Jennifer,
On the student side, Jmol and JSME would be working together. This is no big
deal - very easy. The problem is server side.
Let me think about this. Some important points: Do your existing database
SMILES have stereo chemistry - i.e. / \ and @ notation where appropriate? Are
they all JSME SMILES? Is there a possibility that the database creators may
have drawn explicit hydrogens on carbon in non-stereo contect?
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jul 19, 2016, at 3:37 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu>
> wrote:
>
> 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
> 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> 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
>> http://chemagic.org
>>
>>> On Jul 19, 2016, at 1:23 PM, Jennifer L. Muzyka
>>> <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
>>> http://web.centre.edu/muzyka
>>> http://organicers.org
>>>
>>> 859-238-5413
>>> fax 859-236-7925
>>>
>>>
>>>
>>>
>>>
>>>
>>>> On Jul 18, 2016, at 10:56 PM, Otis Rothenberger <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
>>>> 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
>>>>>
>>>>> 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 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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