baseline_chemprop

Code to obtain the ChemProp results

We use chemprop version 1.5.0

• src/cgr.py is the main script used to train the model for the specified dataset, atom-mapping regime, and split type. It can be run, for example, for the GDB7-22-TS using the True atom-mapping, random splits, and implicit H nodes with

python src/cgr.py --gdb --true

Note that the training creates a lot of directories and output files so it is more convenient to run the script from a dedicated directory.

• src/cgr-repr.py extracts and saves a representation for a given model checkpoint. See example of usage at ../results/repr.
• src/chemprop.patch is the patch we used to bypass the valence check (see below).
• config/ contains the hyperparameters for each dataset taken from doi:10.1039/d3dd00175j (repo).
• results/ contains the submission scripts and the results (MAEs and RMSEs) for all the models trained, as well as the checkpoint file used to generate the t-SNE map (results/gdb-true/fold_0/fold_0/model_0/model.pt, see ../results/repr).

Patch

The original chemprop code cannot process hypervalent Si compounds of the Proparg-21-TS dataset. The patch that disables the valence check can be found at src/chemprop.patch Run

$ patch < src/chemprop.patch

to apply it and

$ patch -R < src/chemprop.patch

to revert. (Modification of the paths may be needed.)