Oh, by the way, you could also set Jmol up on the server end, I think, and
have that functionality on all the mobile devices that ChemDoodle is
planning to be on, just using Jmol as the back end instead of the ChemDoodle
server, and having all the added flexibility of all the interesting things
that Jmol can do. You just have to have your server responding to those
server calls appropriately. I don't know if they've exposed that protocol,
but it would be relatively easy to determine. You could use standard JQuery
connections, either using XHR5 or JSON-P (for older browsers) to make the
connection. If anyone has a server and would like to try this, do let me
know. I'd like to learn how that works.
Bob
On Tue, Jul 26, 2011 at 2:43 AM, Robert Hanson <[email protected]> wrote:
> Sure, that should be easy. I'd like to have an example of that to show
> people.
>
> The WebGL widget can sketch in 3D, but not without the server. To be
> clear: The primary selling point of ChemDoodle 3D is that it works under
> HTML5 and WebGL, components that will soon be available on mobile devices
> and most web browsers. (Right now it is limited to a few cutting-edge
> browsers such as Chrome and Firefox 4, and some Mac browsers, but that is
> expected to improve.) The web-based JavaScript is limited to just the basic
> functionality -- rotating a model, changing its appearance some, that sort
> of thing. The server is called for these services:
>
> contactServer("optimize"...
> contactServer("readSMILES"...
> contactServer("writeSMILES"...
> contactServer("saveFile"...
> contactServer("getMoleculeFromDatabase"...
> contactServer("getOptimizedPDBStructure"...
> contactServer("calculate"...
> contactServer("simulateNMR"...
> contactServer("simulateNMR"...
> contactServer("simulateMassParentPeak"...
>
> Of those, Jmol could do optimizing, reading and writing of SMILES strings,
> saving the file (if it's the signed applet), getting a molecule from the NCI
> or PDB database, and at least adding hydrogens to a PDB structure. The other
> features are more sophisticated and not accessible via Jmol.
>
> For the optimization, you could go with Jmol's load with the 2D->3D
> conversion, but I think a better option would be to have Jmol create the
> SMILES string and just end it to NCI, where they have a better 2D to 3D
> conversion. That's certainly easy enough to do.
>
> For the Jmol 2D->3D conversion, there should be no problem using a
> page-based Jmol instead of the iChemLabs server for 2D to 3D conversion. You
> just write a bit of JavaScript that looks like this:
>
> jmolScript("load DATA \"model\"\n" +
> ChemDoodle.writeMolFileOrSomethingLikeThat() + "\nend \"model\" filter
> '2D'")
>
> I'm not clear on what that ChemDoodle call is to get the mol file, but it
> should be easy.
>
> For the NCI conversion, it would look something like this:
>
> jmolScript("load DATA \"model\"\n" +
> ChemDoodle.writeMolFileOrSomethingLikeThat() + "\nend \"model\" filter
> '2D';load SMILES @{{*}.find('smiles')}")
>
> This just says (1) load the ChemDoodle sketch into Jmol as a 2D structure
> (doing at least a rough minimization); get it's SMILES string, and pass that
> to NCI, loading that structure instead. In pure JmolScript it would look
> like this:
>
> load Data "model"
> string
> __Jmol-12_06161113223D 1 1.00000 0.00000 0
> http://www.ichemlabs.com
> 5 4 0 0 0 0 999 v2000
> -0.8660 -1.0000 0.0000 C 0 0 0 0 0 0
> -0.0000 -0.5000 0.0000 C 0 0 0 0 0 0
> 0.8660 -1.0000 0.0000 C 0 0 0 0 0 0
> -0.0000 0.5000 0.0000 C 0 0 0 0 0 0
> 0.8660 1.0000 0.0000 C 0 0 0 0 0 0
> 1 2 1 0 0 0
> 2 3 1 0 0 0
> 2 4 1 0 0 0
> 4 5 1 0 0 0
> M END
> end "model" filter "2D";load SMILES @{{*}.find('smiles')}
>
>
> Again, for that you need the signed applet. Or, actually you don't, because
> your page will have JQuery on it, and that can do cross-browser server
> calls, as can (Jmol.js by itself, for that matter). But the signed applet is
> better.
>
> So adding Jmol to a page with ChemDoodle is pretty close to trivial but a
> BIT TWISTED. Jmol requires Java; ChemDoodle is hoping to be the solution for
> the cloud-computing "post-Java" era. It's a bit strange.
>
>
> Bob
>
>
>
>
>
> --
> 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
>
--
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
------------------------------------------------------------------------------
Magic Quadrant for Content-Aware Data Loss Prevention
Research study explores the data loss prevention market. Includes in-depth
analysis on the changes within the DLP market, and the criteria used to
evaluate the strengths and weaknesses of these DLP solutions.
http://www.accelacomm.com/jaw/sfnl/114/51385063/
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