[Biopython-dev] Module reorganization for upcoming Bio.PDB enhancements

[Thomas Hamelryck]

Hi,

On Tue, Jun 8, 2010 at 7:10 PM, João Rodrigues <anaryin at gmail.com> wrote:

>
> from Bio.PDB import Protein
> structure = Protein('1ABC.pdb')
> structure.search_ss_bonds()
>

Indeed, that would run into problems for complexes where proteins, RNA, DNA,
etc. occur in the same file. It makes much more sense to have a Structure
centred approach:

proteins=Protein(structure)
chains=proteins.get_chains()
chain_a=chains["A"]
polypeptides=chain_a.get_peptides()

rnas=RNA(structure)

etc.

-Thomas

-- 
Thomas Hamelryck, Assoc. Prof.
Group leader Structural Bioinformatics
Bioinformatics center
Department of Biology
University of Copenhagen
Ole Maaloes Vej 5
DK-2200 Copenhagen N
Denmark
http://wiki.binf.ku.dk/User:Thomas_Hamelryck
http://www.binf.ku.dk/research/structural_bioinformatics/