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

[Peter Cock]

On Tue, May 17, 2011 at 11:14 AM, João Rodrigues <anaryin at gmail.com> wrote:
> Hey,
>
> That's something I noticed too. Some errors still have
> PDBConstructionException as a base class, while most of them have
> PDBConstructionWarning. Only these latter are regulated by the new scheme. I
> believe they were also raised before, but inside the _handle_pdb_exception
> function IIRC.

For backwards compatibility, we still want to use PDBConstructionException
for exceptions (i.e. when permissive=0, or for non-recoverable errors) and
PDBConstructionWarning for warnings (i.e. when permissive=1 or 2). The
filter action may need to convert any PDBConstructionWarning to a
PDBConstructionException.

> Regarding performance, that's something we can easily check with the
> benchmarks. The difference is not big, the PDB branch and 1.57+ differ just
> in that particular detail.

So you don't think this is worth worrying about? OK - if the code is cleaner
this way that's a good justification.

Peter