Re: [Open Babel] Aromaticity

[Craig A. J. <cj...@em...>]

Geoffrey Hutchison wrote:
> What you're saying is that this Kekule SMILES when used as a SMARTS  
> doesn't match. That's fair enough -- that the SMARTS should be  
> transformed.
> 
> I'll file this as a bug.
> 
> Thanks
> -Geoff
> 
> 
>>>> OC1=C2C=CC(=C)N=C2CCC1
>>> Sure. Take a look at Daylight Depict:
>>> http://www.daylight.com/daycgi/depict?4f43313d4332433d4343283d43294e3d433243434331
>>>
>>> The two SMILES have the same depiction (i.e., the ring is  
>>> aromatic). In
>>> SMILES, an exocyclic double bond does not break aromaticity.
>> Well, OK.
>> But if I want to search OC1=C2C=CC(=C)N=C2CCC1 with obgrep in my
>> library, it doesn't match. I must use the aromatic notation.
>> I wonder if perhaps obgrep could run the "SMILES aromaticity detection
>> algorithm" on the smiles/smarts string before searching matching
>> molecules? (Just like the searched library, which contains
>> OC1=C2C=CC(=C)N=C2CCC1 substructures, is converted to aromatic).

This is not a bug, it's just the way SMARTS is defined.  A SMARTS that uses a Kekule form will never match anything; you have to use the aromatic form.

Some applications will try to parse a SMARTS as a SMILES, and if it works, convert it to the aromatic form and re-parse it as a SMARTS.  But that's often impossible, for example, what do you do with "C1=[N,C]C=CC=C1"?  Better to require the user to type in "c1[n,c]cccc1", which is clear.

Craig