[Biopython-dev] CE implementation in Python

[Iddo Friedberg]

Interesting donation from Jason Vertrees. CE is a well-known
structural alignment program from Phil Bourne's lab at UCSD.

-------- Original Message --------
Subject: BiopPython & Structure Alignments
Date: Fri, 17 Oct 2008 23:45:35 -0400
From: Jason Vertrees <jv at cs.dartmouth.edu> <jv at cs.dartmouth.edu>
To: idoerg at burnham.org

Iddo,

I'm not sure if this might be of assitance to the BioPython project, but
I implemented a version of CE Align (structure alignment algorithm) as
an extension to the PyMOL program.  The code is open-source (BSDL) and I
have two versions:
  (1) Pure Python -- slow; essentially unusable, but all Python.  A
typica alignment might take about 30 seconds.
  (2) Mixed Python/C implementation: the math is done in C/C++
(implemented both) so it's very fast.  The good news for BioPython is
that I used distutils and the typical Python Extending procedures to
write the code: BioPython might very easily be able to plug in the code
so you don't have to access a web server to do structure alignments.  A
typical alignment takes about 0.2 seconds.

If you're at all interested, please look at

http://www.pymolwiki.org/index.php/Cealign

as that's there the code lives.

I don't have time to port the code for the project, but I don't think it
would be all that hard given some effort.  I'm happy to answer any
questions.

HTH,

-- Jason Vertrees

--

Jason Vertrees, PhD

Boston U. -- jasonv at bu.edu
Dartmouth -- jv at cs.dartmouth.edu






-- 
Iddo Friedberg, Ph.D.
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