[Biopython-dev] Future of Bio.PDB

[João Rodrigues]

@Eric: p3d, csb, biskit, prody, there are plenty of libraries that
"compete" with Bio.PDB, each focused on a different area or offering
specific features. We should go over them and see what we could implement,
how to implement the parsing, etc. p3d offers a really nice selection API
indeed, I guess more geared towards interactive usage, but maybe a bit
cumbersome for high-throughput applications? (disclaimer, never used it..
). We also have the "support" of EBI, their parsers are probably the most
robust so worth trying to ask how their implementation differs from ours (I
know they have one of their own).

@David: Thanks a lot for the offer, could you make a list of the things you
see outdated or otherwise worth working on? (Maybe we could open a wiki
page / gist for a list of possible areas of improvement?)

@Peter: I thought of that too. Keeping Bio.PDB would be crucial to maintain
backwards compatibility while we could work and offer users the possibility
to test/work with the new module under an "experimental" tag.


2014-02-19 17:41 GMT+01:00 Peter Cock <p.j.a.cock at googlemail.com>:

> On Wed, Feb 19, 2014 at 4:35 PM, David Cain <davidjosephcain at gmail.com>
> wrote:
> > I frequently make use of Bio.PDB, and agree wholeheartedly that certain
> > aspects of it are very dated, or haphazardly organized.
> >
> > The module as a whole would benefit greatly from some extra attention.
> I'm
> > happy to lend a hand in whatever revamp takes place.
> >
> > David Cain
> > +1 (339) 222 4452
>
> Very true, and thanks for the offer.
>
> If we go with the parallel namespace option (Bio.Struct, Bio.structure or
> similar) then we can stick an experimental warning on it and include it
> as a 'beta' module within the next release (while continuing to keep
> Bio.PDB fully backward compatible for now, with the likely goal of
> a formal deprecation in future).
>
> Peter
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