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
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On May 16, 2016, at 6:34 AM, Mike Casey <mike.ca...@ucd.ie> wrote:
>
> Hi Bob,
>
> Sorry, my question was not clear. It arose form the perspective of providing
> feedback to a learner who was being tested on his/her understanding of the
> concept of aromaticity. E.g. a learner could be asked to draw any aromatic
> structure, or a bicyclic aromatic structure, or a five-membered ring that was
> aromatic, etc. Jmol could then be used to analyse the SMILES of the
> learner-drawn structure and 'intelligent' feedback could be provided that
> identified if the answer was correct, or, if not, why the answer was
> incorrect. I suspect that most Jmol users are interested in a Yes/No answer
> to the detection of aromaticity, but it would be very nice to leverage your
> existing algorithm to provide a little more information that would be helpful
> in educational contexts.
>
> From one of your earlier postings I assumed that your algorithm for detecting
> 'strict' aromaticity must be checking the supplied structure against a set of
> criteria (cyclic, uninterrupted pi system, planar, 4n + 2 electrons), so that
> it might be possible for the algorithm (optionally) to return 'flags' (meets,
> or does not meet, each criterion) that could then be used to generate the
> appropriate feedback to the learner. I have now read your pdf on how the
> Jmol SMILES aromaticity algorithm works and, broadly speaking, it does seem
> to function in that manner. So, following the steps listed in your pdf
> document, and thinking particularly about the STRICT directive, would it be
> possible to create an option for the function to return a set of diagnostics,
> as follows?
>
> 1. Criterion 1: Does the structure contain at least one ring?
> 2.a., 2.c. (and 4.?) Criterion 2: Does the structure contain a ring(set) in
> which all the ring atoms are involved in the pi system? (I'm not sure what
> kinds of structures the algorithm is seeking to exclude in Step 4, but I
> think it relates to Criterion 2.)
> 2.b. & 3. Criterion 3: Does the structure contain a ring(set) that meets
> Criterion 2, and is planar?
> 2.c. & 3. Criterion 4: Does the structure contain a ring(set) that meets
> Criteria 2 & 3, and involves 4n+2 electrons, or 4n electrons?
>
> I haven't studied the Jmol code, so I may be mistaken about parts of the
> algorithm, but I hope the general idea is clear. In much the same way as the
> algorithm already assigns each ring a value of -1, 1 or 2, could a more
> comprehensive set of flags be returned for the whole structure? By extending
> the existing algorithm in this way, correct answers could be identified, as
> now, but errors could be diagnosed and more detailed feedback provided for
> incorrect responses.
>
>
> Many thanks for all your work Bob. I'm pleased to read that you are
> preparing a paper on the SMILES and SMARTS functionality of Jmol; those
> powerful capabilities are great and are not available in any other open
> resource, as far as I know, so they deserve to be fully reported.
>
> Mike
>
>
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