[Biopython-dev] PDB tidy script

[Peter]

On Mon, Mar 23, 2009 at 8:39 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Sun, Mar 22, 2009 at 11:53 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>
>>
>> One drawback is that currently Bio.PDB's header parsing leaves a lot to
>> be desired, and very little of the header is output when saving a PDB file
>> (Thomas' focus is/was very much on the 3D data).
>>
>> Peter
>
> I haven't been on this list long enough to know -- is Thomas still
> supporting the PDB module? If so, would he give his blessing to some more
> invasive changes to the PDB module, such as unifying PDBParser and
> parse_pdb_header? That separation has always seemed curiously vestigal to
> me.
> Now that github gives us some flexibility with public branches, it would
> be nice to have a discussion on some longer-term plans for Bio.PDB. I do a
> fair amount of work with PDB files and PyMol at my lab, and if the Biopython
> core devs are open to it, I can start merging enhancements into my public
> branch on github. However, if there's already a plan for the module, it's
> obviously best for me not to publish a divergent branch.

If you look back over the history, there initially was no header parsing,
it was a contribution from Kristian Rother, and I would agree, it is rather
disjoint from the rest of the code.  One thing I personally wanted last
time I was working with PDB files was to have secondary structure
information (for them alpha and beta sheet lines in the header)
mapped onto the residue objects automatically.

And yes, Thomas is supporting the PDB module, but his time has
been rather limited of late.  When I asked him about some of the
open enhancement requests in bugzilla recently (off list) he said
said we needed "a separate class to parse all the info in the header,
not a slew of additions to the core parser class (which is designed
to deal with the 3D data only)."

I would suggest you try and get Thomas involved now for his input
on the design (before you start coding), but if need be press ahead
anyway for your own use, and he can always comment on your
public branch.  I hope the two of you can work together on this, and
if/when Thomas does stand down (or delagate), you could then be
in an excellent position to take over as the Bio.PDB maintainer if
that's what you wanted.

Peter