Version Compatibility

Reference examples tested with: RDKit 2024.09+, RDChiral 1.1+, mmpdb 3.1+, scikit-learn 1.4+, numpy 1.26+.

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Reaction Enumeration

Generate virtual libraries by applying reaction SMARTS to building blocks, enumerate analog series via matched molecular pairs, decompose into R-groups for SAR modeling, or extract transformations from reaction data. Reaction enumeration sits at the intersection of medicinal chemistry, lead optimization, and de novo design; DOGS is one published example of reaction-driven de novo design (Hartenfeller et al. 2012). The two key operations are transform (apply known reactions to make new compounds) and mine (extract rules from observed analog series). RDKit's reaction SMARTS handles the former; mmpdb / Free-Wilson handle analog-series analysis, while mapped-reaction template extraction requires separate tooling such as RDChiral.

For retrosynthetic planning (target-to-starting-material decomposition), see chemoinformatics/retrosynthesis. For ML-driven design, see chemoinformatics/generative-design. For scaffold-based design, see chemoinformatics/scaffold-analysis.

Operation Taxonomy