How do I install the Rdkit skill?

Run npx skillmds@latest add ai4protein/rdkit 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 Rdkit safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Rdkit?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Rdkit free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under BSD-3-Clause.

ai4protein (@ai4protein) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Rdkit by ai4protein — Agent Skill

Name: Rdkit
Author: ai4protein

Rdkit

RDKit cheminformatics via VenusFactory bioinfo scripts and agent_generated_code. Use for SMILES/SDF, descriptors, fingerprints, substructure filters, similarity. Do NOT use for ChEMBL bioactivity download (chembl_database) or openFDA (fda). No dedicated rdkit_* LangChain tool — run scripts or import modules.

ai4protein 64d0603 5 files · 59.9 KB Updated Sep 17, 2026

File contents

RDKit Cheminformatics

Overview

Fine-grained molecular control in Python. Platform helpers live under src/tools/bioinfo/rdkit/ (CLI + importable functions). Prefer them over re-implementing RDKit from scratch.

VenusFactory execution

No rdkit_* @tool in the hub — use agent_generated_code (or python_repl) and import the modules below.
Extended tutorials: read_skill("rdkit", relative_path="references/legacy_guide.md").
Bioactivity from ChEMBL first → chembl_database, then RDKit for chemistry ops.

Project scripts (src/tools/bioinfo/rdkit/)

Script	Purpose
`molecular_properties.py`	MW, LogP, TPSA, Lipinski, QED → CSV
`substructure_filter.py`	SMARTS/SMILES include/exclude filters
`similarity_search.py`	Morgan/RDKit/MACCS fingerprints + Tanimoto

from src.tools.bioinfo.rdkit import calculate_properties, filter_molecules, similarity_search
# loaders: substructure_filter.load_molecules / similarity_search.load_molecules

python -m src.tools.bioinfo.rdkit.molecular_properties "CCO"
python -m src.tools.bioinfo.rdkit.similarity_search "CCO" database.smi --threshold 0.7 -o hits.csv

When NOT to use

Download ChEMBL molecules/activities → chembl_database
Simple FDA label search → fda / query_fda

Common mistakes

Importing load_molecules from package root (use module-specific loaders)
Assuming a LangChain tool named rdkit_* exists
Sanitization failures on dirty SMILES — handle None mols

References

references/api_reference.md, descriptors_reference.md, smarts_patterns.md
references/legacy_guide.md — full capability cookbook

---name: rdkitdescription: RDKit cheminformatics via VenusFactory bioinfo scripts and agent_generated_code. Use for SMILES/SDF, descriptors, fingerprints, substructure filters, similarity. Do NOT use for ChEMBL bioactivity download (chembl_database) or openFDA (fda). No dedicated rdkit_* LangChain tool — run scripts or import modules.license: BSD-3-Clause---# RDKit Cheminformatics## OverviewFine-grained molecular control in Python. Platform helpers live under `src/tools/bioinfo/rdkit/` (CLI + importable functions). Prefer them over re-implementing RDKit from scratch.## VenusFactory execution- No `rdkit_*` `@tool` in the hub — use **`agent_generated_code`** (or `python_repl`) and import the modules below.- Extended tutorials: `read_skill("rdkit", relative_path="references/legacy_guide.md")`.- Bioactivity from ChEMBL first → `chembl_database`, then RDKit for chemistry ops.## Project scripts (src/tools/bioinfo/rdkit/)| Script | Purpose ||--------|---------|| `molecular_properties.py` | MW, LogP, TPSA, Lipinski, QED → CSV || `substructure_filter.py` | SMARTS/SMILES include/exclude filters || `similarity_search.py` | Morgan/RDKit/MACCS fingerprints + Tanimoto |```pythonfrom src.tools.bioinfo.rdkit import calculate_properties, filter_molecules, similarity_search# loaders: substructure_filter.load_molecules / similarity_search.load_molecules``````bashpython -m src.tools.bioinfo.rdkit.molecular_properties "CCO"python -m src.tools.bioinfo.rdkit.similarity_search "CCO" database.smi --threshold 0.7 -o hits.csv```## When NOT to use- Download ChEMBL molecules/activities → `chembl_database`- Simple FDA label search → `fda` / `query_fda`## Common mistakes- Importing `load_molecules` from package root (use module-specific loaders)- Assuming a LangChain tool named `rdkit_*` exists- Sanitization failures on dirty SMILES — handle `None` mols## References- `references/api_reference.md`, `descriptors_reference.md`, `smarts_patterns.md`- `references/legacy_guide.md` — full capability cookbook

Frequently asked questions