[BioRuby] Bio::PDB::Residue patch
GOTO Naohisa
ngoto at gen-info.osaka-u.ac.jp
Mon Apr 23 16:03:43 UTC 2007
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
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