgan fingerprint, generate FCFP-type invariants. More... | |
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::MorganFingerprint::getMorganGenerator | ( | const MorganArguments & | args, |
AtomInvariantsGenerator * | atomInvariantsGenerator = nullptr , |
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BondInvariantsGenerator * | bondInvariantsGenerator = nullptr , |
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bool | ownsAtomInvGen = false , |
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bool | ownsBondInvGen = false |
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator< OutputType > * RDKit::MorganFingerprint::getMorganGenerator | ( | unsigned int | radius, |
bool | countSimulation, | ||
bool | includeChirality, | ||
bool | useBondTypes, | ||
bool | onlyNonzeroInvariants, | ||
bool | includeRedundantEnvironments, | ||
AtomInvariantsGenerator * | atomInvariantsGenerator = nullptr , |
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BondInvariantsGenerator * | bondInvariantsGenerator = nullptr , |
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std::uint32_t | fpSize = 2048 , |
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std::vector< std::uint32_t > | countBounds = {1, 2, 4, 8} , |
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bool | ownsAtomInvGen = false , |
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bool | ownsBondInvGen = false |
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) |
Get a fingerprint generator for Morgan fingerprint.
OutputType | determines the size of the bitIds and the result, can be 32 or 64 bit unsigned integer |
radius | the number of iterations to grow the fingerprint |
countSimulation | if set, use count simulation while generating the fingerprint |
includeChirality | if set, chirality information will be added to the generated bit id, independently from bond invariants |
onlyNonzeroInvariants | if set, bits will only be set from atoms that have a nonzero invariant |
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 |
countSimulation | if set, use count simulation while generating the fingerprint |
includeChirality | sets includeChirality flag for both MorganArguments and the default bond generator MorganBondInvGenerator |
useBondTypes | if set, bond types will be included as a part of the default bond invariants |
onlyNonzeroInvariants | if set, bits will only be set from atoms that have a nonzero invariant |
includeRedundantEnvironments | if set redundant environments will be included in the fingerprint |
atomInvariantsGenerator | custom atom invariants generator to use |
bondInvariantsGenerator | custom bond invariants generator to use |
ownsAtomInvGen | if set atom invariants generator is destroyed with the fingerprint generator |
ownsBondInvGen | if set bond invariants generator is destroyed with the fingerprint generator |
This generator supports the following AdditionalOutput
types:
atomToBits
: which bits each atom is the central atom foratomCounts
: how many bits each atom setsbitInfoMap
: map from bitId to (atomId, radius) pairs FingerprintGenerator< OutputType > * RDKit::MorganFingerprint::getMorganGenerator | ( | unsigned int | radius, |
bool | countSimulation = false , |
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bool | includeChirality = false , |
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bool | useBondTypes = true , |
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bool | onlyNonzeroInvariants = false , |
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AtomInvariantsGenerator * | atomInvariantsGenerator = nullptr , |
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BondInvariantsGenerator * | bondInvariantsGenerator = nullptr , |
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std::uint32_t | fpSize = 2048 , |
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std::vector< std::uint32_t > | countBounds = {1, 2, 4, 8} , |
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bool | ownsAtomInvGen = false , |
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bool | ownsBondInvGen = false |
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) |
Get a fingerprint generator for Morgan fingerprint.
OutputType | determines the size of the bitIds and the result, can be 32 or 64 bit unsigned integer |
radius | the number of iterations to grow the fingerprint |
countSimulation | if set, use count simulation while generating the fingerprint |
includeChirality | if set, chirality information will be added to the generated bit id, independently from bond invariants |
onlyNonzeroInvariants | if set, bits will only be set from atoms that have a nonzero invariant |
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 |
countSimulation | if set, use count simulation while generating the fingerprint |
includeChirality | sets includeChirality flag for both MorganArguments and the default bond generator MorganBondInvGenerator |
useBondTypes | if set, bond types will be included as a part of the default bond invariants |
onlyNonzeroInvariants | if set, bits will only be set from atoms that have a nonzero invariant |
atomInvariantsGenerator | custom atom invariants generator to use |
bondInvariantsGenerator | custom bond invariants generator to use |
ownsAtomInvGen | if set atom invariants generator is destroyed with the fingerprint generator |
ownsBondInvGen | if set bond invariants generator is destroyed with the fingerprint generator |
This generator supports the following AdditionalOutput
types:
atomToBits
: which bits each atom is the central atom foratomCounts
: how many bits each atom setsbitInfoMap
: map from bitId to (atomId, radius) pairs Definition at line 316 of file MorganGenerator.h.