[Biopython-dev] CE implementation in Python

Peter biopython at maubp.freeserve.co.uk
Mon Oct 27 09:57:06 UTC 2008

On Sun, Oct 26, 2008 at 9:34 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
> Interesting donation from Jason Vertrees. CE is a well-known
> structural alignment program from Phil Bourne's lab at UCSD.

This sounds interesting - presumably to integrate it into Biopython we
would need to make it work on the Bio.PDB chain/structure objects.
For example, I would expect the CE code would need to be able to get
the secondary structure of each residue (i.e. where did the PDB file
say the alpha helices and beta sheets were).  However, I will not have
the time nor the motivation to do this myself.

Its nice that in addition to pure python he has both C and C++ back
ends. My gut instinct is to avoid the C++ code and stick with the C
code (given previous cross platform fun with C++).  Its a little
surprising his python code is so much slower - but maybe it doesn't
take full advantage of numpy at the moment?


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