Hi,
On Wed, Jan 9, 2013 at 9:08 PM, Simon Norberg <[email protected]> wrote:
> Hi,
>
> I have a project where i need to generate nice looking molecule images
> from preferable SMILES format, other similar formats could be OK as
> input. In the avogadro gui its possible to do exactly this, but the
> problem is that it requires several manual step and for the amount of
> molecules i need to generate it will be too cumbersome. From searching
> the avogadro wiki i cant find that it exist any cli that would alow me
> to do this, but i have found that there is python bindings that support
> automatize some operation. Would it be possible to to this from python
> using libavogadro?
> I have testet the python example in avogadro github repository
> "avogadro/libavogadro/examples/python/standalone.py" by using this it
> looks likes it possible automatize the first part - loading the
> molecule, but I cant see any possibility to export this in the api, is
> it missing or is it just me not looking after it in the correct place?
> If its not yet possible to export with the api, would adding that
> feature be hard? and where in the code should i start to look to do it.
>
Avogadro uses OpenBabel for this (http://openbabel.org). It supports batch
conversions for files using the (o)babel program. If you have Avogadro
installed, this is most likely installed on your system too.
babel mysmiles.smi foo.png -m
The -m option turns the multi-molecule file into seperate png files
(foo1.png, foo2.png, ...). There is also support for SVG output.
Hope this helps,
Tim
> Regards,
> Simon
>
>
>
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