[chimera-dev] python equivalent for Axis

[Eric Pettersen]

Hi JD,
	The StructMeasure.bestLine routine almost does what you want, but  
although it returns the eigenvectors, it doesn't return the  
eigenvalues (!) which makes it kind of useless.  I'll be fixing that  
in tonight's build.  At any rate, you can just conscript the  
underlying code:  if your list of atoms is in the variable "atoms",  
then this will get you the eigenvectors/values:

	coords = chimera.numpyArrayFromAtoms(atoms)
	centroid = coords.mean(0)
	centered = coords - centroid
	from numpy.linalg import svd
	ignore, vals, vecs = svd(centered)

--Eric

On Nov 8, 2008, at 7:00 AM, Dr. Jean-Didier Maréchal wrote:

> Dear all,
>
> Sorry to bother you again with a similar kind of question, but I'd  
> like my
> script to stock in an array the three resulting vectors of the new
> implemented calculation of the axes for a given set of selected  
> atoms. The
> truth is that I find the right python call for the axis function. I  
> imported
> StructMeasure and tried different ways around but I can't find my way
> through. I don't know if I don't give the wrong arguments or have  
> the wrong
> syntaxes.
>
> Thanks a lot for any help,
>
> JD
>
>
> -----Mensaje original-----
> De: chimera-dev-bounces at cgl.ucsf.edu
> [mailto:chimera-dev-bounces at cgl.ucsf.edu] En nombre de
> chimera-dev-request at cgl.ucsf.edu
> Enviado el: jueves, 06 de noviembre de 2008 21:00
> Para: chimera-dev at cgl.ucsf.edu
> Asunto: Chimera-dev Digest, Vol 58, Issue 2
>
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> Today's Topics:
>
>   1. atom spec. in BNF (David A. C. Beck)
>   2. Re: atom spec. in BNF (Eric Pettersen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST)
> From: "David A. C. Beck" <dacb at u.washington.edu>
> Subject: [chimera-dev] atom spec. in BNF
> To: chimera-dev at cgl.ucsf.edu
> Message-ID:
> 	<Pine.LNX.4.64.0811051401230.9881 at homer23.u.washington.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Does anyone have BNF notation for the atom specification 'language'  
> used
> by Chimera?  Thanks,
>  - David
>
> --
> David A. C. Beck, Ph.D.
> dacb at u.washington.edu
> Valerie Daggett Laboratory
> University of Washington, Seattle
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 5 Nov 2008 14:26:16 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [chimera-dev] atom spec. in BNF
> To: "David A. C. Beck" <dacb at u.washington.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> On Nov 5, 2008, at 2:03 PM, David A. C. Beck wrote:
>
>> Does anyone have BNF notation for the atom specification 'language'
>> used
>> by Chimera?
>
> I don't think so.  What's the use case here?  If you're in the context
> of Chimera, you should be able to use Chimera's own atom-spec parsing
> facilities, e.g. chimera.specifier.evalSpec().  Outside of Chimera,
> I'm aware of a pretty extensive but not totally complete parser in
> perl:  Chemistry::MidasPattern - Select atoms in macromolecules -
> search.cpan.org
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
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