This repo provides the necessary code and data to reproduce the results in the reply to comment on "Physics-based representations for machine learning properties of chemical reactions". This paper as well as the associated code explore the dependency of reaction barrier prediction to the atom-mapping quality.
The datasets focussed on here are the Cyclo-23-TS, GDB7-22-TS and Proparg-21-TS. For each dataset, the following information is available
- The xyz structures of reactants and products, and computed barriers
- Atom maps for the original-mapped reactions (where available), RXNMapper reactions, and randomly mapped reactions.
- Corresponding submission csv files for chemprop
- The results of a 10-fold CV run of physics-based model SLATM+KRR
The codes in src/
provide:
- Means to atom map the reactions using RXNMapper, using the files
mapper.py
andprocess_maps.py
- Random mappings are generated using
random_mapper.py
- The files
learning.py
andreaction_reps.py
are support files forslatm_krr.py
which performs the 10-fold CV prediction with 80/10/10 splits of the SLATM+KRR model
Results of the CGR runs are saved to results/
.
To run CGR models yourself, you will need to do so using chemprop, with the csv files in the data directory.