[Biopython-dev] Features of the GSOC branch ready to be merged

[João Rodrigues]

Hey Kristian, all,

What about this: creating a new file under Bio.PDB called Misc.py or
Utilities.py that contains functions like renumber_residues. I'm thinking on
other functions like joining PDB files, extracting chains from PDB files,
renaming chains etc.

These are all operations that one can easily do programatically using
Bio.PDB, however they do require coding (10 lines each I'd say). This
"collection" of useful snippets could be included in a separate file and
even provide an interface to the command line. This was one of Eric's ideas
for GSOC I didn't pursue in my project.

Regarding renumber_residues explicitly, this would allow using it
structure-wide or chain-wide without duplicating code (Right now it sits on
Structure.py). I can also keep it as is now and just add chain, from_id, and
to_id arguments.

Let me know of your opinions,

Cheers

João [...] Rodrigues
http://doeidoei.wordpress.com



On Mon, Dec 13, 2010 at 4:13 PM, Kristian Rother <krother at rubor.de> wrote:

>
> Hi Joao,
>
> I agree with Eric that renumbering residues should be possible chain-wise.
>
> In my daily work, I am frequently using an interface similar to
>
> renumber( chain, start_id )
>
> rather than
>
> renumber( structure, start_id )
>
> But having these two in BioPython would be quite cool. We also do
> numbering of portions
>
> renumber (chain, start_id, from_id, to_id)
>
> and using insertion codes --> 1A, 1B, 1C, 1D...
> But I agree these are not so important.
>
> Best regards,
>    Kristian
>
>
>
>
>
> > Hello Eric,
> >
> > Regarding renumber_residues, I could add the following arguments to make
> > it
> > more flexible:
> > - *first *and *last*: to allow renumbering of specific sections of the
> > structure
> > - *chain* : to limit the renumbering to one chain only.
> >
> > As for the biological units I'll have to look at them again... to be
> > honest
> > I really need to retest them :x
> >
> > Thanks for the comments :)
> >
> > Best!
> >
> > João
> >
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> >
>
>