[Biopython-dev] Benchmarking PDBParser

[João Rodrigues]

Hello all,

Following a few discussions, I'm tempted to benchmark the current
implementation of the PDBParser and see how it fares against an old
implementation (I think I'll use 1.48 since older versions need Numerical
Python). The main objective is to see if the recent developments have a
significant impact in its speed.

I thought of downloading the entire PDB but since it would take several
days, I downloaded the CATH domain list instead. Those are just protein ATOM
records, without any header, but since all modifications were essentially
dealing with ATOM records, etc, I think it might be as valid.

I'll be running tests today and tomorrow and I'll put the results up
somewhere later on. I'm also making the scripts available so it is easy to
benchmark it later on.

Thoughts or suggestions?

Cheers,

João