[Biopython-dev] Benchmarking PDBParser

[João Rodrigues]

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.