[Biopython-dev] Adding QUIET argument to PDBParser()

[João Rodrigues]

Hello all,

Not to let this die.

I've added PERMISSIVE=2 to PDBParser. I also changed the code to remove the
_handle_pdb_exception method and replace it by the warnings module.

This was done in two commits in my branch:

https://github.com/JoaoRodrigues/biopython/commit/5b44defc3eb0a3505668ac77b59c8980630e6b07
https://github.com/JoaoRodrigues/biopython/commit/7383e068e41dd624458b3904fcd61a04c3f319c4


Sorry to be insistent, but I don't really wish QUIET to live long if we have
such an elegant alternative.

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2011/5/6 Peter Cock <p.j.a.cock at googlemail.com>

> On Fri, May 6, 2011 at 5:23 PM, Eric Talevich <eric.talevich at gmail.com>
> wrote:
> > On Fri, May 6, 2011 at 3:54 AM, João Rodrigues <anaryin at gmail.com>
> wrote:
> >
> >> Hello all,
> >>
> >> The PDBParser is sometimes a bit too loud, making meaningful output
> drown
> >> in
> >> dozens of warnings messages. This is partly (mostly) my fault because of
> >> the
> >> element guessing addition. Therefore, I'd suggest adding a QUIET
> argument
> >> (bool) to PDBParser that would supress all warnings. Of course, default
> is
> >> False. It might come handy for batch processing of proteins.
> >>
> >> I've added it to my pdb_enhancements branch so you can take a look:
> >>
> >>
> >>
> https://github.com/JoaoRodrigues/biopython/commit/5405d8a4cc555bcfce6ad0915db62a131cee9493
> >>
> >>
> > Since the PERMISSIVE argument is already an integer, could we consolidate
> > these by letting (PERMISSIVE=2) behave as (PERMISSIVE=1, QUIET=1) ?
> >
>
> I'm OK with that,
>
> Peter
>