[Bioperl-l] A perl regex query

Chris Fields cjfields at uiuc.edu
Tue Sep 18 11:38:04 EDT 2007

On Sep 18, 2007, at 8:05 AM, Stefan Kirov wrote:

> neeti somaiya wrote:
>> ...
> It seems to me you are trying to match 2 collections of chemical
> compounds. If you need to do this reliably you need to use canonical
> smiles (perhaps there are other solutions but I am not aware of them).
> There are many resources for that, including open-source:
> http://openbabel.sourceforge.net/wiki/Main_Page
> It is not really bioperl's cup of tea, this is much more a
> chemi-informatics problem. I am not sure if there is a need for  
> bioperl
> to be extended this way- any thoughts on that?
> Hope this helps, regards
> Stefan

I would vote nyet myself unless I was convinced that this would be  
beneficial to bioperl core.  Right now I'm not yet there, primarily b/ 
c of the already available OpenBabel (with available CPAN interface)  
and other resources, not to mention there are too many areas in  
bioperl which need more focus (tests, documentation, etc).

However, if we do want to incorporate chemi-informatics at some point  
it could be something which is not integrated into the core  
architecture and can be installed separately (like network, ext, db,  


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