for the list: I commented on these on the github issue:
https://github.com/rdkit/rdkit/issues/2258
On Tue, Feb 12, 2019 at 6:36 PM Steven Kearnes <kear...@google.com> wrote:
> 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
>>>
>>
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