How do I install the Pharmaclaw Catalyst Design skill?

Run npx skillmds@latest add dvcrn/pharmaclaw-catalyst-design in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Pharmaclaw Catalyst Design safe to use?

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Which AI agents work with Pharmaclaw Catalyst Design?

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Is Pharmaclaw Catalyst Design free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Pharmaclaw Catalyst Design?

dvcrn (@dvcrn) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pharmaclaw Catalyst Design by dvcrn

Name: Pharmaclaw Catalyst Design
Rating: 4.2 (5 reviews)
Author: dvcrn

Pharmaclaw Catalyst Design

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.

dvcrn Updated Sep 8, 2026 32 repo stars

File contents

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.

---name: pharmaclaw-catalyst-designdescription: 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## OverviewRecommends 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 couplingpython 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 PPh3python scripts/ligand_designer.py --scaffold PPh3 --strategy all --draw# Full chain: reaction → catalyst → ligand optimizationpython 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 AliasesPPh3, PCy3, dppe, dppp, NHC_IMes, NHC_IPr — resolved automatically to SMILES.

Frequently asked questions