bio-reaction-enumeration

## Version Compatibility Reference examples tested with: RDKit 2024.03+ 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 a combinatorial library from my building blocks"** → Enumerate virtual compound libraries by applying reaction SMARTS transformations to sets of building-block molecules, producing and validating all product combinations for a defined synthetic route. - Python: `AllChem.ReactionFromSmarts()`, `rxn.RunReactants()` (RDKit) Generate virtual compound libraries using reaction SMARTS. ## Reaction SMARTS Basics ```python from rdkit import Chem from rdkit.Chem import AllChem # Define reaction (reactants >> products with atom mapping) # Amide coupling: carboxylic acid + amine -> amide amide_rxn = AllChem.ReactionFromSmarts( '[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]' ) # Validate reaction definition n_errors = amide_rxn.Validate() if n_errors[0] == 0: print('Reaction is valid') # Run reaction acid = Chem.MolFromSmiles('CC(=O)O') amine = Chem.MolFromSmiles('CCN') products = amide_rxn.RunReactants((acid, amine)) # products is a tuple of tuples: ((product1,), (product2,), ...) for prod_set in products: for prod in prod_set: Chem.SanitizeM...