[Biopython] BioJava-like seqres alignment for Bio.PDB

[Rodrigo Faccioli]

Hi,

About the SEQRES implementation for BioPython, I've developed it. Please,
see it in [1]. I hope this implementation could help you.

[1]
http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/fcfrp/PDBParser.py

Best,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Fri, Jul 2, 2010 at 4:25 PM, João Rodrigues <anaryin at gmail.com> wrote:

> Hey!
>
> >> Does anyone have any code for easy alignment between the SEQRES entry
> > >> in a pdb file and the actual ATOM/HETATM entries in the chain?
> >
>
> There's not parsing for SEQRES yet in parse_header_pdb but it wouldn't be
> hard to.
>
>
> >  >> In biojava, this is just one of the options when you parse a PDB
> file,
> > >> it would certainly be useful.
> >
>
> Indeed it would.
>
>
> That looks like a good reason to have a PDB XML parser (as trying to do
> > this from the plain text PDB is probably fiddly).
> >
>
> I don't know if people have started working on such a parser but I have
> some
> sort of a head start. Check here:
>
>
> http://github.com/JoaoRodrigues/biopython/blob/GSOC2010/Bio/Struct/WWW/WHATIFXML.py
>
> Warning, very ugly :)
>
>
>
> > > In any case, having function that provides this mapping (both
> directions)
> > in
> > > BioPython would be extremely useful.
> >
> > Maybe something for the GSoC project TODO list? ;)
> >
>
> Hmm, I was working on something more or less like this a while back and it
> didn't work that well. But it might be a good idea. It seems however that
> Bryan already did it :) No?
>
> João
>
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