RDKit conformation generation script (Python 3)

At Pharmacelera we have written a python script to generate conformations with RDKit,
one of the best freely available tools for conformer generation due to
its accuracy reproducing experimentally determined structures and its
reasonable computing requirements. You can learn more about this script here.

New features from the previous version are:

  • Calculation of conformer energy and difference with minimum energy one.
  • Better control about what is happening if a molecule fails.
  • Possibility to generate a log file to check the different steps done
  • If MMFF does not work, automatic calculation with UFF (and warning of the molecule).
  • Better control of stereochemistry configuration according to the input molecule.
RDKit conformer generation




Torre R, 4a planta, Despatx A05, Parc Científic de Barcelona (PCB). C/ Baldiri Reixac 4-8 08028 Barcelona