On Mon, Apr 2, 2012 at 12:35 PM, Kevin Theisen <ke...@ichemlabs.com> wrote:
> I think these are all good points. In order to create a Jmol app for
> iPads, one would need to completely port the project to Objective-C, no
> easy task. To publish in Apple's App Store also costs money (99$/year), is
> very, very complicated and requires constant attention. And regardless of
> whether such an app would exist, Jmol authors would still need to
> "recreate" their content to work in these apps; the applets on their
> websites would still not work. So we are focusing on HTML5/WebGL as the
> solution.
>
> Most of the performance issues with the ChemDoodle Web Components and
> large proteins have been addressed, and the toolkit should never crash when
> parsing any sized PDB file at this point. However, when using the backend
> services, a PDB file may take a while to parse, and our Apache server
> automatically terminates connections after 60 seconds, resulting in an
> error. This is due to the fact that our Java backend is based on the
> ChemDoodle desktop API, and therefore has overhead for working with the GUI
> and for creating 2D graphics. We are currently in the process of separating
> this logic out, so that really intensive functions become much more
> efficient.
>
> I should note that our graphics are not limited to just proteins, the
> ChemDoodle Web Components library handles small molecules, macromolecules,
> crystals, spectra, and 2D as well as 3D (MOL/PDB/CIF/JCAMP/XYZ). We are
> also working on surfaces (an experimental API is already included). Maybe
> this is a good time to really push for an integration of Jmol functionality
> on our backend though. We are still working on an efficient marching cubes
> algorithm in Javascript, and until that is complete, we could use Jmol
> instead. We would just need to know how to call it and export the necessary
> information. I think with your help, Bob, we could have this in a few days.
>
Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if
you want something like that, use JmolData.jar. That's headless and can run
any script not involving image creation or font use. So creation of
isosurfaces is fine. Jmol's marching cubes algorithm is highly efficient,
now processing just about everything "progressively" meaning as a data
stream, never actually creating a huge cube of data. It's possible
exporting it as some other format would work.
Kevin, could you tell us about some of your ideas for scriptability of
ChemDoodle? I'm sure that's come a long way since I talked with you last.
--
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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