[Bioperl-l] PDB ATOM records: name, segid, etc.

[Andrew Dalke]

Kris Boulez:
> Does anyone know if OpenBabel is more then a converter (i.e. could we
> use to read data in and let it create Structure objects) ?

That could be done.  OpenBabel is built on OELib, and there are
bindings from Python to OELib (done by Bob Tolbert, then at
Boehringer-Ingelheim), so I don't see any technical reason why there
couldn't be bindings to Perl.

There are social reasons.  Do you want bindings to a largish C++
toolkit?  How important is it?  Should that instead be a distinct
project from bioperl (like FROWNS is from Biopython)?

I think it's easiest to use OpenBabel as an external application,
and that that's the right thing to do.

> > A related issue, what do you think about incorporating bond, angle, etc.
> > data, and forcefield parameters?  And things like non-bonded
> > interaction analysis, H-bond detection, etc? We have various bits of
> > Perl code that we are trying to organize, and BioPerl's PDB module
> > would be a good place to put it.
> > 
> I think Bio::Structure is certainly the place these belong under. Which
> data/analysis are you exactly thinking about ?

We should definitely have a Structure BoF at BOSC this year.

One thing I did in VMD (a structure visualization and analysis program I
helped develop) was a pretty powerful atom selection language, which was
tied in with a way to extract different properties from the structure.

  http://www.ks.uiuc.edu/Research/vmd/current/ug/node78.html#ug:topic:selections

With that it became pretty easy to develop all sorts of different
analysis functions.

					Andrew