[BioRuby] bug in residue.rb

[Moses M. Hohman]

Hi Goto and Mikael,

I'd be happy to help write more unit tests for the PDB parser if that  
would be helpful. Please let me know (I am already a bioruby  
committer - I haven't done much in quite a while though).

Moses

On Apr 13, 2006, at 10:27 AM, GOTO Naohisa wrote:

> Hi,
> Thank you for reporting bugs.
> Because we extremely changed PDB parser from 0.6.4 to 1.0,
> there might be more and more bugs.
>
> On Thu, 13 Apr 2006 08:42:09 -0400
> Mikael Borg <mikael.borg at utoronto.ca> wrote:
>
>> Hi, the [] method for Bio::PDB::Residue stopped working when I  
>> upgraded from
>> bioruby-0.6.4 to bioruby-1.0.
>>
>> I believe the problem lies in line 86 of bio-1.0.0/lib/bio/db/pdb/ 
>> residue.rb:
>>
>>       #Keyed access to atoms based on element e.g. ["CA"]
>>       def [](key)
>>         atom = @atoms.find{ |atom| key == atom.element }
>>       end
>>
>> Should this be something like
>>
>>       #Keyed access to atoms based on element e.g. ["CA"]
>>       def [](key)
>>         atom = @atoms.find{ |atom| key == atom.name.strip}
>>       end
>>
>> as atom.element==nil when I read in a pdb file?
>>
>> When a pdb file is parsed, the white space surrounding the atom.name
>> record is not removed, so e.g. atom.name=" CA ", which is why I  
>> had to strip
>> atom.name.
>
> I previously thought that the white spaces may have some literal
> meanings, but I'm now feeling inconvenience for the spaces.
> I'll change atom.name (and other methods like this) to return a
> stripped string (e.g. "CA"), if this dosn't make fatal errors.
>
> -- 
> Naohisa GOTO
> ngoto at gen-info.osaka-u.ac.jp
> Department of Genome Informatics, Genome Information Research Center,
> Research Institute for Microbial Diseases, Osaka University, Japan
>
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