[cctbxbb] programmatic access to PDB through cctbx?
Gabor Bunkoczi
gb360 at cam.ac.uk
Wed Apr 1 08:48:36 PDT 2015
Coincidentally, the EBI has put the new API into production today, so
the URL is now:
http://www.ebi.ac.uk/pdbe/api/doc
I will update the pdbe module, although there is possibly a redirection
in place.
BW, Gabor
On 2015-04-01 12:54, Gabor Bunkoczi wrote:
> Hi Kaushik,
>
> the EBI has rolled out a new web API:
>
> http://wwwdev.ebi.ac.uk/pdbe/api/doc/
>
> We have a modules that allows specific queries, and more can be
> defined fairly simply. Check out iotbx/pdb/pdbe.py, this defines
> interfaces to access the STATUS query (on the PDB tab) and the CATH
> and SCOP queries (on the SIFTS tab).
>
> There is also a possibility to do searches using Solr. Check out these
> notebooks (presented at a workshop last November) about usage. Note,
> you need to install the MySolr Python module for these to work.
>
> http://nbviewer.ipython.org/github/PDBeurope/PDBe_Programming/tree/master/search_interface/notebooks/
>
> BW, Gabor
>
> On 2015-04-01 12:11, Kaushik Hatti wrote:
>> Hello,
>>
>> Sorry if this is not relevant to this mailing list.
>>
>> I was wondering if there are any modules available under cctbx to
>> query PDB database programmatically.
>>
>> There was an option to SQL-query PDBe (from here
>> :http://www.ebi.ac.uk/pdbe-as/pdbedatabase/ [1] ). But, this service
>> has been retired since Mar 2015. How else could complex query on PDB
>> possible?
>>
>> An example query could be:
>>
>> list of PDBid with SCOPid="1hba" and (Resolution < 2 and R/Rfree <
>> 15/20) or (Resolution < 3 and R/Rfree < 20/25 ) and Completeness < 95%
>> and structureFactorAvailability="Y"
>>
>> Such a query was possible via above mentioned SQL link. However, I am
>> unable to find any other means now.
>>
>> Thanks in advance,
>> Kaushik Hatti,
>> Molecular Biophysics Unit,
>> Indian Institute of Science,
>> Bangalore, India
>>
>> --
>> People living deeply have no fear of death - Anais Nin
>> Caution: I am still the dumbest person I have ever known :-)
>>
>> Links:
>> ------
>> [1] http://www.ebi.ac.uk/pdbe-as/pdbedatabase/
>>
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>
>
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