[Biopython] topology of transmembrane proteins in BioPython

[João Rodrigues]

Hey Afonso,

In Bio.PDB there is not for sure. Bio.Graphics *might* be adapted to deal
with such files but I can't tell you how straightforward it can be. Have a
look here:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc200
http://www.bio-cloud.info/Biopython/en/ch15.html

Also, are you by any chance parsing PDBTM files? That could be a useful
addition for Bio.PDB.

Abraço,

João


2012/11/20 Afonso Duarte <aduarte at itqb.unl.pt>

> Dear All,
>
>
>
> I´m a newbie in BioPython
>
> I have a list of transmembrane proteins (in XML or txt format that include:
> name/sequence number/sequence/ secondary structure prediction/
> transmembrane
> regions) that I would like to draw a topology picture from.
>
> As I have a large number I would like to implement it in Biopython. Is
> there
> any package/model  that allow to run this task automatically? if not (I
> searched but did not found one that would do it), is there a graphical
> module that can be adapted to draw such kind of files ? (i.e. just need to
> draw rectangles / arrows and connecting lines and allow these to be fully
> manipulated)
>
>
>
> Thanks!
>
>
>
> Afonso
>
>
>
>
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