Thanks; here's a couple more (not related to aromaticity):
[H]=N(C)C
[H]#N(C)C
On Sat, Feb 9, 2019 at 7:53 AM Greg Landrum <greg.land...@gmail.com> wrote:
> Yeah, I'm also a bit surprised by this.
> I need to investigate a bit, but I guess that it's an unexpected
> interaction between a couple different pieces of code connected with
> valence detection and aromaticity perception.
> Here's a bit of support for that:
>
> In [11]: m2 = Chem.MolFromSmiles('C#n1ccnc1')
>
>
> In [12]: Chem.Kekulize(m2,clearAromaticFlags=True)
>
>
> In [14]: m2.UpdatePropertyCache()
>
> [16:52:39] Explicit valence for atom # 1 N, 5, is greater than permitted
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)
> <ipython-input-14-504441a3d62f> in <module>
> ----> 1 m2.UpdatePropertyCache()
>
> ValueError: Sanitization error: Explicit valence for atom # 1 N, 5, is
> greater than permitted
>
>
> Thanks for reporting the problem!
>
> On Sat, Feb 9, 2019 at 2:59 AM Steven Kearnes via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
>> I thought more about this as I was driving home. AFAICT neither of these
>> structures obeys Huckel's rule. Also, I noticed that both nitrogens have
>> GetTotalValence() == 3, which really seems odd.
>>
>> On Fri, Feb 8, 2019 at 5:03 PM Steven Kearnes <kear...@google.com> wrote:
>>
>>> C=n1ccnc1
>>> C#n1ccnc1
>>>
>>> I get that the extracyclic bonds contribute pi systems that enable
>>> aromaticity, but I don't know why the nitrogens don't have formal charges
>>> in the resulting Mol object. Note that only the first molecule matches
>>> anything in PubChem
>>> <https://pubchem.ncbi.nlm.nih.gov/compound/91511624#section=Top>, and
>>> it has a formal charge there.
>>>
>>> Thanks,
>>> Steve
>>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
