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

[Hilmar Lapp]

Sounds good.

ISMB: the breaking news is Chris took down (he left this morning) 
the OPENBIO wireless reaching out into the auditorium ...

	-hilmar

On Wednesday, August 7, 2002, at 12:41  AM, Steve Chervitz wrote:

> I don't like the name "StructureDBI" because people may think it is 
> somehow
> related to DBI.pm (e.g., a subclass). Bio::DB::StructureDatabaseI and
> Bio::DB::SeqDatabaseI would avoid this problem.
>
> How's ISMB going? Any breaking news?
>
> Steve
>
> --- Hilmar Lapp <hlapp@gnf.org> wrote:
>> 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
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>>>>
>>>
>>> -----------------------------------------------------------------
>>> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
>>> <birney@ebi.ac.uk>.
>>> -----------------------------------------------------------------
>>>
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>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
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>
>
> =====
> Steve Chervitz
> sac@bioperl.org
>
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------