[Bioperl-l] Parsing PDB entries in BioPerl

[Ann Loraine]

> therefor I would want to ask you which data in a PDB entry you're
> typically intrested in and which questions you want to ask to such an
> object.

Dear Kris,

I'd be very interested in being able to parse out which residues are
post-translationally modified as well as which residues are involved in
catalysis - the active sites.

Any kind of feature information on one or more protein sequences would be
great.  Seems like these could be abstracted into two types of features:

1. SingleSpanFeatures - features that refer to a 1-or-more residue spans
on a single chain

2. CompoundFeatures - groups of SingleSpanFeatures

	(such as contact points across multiple chains)

Also, to model PDB files that describe a protein complex, you might want
to build a MultiMoleculeSeq, a container for multiple sequences, each of
which would be decorated with CompoundFeatures and SingleSpanFeatures.

Yours,

Ann