[BioRuby] Bio::PDB::Residue patch
Alex Gutteridge
alexg at kuicr.kyoto-u.ac.jp
Mon Apr 23 08:40:18 UTC 2007
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
>
>
> _______________________________________________
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> BioRuby at lists.open-bio.org
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Alex Gutteridge
Bioinformatics Center
Kyoto University
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