[Biopython-dev] Optimization of PDBParser and friends

Peter Cock p.j.a.cock at googlemail.com
Tue Sep 4 12:16:26 UTC 2012

On Tue, Sep 4, 2012 at 7:11 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Peter, João,
> Just a little FYI. I ran into the OrderedDict issue when I started writing
> SearchIO a few months ago as well, so I added an OrderedDict implementation
> in Bio._py3k
> (https://github.com/bow/biopython/commit/34f873b2d21136487a0b925be898c52daa0cc61c).
> The code is from the ordereddict module from PyPI at that time. I haven't
> checked if it's the same as the one shown in the link (there may have been
> some updates), but it seems to work fine up to now.
> Hope this is useful :),
> Bow

Given the OrderedDict will be useful for Bio.PDB and Bow's SearchIO,
that seems quite a good case for including it. How does this look
(on the 'od' branch in my repository)?


This differs from Bow's version in that I put the module in as a separate
file (Bio/_ordereddict.py), and that it will prefer the ordereddict package
if already installed (e.g. from PyPI).


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