[BioRuby] BioRuby PDB Classes

[Alex Gutteridge]

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