[Biopython] PDBParser-chain breaks

[João Rodrigues]

For some reason however, I didn't get the discontinuous error .. That's why
I proposed this alternative.

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



2012/5/9 Eric Talevich <eric.talevich at gmail.com>

> The warnings module also lets you convert any warning to an error (or
> ignore it, etc.). Use a regular expression to match the warning message:
>
> from Bio import PDB
> import warnings
> warnings.filterwarnings('error', message='.*discontinuous at.*')
> p = PDB.PDBParser()
> s = p.get_structure("", "3BEG.pdb")
>
>
>
> On Tue, May 8, 2012 at 3:39 PM, João Rodrigues <anaryin at gmail.com> wrote:
>
>> Of course. Since they throw a warning just make sure to count the
>> warnings,
>> parse the chain break ones, and if they are more than 0, you have chain
>> breaks.
>>
>> Cheers,
>>
>> João [...] Rodrigues
>> http://nmr.chem.uu.nl/~joao
>>
>>
>>
>> 2012/5/8 George Devaniranjan <devaniranjan at gmail.com>
>>
>> > Hi João,
>> >
>> > Is there a way though to find PDB's with chain breaks? using biopython?
>> >
>> > Thank you,
>> > George
>> >
>> > On Tue, May 8, 2012 at 3:34 PM, João Rodrigues <anaryin at gmail.com>
>> wrote:
>> >
>> >> Hi George,
>> >>
>> >> Chain breaks are pretty "harmless" and usually do not represent a
>> faulty
>> >> PDB file. The PERMISSIVE flag is for "features" like missing b-factors.
>> >>
>> >> Cheers,
>> >>
>> >> João [...] Rodrigues
>> >> http://nmr.chem.uu.nl/~joao
>> >>
>> >>
>> >>
>> >> 2012/5/8 George Devaniranjan <devaniranjan at gmail.com>
>> >>
>> >>>  Hi,
>> >>>
>> >>> I thought using PERMISSIVE=0 would raise an exception if I pass a PDB
>> >>> with
>> >>> chain breaks.
>> >>> However, nothing like that seems to happen.....
>> >>>
>> >>> For instance
>> >>>
>> >>> P=PDBParser(PERMISSIVE=0)
>> >>> structure=P.get_structure('test', '7ODC.pdb')
>> >>>
>> >>>
>> >>> 7ODC has 3 chain breaks but it does not raise an exception.
>> >>>
>> >>> Thank you
>> >>> George
>> >>> _______________________________________________
>> >>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> >>> http://lists.open-bio.org/mailman/listinfo/biopython
>> >>>
>> >>
>> >>
>> >
>>
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>
>