avogadro-devel

[Avogadro-devel] Possible to generate png from SMILES without using the GUI

[Simon N. <si...@da...>]

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?


Regards,
Simon

Re: [Avogadro-devel] Possible to generate png from SMILES without using the GUI

[Tim V. <tim...@gm...>]

Hi,

On Wed, Jan 9, 2013 at 9:08 PM, Simon Norberg <si...@da...> 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
>
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. SALE $99.99 this month only -- learn more at:
> http://p.sf.net/sfu/learnmore_122412
> _______________________________________________
> Avogadro-devel mailing list
> Avo...@li...
> https://lists.sourceforge.net/lists/listinfo/avogadro-devel
>

Re: [Avogadro-devel] Possible to generate png from SMILES without using the GUI

[Simon N. <si...@da...>]

> 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
Hi Tim,
Thansk for the hint, but I guess I didn’t specify what i meant with nice 
looking images Avogadro generates well enough, the image i want to 
create is a image of a 3d molecule. Similar to what you export from 
avogadro when you choose to export a PNG.
OpenBabel is only able to generate 2d text based image AFAIK. One 
possibility i have tested is to use OpenBabel to generate a .pdb file 
and then use raster3D to generate a 3d molecule image.
The image raster3d generate isn’t as nice as avogadros, and i have a 
hard time to render a atom of constant size. I want to have a Carbon 
atom to be the same size in pixels regardless of generating a simple CO 
or a more complex molecule. I dont know if avogadro supports this 
either, but at least if i could hack a python script i might be able to 
fix it myself in avogadro.

Regards,
Simon

Re: [Avogadro-devel] Possible to generate png from SMILES without using the GUI

[Marcus D. H. <mar...@ki...>]

On Tue, Jan 15, 2013 at 11:32 AM, Simon Norberg <si...@da...> wrote:
>
>> 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
> Hi Tim,
> Thansk for the hint, but I guess I didn’t specify what i meant with nice
> looking images Avogadro generates well enough, the image i want to
> create is a image of a 3d molecule. Similar to what you export from
> avogadro when you choose to export a PNG.
> OpenBabel is only able to generate 2d text based image AFAIK. One
> possibility i have tested is to use OpenBabel to generate a .pdb file
> and then use raster3D to generate a 3d molecule image.
> The image raster3d generate isn’t as nice as avogadros, and i have a
> hard time to render a atom of constant size. I want to have a Carbon
> atom to be the same size in pixels regardless of generating a simple CO
> or a more complex molecule. I dont know if avogadro supports this
> either, but at least if i could hack a python script i might be able to
> fix it myself in avogadro.
>
Avogadro doesn't have that level of control from the command line, the
Python bindings might be enough to allow you to accomplish what you
need (and I remember Tim writing some blog posts about doing similar
things there).

Thanks,

Marcus