Thanks, Mike. Your explanation finally helps me understand why Otis is so
focused on having Jmol do the comparisons rather than going back to the
database. I didn’t get that until now. The potential complication for me is
that I’m hoping to eventually implement these questions in a graded homework
system. I realize that students are resourceful and having the SMILES in the
page’s JavaScript would make it possible (not actually easy) for students to
cheat. So I’m reluctant to have the SMILES in the page. Is there a way to do
the Jmol SMILES comparison on the server side?
Jennifer
On Jul 20, 2016, at 7:09 AM, Mike Casey
<mike.ca...@ucd.ie<mailto:mike.ca...@ucd.ie>> wrote:
Hi Jennifer & Otis,
I'm a relatively inexperienced programmer so please treat the following with
caution. However, FWIW, I use the approach that Otis is recommending (if I
understand him correctly). Users make selections, ajax is used once to
retrieve all the data relevant to a problem of the appropriate type from a
database (as a JSON object that is easy to work with in Javascript). The
structures drawn by the user in JSME are then checked by comparison of the user
SMILES from JSME against the correct SMILES, retrieved from the database with
the other problem data, using Jmol (which is in a hidden div on the page. As
Otis says, Jmol matches different SMILES strings from different sources as long
as the structures are the same. My site is not in the wild yet (it is a major
upgrade of http://www.ucd.ie/chem/chemint/), but I would be happy to send the
code to you if that would be helpful.
Mike
Dr Mike Casey
School of Chemistry
UCD
Dublin
01 716 2420
On 20 July 2016 at 01:58, Otis Rothenberger
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:
Jennifer,
The student SMILES and the answer SMILES need to be compared on the client
(browser) side via JavaScript. The student answer SMILES is already on the
client side. All we would need is the answer SMILES there also.
Having said this, I know that Bob H once mentioned running the Java app on the
server to do server side tasks, but running the Java app on the server is way
beyond my programming skills.
With the power of modern JavaScript and HTML5, I’m not sure I see why the
computer jocks are more comfortable with a second hit on the server. The fact
is that the server cannot do the SMILES comparison as elegantly as Bob’s JSmol
SMILES comparison, that is unless the Jmol Java App is run on the server. With
the client side JavaScript/HTML5 power, it seems to me going back to the server
is just going back to the server in order to go back to the server!
All of this, of course, is dependent on getting the answer SMILES into the
working webpage.
Whichever route you go, that still leaves you with a database with some SMILES
issues. Here’s a suggestion: How soon is Bob B’s cheminformatics course going
into action again? Reconstructing your database entirely from Resolver (maybe
PubChem) by an automated process would be a great real world project for one of
the student teams. ( cc to Bob B)
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016, at 8:22 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
Otis,
What you are describing is essentially how I handle the code for the page where
students draw the product structure. It's certainly doable for the starting
material structure as well. I would just need to work out the different query
and JavaScript. My computer science colleagues would probably consider that
the brute force method, unlike the more elegant Ajax method that goes back and
queries the database a second time. Is there some advantage to keeping all of
the code within the page rather than going back to the database? Those use PHP
and MySQL.
Jennifer
Sent from my iPad
On Jul 19, 2016, at 6:00 PM, Otis Rothenberger
<osrot...@icloud.com<mailto:osrot...@icloud.com>> wrote:
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<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016, at 4:35 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto: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<mailto: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<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016, at 4:01 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto: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<mailto: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<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016, at 3:37 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto: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<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<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
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
