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

[João Rodrigues]

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