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Contains an implementation of Topological-torsion fingerprints, as described in: R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan; "Topological Torsion: A New Molecular Descriptor for SAR Applications. Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
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GetTopologicalTorsionFingerprintAsIntVect = rdMolDescriptors.G
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Imports: Chem, rdMolDescriptors, Utils, GetTopologicalTorsionFingerprint, GetHashedTopologicalTorsionFingerprint
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Returns a score for an individual path. >>> m = Chem.MolFromSmiles('CCCCC') >>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0),1) >>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1),2) >>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2),2) >>> c4 = Utils.GetAtomCode(m.GetAtomWithIdx(3),1) >>> t = c1 | (c2 << rdMolDescriptors.AtomPairsParameters.codeSize) | (c3 << (rdMolDescriptors.AtomPairsParameters.codeSize*2)) | (c4 << (rdMolDescriptors.AtomPairsParameters.codeSize*3)) >>> pyScorePath(m,(0,1,2,3),4)==t 1 The scores are path direction independent: >>> pyScorePath(m,(3,2,1,0),4)==t 1 >>> m = Chem.MolFromSmiles('C=CC(=O)O') >>> c1 = Utils.GetAtomCode(m.GetAtomWithIdx(0),1) >>> c2 = Utils.GetAtomCode(m.GetAtomWithIdx(1),2) >>> c3 = Utils.GetAtomCode(m.GetAtomWithIdx(2),2) >>> c4 = Utils.GetAtomCode(m.GetAtomWithIdx(4),1) >>> t = c1 | (c2 << rdMolDescriptors.AtomPairsParameters.codeSize) | (c3 << (rdMolDescriptors.AtomPairsParameters.codeSize*2)) | (c4 << (rdMolDescriptors.AtomPairsParameters.codeSize*3)) >>> pyScorePath(m,(0,1,2,4),4)==t 1 |
>>> m = Chem.MolFromSmiles('C=CC') >>> score=pyScorePath(m,(0,1,2),3) >>> ExplainPathScore(score,3) (('C', 1, 0), ('C', 2, 1), ('C', 1, 1)) Again, it's order independent: >>> score=pyScorePath(m,(2,1,0),3) >>> ExplainPathScore(score,3) (('C', 1, 0), ('C', 2, 1), ('C', 1, 1)) >>> m = Chem.MolFromSmiles('C=CO') >>> score=pyScorePath(m,(0,1,2),3) >>> ExplainPathScore(score,3) (('C', 1, 1), ('C', 2, 1), ('O', 1, 0)) >>> m = Chem.MolFromSmiles('OC=CO') >>> score=pyScorePath(m,(0,1,2,3),4) >>> ExplainPathScore(score,4) (('O', 1, 0), ('C', 2, 1), ('C', 2, 1), ('O', 1, 0)) >>> m = Chem.MolFromSmiles('CC=CO') >>> score=pyScorePath(m,(0,1,2,3),4) >>> ExplainPathScore(score,4) (('C', 1, 0), ('C', 2, 1), ('C', 2, 1), ('O', 1, 0)) >>> m = Chem.MolFromSmiles('C=CC(=O)O') >>> score=pyScorePath(m,(0,1,2,3),4) >>> ExplainPathScore(score,4) (('C', 1, 1), ('C', 2, 1), ('C', 3, 1), ('O', 1, 1)) >>> score=pyScorePath(m,(0,1,2,4),4) >>> ExplainPathScore(score,4) (('C', 1, 1), ('C', 2, 1), ('C', 3, 1), ('O', 1, 0)) >>> m = Chem.MolFromSmiles('OOOO') >>> score=pyScorePath(m,(0,1,2),3) >>> ExplainPathScore(score,3) (('O', 1, 0), ('O', 2, 0), ('O', 2, 0)) >>> score=pyScorePath(m,(0,1,2,3),4) >>> ExplainPathScore(score,4) (('O', 1, 0), ('O', 2, 0), ('O', 2, 0), ('O', 1, 0)) |
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GetTopologicalTorsionFingerprintAsIntVect
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