> .. that is the first atom in the system. How do I change its color?
Colors in Avogadro 1.0.x are defined by a color plugin, not the atom. In
Avogadro 1.1.x, there's a new property:
atom.setCustomColorName("red")
http://avogadro.cc/api/dev/classAvogadro_1_1Atom.html
>> dir(at)
>
> Does not give any list of methods or variables of the object "at". This
> makes it difficult to "play around" (thats the way I learn, at least) with
> the methods, etc.
I think this is a limitation of Boost::Python which is currently used for the
Python interface.
> Is there a way to read in a coordinate file from the ipython console,
> using some method of the Avogadro class..?
You probably want Avogadro.MoleculeFile.readMolecule()
http://avogadro.cc/api/dev/classAvogadro_1_1MoleculeFile.html
> 2) I am not able to change the color of the hydrogen bonds either.. I go
> to hydrogen bonds => hydrogen bond settings => colors => custom color
> .. i change it to black .. nothing happens (its still ugly yellow).
Ooh, that's weird. I can certainly address that for Avogadro 1.1.x, but not
> 3) In general, I am interested in the following..
>
> a) Read a coordinate file to avogadro (btw, why doesn't it recognize
> ".xmol" extension - its the same things as ".xyz" ?)
Avogadro recognizes extensions used through Open Babel. No one has ever
suggested that Open Babel recognize .xmol. I've certainly never seen one "in
the wild," although I've seen many flavors of ".xyz" files.
> b) Meanwhile, manipulate that coordinate file with my custom python
> scripts to study various things .. (outside avogadro)
Right.
> c) Color / draw bonds on the avogadro view, say, my own custom hydrogen
> bonds, etc.
At the moment, I'm not sure the hydrogen bond engine is sufficient for that,
but it's a good feature request.. mark various pairs of atoms as hydrogen
bonds. There have been proposals for recognizing various "zero order" bonds to
save to files (e.g., CML and SDF).
Please feel free to spam. I don't think the Python interface is getting enough
exercise and it should definitely be able to do what you're describing. That
was the whole point.
Thanks,
-Geoff
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