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

[Hilmar Lapp]

I agree. The name of the generic interface should maybe better be 
Bio::DB::StructureDBI, or Bio::DB::RandomAccessStructureI. This BTW 
also tells us that Bio::DB::RandomAccessI isn't the best name; it 
should rather be Bio::DB::SeqDBI or Bio::DB::RandonAccessSeqI for 
consistency ...

Just my Can$0.02 (still at ISMB).

	-hilmar

On Tuesday, August 6, 2002, at 03:27  AM, Ewan Birney wrote:

> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>>
>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------