Jennifer,
The default is that JSME keeps explicit hydrogens to carbon, and these will
show up in brackets. An option can be used to turn this off.
It sounds like you have a mix of SMILES that may have been created by options
variations in the JSME implementations being used. That's a problem.
One more question, and then I'll do some more thinking. What other items or
keys are in the database?
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jul 19, 2016, at 4:01 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu>
> wrote:
>
> Otis,
> 1200 of the compounds have SMILES that agree with the JSME version. Those
> were generated by a buddy of mine. Then when I found some disagreed, I went
> through them one by one to fix the ones that disagree.
>
> The next 3800 came from some other source than JSME when one of my students
> imported the compounds into the database. Most of those are not involved in
> reactions so those compounds might not be relevant. I anticipate that I
> would change them one by one if needed so that they agree with JSME. None of
> those have SMILES that look like the stuff with brackets and H’s that JSME
> produces. They tend to use the slashes to indicate double bond
> stereochemistry and @ to indicate chirality at stereocenters. (People who
> are more proficient programmers than I am could probably complete the task
> more rapidly by automating it.)
>
> Now I’m adding new reactions to accompany the question type where students
> draw the starting material rather than the product, I’m adding new compounds
> one by one. I’m getting the SMILES for each of those compounds from the JSME
> 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 3:51 PM, Otis Rothenberger <osrot...@icloud.com> wrote:
>>
>> 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
>>>
>>>
>>>
>>>
>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> 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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