[Biopython-dev] Benchmarking PDBParser

[João Rodrigues]

Hey Chad,

That's exactly what I ended up doing and it is done ;) Pretty quick, I was
hoping for a day or so!

Best,

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



On Wed, May 4, 2011 at 3:55 PM, Chad Davis <chad.a.davis at gmail.com> wrote:

> I'd be very interested in this as well.
> I'm working on some modifications (in the alpha stages still) to the
> BioPerl PDB parser (based on the Perl Data Language, analogous to
> NumPy) and would be interested to compare all of them (BioPython old
> and new, BioPerl old and new).
>
> In my experience, downloading the PDB, just the divided structures,
> works best with rsync, and I believe it should only take several
> hours, not several days, the first time. It should be as easy as:
>
> rsync -a rsync.wwpdb.org::ftp_data/structures/divided/pdb/ ./pdb
>
> Other options:
> http://www.wwpdb.org/downloads.html
>
> Chad
>
>
> On Wed, May 4, 2011 at 15:23, João Rodrigues <anaryin at gmail.com> wrote:
> > Just a word of advice. I tried to download the whole PDB with PDBList.py
> and
> > I ran into an error. Their server shut me down due to too many
> connections.
> > Perhaps adding an exception catcher like the one we have for NCBI servers
> > would be useful?
> >
> > Preliminary results show some degradation of speed..
> >
> > ==> benchmark_CATH-biopython_149.time <==
> > Total time spent: 530.686s
> > Average time per structure: 46.839ms
> >
> > ==> benchmark_CATH-biopython_current.time <==
> > Total time spent: 686.176s
> > Average time per structure: 60.563ms
> >
> > I'll write a full summary when I finish downloading the PDB and testing
> it.
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> >
>