/RetroRules

Extract the reaction rule SMILES from https://retrorules.org/

Primary LanguagePythonMIT LicenseMIT

RetroRules

Retrieve the reaction rules from RetroRules

Input

  • -rule_type: (string) Valid options: retro, forward, all. Return the rules that are in reverse, forward or both direction
  • -diamters: (integer list): Valid options: 2, 4, 6, 8, 10, 12, 14, 16. The diameter of the rules to return
  • -output_format: (string) Valid options: tar, csv. Format output

Ouput

  • -output: (string): Path of the output file. Either a TAR (containing a CSV) or CSV list of reaction rules that are in a RetroPath2.0 friendly format

Dependencies

Building the docker

docker build -t brsynth/retrorules-standalone .

Running the test

To run the test, run the following command:

python run.py -rule_type retro -output rules.tar -diameters 2,8 -output_format tar

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Version

v0.1

Authors

  • Thomas Duigou
  • Melchior du Lac

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

  • Joan Hérisson

How to cite RetroRules?

Please cite:

Duigou, Thomas, et al. "RetroRules: a database of reaction rules for engineering biology." Nucleic acids research 47.D1 (2019): D1229-D1235.