Hi all,
I initially wrote an fmoc smarts reaction to deprotect molecules as the
following:
reaction_smarts='[#7:1]C(=O)OCC1c2ccccc2-c3ccccc13>>[#7:1]'
Here's an example where this fails:
from rdkit import Chem
from rdkit.Chem import AllChem
mol=Chem.MolFromSmiles('O=C(O)COC1(Cc2cc[nH]n2)CN(C(=O)OCC2c3ccccc3-c3ccccc32)C1')
mol
[image: image.png]
reaction_smarts='[#7:1]C(=O)OCC1c2ccccc2-c3ccccc13>>[#7:1]'
rxn = AllChem.ReactionFromSmarts(reaction_smarts)
products = rxn.RunReactants((mol,))
products[0][0]
[image: image.png]
Now this gets solved by rewriting my smarts
to '[#7;$([#7]C(=O)OCC1c2ccccc2-c3ccccc13):1]>>[#7:1]' but I don't
understand what was wrong with the initial one and how it could create that
result. This does not happen systematically to the building blocks I've
been working with. Does anyone have an explanation for this or is it a bug?
Thank you for your help!
Fio
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