[BioRuby] bug in pdb.rb bio-1.0.0
ngoto at gen-info.osaka-u.ac.jp
Mon Apr 23 15:25:28 UTC 2007
The patch have been committed into CVS.
ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp
On Sat, 14 Apr 2007 14:52:26 +0900
Toshiaki Katayama <ktym at hgc.jp> wrote:
> Hello Mikael,
> Thank you for your patch.
> Could you prepare your patch in unified diff format? (diff -u)
> Alex or Goto-san, could you confirm this patch fixes the problem?
> (as I don't use PDB usually).
> On 2007/04/14, at 7:23, Mikael Borg wrote:
> > Hello bioruby,
> > I think I discovered a bug in the pdb parser. Below, a description of
> > the bug and a one-liner fix that I hope corrects the problem.
> > When parsing a pdb file with many models, but only one chain per model,
> > all atoms are added to residues in the first Bio::PDB::Model of the
> > Bio::PDB structure.
> > The reason is that the pdb parser doesn't reset the variable for the
> > current chain (cChain) when the 'MODEL' keyword is encountered, so atoms
> > keep getting assigned to the chains in the first model.
> > Suggested patch:
> > # diff pdb.rb pdb.rb.orig
> > 1506d1505
> > < cChain = nil
> > Thank you for your efforts, I am looking forward to the next release!
> > Regards,
> > Mikael Borg
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
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