[Kalzium] [Avogadro-devel] gsoc summer project, animation in Kalzium, call for feedback

[Benoît Jacob]

Hi Naomi,

it is a great idea to have written to these lists.

I can't really comment on the specific ideas that you're proposing below, as I 
am no chemist (have mostly been working on 3D-geomtrical and OpenGL aspects, 
and on the Eigen library).

But I'd like to make a few general comments:

It is fully expected that the end result of any SoC will be different from its 
initial plan. It is natural that your goals evolve as the project itself 
evolves, even Google's mentor forms say that. Therefore, it is not so 
important for you to collect a lot of feedback on your initial goals list 
before you start coding. In fact, until you send code, I don't think that 
anybody else can get a precise enough idea of where you're going, to be able 
to give good feedback. So what's much more important is that while you are 
coding, you discuss and interact very frequently with other avogadro people, 
so you evolve in real-time with the rest of the project. Concretely, that 
means that once you've coded something you send a patch to this list, and 
then indeed you can expect much more feedback. Of course if it doesn't break 
things you can commit right away to svn and then ask for feedback.

You can perfectly do things in avogadro that were not at all part of your 
initial plan, and expect this to be taken into account when evaluating your 
SoC's success. This happened with Marcus, he quickly started contributing 
things that were not at all part of his initial SoC plan, and of course I 
took this into account when evaluating his SoC (Google's forms encouraged me 
to, btw). So if you find an annoying bug and fix it, that's great, everybody 
will be thankful. Just make sure to keep a record of things you did, although 
svn itself will remember that. Likewise don't hesitate to participate in any 
discussions on this list.

One last thing, if you like IRC, there are #avogadro and #kalzium on Freenode, 
where these days you'll frequently see Marcus, Carsten, Tim, Jordan among 
others. I will be away for most of the 3 next weeks. Of course IRC is not at 
all mandatory, e.g. Geoff and Donald seldom connect these days, but if you 
hang around you'll see a lot of opportunities to get better insight into the 
project and see what's in the air.

Cheers,
Benoit

On Friday 16 May 2008 16:35:09 Naomi Fox wrote:
> Hi,
>
> I'm working on a Google summer of code project (gsoc) to add animation
> features into libAvogadro, which provides the molecular viewer
> functionality of Kalzium.  My mentor is Marcus Hanwell, who worked on
> libAvogadro as a gsoc project last summer.
>
> As part of Kalzium as an educational tool, I think the ability to view
> molecules in motion is a powerful tool for providing insight into how
> biological functions happen.
>
> My idea is to provide users with the ability to try different techniques
> for motion generation of molecules (especially proteins) and be able to
> visualize them with Kalzium.  The current best system I've found for doing
> this is VMD <http://www.ks.uiuc.edu/Research/vmd/>, developed at UIUC.
>
> Below is a list of tasks I've outlined for the project.  I'd love to get
> feedback on what features developers and users might find useful.
>
> Thanks,
> Naomi
>
>
> Tasks:
> The main goals are to implement task 1 (non-interactive motion) and task 3
> (VCR-type functionality). I plan to start on task 2 (interactive motion)
> only when the functionalities of task 1 and task 3 are well tested and
> stable.
>
> Task 1. non-interactive motion functionality. (This will involve using
> OBMol's support for multiple conformers.)
>
> (a) implement ability to implement their motion generator by extending
> classes in libAvogadro
> (b) using part a, provide a file-input way to animate a molecule by reading
> in files with coordinates of different conformers and displaying
> (c) add support for some popular molecular simulation applications:
> (examples rosetta, namd). Either use option (b), or some other. Options for
> animation will differ on the type of simulation being done (Monte Carlo,
> Molecular Dynamics).
>
>
> Task 2. interactive motion (i.e. a user can select an atom or residue and
> apply-force):
>
> (a) get user input for atom selection and vector for direction and
> magnitude (b) decide how to pass information back to motion simulator (need
> to _gure out the best way to do this type of communication, based on what
> was chosen for 1(a))
> (c) add support for popular interactive molecular dynamics applications (ex
> namd). This should be one chosen from one support was added for
> non-interactive simulation for 1(a).
>
>
> Task 3. VCR functionality
>
> (a) fast-forward, rewind, play-back
> (b) record to file to be played back in Kalzium
> (c) record to some type of movie file that can be played in an external
> player (.mov?)


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