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 at
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
[email protected]<mailto:[email protected]>
http://web.centre.edu/muzyka
http://organicers.org
859-238-5413
fax 859-236-7925
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