[BioRuby] BioRuby PDB Classes
GOTO Naohisa
ngoto at gen-info.osaka-u.ac.jp
Fri Feb 13 00:29:11 EST 2004
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
More information about the BioRuby
mailing list