Bob,
I think we still run into the cross domain security violation with the St
Olaf server.
One possibility is to offer Jmol users simple server side scripts. ISU has
certainly opened server side scripting for faculty. I suspect this may be
true at other institutions. I only have experience with Windows servers.
What would cover most bases if we went this route? Would Windows, Unix, and
Mac get the job done?
I don't think I can handle the Mac and Unix side of this, but I'd certainly
share my Resolver/PubChem ASP.NET script with anyone interested in this. If
there are any Mac server of Unix server people who would like to give this
a try, let me know, and I'll send you the script. The only condition is
that you don't laugh at my chaotic scripting style.
Another Point: After our discussion a few weeks ago when you pointed out
that Jmol script is completely synchronous, I've found that I no longer
need AJAX. Jmol Script is AJAX! Actually, It's better. You don't need to
keep saying, "Wait your turn." Every server touch waits patiently in a
normal Jmol script line for its turn - no complaining no whining. It's
great.
Some Continued Questions Related to Michael's Note:
1) Do you know if the applet running locally with a local file address is
subject to disk writing restrictions?
2) Ignoring item 1 above entirely for a minute, what Michael suggests might
be possible on a server. I'm effectively writing from Jmol to my server now
by using server side scripting to write Jmol state. I should be able to
write anything the Jmol puts into a string. That's half the battle.
Michael, do you know if VB (more importantly for applications VBA) can
read/write text to a Web server?
One Final Clarification:
When remote data comes into Jmol, I am no longer using AJAX - not for the
query or the returned data. I am, of course, using the above ASP.NET
script.
For a local database on my server, I am using AJAX. But this is only
because I must first create a JSON structure and use it in JavaScript prior
to Jmol coming into the picture.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Robert Hanson" <hans...@stolaf.edu>
Sent: Tuesday, March 15, 2011 7:30 AM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public
Databases
Speaking of public databases, this might be a time to test the facility
that has been in Jmol for quite some time -- the ability of the UNSIGNED
applet to access remote files via a JavaScript interface. I don't think
anyone has capitalized on this, but there is a St. Olaf server that is
built into Jmol.js.
<JavaScript_here>
jmolLoadAjax_STOLAF_RCSB
</JavaScript_here>
Could we adapt this, Otis, to get small molecules into any applet?
Bob
On Mon, Mar 14, 2011 at 10:39 PM, Otis Rothenberger <osrot...@chemagic.com>
wrote:
All-
Chemical Entities of Biological Interest (ChEBI) is dictionary of small
molecular entities. While it understands SMILES, it does not have Jmol's
ability to FIND SMILES. Nevertheless, one can query the dictionary with an
InChiKey. With the help of NIH/NCI Resolver, therefore, a Jmol model can be
used to directly query the dictionary:
http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='InChIKey=BSYNRY
MUTXBXSQ-UHFFFAOYSA-N'
with Resolver making the SMILES to InChiKey translation.
ChERBI is a user driven database that currently contains 18000 compounds. A
brief discussion of ChEBI is here:
http://precedings.nature.com/documents/3525/version/1
>From a teaching perspective, this attracted my attention because it is a
nice way to include bioinformatics into an instructional setting under the
Jmol umbrella. While there are query accessible molfiles available via
ChERBI, this is not the main point. Resolver and PubChem are much better
general sources. The main point is that with one click in Jmol make the
query, "Is the small molecule in my Jmol window of biological interest?" I
have not yet hooked the CheMagic model kit to this site, but I expect to do
so sometime this week.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
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St. Olaf College
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http://www.stolaf.edu/people/hansonr
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If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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