atom_descriptors

[Xu22]

How can I add atom_descriptors to your model?

[hesther]

You can load atom descriptors from a sdf, npz or pkl file via the command line option --atom_descriptors_path <path_to_file> and use the descriptors either via --atom_descriptors feature (as extra atom features during the molecule featurization, that is, they are added to the regular atom features before the MPNN) or via --atom_descriptors descriptor (atomic descriptors are concatenated to the atomic feature vector after MPNN before aggregating the atoms to a molecule).

The data file should look like:

• .npz descriptors are saved as 2D array for each molecule in the order of that in the data.csv
• .pkl / .pckl / .pickle containing a pandas dataframe with smiles as index and numpy array of descriptors as columns
• .sdf containing all mol blocks with descriptors as entries

Hope this helps!

[Xu22]

Thanks a lot!