[BioRuby] bug in pdb.rb bio-1.0.0

[Toshiaki Katayama]

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).

Thanks,
Toshiaki


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