>
> I was thinking that some simple format like
>
> write xxx.vrml
Thanks, I'll look into the Java API later today. Basically, I would like to
call it via Java rather than the script. I will definitely have some questions
for you, I'll send them offline.
>
> ? Those are pretty simple operations, of course. But I think they are
> representative of what I'm talking about. Are there any web pages out there
> using ChemDoodle that have simple scripting like this?
I think we are saying the same thing. We don't have as many convenience actions
as Jmol has, but we will be able to improve upon that as development continues.
See the following pages for more information on manipulating the ChemDoodle Web
Components:
http://web.chemdoodle.com/tutorial
http://web.chemdoodle.com/tutorial/input-events
http://web.chemdoodle.com/tutorial/animations
http://web.chemdoodle.com/tutorial/advanced/visual-specifications
http://web.chemdoodle.com/tutorial/advanced/working-with-pdb-files
-Kevin
On Apr 2, 2012, at 7:59 PM, Robert Hanson wrote:
>
>
> On Mon, Apr 2, 2012 at 3:20 PM, Kevin Theisen <ke...@ichemlabs.com> wrote:
>> 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?
>
>
> I was thinking that some simple format like
>
> write xxx.vrml
>
> This is a very simple format that I would think would be easily parsed by
> your JavaScript. It includes vertices, normals, and faces.
>
> Transform{children Transform{translation .449 -.189 .065
> children [
> Shape {
> appearance DEF _0 Appearance{material Material{diffuseColor 1 .648 0
> transparency 0}} geometry IndexedFaceSet {
> coord Coordinate {
> point [
> 4.262 1.094 .447
> 4.262 1.068 .484
> 4.275 1.068 .447
> 4.262 1.2 .191
> 4.338 1.068 .191
> ...
> -5.071 -1.439 .702
> -5.087 -1.439 .447
> -5.033 -1.439 .191
> ]
> }
> coordIndex [
> 2 0 1 -1
> 3 0 4 -1
> 4 0 2 -1
> ...
> 3988 4019 3990 -1
> 3990 4019 3982 -1
> ]
> solid FALSE
> normalPerVertex TRUE
> normal Normal {
> vector [
> .836 .456 .305
> .836 .539 .101
> .889 .43 .154
> ...
> 3150 3127 3125 -1
> 3125 3127 3127 -1
> 3127 3127 3119 -1
> ]
> }
> }
>
>
>
>
>>
>> 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.
>
>
> Ah, well, actually web developers have full access to the Viewer class, so
> they can do anything with it they want, if they chose to. However, they would
> never choose to.
>
> > Does this make sense?
>
> No, sorry, it still doesn't! :) I think I just need a "for instance":
>
> I have a page with a ChemDoodle version of caffeine.
>
> What do I do in ChemDoodle that would be equivalent to this in Jmol:
>
> select {carbon}; color red
>
> or
>
> rotate x 30
>
> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do
> this?
>
> select *; wireframe only
> select {helix}; cartoons only
>
> ? Those are pretty simple operations, of course. But I think they are
> representative of what I'm talking about. Are there any web pages out there
> using ChemDoodle that have simple scripting like this?
>
>
> Bob
>
>
> -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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>
>
> --
> 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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