[BioRuby] BioRuby PDB Classes

[Toshiaki Katayama]

Hi Alex,

Sounds great!

You can post your codes here so that everyone can try your module
and committers can discuss how to migrate your efforts.

(Note that this list is configured to restrict binary attachments.)

I think current PDB code is maintained by N. Goto and he will join
the discussion.

P.S.
It's also nice to hear that Ruby is used in EBI. :)

Thanks,
--
Toshiaki Katayama        ktym at hgc.jp, k at bioruby.org
tel://+81-3-5449-5614    Human Genome Center, Institute of Medical 
Science
fax://+81-3-5449-5434    University of Tokyo
http://bioruby.org/~k/   4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, 
Japan


On 2004/02/13, at 0:53, Alex Gutteridge wrote:

> 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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