Otis,
The SMILES database has about 5000 compounds in it. I’m confused about how
JSmol works here. Would there be a JSmol drawing interface rather than JSME?
I guess I need to go read the Jmol documentation about how to get the SMILES
stuff working. Is there some automated process to get the Jmol versions of the
SMILES to update the database?
Jennifer
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://organicers.org
859-238-5413
fax 859-236-7925
On Jul 19, 2016, at 2:00 PM, Otis Rothenberger
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:
Jennifer,
For the most part, there is no cross application canonical SMILES. Daylight
never released the technical details to their reduction to canonical algorithm.
Consequently, uniqueness exists only within a given “copycat” application. I
believe PubChem uses Open Eye SMILES. If you were comparing Open Eye unique
SMILES to Open Eye unique SMILE, you could do a simple string comparison.
JSME is top notch in my opinion. I would not use any other online drawing
software, but with JSME, you cannot have canonical (unique) SMILES AND
stereochemistry. If you want simple string comparison, both SMILES (sever and
student drawn) will have to be JSME without E/Z and stereo chemistry. I’m
almost certain that this has not changed since the "old doc" in the previous
email. I think this means that you are going to have to use these explicit
options in server and client JSME SMILE creation: noquery (this is default),
noautoez, canonize (this is default), nostereo. I’d list all explicitly.
This probably not what you actually want, and that’s the absolute beauty of
what Bob created in JSmol! With Bob’s approach, the cross application unique
SMILES barriers do not matter. Bob took the expression “unique SMILES” and made
it obsolete!
To do this (include stereochemistry via Bob’s approach) you will also have to
make some options selections in JSME, but you will also be able to use E/Z and
stereochemistry.
How large is your SMILES database?
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org
On Jul 19, 2016, at 1:23 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
Otis,
The SMILES goes back to the MySQL database for comparison rather than just
running JavaScript within the browser. The stuff in the database was all
generated with JSME. (So I’m confused about how adding Jmol to the mix will
help.) The “canonical” SMILES generated by JSME sure doesn’t look like the
canonical SMILES provided in PubChem. But maybe I’m actually getting SMARTS?
I will go read the documentation you have pointed out.
Jennifer
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://organicers.org<http://organicers.org/>
859-238-5413
fax 859-236-7925
On Jul 18, 2016, at 10:56 PM, Otis Rothenberger
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:
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
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<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 18, 2016, at 4:22 PM, Otis Rothenberger
<osrot...@icloud.com<mailto: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
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<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 18, 2016, at 3:39 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto: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 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
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