Dear list,
I have been trying to replace this SMARTS pattern in a ring:
'c(=O)[nH]'
By this SMILES fragment:
'c(O)n'
My trials using a single SMARTS pattern search then replace
break open the ring, which is not what I want.
My not working trial code:
---
mol = Chem.MolFromSmiles('O=c1[nH]cccc1')
pat = Chem.MolFromSmarts('c(=O)[nH]')
rep = Chem.MolFromSmarts('c(O)n')
res = AllChem.ReplaceSubstructs(mol,pat,rep)
Chem.MolToSmiles(res[0])
'ccccc(n)O'
---
The example molecule is just an example; the ring might be smaller
and/or have more heteroatoms.
Should I use a chemical reaction for this?
Am I forced to describe full rings in both SMARTS patterns?!
I don't want to have to enumerate all the possibilities...
I can make it ~work~ using two replacements:
first 'c(=O)' to 'c(O)'
then
'[nH]' to 'n'
But this is less precise than what I really want
and I believe it will change molecules or places I don't want to change.
Thanks a lot and happy new year!
F.
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