pdb2sql

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.

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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.

Keywords
Programming languages
  • Python 93%
  • TeX 7%
License
  • Apache-2.0
</>Source code

Participating organisations

Netherlands eScience Center

Mentions

Contributors

Contact person

Nicolas Renaud

Nicolas Renaud

Netherlands eScience Center
Cunliang Geng
Cunliang Geng
Netherlands eScience Center
Nicolas Renaud
Nicolas Renaud
Netherlands eScience Center

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