[Biopython] PDBParser-chain breaks

[Eric Talevich]

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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