Re: [chimera-dev] python equivalent for Axis

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@cgl.ucsf.edu [mailto:chimera-dev-bounces@cgl.ucsf.edu] En nombre de chimera-dev-request@cgl.ucsf.edu Enviado el: jueves, 06 de noviembre de 2008 21:00 Para: chimera-dev@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)

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Message: 1 Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST) From: "David A. C. Beck" Subject: [chimera-dev] atom spec. in BNF To: chimera-dev@cgl.ucsf.edu Message-ID: 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@u.washington.edu Valerie Daggett Laboratory University of Washington, Seattle

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Message: 2 Date: Wed, 5 Nov 2008 14:26:16 -0800 From: Eric Pettersen Subject: Re: [chimera-dev] atom spec. in BNF To: "David A. C. Beck" Cc: chimera-dev@cgl.ucsf.edu Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D@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