I usually convert SMILES to SDF.
In my current project, I didn't call the flag -aa. Would that have affected
the aromaticity of the compounds or the default attempt would have worked?
I didn't see any warnings about failing attempts to fix the aromaticity.
What's the general rule of thumb here? Do you recommend any means to check
the correctness of aromaticity after the conversion?
Thanks,
Sundar
On Mon, Dec 4, 2017 at 7:18 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> HI Jubilant,
>
> The development version has rewritten handling of aromaticity, and as this
> will be the next release, I will focus on this. The following talk gives an
> overview of the process:
> https://baoilleach.blogspot.co.uk/2017/08/my-acs-talk-on-
> kekulization-and.html
>
> Your question didn't mention what conversion you are doing. When reading
> aromatic SMILES, we attempt to kekulize the aromatic bonds provided. If
> this is not possible, we don't fix it (which is not possible in the general
> case) - but instead produce a warning.
>
> When writing aromatic SMILES, we perceive aromaticity by default using the
> Daylight model described in the talk (to be exact, it's an extension of
> Daylight). If instead, you would like to use the aromaticity as present in
> the input SMILES, you can specify "-aa" when reading.
>
> Regards,
> - Noel
>
> On 1 December 2017 at 06:38, Sundar <jubilantsun...@gmail.com> wrote:
>
>> Hi all,
>>
>> I was looking for a documentation for how openbabel works on detecting
>> aromaticity and what is the flag to choose while converting molecules. Does
>> obabel detect and fix aromaticity by default? If yes, what are the default
>> options and what other options are available?
>>
>> Please, direct me to the documentation page.
>>
>> Thanks,
>> Jubilant
>>
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