I do not know the valence model of RDkit. Therefore below there is an
ugly but working solution: set to the S+ atom NoImplicit.
mol = Chem.MolFromSmiles('CC(C)(C)SC')
rxn =
AllChem.ReactionFromSmarts('[CH0:1][S:2][CH3:3]>>[C:1][SH0+:2].[CH3-:3]')
ps = rxn.RunReactants((mol,))
print(Chem.MolToSmiles(ps[0][0]))
print(Chem.MolToSmiles(ps[0][1]))
for a in ps[0][0].GetAtoms():
if a.GetAtomicNum() == 16 and a.GetFormalCharge() == 1:
a.SetNoImplicit(True)
print(Chem.MolToSmiles(ps[0][0]))
print(Chem.MolToSmiles(ps[0][1]))
Pavel.
On 05/28/2017 08:26 AM, Nitzan Tzanani wrote:
mol = Chem.MolFromSmiles('CC(C)(C)SC')
rxn =
AllChem.ReactionFromSmarts('[CH0:1][S:2][CH3:3]>>[C:1][SH0+:2].[CH3-:3]')
ps = rxn.RunReactants((mol,))
print Chem.MolToSmiles(ps[0][0])
print Chem.MolToSmiles(ps[0][1])
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