[BioRuby-cvs] bioruby/lib/bio/db/pdb residue.rb,1.12,1.13

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv22990/lib/bio/db/pdb

Modified Files:
	residue.rb 
Log Message:
Bio::PDB::Residue#[] (and Bio::PDB::Heterogen#[]) are changed to use the
name field for selecting atoms, because the element field is not useful
for selecting atoms and is not used in many pdb files.
(reported by Alex Gutteridge in [BioRuby] Bio::PDB::Residue patch)


Index: residue.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** residue.rb	5 Apr 2007 23:35:41 -0000	1.12
--- residue.rb	23 Apr 2007 16:03:25 -0000	1.13
***************
*** 66,72 ****
        alias id residue_id
  
!       #Keyed access to atoms based on element e.g. ["CA"]
        def [](key)
!         atom = @atoms.find{ |atom| key == atom.element }
        end
  
--- 66,72 ----
        alias id residue_id
  
!       #Keyed access to atoms based on atom name e.g. ["CA"]
        def [](key)
!         atom = @atoms.find{ |atom| key == atom.name }
        end