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Generation of Murcko scaffolds from a molecule
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murckoTransforms = [AllChem.ReactionFromSmarts('[*:1]-[!#1;D1]
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murckoQ = Chem.MolFromSmarts(murckoQ)
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murckoPatts = [Chem.MolFromSmarts(x) for x in murckoPatts]
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aromaticNTransform = AllChem.ReactionFromSmarts('[n:1]-[D1]>>[
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Makes a Murcko scaffold generic (i.e. all atom types->C and all bonds ->single >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('c1ccccc1'))) 'C1CCCCC1' >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('c1ncccc1'))) 'C1CCCCC1' The following were associated with sf.net issue 246 >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('c1[nH]ccc1'))) 'C1CCCC1' >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('C1[NH2+]C1'))) 'C1CC1' >>> Chem.MolToSmiles(MakeScaffoldGeneric(Chem.MolFromSmiles('C1[C@](Cl)(F)O1'))) 'CC1(C)CC1' |
Return molecule object containing scaffold of mol >>> m = Chem.MolFromSmiles('Cc1ccccc1') >>> GetScaffoldForMol(m) <rdkit.Chem.rdchem.Mol object at 0x...> >>> Chem.MolToSmiles(GetScaffoldForMol(m)) 'c1ccccc1' >>> m = Chem.MolFromSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1') >>> Chem.MolToSmiles(GetScaffoldForMol(m)) 'c1ccc(Oc2ccccn2)cc1' |
Returns MurckScaffold Smiles from smiles >>> MurckoScaffoldSmilesFromSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1') 'c1ccc(Oc2ccccn2)cc1' |
Returns MurckScaffold Smiles from smiles >>> MurckoScaffoldSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1') 'c1ccc(Oc2ccccn2)cc1' >>> MurckoScaffoldSmiles(mol=Chem.MolFromSmiles('Cc1cc(Oc2nccc(CCC)c2)ccc1')) 'c1ccc(Oc2ccccn2)cc1' |
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murckoTransforms
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aromaticNTransform
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