MOL files that represent molecules store kekule bond representations, not
aromatic bonds, so there is nothing to check.
First of all, if you are worried about aromaticity problems, you should use
the development version of Open Babel.
I wouldn't worry about the "-aa" option - it's only in the development
version and its main use is to speed up reading aromatic SMILES (by
avoiding subsequent aromaticity perception). It's better to use it only
when necessary.
The development version will always correctly kekulize the molecule; if it
fails to kekulize, that's an error in the input SMILES and it will produce
either an error or a warning (I'm still thinking about which is better
here).
Regarding testing correctness, a key test is whether a molecule written by
toolkit A will be read as the same molecule by toolkit B. Essentially this
boils down to the question of whether the aromatic SMILES generated by
toolkit A can be kekulized, and secondly, do all the atoms have the correct
number of hydrogens when read by toolkit B. I have done some work on
benchmarking the ability of different toolkits to read aromatic SMILES over
at https://github.com/nextmovesoftware/smilesreading.
Regards,
- Noel
On 4 December 2017 at 18:54, Sundar <jubilantsun...@gmail.com> wrote:
> 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-kek
>> ulization-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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>>
>
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