Limitations and known issues¶

• Very large molecules are skipped in some workflows. A molecule with more than 30 non-ring single bonds is not mutated, and a molecule with more than 100 hydrogen atoms is not processed by grow or link.

• Database compatibility depends on the RDKit version. Context canonicalization uses RDKit's SMILES representation. A change in how RDKit writes SMILES can make a database built with one RDKit version unusable from a different version. We did not observed this in the past, but recommend to pin RDKit (>=2025.3.5) when sharing databases across environments.