Jennifer,
You have to set SMILES settings in the JSME options part of your JSME set-up to
invoke stereochemistry and E/Z. This page explains all of the options and the
set up procedure:
http://peter-ertl.com/jsme/JSME_2015-06-14/doc.html
BUT, BUT, it looks like you are doing SMILES comparisons, and with
stereochemistry and E/Z invoked, I’m pretty sure JSME SMILES are not unique.
The best way to compare SMILES is with JSmol. In the case of your page, you
could hide JSmol on the page. Comparison can be done in JavaScript:
function compSmiles(key, ans) {
key = key.replace(/\\/g, '\\\\');
ans = ans.replace(/\\/g, '\\\\');
return Jmol.evaluateVar(jmolApplet0. "'" + key + "'.find('SMILES','" +
ans + "') > 0");
}
My quotes above are hard to read, so here’s the function with spaces to
emphasis the quotes:
function compSmiles(key, ans) {
key = key.replace(/\\/g, ' \\\\ ');
ans = ans.replace(/\\/g, ' \\\\ ');
return Jmol.evaluateVar(jmolApplet0. " ' " + key + " '.find('SMILES','
" + ans + " ') > 0");
}
The replace statements above are needed to place the SMILES \ notation into a
JavaScript string - i.e. correct the fact that \ in a character escape in
JavaScript.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jul 18, 2016, at 3:39 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu>
> wrote:
>
> I’m not sure if this listserv is the proper place for me to ask this
> question, but I’m not sure where else to ask. I’m using the JSME embedded
> within Jmol/JSmol to let students practice reaction questions where they can
> draw products. The ability to draw starting materials is currently in
> development. My problem is that JSME generates some quirky SMILES strings.
> Cis and trans-3-hexene both generate [H]C(CC)=C([H])CC, so it’s not possible
> to distinguish the stereoisomers. If I don’t draw in the stereochemistry
> explicitly, I get the canonical SMILES. (If you’d like to see the page in
> development, feel free to check it out
> athttp://chemserv.centre.edu/muzyka/reactionzoo/jsmol/jsme/JSMEreaction17.php
> <http://chemserv.centre.edu/muzyka/reactionzoo/jsmol/jsme/JSMEreaction17.php>)
>
> The documentation for JSME says it generates canonical SMILES, but I haven’t
> seen any other SMILES that use the brackets with the H atoms.
>
> If you guys can point me to an alternate location to ask this question, I’d
> appreciate it.
> Thanks
>
>
>
>
> Jennifer Muzyka
> H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY 40422
>
> jennifer.muz...@centre.edu <mailto:jennifer.muz...@centre.edu>
> http://web.centre.edu/muzyka <http://web.centre.edu/muzyka>
> http://organicers.org <http://organicers.org/>
>
> 859-238-5413
> fax 859-236-7925
>
>
>
>
>
>
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