[cctbxbb] programmatic access to PDB through cctbx?

[Gabor Bunkoczi]

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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