Jennifer,
I knew this statement was out there. It took me a while to find the Web doc:
"public String JME.smiles()
returns a SMILES string of the current molecule(s) or reaction. For single
molecule without stereochemistry the SMILES is unique, unification is not yet
implemented for molecules with stereochemistry and for reactions.”
http://www.molinspiration.com/jme/doc/jme_functions.html
<http://www.molinspiration.com/jme/doc/jme_functions.html>
It’s an old doc, but I’m sure it still applies.
Since canonize is the default in JSME, you’re going to have to select
nocanonize!
Also, your current option setting sets the “query” option. That sets up SMARTS
mode. I don’t think that is what you want?
Although it’s commented out in your current HTML, it looks like you are set of
for a simple string comparison. That’s not going to work. This is where Bob’s
JSmol .find approach comes into play - my previous email.
I’ve been using a Jmol/JSME SMILES comparison for quite a while, so don’t
hesitate to ask if you need more specific information.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jul 18, 2016, at 4:22 PM, Otis Rothenberger <osrot...@icloud.com> wrote:
>
> 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
> <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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