[BioRuby] BioRuby PDB Classes
Alex Gutteridge
alexg at ebi.ac.uk
Thu Feb 12 10:53:40 EST 2004
Hi,
I'm a structural bioinformatics graduate student at the EBI. I have
very little Ruby experience (< a month), but do have some experience
with Perl, BioPerl and PDB parsing. I checked BioRuby to see if it had
a PDB parsing module and found that it did, but with some caveats: The
current module is excellent at parsing the annotation records, but
doesn't provide any easy way to get at the co-ordinate data (which is
the real meat of the PDB).
So, with this in mind, I have written a new PDB parsing module which
builds on the (excellent) parsing framework that's already there.
Essentially it adds a series of classes to represent the different
levels of structure within a PDB file - models, chains, residues and
atoms. I've also added some utility methods for calculating distances,
centre of gravity, searching etc...
I've also added (a lot!) of comments to the current code which might be
useful to people.
My question(s) to the list are:
1. Am I treading on other peoples toes here? Is someone else actively
developing the pdb.rb module? Naohisa Goto?
2. If not, should I post the code to the mailing list, or somewhere
else? I'm sure it needs some tidying up and bioruby-fication. It would
be great if someone more experienced than I could give some
comments/criticisms.
Thanks for your time.
Alex Gutteridge
European Bioinformatics Institute
Cambridge CB10 1SD
UK
Tel: 01223 492550
Email: alexg at ebi.ac.uk
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