Mike,
Although it’s not in the Resolver docs, Resolver can do this (below). This is
all going to be dependent on CATVS aromatic SMILES rules. Notice that Oc1ccccc1
<https://cactus.nci.nih.gov/chemical/structure/Oc1ccccc1/aromatic> and
C1=CC=CC(O)=C1
<https://cactus.nci.nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic> are
both recognized as aromatic, consistent with another bit of old wisdom on the
Daylight site:
When should I specify a structure as aromatic?
You never need to do so. If you find yourself typing in SMILES, it's a bit
easier to type "c1ccccc1" for benzene instead of "C1=CC=CC=C1" cyclohexatriene,
but it's just a matter of convenience, since they mean exactly the same thing.
https://cactus.nci.nih.gov/chemical/structure/cyclohexane/aromatic
<https://cactus.nci.nih.gov/chemical/structure/cyclohexane/aromatic> NO
https://cactus.nci.nih.gov/chemical/structure/phenol/aromatic
<https://cactus.nci.nih.gov/chemical/structure/phenol/aromatic> YES
https://cactus.nci.nih.gov/chemical/structure/Oc1ccccc1/aromatic
<https://cactus.nci.nih.gov/chemical/structure/Oc1ccccc1/aromatic> YES
https://cactus.nci.nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic
<https://cactus.nci.nih.gov/chemical/structure/C1=CC=CC(O)=C1/aromatic> YES
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On May 16, 2016, at 1:49 PM, Otis Rothenberger <osrot...@icloud.com> wrote:
>
> Mike,
>
> The idea of “intelligent” feedback is intriguing. We played around with this
> concept in a large section at ISU years ago. It was fun, but frustrating! I
> don’t know if Bob can do what you ask with Jmol SMILES or not. For my part, I
> learned two things form this email chain:
>
> 1) It forced me to look at Bob’s SMILES/SMARTS docs, and I now understand why
> cyclopentadienone is aromatic - or not depending on the Jmol SMILES setting!
>
> 2) I also learned that Daylight had a sense on humor on the subject at hand.
> From their docs:
>
> QUOTE
> What does "aromatic" mean, anyway?
>
> "Aromatic" means "it smells nice". No kidding, that's the only defensible
> definition. There is no single rigorous definition of aromaticity in
> chemistry. To a synthetic chemist, aromaticity implies something about
> reactivity; to a thermodynamicist, about heat of formation; to a
> spectroscopist, about NMR ring current; to a molecular modeler, about
> geometrical planarity; to a cosmetic chemist, it probably means "smells
> nice". The SMILES definition of aromaticity has nothing to do with the other
> definitions, except that we'd all agree that benzene is "aromatic".
> END QUOTE
>
> In a 2007 blog, Rich Apodaca (ChemWriter Application) took a look at the
> history of SMILES and aromaticity. It’s an interesting read:
>
> http://depth-first.com/articles/2007/11/28/smiles-and-aromaticity-broken/
> <http://depth-first.com/articles/2007/11/28/smiles-and-aromaticity-broken/>
>
> Otis
>
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