[Bioperl-l] module proposal Bio::DB::PDB

[Ewan Birney]

On Tue, 6 Aug 2002 lsprilus@bioinformatics.weizmann.ac.il wrote:

> Hi,
> 
> We are considering to develop a Bio::DB::PDB module for allowing access   
> (search, retrieval, analysis) to OCA and PDB databases.

I would suggest setting up an abstract interface with methods like:

   $db->get_Structure_by_id();

   $query = $db->get_Structure_by_query($string);

   where $query has methods ->next_structure, like StructureIO

(Lincoln and others - should we stick to the convention get_XXXX_by_YYYY?)


Then PDB and OCA databases (don't known what OCA is!) are implementations
of Bio::DB::StructureI (ie, Bio::DB::PDB implements Bio::DB::StructureI)




> 
> I would appreciate comments and suggestions.
> 
> Jaim
> -- 
>  Dr Jaime Prilusky                | Jaime.Prilusky@weizmann.ac.il
>  Weizmann Institute of Science    | fax: 972-8-9344113
>  76100 Rehovot - Israel           | tel: 972-8-9344959
> 
>  info URL http://bioinformatics.weizmann.ac.il/jaime_prilusky.html
>  OCA is at http://bioinformatics.weizmann.ac.il:8500
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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