Hi there RDkitters,
I have a molecule defined in aromatic form ("c1n[nH]nn1") and I am
trying to do a replace substructs on it using the equivalent kekule
form as a query ("'C1=N[NH1]N=N1"). However the substitution does not
happen. As shown by the following code:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('c1n[nH]nn1')
r = Chem.MolFromSmiles('c1[n-]nnn1', sanitize=False) # some arbitrary tautomer
q = Chem.MolFromSmarts('C1=N[NH1]N=N1')
replaced = AllChem.ReplaceSubstructs(mol, q, r, replaceAll=True)[0]
print Chem.MolToSmiles(replaced)
Any ideas why this is the case/what I am doing wrong?
Many thanks,
-
Jean-Paul Ebejer
Early Stage Researcher
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