Here's a detail about Daylight's aromaticity detection that you might not
be able to deduce by looking at results. (This is not a trade secret; Dave
described this in public at several MUG meetings.)
1. Read the SMILES, SDF, or other format into an object.
2. Deduce the orbital configuration of EVERY atom (1s, 2s, 2p, sp, sp2,
etc.).
3. Discard all bond information. (I.e. completely ignore the original bond
specifications.)
4. Recalculate the electron assignments (single, double, triple, quadruple)
from the atoms' orbitals.
5. Detect aromaticity using the "extended Huckle's rule" (the details of
which were never published to my knowledge).
Craig
On Mon, Dec 4, 2017 at 5:18 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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>
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--
---------------------------------
Craig A. James
Chief Technology Officer
eMolecules, Inc.
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