Michael,
OK, you definitely have my attention. Communication between Jmol and local
applications is a great idea. I have a few questions:
1) Are you doing this with the applet or the application?
2) It sounds like you are currently "talking" to Jmol with your VB code
independent of traditional applications - e.g. Excel, Word, etc. Is that
correct?
3) Have you attempted to do this with an application, say Excel, using
VBA?
>From Jmol's perspective, I think I understand why the file has to be
written, but I don't see that as a big problem. I have a few other
questions, but they are in the context of a reply to Bob's note. I think
I'll post them in another email to this chain.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Michael Marden" <michael.mar...@inserm.fr>
Sent: Tuesday, March 15, 2011 11:05 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public
Databases
Two items concerning communication with Jmol caught my attention.
this one (Continuing Saga of Jmol Talking to Public Databases)
and "Command line communication with the Jmol application?"
I'm not sure if it is really relevant to the method that I'm using.
I'm using visual basic (VB) as a front end, and Jmol shows up within
a browser (within a VB window).
So I can do all my set-up, calculations etc, and then send commands
to Jmol
Bob Hansen helped me set this up, using the Jmol.js and
JmolApplet.jar files.
The VB program writes a text file to disk that contains the
command. Jmol is waiting and reads it back.
So essentially I continuously pump commands to modify the molecule
being presented.
I would prefer a way to avoid the round to the hard disk, but it
seems to work well.
As Jmol is now mature, it would be good to consider communication
with other programs.
Michael Marden
INSERM, University Paris 11, France
On 15/03/2011 12:30, Robert Hanson wrote:
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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If nature does not answer first what we want,
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