sorry -- crossed threads.
Sure, from the app, you should be able to just do something like this:
load $someChemicalName
like
load $cholesterol
or a SMILES string:
load $CCC(C)CCO
On Fri, Mar 18, 2011 at 11:38 AM, Charles Harrison Shubert <cshub...@mit.edu
> wrote:
> Hi Bob,
>
> Is there a way I can access this type of JavaScript functionality from my
> Java app that embeds Jmol and talks to it through the JmolViewer?
>
> JmolViewer jmolViewer = JmolViewer.allocateViewer(this,
> newSmarterJmolAdapter(),
> null, null, null, null, null);
>
> Thanks,
>
> --Chuck
>
> On Mar 15, 2011, at 3:54 PM, Robert Hanson wrote:
>
> So, Otis, what I am wondering about is whether you would allow us to add
>
> jmolLoadAjax_STOLAF_NIH
>
> to Jmol.js. It would allow any applet (or knowledgeable user on any
> applet's page) to load any of the NIH models into Jmol directly, without
> need for the signed applet. You can try this yourself for the PDB. Just go
> to any page on the web that uses Jmol and a relatively recent (3 years?)
> version of Jmol.js, and enter on the URL line:
>
> javascript:void(jmolLoadAjax_STOLAF_RCSB())
>
> As I said, this hasn't been tested much with recent browsers.
>
> Bob
>
>
> On Tue, Mar 15, 2011 at 6:30 AM, Robert Hanson <hans...@stolaf.edu> 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=BSYNRYMUTXBXSQ-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
>>>
>>> ------------------------------------------------------------------------------
>>> Colocation vs. Managed Hosting
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>>> for your organization - today and in the future.
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>>> _______________________________________________
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: <507-786-3107> <507-786-3107>507-786-3107
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: <507-786-3107>507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> <ATT00001..c><ATT00002..c>
>
>
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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