Skill: cheminem/pharmaclaw-catalyst-design (version 1.0.0)

--- name: pharmaclaw-catalyst-design description: Organometallic catalyst recommendation and novel ligand design for drug synthesis reactions. Recommends catalysts (Pd, Ru, Rh, Ir, Ni, Cu, Zr, Fe) for reaction types (Suzuki, Heck, Buchwald-Hartwig, metathesis, hydrogenation, click, etc.) from curated database with scoring. Designs novel ligand variants via RDKit (steric, electronic, bioisosteric modifications). Chains from chemistry-query/retrosynthesis (receives reaction type + substrate) and feeds into IP Expansion (novel ligands as patentable inventions). Triggers on catalyst, ligand, organometallic, cross-coupling catalyst, reaction conditions, catalyst selection, ligand design, cone angle, bite angle, phosphine, NHC, palladium catalyst, ruthenium catalyst. --- # 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 ```bash # 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.


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: suspicious (MEDIUM)