Hi Fiorella,
I don't believe your initial solution is actually wrong; I think it may
just be the drawing of RDKit that is throwing you off. Whenever a red
circle shows up in a mol image, that indicates the perfect overlap of two
atoms. In this case, it is extra confusing because one of the atoms is a
red O itself.
If I do `Chem.MolToSmiles(products[0][0])` on your code, I get
`O=C(O)COC1(Cc2cc[nH]n2)CNC1`,
which gives the following image in ChemDraw.
[image: Screen Shot 2021-06-27 at 5.20.55 PM.png]
Hopefully that's all that it was, but please let me know if there was some
other error you noticed.
Best,
Matt
On Sun, Jun 27, 2021 at 3:34 PM Fiorella Ruggiu <ruggiu.fiore...@gmail.com>
wrote:
> 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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