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

[Eric Talevich]

Looks good to me. I can't guarantee I'll be able to merge this right
away since I'm going to be traveling for the next week. Anyone else
want to try it?
-Eric

On 5/13/11, João Rodrigues <anaryin at gmail.com> wrote:
> 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
>>
>