Symmetry and MacMolPlt

I’ve just watched screencast about SN2 (http://blip.tv/file/2188480) and seen MacMolPlt program used there. I’ve installed it and found it’s great thing! It can find symmetry elements, visualize them, symmetrize structure. Also it can build z-matrix (but this feature seems not to be convenient to use). Program is licensed under GPL2 or later (it’s not stated in UI and website, but I’ve found license in source package)
What about integration of Avogadro with MacMolPlt (e.g. export -> determine point group -> show elements -> apply point group-> import back)?

Regards,
Konstantin

What about integration of Avogadro with MacMolPlt (e.g. export -> determine point group -> show elements -> apply point group-> import back)?

I like that you’re coming up with lots of good ideas. I think it’s fine to suggest a shared clipboard format (e.g., MDL Molfile or XYZ) to allow users to copy/paste between Avogadro and MacMolPlt. That’s good for users – it’s basically the “primary GUI” for the GAMESS package, and we should enable that kind of integration. Marcus and I have worked with QUI for the Q-Chem program similarly.

But didn’t you say you had improved symmetry detection code? Why don’t you send that to me, and I’ll see about integrating it into Open Babel. As I mentioned to you off-list, I also have some Java code which offers these features (determine point group, track symmetry elements, symmetrize).

For this type of functionality, which many people want in Avogadro, I think we should do it, rather than telling people to use another program. Integration is good. Dependence is not good.

Just my $0.02,
-Geoff

What about integration of Avogadro with MacMolPlt (e.g. export -> determine point group -> show elements -> apply point group-> import back)?
I like that you’re coming up with lots of good ideas.

My pleasure :slight_smile: I usually have more ideas than time to implement them

I think it’s fine to suggest a shared clipboard format (e.g., MDL Molfile or XYZ) to allow users to copy/paste between Avogadro and MacMolPlt. That’s good for users – it’s basically the “primary GUI” for the GAMESS package, and we should enable that kind of integration. Marcus and I have worked with QUI for the Q-Chem program similarly.
But didn’t you say you had improved symmetry detection code? Why don’t you send that to me, and I’ll see about integrating it into Open Babel.

Sorry. I’ve thought I should integrate it myself, and was a bit lazy to it (it works fine for me currently :). If you’d like to hack it yourself (or anybody else), source is attached. I’ve also mentioned that it’s published as part of OpenThermo (http://openthermo.sourceforge.net, symmetry.cpp in root of source tree)

I thought to work on it as a part of symmetry extension. However, you said that “Todo for 1.1” is for whole 1.1.x series (AFAIU, effectively 1.2.0), so I didn’t promise to do it just now

As I mentioned to you off-list, I also have some Java code which offers these features (determine point group, track symmetry elements, symmetrize).

I looked through it. It seems not to be “self-sufficient” (relies on CDK), otherwise it could be easily converted or compiled as such with gcj to native code

For this type of functionality, which many people want in Avogadro, I think we should do it, rather than telling people to use another program. Integration is good. Dependence is not good.

IMHO, it’s better to have a dependence than re-invent the wheel. Don’t you like Unix way?


Regards,
Konstantin