[BioRuby] BioRuby PDB Classes

[GOTO Naohisa]

Hi,

On Thu, 12 Feb 2004 15:53:40 +0000
Alex Gutteridge <alexg at ebi.ac.uk> wrote:

> 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).

As you said, currently, Bio::PDB in BioRuby is literally a parser, 
processing texts. Co-ordinate data is provided only as a sets of numbers.
Some higher-level classes for molecular structures are needed,
but not written yet.

> 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.

Great!

In addition, some template or abstract classes might be needed,
because there are mmCIF and other data formats for molecular structure.

> 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?

I'm Naohisa Goto, but I'm not actively developing the pdb.rb now,
and no one (except you) are doing, as far as I know.
So, you can freely modify the pdb.rb.

If you want to change existing class/method's name, or massively change
existing class/method's specification or definition, please tell us.

> 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.

If the code is short, please post to the mailing list.
For long codes, please send to staff at bioruby.org, or you can use
the BioRuby Project Wiki page (http://wiki.bioruby.org/English/).

Regards,
-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Genome Information Research Center, Osaka University, Japan