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

[Kristian Rother]

Hi guys,

I'm fine with your ideas regarding different wrappers for
Bio.PDB.Structure objects discussed last week, in particular:

- creating Bio.Struct.RNA or Bio.PDB.RNA with a Structure instance.
- having a structure.as_rna() helper method as suggested by Eric (but this
is no must).

I'd like to take what Joao does for proteins and add some basic equivalent
for RNA structures shortly after.

Best Regards,
    Kristian



Quoting Thomas Hamelryck <thomas.hamelryck at gmail.com>:

> 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