Hi there,
I have a list of molecules of which I want all to be in the same
tautomeric (does this word even exist?) form.
This "cheat" works fine using ReplaceSubstructs on my 100+ molecule
with the exception of one case, where the resulting molecule is being
fragmented. Can someone explain why this is the case?
Now to code:
#!/usr/bin/env python
from rdkit import Chem
from rdkit.Chem import AllChem
mol =
Chem.MolFromSmiles("COc1c(/N=C2\C(=O)c3c(cccc3)C(O)=C2n2nnc3ccccc23)cccc1")
q = Chem.MolFromSmarts("OC1=CC(=N)C(=O)c2ccccc12")
r = Chem.MolFromSmiles("NC1=CC(=O)c2ccccc2C1=O", sanitize=False)
modified = AllChem.ReplaceSubstructs(mol, q, r, replaceAll=True)[0]
# the following gives COc1ccccc1.NC1=CC(=O)c2ccccc2C1=O.n1nc2ccccc2n1
# fragmented ?! WHY ?!
print Chem.MolToSmiles(modified)
-
Jean-Paul Ebejer
Early Stage Researcher
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