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 <
[email protected]> 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 <[email protected]> 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
>>
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