RDKit Cheminformatics Guide
Lets the agent analyze molecules: parse SMILES, compute descriptors, fingerprints and substructure searches with RDKit.
- Repository
- aiming-lab/AutoResearchClaw
- Stars
- 14,802
- Licence
- MIT
- Files
- 1 file
What it does
This skill gives the agent a reference of best practices for RDKit, a widely used open-source chemistry toolkit. Once installed, when a request involves molecules written as SMILES strings, drug-like compounds, or chemical structure comparison, the agent knows how to load molecules, check for invalid input, calculate properties such as molecular weight and LogP, compare molecules by fingerprint similarity, and search for functional groups. It is guidance text, not a standalone tool: the agent still writes and runs its own Python code.
Great for
- Researchers or students doing basic cheminformatics or drug-discovery screening in Python
- Developers building molecule-filtering or compound-library pipelines with RDKit
- Anyone who wants an agent to apply Lipinski-style filters or similarity searches correctly
Skip it if
- Medical, safety or clinical decisions: the descriptors and rules of thumb here are screening heuristics, not validated predictions of toxicity or efficacy
- Users without Python and RDKit installed, since the examples cannot run without them
- Synthesis or hazardous-chemical work: the skill does not address safety, regulation or lab handling
Try asking
- “Check whether these SMILES strings are valid and give me their molecular weight and LogP”
- “Find all molecules in this SDF file that contain a carboxylic acid group”
- “Compare these compounds to my reference molecule using Morgan fingerprints and Tanimoto similarity”
- “Filter this compound library by Lipinski's Rule of 5 and export the passing molecules to a new SDF file”
Install in 3 steps
- 1
Download the skill
The ZIP contains the 1 original files, the MIT licence and an attribution note.
chemistry-rdkit.zip - 2
Add it to your agent
Claude Code (all projects)
mkdir -p ~/.claude/skills && unzip chemistry-rdkit.zip -d ~/.claude/skills/Claude Code / Agent SDK (this project only)
mkdir -p .claude/skills && unzip chemistry-rdkit.zip -d .claude/skills/Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.
- 3
Ask for the task
No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.
Get better results
- Provide SMILES or SDF files directly, and ask the agent to report invalid entries rather than silently skipping them
- Specify the fingerprint type and similarity threshold you want, since the skill's 0.7 Tanimoto cutoff is only a rough guide
- Verify results against a second tool or a chemist's review before relying on them for any decision
What's inside
- SKILL.md
Redistributed unmodified from aiming-lab/AutoResearchClaw under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.