[chimera-dev] python for finding clashes

[Dr. Jean-Didier Maréchal]

Hi Elaine,

Thanks a lot for the input. The thing is that I'd like to store the value in
an array if it is possible. 

Cheers,
JD

-----Mensaje original-----
De: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Enviado el: martes, 28 de octubre de 2008 17:29
Para: JeanDidier.Marechal at uab.es
CC: chimera-dev at cgl.ucsf.edu
Asunto: Re: [chimera-dev] python for finding clashes

Hi JD,
Many (all?) options are available from the Chimera command "findclash"  
itself,

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

for example "log true" to send information to the Reply Log or  
"saveFile pathname" to write it to a text file with location/name  
pathname.

Is that what you needed, or does the information need to be stored in  
an array or variable?
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Oct 28, 2008, at 7:15 AM, Jean Didier Pie Marechal wrote:

> Hi everyone,
> I am writing a script for which I need the number of clashes for a  
> given selection for continuing.
>
> My first thought was to simply run in my script:
> runCommand("findclash selection ignoreIntraRes false")
> after having selected the region I was interested in.
> However, I realize that I come to the recurrent problem: having the  
> information I am interested in printed in the reply log. I don't  
> know how to have the info passed into an array or any kind of  
> variable in the  python environment. Could you tell me how to do so  
> please?
>
> On the other side, I would be pleased if you could tell me what is  
> the correct arguments I have to pass and syntax I have to use for  
> the functions  detectClash and/or cmdDetectClash (which I guess is  
> the basis of the same findclash).
>
> All the best,
> JD