> 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.
Exporting it to a format is not necessary. We just need to send Jmol atoms, and
then extract the vertices, normals and mesh connectivity of the surface. That
information will be ajaxed down as JSON, and immediately rendered. Is this
possible?
>
> 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.
I'm sure we will butt heads again on this, but this is a fundamental difference
between Jmol and ChemDoodle. Jmol's scripting system is necessary because
authors cannot manipulate Java at runtime, and therefore would have no way to
programmatically interact with Jmol. The ChemDoodle Web Components library is
pure Javascript, and can be manipulated in any way, at any time, including
runtime. So a script for the ChemDoodle Web Components is not necessary, but
that does not mean an author can't achieve the same behavior in both
environments.
For instance, a Jmol script call would look like this:
jmol.runScript('actionA actionB');
While a ChemDoodle script would look like this:
component.actionA();
component.actionB();
It is actually more powerful in Javascript, because any aspect of the
functionality may be tweaked this way (for instance, we can rename classes,
create subclasses, add in our own functions), and does not require an explicit
script language to be developed. Maybe the more pressing issue is the reuse of
all the Jmol scripts. And maybe this is worth investigating, a Jmol script
parser for ChemDoodle that will do the same actions. Does this make sense?
-Kevin
On Apr 2, 2012, at 2:31 PM, Robert Hanson wrote:
>
>
> 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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