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Contains an implementation of Atom-pair fingerprints, as described in: R.E. Carhart, D.H. Smith, R. Venkataraghavan; "Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications" JCICS 25, 64-73 (1985). The fingerprints can be accessed through the following functions: - GetAtomPairFingerprint - GetHashedAtomPairFingerprint (identical to GetAtomPairFingerprint) - GetAtomPairFingerprintAsIntVect - GetAtomPairFingerprintAsBitVect
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GetAtomPairFingerprintAsIntVect = rdMolDescriptors.GetAtomPair
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numPathBits = rdMolDescriptors.AtomPairsParameters.numPathBits
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_maxPathLen = 1 << numPathBits-1
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numFpBits = numPathBits+ 2* rdMolDescriptors.AtomPairsParamete
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fpLen = 1 << numFpBits
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Imports: DataStructs, rdMolDescriptors, Utils, GetAtomPairFingerprint, GetHashedAtomPairFingerprint
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Returns a score for an individual atom pair. >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCCC') >>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0)) >>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1)) >>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2)) >>> t = 1 | min(c1,c2)<<numPathBits | max(c1,c2)<<(rdMolDescriptors.AtomPairsParameters.codeSize+numPathBits) >>> pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1)==t 1 >>> pyScorePair(m.GetAtomWithIdx(1),m.GetAtomWithIdx(0),1)==t 1 >>> t = 2 | min(c1,c3)<<numPathBits | max(c1,c3)<<(rdMolDescriptors.AtomPairsParameters.codeSize+numPathBits) >>> pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2)==t 1 >>> pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2, ... atomCodes=(Utils.GetAtomCode(m.GetAtomWithIdx(0)),Utils.GetAtomCode(m.GetAtomWithIdx(2))))==t 1 |
>>> from rdkit import Chem >>> m = Chem.MolFromSmiles('C=CC') >>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1) >>> ExplainPairScore(score) (('C', 1, 1), 1, ('C', 2, 1)) >>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2) >>> ExplainPairScore(score) (('C', 1, 0), 2, ('C', 1, 1)) >>> score = pyScorePair(m.GetAtomWithIdx(1),m.GetAtomWithIdx(2),1) >>> ExplainPairScore(score) (('C', 1, 0), 1, ('C', 2, 1)) >>> score = pyScorePair(m.GetAtomWithIdx(2),m.GetAtomWithIdx(1),1) >>> ExplainPairScore(score) (('C', 1, 0), 1, ('C', 2, 1)) We can optionally deal with chirality too >>> m = Chem.MolFromSmiles('C[C@H](F)Cl') >>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1) >>> ExplainPairScore(score) (('C', 1, 0), 1, ('C', 3, 0)) >>> score = pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1,includeChirality=True) >>> ExplainPairScore(score,includeChirality=True) (('C', 1, 0, ''), 1, ('C', 3, 0, 'R')) >>> m = Chem.MolFromSmiles('F[C@@H](Cl)[C@H](F)Cl') >>> score = pyScorePair(m.GetAtomWithIdx(1),m.GetAtomWithIdx(3),1,includeChirality=True) >>> ExplainPairScore(score,includeChirality=True) (('C', 3, 0, 'R'), 1, ('C', 3, 0, 'S')) |
Returns the Atom-pair fingerprint for a molecule as a SparseBitVect. Note that this doesn't match the standard definition of atom pairs, which uses counts of the pairs, not just their presence. **Arguments**: - mol: a molecule **Returns**: a SparseBitVect >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCC') >>> v = [ pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(1),1), ... pyScorePair(m.GetAtomWithIdx(0),m.GetAtomWithIdx(2),2), ... ] >>> v.sort() >>> fp = GetAtomPairFingerprintAsBitVect(m) >>> list(fp.GetOnBits())==v True |
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GetAtomPairFingerprintAsIntVect
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numFpBits
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