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/se...
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/
_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb