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:

--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

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.