Errata: My previously given solution actually doesn't work.
On Sun, Jun 27, 2021 at 12:10 PM Fiorella Ruggiu <ruggiu.fiore...@gmail.com>
wrote:
> 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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