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Reaction SMILES postprocessing

AV Alain C. Vaucher
PS Philippe Schwaller
JG Joppe Geluykens
VN Vishnu H. Nair
AI Anna Iuliano
TL Teodoro Laino
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The Pistachio database provides reaction SMILES strings parsed into reactant, reagent, and product molecules. We merged the reactant and reagent molecules into a list of precursor molecules, and all the SMILES strings were canonicalized with RDKit33. For both lists of precursor and product SMILES, we removed the duplicates and reordered the lists alphabetically. The concatenation of the SMILES strings produced the reaction SMILES used for training. Following the reaction SMILES notation, we separated the molecules within the same class using dots (“.”), while the precursor and product lists were separated by “>>”. For fragment bonds, we adopted the convention of using the tilde symbol (“~”) instead of a dot.

For use in language-based models, the reaction SMILES is tokenized by inserting spaces between the SMILES tokens.

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