[Biopython-dev] Optimization of PDBParser and friends

[Peter Cock]

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)?

https://github.com/peterjc/biopython/commit/52b011aa8ddce06e636de776d8cea8e62845853f

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).

Peter