[BioRuby] Bio::PDB::Residue patch

[GOTO Naohisa]

Hi Alex,

I've applied the patch into the CVS.
I've also wrote a description to doc/Changes-0.7.rd, 
because this is imcompatible with the older version,
though the function in the older version is somehow broken.

Thanks,

Naohisa Goto
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp

On Mon, 23 Apr 2007 17:40:18 +0900
Alex Gutteridge <alexg at kuicr.kyoto-u.ac.jp> wrote:

> Hmmm. Attachment didn't seem to work. Here is the patch:
> 
> --- residue.rb  2007-04-23 15:17:37.000000000 +0900
> +++ residue.new.rb      2007-04-23 15:17:13.000000000 +0900
> @@ -65,9 +65,9 @@
>         # Now, Residue#id is an alias of residue_id.
>         alias id residue_id
> -      #Keyed access to atoms based on element e.g. ["CA"]
> +      #Keyed access to atoms based on atom name e.g. ["CA"]
>         def [](key)
> -        atom = @atoms.find{ |atom| key == atom.element }
> +        atom = @atoms.find{ |atom| key == atom.name }
>         end
>         # Updates residue id. This is a private method.
> 
> AlexG
> 
> On 23 Apr 2007, at 15:24, Alex Gutteridge wrote:
> 
> > Hi All,
> >
> > I've attached a tiny patch for 'bio/db/pdb/residue.rb' which fixes  
> > some broken functionality. The keyed access to residue atoms was  
> > using the element field rather than the name field. The element  
> > field is not useful for selecting atoms and is not used in many pdb  
> > files. Can someone with commit access please check and apply the  
> > patch?
> >
> >
> > Alex Gutteridge
> >
> > Bioinformatics Center
> > Kyoto University
> >
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby