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The Kalzium Molecular Editor

Posted by Marcus D. Hanwell on

Some of you with long memories may recall that I worked on the Kalzium molecular editor for my Google Summer of Code (TM) project last summer. The observant among you may have also noticed that Kalzium in KDE 4.0 featured a molecular viewer. Well the freeze meant that much of my work didn't make it into KDE 4.0. This is the case with many of our current GSoC students (Naomi among them) who are just starting to code as KDE 4.1 is being frozen and released.

Since last summer life has been really hectic, the shipment of my household possessions from the UK to the US was delayed significantly by an incompetent shipping company which also proceeded to break many things... This led to me having no Linux system to develop on for quite some time, and then less time to develop due to having to deal with the fallout of a botched delivery. Still, I am very pleased to be able to show off some of my latest work which made it into KDE 4.1 and will be in KDE 4.1 beta1 (due out in a few days).

Kalzium 4.1 molecular editor

I was able to expose some of the extra display types I added along with support for drawing and editing molecules. You can also measure distances and angles of the molecule you are looking at and do some geometry optimisation. Given a little more time I would have liked to expose some of the manipulation features but this new six month cycle was so short and my time was constrained anyway. It will make it into 4.2 at least.

I am looking forward to seeing the animation support Naomi is working on now and am very happy to be able to mentor her over the summer. I think high quality, open source educatonal programs are very important and hope that this editor will be useful in that role. The Avogadro library and application should hopefully be able to satisfy college students and researchers. With the scripting support and open source nature of the two projects I think they interact very well and complement one another.

As always I would love to hear your feedback on the Kalzium changes and the other work we are doing.

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Kevin Kofler on :

Kevin KoflerWell, you asked for feedback, so: it would be great if Kalzium in KDE betas didn't require always the very latest SVN HEAD of trunk of OpenBabel, which hasn't even been released as a beta yet. :-( Kalzium from KDE 4.1 Beta 1 doesn't build against OpenBabel 2.2.0 Beta 4, the latest beta from OpenBabel (or at least so claims their site), without patching. This is really annoying when getting the betas into Fedora Rawhide.

Geoffrey Hutchison on :

Geoffrey HutchisonWe don't release versions of Avogadro (or Kalzium) without corresponding versions of Open Babel. In this case, there is a 2.2.0b5, which was released with Avogadro 0.8, and well before Kalzium's snapshot from KDE Beta 1.

http://sourceforge.net/project/showfiles.php?group_id=40728&package_id=154019

I apologize that the releases have been in sync, but Avogadro has pushed a lot of bug-fixes in Open Babel. The problem should go away shortly since OB-2.2.0 is nearing completion.

I don't know where you're seeing 2.2.0b4 is the latest Open Babel though. The beta snapshot was placed in the exact same place for downloads as all the rest. If you have some complaint about this, please contact me via the openbabel-devel mailing list -- it's not really a Kalzium issue

Kevin Kofler on :

Kevin Koflerhttp://openbabel.org/wiki/Get_Open_Babel still links to b4.

Marcus D. Hanwell on :

Marcus D. HanwellSorry about that - that page was obviously forgotten. We have updated it now, thanks for pointing it out.

Marcus D. Hanwell on :

Marcus D. HanwellI see Geoff beat me to replying - I have been stuck in the basement of an engineering building all morning... As Geoff said, the OpenBabel beta had been released well before the changes I made to Kalzium. We are working towards a final release of OpenBabel but the development of Kalzium's 3d molecular editor, Avogadro and OpenBabel are all quite closely linked. If I can make packaging Kalzium easier then I certainly will but I am afraid that the way we are releasing is necessary.

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