[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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