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How to get the coordinates of every generated conformer?

Hello everyone,

I have been using avogadro for the generation of conformers. After the
conformer search is there a way (through the GUI or using the python
terminal) to save all coordinates without having to select each one from the
list ? I have looked into the manual and even tried to find that information
in the python scripting page (in the wiki), to no avail … I dont need that
every conformer saves its coordinates to a single file, I just want a way to
export the list of coordinates for every conformer.

Thanks a lot and sorry if this is a naïve question,
Paulo


Paulo E. Abreu
Professor Auxiliar
Departamento de Química
Faculdade de Ciências e Tecnologia da Universidade de Coimbra

On Thu, Oct 29, 2009 at 3:03 PM, Paulo E. Abreu paulo.abreu@ci.uc.pt wrote:

Hello everyone,

Hi,

I have been using avogadro for the generation of conformers. After the
conformer search is there a way (through the GUI or using the python
terminal) to save all coordinates without having to select each one from the
list ? I have looked into the manual and even tried to find that information
in the python scripting page (in the wiki), to no avail … I dont need that
every conformer saves its coordinates to a single file, I just want a way to
export the list of coordinates for every conformer.

This should be possible using a python extension. I’ll try this and
add it to the wiki if I find time tonight or tomorrow.

Cheers,
Tim

Thanks a lot and sorry if this is a naïve question,
Paulo


Paulo E. Abreu
Professor Auxiliar
Departamento de Química
Faculdade de Ciências e Tecnologia da Universidade de Coimbra


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On Thu, Oct 29, 2009 at 5:03 PM, Tim Vandermeersch
tim.vandermeersch@gmail.com wrote:

On Thu, Oct 29, 2009 at 3:03 PM, Paulo E. Abreu paulo.abreu@ci.uc.pt wrote:

Hello everyone,

Hi,

I have been using avogadro for the generation of conformers. After the
conformer search is there a way (through the GUI or using the python
terminal) to save all coordinates without having to select each one from the
list ? I have looked into the manual and even tried to find that information
in the python scripting page (in the wiki), to no avail … I dont need that
every conformer saves its coordinates to a single file, I just want a way to
export the list of coordinates for every conformer.

This should be possible using a python extension. I’ll try this and
add it to the wiki if I find time tonight or tomorrow.

I’ve added the example to the wiki:
http://avogadro.openmolecules.net/wiki/Saveconformers.py

However, it requires this commit


to work. If you are using linux you can easily rebuild. In case you
are using windows, you’ll have to wait for 1.0.1 which will be
released in the near future.

Cheers,
Tim

Thanks a lot and sorry if this is a naïve question,
Paulo


Paulo E. Abreu
Professor Auxiliar
Departamento de Química
Faculdade de Ciências e Tecnologia da Universidade de Coimbra


Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference


Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss