[chimera-dev] python for finding clashes

[Eric Pettersen]

Hi JD,
	I misunderstood: I thought you meant that you had an actual Selection  
object you were working with.  If what you have done is select the  
atoms you want to work with, then chimera.selection.currentAtoms() is,  
as you pointed out, a list of those atoms.  Therefore you can just do  
this:

	clashes = detectClash(chimera.selection.currentAtoms())

--Eric
                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Oct 29, 2008, at 11:40 AM, Dr. Jean-Didier Maréchal wrote:

> Hi Eric and others,
>
> I am having problems with the selection, is it a list or a variable ? 
> … sorry.
>
>
> I selected some atoms and then open the IDLE.
>
> Then goes the script :
> >> import chimera
> >>> from DetectClash import detectClash
> >>> at=chimera.selection.currentAtoms() – this stocks in at a list  
> of atoms.
> >>> clashes=detectClash(at.atoms()) – I do what you say
>
> And the message error :
> Traceback (most recent call last):
>   File "<pyshell#3>", line 1, in <module>
>     clashes=detectClash(at.atoms())
> AttributeError: 'list' object has no attribute 'atoms'
>
> I played around between list and variables but can’t find the right  
> way to move forward. Could you throw me a cable please .
>
> Best,
> jd
>
> De: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
> Enviado el: martes, 28 de octubre de 2008 19:18
> Para: JeanDidier.Marechal at uab.es
> CC: chimera-dev at cgl.ucsf.edu
> Asunto: Re: [chimera-dev] python for finding clashes
>
> Hi JD,
>             You should use DetectClash.detectClash().  The only  
> mandatory argument is a list of atoms.  So if your selection was in  
> a variable named 's', you might call the function like so:
>
>             from DetectClash import detectClash
>             clashes = detectClash(s.atoms())
>
> The return value is a dictionary.  The keys of the dictionary are  
> atoms that have clashes.  The values are dictionaries.  These  
> dictionaries have keys which are the atoms that clash with the  
> original key atom.  The values are the amount of the clash.  So to  
> get the number of clashes, you would use something like this:
>
>             sum = 0
>             for clashDict in clashes.values():
>                         sum += len(clashDict)
>             numClashes = sum / 2
>
>             Now, there are a lot of optional keyword arguments to  
> the detectClash() function.  They are pretty well documented in the  
> doc string of the function.  So you should look through the doc  
> string and post any questions that you might still have...
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
>
> 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
>
> Dr. Jean-Didier Maréchal
> Lecturer
> Computational Bioorganic and Bioionorganic Chemistry @ Transmet
> Unitat de Química Física
> Departament de Química
> Universitat Autònoma de Barcelona
> Edifici C.n.
> 08193 Cerdanyola (Barcelona)
> Tel: +34.935814936
> e-mail: JeanDidier.Marechal at uab.es
>
>
>
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>

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