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RDKit
Open-source cheminformatics and machine learning.
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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 | ( | 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 305 of file MorganGenerator.h.
1.9.8