AL
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BI
bio-reaction-enumeration
Maintainer FreedomIntelligence · Last updated April 1, 2026
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-reaction-enumeration
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: AllChem.ReactionFromSmarts(), rxn.RunReactants() (RDKit).
- 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.
- amide_rxn = AllChem.ReactionFromSmarts( 'C:1O.[N:3]>>C:1[N:3]' ).
Source Doc
Excerpt From SKILL.md
Reaction SMARTS Basics
from rdkit import Chem
from rdkit.Chem import AllChem
## 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))
Use cases
- Use when creating combinatorial libraries or enumerating products from synthetic routes.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- molecular-io - Save enumerated libraries
- molecular-descriptors - Filter by properties
- admet-prediction - Screen for drug-likeness
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