Hi Matt,
Thank you for this. You are indeed right that I got caught by the
visualization and didn't check my smiles yesterday. I thought the red was
indicating an obvious valence error on the oxygen there and that molecule
just made no sense. I appreciate the swift answer.
Thank you,
Fio
On Sun, Jun 27, 2021 at 2:22 PM Matthew Robinson <
matthew67robin...@gmail.com> wrote:
> 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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>> Rdkit-discuss@lists.sourceforge.net
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>>
>
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