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SparseIntVect< boost::uint32_t > * | getFingerprint (const ROMol &mol, unsigned int radius, std::vector< boost::uint32_t > *invariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, bool useChirality=false, bool useBondTypes=true, bool useCounts=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=0) |
| returns the Morgan fingerprint for a molecule More...
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SparseIntVect< boost::uint32_t > * | getHashedFingerprint (const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=0) |
| returns the Morgan fingerprint for a molecule More...
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ExplicitBitVect * | getFingerprintAsBitVect (const ROMol &mol, unsigned int radius, unsigned int nBits, std::vector< boost::uint32_t > *invariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=0) |
| returns the Morgan fingerprint for a molecule as a bit vector More...
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void | getConnectivityInvariants (const ROMol &mol, std::vector< boost::uint32_t > &invars, bool includeRingMembership=true) |
| returns the connectivity invariants for a molecule More...
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void | getFeatureInvariants (const ROMol &mol, std::vector< boost::uint32_t > &invars, std::vector< const ROMol * > *patterns=0) |
| returns the feature invariants for a molecule More...
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SparseIntVect<boost::uint32_t>* RDKit::MorganFingerprints::getFingerprint |
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const ROMol & |
mol, |
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unsigned int |
radius, |
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std::vector< boost::uint32_t > * |
invariants = 0 , |
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const std::vector< boost::uint32_t > * |
fromAtoms = 0 , |
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bool |
useChirality = false , |
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bool |
useBondTypes = true , |
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bool |
useCounts = true , |
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bool |
onlyNonzeroInvariants = false , |
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BitInfoMap * |
atomsSettingBits = 0 |
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) |
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returns the Morgan fingerprint for a molecule
These fingerprints are similar to the well-known ECFP or FCFP fingerprints, depending on which invariants are used.
The algorithm used is described in the paper Rogers, D. & Hahn, M. Extended-Connectivity Fingerprints. JCIM 50:742-54 (2010) http://dx.doi.org/10.1021/ci100050t
The original implementation was done using this paper: D. Rogers, R.D. Brown, M. Hahn J. Biomol. Screen. 10:682-6 (2005) and an unpublished technical report: http://www.ics.uci.edu/~welling/teaching/ICS274Bspring06/David%20Rogers%20-%20ECFP%20Manuscript.doc
- Parameters
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mol | the molecule to be fingerprinted |
radius | the number of iterations to grow the fingerprint |
invariants | : optional pointer to a set of atom invariants to be used. By default ECFP-type invariants are used (calculated by getConnectivityInvariants()) |
fromAtoms | : if this is provided, only the atoms in the vector will be used as centers in the fingerprint |
useChirality | : if set, additional information will be added to the fingerprint when chiral atoms are discovered. This will causeC[C@H](F)Cl,
C[C@@H](F)Cl, and CC(F)Cl to generate different fingerprints. |
useBondTypes | : if set, bond types will be included as part of the hash for calculating bits |
useCounts | : if set, counts of the features will be used |
onlyNonzeroInvariants | : if set, bits will only be set from atoms that have a nonzero invariant. |
atomsSettingBits | : if nonzero, this will be used to return information about the atoms that set each particular bit. The keys are the map are bit ids, the values are lists of (atomId, radius) pairs. |
- Returns
- a pointer to the fingerprint. The client is responsible for calling delete on this.
SparseIntVect<boost::uint32_t>* RDKit::MorganFingerprints::getHashedFingerprint |
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const ROMol & |
mol, |
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unsigned int |
radius, |
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unsigned int |
nBits = 2048 , |
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std::vector< boost::uint32_t > * |
invariants = 0 , |
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const std::vector< boost::uint32_t > * |
fromAtoms = 0 , |
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bool |
useChirality = false , |
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bool |
useBondTypes = true , |
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bool |
onlyNonzeroInvariants = false , |
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BitInfoMap * |
atomsSettingBits = 0 |
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) |
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returns the Morgan fingerprint for a molecule
These fingerprints are similar to the well-known ECFP or FCFP fingerprints, depending on which invariants are used.
The algorithm used is described in the paper Rogers, D. & Hahn, M. Extended-Connectivity Fingerprints. JCIM 50:742-54 (2010) http://dx.doi.org/10.1021/ci100050t
The original implementation was done using this paper: D. Rogers, R.D. Brown, M. Hahn J. Biomol. Screen. 10:682-6 (2005) and an unpublished technical report: http://www.ics.uci.edu/~welling/teaching/ICS274Bspring06/David%20Rogers%20-%20ECFP%20Manuscript.doc
- Parameters
-
mol | the molecule to be fingerprinted |
radius | the number of iterations to grow the fingerprint |
invariants | : optional pointer to a set of atom invariants to be used. By default ECFP-type invariants are used (calculated by getConnectivityInvariants()) |
fromAtoms | : if this is provided, only the atoms in the vector will be used as centers in the fingerprint |
useChirality | : if set, additional information will be added to the fingerprint when chiral atoms are discovered. This will causeC[C@H](F)Cl,
C[C@@H](F)Cl, and CC(F)Cl to generate different fingerprints. |
useBondTypes | : if set, bond types will be included as part of the hash for calculating bits |
onlyNonzeroInvariants | : if set, bits will only be set from atoms that have a nonzero invariant. |
atomsSettingBits | : if nonzero, this will be used to return information about the atoms that set each particular bit. The keys are the map are bit ids, the values are lists of (atomId, radius) pairs. |
- Returns
- a pointer to the fingerprint. The client is responsible for calling delete on this.