Kalzium Molecular Viewer, Editors, and Avogadro

Development
1

Hi Carsten,

I was reading your weblog this morning (http://
cniehaus.livejournal.com/) and am really impressed by the progress in
the Kalzium molecular viewer.

I’m writing because I’ve been in a hacking/planning mood and have
been working on a plan for “Avogadro” which is a "next generation"
molecular editor/modeling tool. It seems it will be based on Qt and
Open Babel. Qt because it’s cross-platform, GPL, and much more
logical. Open Babel because it’s fast, cross-platform, and I develop
it. (I won’t say it’s as logical or well-documented as Qt. Not yet. :slight_smile:

I had looked at libQGLViewer for simplifying the Qt/OpenGL since it’s
also GPL and has some nice features for animation, selection
(including “rubber band”) and saving bitmap or other graphical
representations. If you don’t know of this, I suggest taking a look.

Now I see how much Kalzium has done for their molecular viewer and I
feel like I should get busy!

So let me explain the ideas for Avogadro and maybe you can provide
some input and/or interest. The main idea is inspired by programs
like GIMP or Photoshop or Eclipse. People use editors for different
reasons. So these projects have lots of plugins for different needs.

So my idea for Avogadro is that:
a) The C++ inheritance should allow fast coding for new tasks (e.g.,
new rendering modes)
In particular, render subclasses are passed an object (e.g.,
molecule, grid/cube/volume, protein) which is their "specialty"
b) It should easily allow loadable plugins and scripting.

This is also nice for development – once the core functionality is
done, additional features can be added with plugins.

I’m curious. Is Kalzium seriously interested in adding a molecular
editor? Or would it be OK if there just happened to be a separate
project that probably shares a lot of code with Kalzium. (I intend to
shamelessly borrow/adapt/steal the viewer code.)

Would it make sense to work together? For example, that the
rendering, etc. is all the same, but Avogadro adds editing features
and plugins? If there’s interest, I’ll be glad to e-mail my more
detailed plan.

Cheers,
-Geoff

2

Am Mittwoch 05 Juli 2006 20:09 schrieb Geoffrey Hutchison:

I’m curious. Is Kalzium seriously interested in adding a molecular
editor?

It was not until 2 minutes ago :wink:

Or would it be OK if there just happened to be a separate
project that probably shares a lot of code with Kalzium. (I intend to
shamelessly borrow/adapt/steal the viewer code.)

I won’t sue you :wink: Seriously: I think that the only sane thing you can do is
to use all of our opengl-code. Benoit (the one who send you the math-mail
yesterday) is doing all the 3D and OpenGL-stuff. We are trying to use as much
as possible of OpenBabel2.1. It seems that we already reach the limits in
some cases, I hope Benoit will find time and motivation to improve that stuff
in OpenBabel.

Would it make sense to work together?

Beware: Kalzium is now using Qt 4.2.

For example, that the
rendering, etc. is all the same, but Avogadro adds editing features
and plugins? If there’s interest, I’ll be glad to e-mail my more
detailed plan.

Of course it would be cool if you would code Avogadro in a way that Kalzium
would just use it (on compiletime check if libavogadro is available and then
activate it). There is a lot going on in the 3D/GL-Stuff of Benoit. All of
our code is in KDE’s repository. Not sure how to handle codesharing…

I want Kalzium to improve and mature into a more “professional” way. I am a
teacher of biology and chemistry and always have that in my personal roadmap.
I think editing fits well.

Btw: Do you have ICQ or preferably Jabber? cniehaus@jabber.org

–
Gruß,
Carsten Niehaus