Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.

276 commits | Last update: April 04, 2020

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What pdb2sql can do for you

  • a powerful pdb2sql object to convert biomolecular structure data (in PDB format) in SQL database
  • strcuture transformation functions (rotations, translations...)
  • to calcualte structure interface (contact atoms and residues)
  • to calculate structure similarity (iRMSD, lRMSD, FNAT, DockQ...)

pdb2sql easily allows to load a PDB file in an object. Once loaded, the data can be parsed using SQL queries. To facilitate the adoption of the tool simple methods have been developped to wrap the SQL queries in simple methods. Quick examples and documentation are available on https://pdb2sql.readthedocs.io.

Read more
  • Optimized data handling
  • Big data
Programming Language
  • Python
  • SQL
  • Apache-2.0
Source code

Participating organizations


  • Cunliang Geng
    Netherlands eScience Center
  • Nicolas Renaud
    Netherlands eScience Center
Contact person
Nicolas Renaud
Netherlands eScience Center