Re: Kalzium looks promising

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Re: Kalzium looks promising
by Benoit Jacob on Wednesday 31/Jan/2007, @00:24

We use OpenBabel to load molecule files, and OpenBabel supports 62 file formats as Troy counted. I checked, PDB is among the supported formats.

http://openbabel.sourceforge.net/wiki/Category:Formats

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Re: Kalzium looks promising
by Rithvik on Wednesday 31/Jan/2007, @03:49

That is understood. Openbabel does convert and support many formats, but it looses a lot of annotations on the way, such as residue information.
The 'molecule' screensaver in xscreensaver does a similar thing by showing PDB files. But PDB viewers show more than just the atoms in the molecule as most molecule viewers do. e.g secondary structure as ribbons, backbone trace, residue annotations etc. A PDB viewer is more than a molecule viewer. There are a lot of pdb viewers there, but none which integrate with KDE or konqueror like Chime (http://www.mdl.com/products/framework/chime/) does with IE on windows (jmol (jmol.sourceforge.net) is good enough though). A Plugin or kpart like that could help such projects like the gromacs gui ( http://kde-apps.org/content/show.php?content=47665 ). This doesn't make sense for kalzium maybe, but the libavogadro thingie looks promising.

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Re: Kalzium looks promising
by Benoit Jacob on Wednesday 31/Jan/2007, @04:46

ah ok, thanks for explaining. I'm no chemist and I'm only doing the math and OpenGL stuff here, but I'll point Carsten and Donald to your comment.

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Re: Kalzium looks promising
by Carsten Niehaus on Wednesday 31/Jan/2007, @07:09

Well, there is Bioclipse (http://www.bioclipse.net/): http://bioclipse.net/index.php?option=com_content&task=view&id=11&Itemid=5

Of course, that is not in Konq, but for that you can of course use JMol (http://jmol.sourceforge.net/). Look at the screenies if you want to see it in action: http://jmol.sourceforge.net/screenshots/

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Re: Kalzium looks promising
by Rithvik on Wednesday 31/Jan/2007, @07:53

I have mentioned and use jmol. I didn't know of bioclipse. Thanks.

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Re: Kalzium looks promising
by dcurtis on Wednesday 31/Jan/2007, @11:18

I've been working on pulling some extra information (annotations?) into OpenBabel. I know that there is already work for residue information (although i haven't worked on that directly). libavogadro will support it, and thus kalzium.

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that's the spirit. thank *you* all
by eMPe on Wednesday 31/Jan/2007, @16:47

just a short note the feature is coming to a library that is used by a library that is used by our favorite KDE application AND 'competing' apps.. That's the real power of FOSS. Sh1t, I just love this. It's like 'sweets hitting the fan' or so...lol.

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Re: that's the spirit. thank *you* all
by Carsten Niehaus on Thursday 01/Feb/2007, @01:56

When I started that 3D-feature I wrote my own cml-parser. After some days I thought that is a really stupid idea and ported Kalzium to OpenBabel. It took me about 2 hours and five emails.

In the end OpenBabel has a couple of bugs left, the API-docs are now cleaner (because of my stupid questions ;-) and OB even has some new features I needed. Avogadro is also using OB, as is GHemical and others.

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Re: Open Babel problems?
by Geoff Hutchison on Thursday 01/Feb/2007, @07:28

If you have particular "problems" with Open Babel, you really should report them to the bug tracker. Please don't just gripe about the project on a random forum -- your bugs won't be fixed that way. Better yet, please give us example files of stripping out annotations and tell us what we should do instead. Residue information certainly should be retained when reading a PDB file. Check out PDB -> Mol2 for example.

Yes, Avogadro does have options for rendering a residue at a time, or secondary structure, etc. We've planned it that way. But Avogadro is also based on Open Babel, so if you really think there are problems in the underlying library, it'll be a problem with Kalzium, Avogadro... well quite a few viewers.

I like to think Open Babel as a project is pretty good about responding to critiques and suggestions. So please tell us what we're doing wrong so we can fix them!

http://sourceforge.net/projects/openbabel

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