Catalyst Design Agent v1.0.0
Overview
Recommends organometallic catalysts for drug synthesis steps and designs novel ligand modifications. Two core workflows: recommend (find the right catalyst) and design (create novel ligand variants).
Quick Start
# Recommend catalysts for a Suzuki coupling
python scripts/catalyst_recommend.py --reaction suzuki
# Recommend with constraints (prefer cheap, earth-abundant)
python scripts/catalyst_recommend.py --reaction "C-N coupling" --constraints '{"prefer_earth_abundant": true, "max_cost": "medium"}'
# Design novel ligand variants from PPh3
python scripts/ligand_designer.py --scaffold PPh3 --strategy all --draw
# Full chain: reaction → catalyst → ligand optimization
python scripts/chain_entry.py --input-json '{"reaction": "suzuki", "context": "retrosynthesis"}'
Scripts
scripts/catalyst_recommend.py
Scores and ranks catalysts from curated database (12 catalysts, 28 reaction types).
--reaction <type> Required. e.g., suzuki, metathesis, C-N coupling, hydrogenation
--substrate <SMILES> Optional. Substrate context
--constraints <JSON> Optional. {prefer_metal, max_cost, prefer_earth_abundant}
--enantioselective Flag. Prioritize chiral catalysts
Scoring (0-100): reaction match (50), cost (15), metal preference (10), enantioselectivity (10), loading efficiency (5), advantages (5), earth-abundance (5).
scripts/ligand_designer.py
Generates novel ligand variants via three strategies:
| Strategy | Method | Output |
|---|---|---|
| steric | Add methyl/iPr/tBu to aromatic rings | Modified SMILES + properties |
| electronic | Add OMe/F/CF3 substituents | Modified SMILES + properties |
| bioisosteric | P→NHC, phenyl→pyridyl, phosphine→phosphite | Conceptual suggestions + rationale |
--scaffold <SMILES|name> Required. PPh3, NHC_IMes, NHC_IPr, PCy3, dppe, dppp, or raw SMILES
--strategy <type> steric|electronic|bioisosteric|all (default: all)
--draw Generate 2D grid PNG of variants
--output <path> Save JSON results to file
scripts/chain_entry.py
Standard PharmaClaw chain interface. Accepts JSON, routes to recommend/design/both.
Input keys: reaction, scaffold/ligand, substrate/smiles, constraints, enantioselective, strategy, draw, context
If only reaction is given, also auto-runs ligand optimization on the top recommended catalyst's ligand.
Chaining
| From | Input | To | Output |
|---|---|---|---|
| Chemistry Query / Retrosynthesis | Reaction type needed for a synthesis step | Catalyst Design | Ranked catalysts + conditions |
| Catalyst Design | Top catalyst ligand SMILES | Ligand Designer | Novel ligand variants |
| Catalyst Design | Novel ligand SMILES | IP Expansion | Patent landscape check |
| Catalyst Design | Recommended conditions | Chemistry Query | Forward reaction simulation |
Database
references/catalyst_database.json — 12 catalysts, 8 metals, 28 reaction types. Includes SMILES, conditions, loading ranges, cost ratings, advantages/limitations, and literature DOIs.
Expandable: add entries following the existing schema.
Ligand Aliases
PPh3, PCy3, dppe, dppp, NHC_IMes, NHC_IPr — resolved automatically to SMILES.