Jennifer,
On your page, students make several choices to set up a problem. It appears
that each choice does a GET and reloads the page from sever with appropriate
page modification. How hard would it be to return the correct SMILES on each of
these GETS?
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jul 19, 2016, at 4:35 PM, Jennifer L. Muzyka <jennifer.muz...@centre.edu>
> wrote:
>
> Otis,
> Other information in the database includes: CAS RN, InChI, InChiKey, and
> ChemSpider ID. I’m aware that the different sources for SMILES is a
> potential issue, having already dealt with that. I’m also aware that
> compounds can have more than one CAS number and more than one ChemSpider ID
> even though I learned that CAS numbers were unique back when I was in
> college. An unfortunate reality is that I don’t have all of the keys for
> every compound. Another potential problem with the database is that I might
> not have removed all of the situations where a single compound appeared more
> than once. There are other things in the database (gifs, pdbs, jcamp
> spectra) for some compounds.
> Jennifer
>
>
>
>
>
>> On Jul 19, 2016, at 4:22 PM, Otis Rothenberger <osrot...@icloud.com> wrote:
>>
>> 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
>>>
>>>
>>>
>>>> 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
>
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