Hi,
Geoffrey, thanks for your reply.
The Avogadro version in the (ubuntu) repos is unfortunately 1.0.x..
So, I installed manually the latest 1.1 version. There was a dependency
hell of all sort
of packages not mentioned anywhere (qttools5-dev-tools ..), but never
mind, I got through it.
I started Avogadro 1.1., however, the python console was not available
anywhere .. although it should
be installed by default?
After opening some menus, Avogadro froze up and I got ..
QStackedLayout::setCurrentWidget: Widget 0x1f5b550 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
*** Error in `avogadro': realloc(): invalid next size:
0x000000000403fd40 ***
So in the end I have already spent an hour and a half in just trying to
change the color of a single atom .. ;)
.. I guess I'll give up on Avogadro for the moment. Seems like a great
program though.
How is it with Avogadro 2.. is there any python support yet .. ?
Regards,
S.
On 02/17/2014 10:51 PM, Geoffrey Hutchison wrote:
>> .. 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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