Thanks Paolo, I'll try that. Sorry about the misleading title of my email,
I forgot to change it.
Best,
Alexis
On Fri, 4 Dec 2020 at 13:40, Paolo Tosco wrote:
> Hi Alexis,
>
> you may cast the _vectdouble to a list or a tuple and then you'll be able
> to pickle it.
> The 2020.09.01 is just an
Hi Alexis,
you may cast the _vectdouble to a list or a tuple and then you'll be able
to pickle it.
The 2020.09.01 is just an oversight; you are indeed the 2020.09.02 version.
Cheers,
p.
On Fri, Dec 4, 2020 at 1:32 PM Alexis Parenty
wrote:
> Dear Rdkiters,
>
> I could not pickle my models
Dear Rdkiters,
I could not pickle my models when using the new chemical descriptors,
therefore, I have re-installed the latest patched version of rdkit
2020.09.02 through conda-forge. (ref Fixes #3511 #3513)
https://anaconda.org/conda-forge/rdkit
However, this new version still does not let me
he issue isn’t the aromaticity of the
>>> imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’
>>> second molecule is identical to the first except that one bond in the
>>> 5-membered ring was broken, and that (to my eyes at least) should not
>>
yes at least) should not
>> affect whether the 6-membered ring is seen as aromatic.
>>
>>
>>
>> Regards,
>>
>> Mark.
>>
>>
>>
>> *From:* Paolo Tosco
>> *Sent:* 27 November 2020 17:04
>> *To:* Alexis Parenty
>> *Cc:
molecules
returning two different forms (kekule and aromatic)
Hi Alexis,
The second molecule (smiles2) is indeed aromatic, but the first (smiles1) is
not, as the imidazole ring condensed to the pyridine is partially saturated.
The smiles1a analogue where I have added a double bond is aromatic
er the 6-membered ring is seen as aromatic.
>
>
>
> Regards,
>
> Mark.
>
>
>
> *From:* Paolo Tosco
> *Sent:* 27 November 2020 17:04
> *To:* Alexis Parenty
> *Cc:* RDKit Discuss
> *Subject:* Re: [Rdkit-discuss] canonicalization of two aromatic molecules
5-membered ring was broken, and that (to my eyes at least) should not
> affect whether the 6-membered ring is seen as aromatic.
>
>
>
> Regards,
>
> Mark.
>
>
>
> *From:* Paolo Tosco
> *Sent:* 27 November 2020 17:04
> *To:* Alexis Parenty
> *Cc:* RDKit Discuss
> *
Hi Paolo,
Many thanks for your response. I suspected that the dihydro-imidazol ring
was involved in this behaviour.
Still can't get my head around this aromaticity behaviour, but I trust you!
It seems that the fused dihydro-imidazol is somehow "stealing" the
aromaticity of the pyridine ring...
Hi Alexis,
The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
is not, as the imidazole ring condensed to the pyridine is partially
saturated.
The smiles1a analogue where I have added a double bond is aromatic, and
upon canonicalization it yields an aromatic SMILES as
Hi everyone,
Why is it that when I canonicalize the following smiles_1 I get its
unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
get its expected aromatic form?
>From rdkit import Chem
smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
smiles
==> 'C1=CC2=NCCN2C=C1'
smiles2
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