The RDKit is fairly strict in checking that the charge + valence don't
exceed reasonable values for the element, but it does not go so far as to
catch these extreme cases.
It's worth thinking about how to add this kind of sanity checking to the
RDKit itself while still allowing "reasonable" hypervalent species, but
this is unlikely to happen quickly.
In the near term it seems like something that could be reasonable for
either MolVS or the standardizer to handle.
Best,
-greg
On Mon, Apr 16, 2018 at 10:35 AM, Colin Bournez <
[email protected]> wrote:
> Hello everyone,
>
> I was working with molecules generated from fragment and I saw a molecule
> not right, here is the smiles :
> 'CC1(C)CC(N)CC(C)(C)[NH2+2]1[O-]'
> I tried to 'clean it' with Cleanup, Sanitize, molsvs or standardizer but I
> could not change the N with 5 bounds.
>
> So, I also tried to create other molecule to see and you can do the same
> with this code in a notebook :
> m = Chem.MolFromSmiles('CC1(C)CC(N)CC(C)(C)[NH15+15]1(CCC)')
> m=Chem.AddHs(m)
> m
>
> It seems that there is no problem for RDKit if you add Hs to N with charge
> (if you try m = Chem.MolFromSmiles('CC1(C)CC(N)CC(C)(C)[NH15]1(CCC)') it
> won't work. Also, if you have less charge than H it won't work.
>
> Any idea how to avoid that?
> Rdkit version is 2017.09.3
>
> --
> *Colin Bournez*
> PhD Student, Structural Bioinformatics & Chemoinformatics
> Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
> d'Orléans 7311
> Rue de Chartres, 45067 Orléans, France
> T. +33 238 494 577
>
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