Rdkit
RdKit allows you to generate chemical structures and perform molecular calculations, streamlining research in chemistry and drug discovery.
Install on your platform
We auto-selected Claude Code based on this skill’s supported platforms.
Run in terminal (recommended)
claude mcp add rdkit npx -- -y @trustedskills/rdkit
Or manually add to ~/.claude/settings.json
{
"mcpServers": {
"rdkit": {
"command": "npx",
"args": [
"-y",
"@trustedskills/rdkit"
]
}
}
}Requires Claude Code (claude CLI). Run claude --version to verify your install.
About This Skill
What it does
This skill provides access to RDKit, an open-source cheminformatics toolkit. It allows AI agents to perform molecular manipulations like generating 2D depictions of molecules, calculating molecular properties (e.g., logP, molecular weight), and performing chemical reactions. This is useful for tasks involving drug discovery, materials science, or any application requiring analysis and manipulation of chemical structures.
When to use it
- Drug Discovery: Predicting the properties of potential drug candidates based on their molecular structure.
- Materials Science: Analyzing the composition and characteristics of novel materials.
- Chemical Reaction Prediction: Predicting products or reactants for a given chemical reaction.
- Molecular Visualization: Generating images and representations of molecules for reports or presentations.
Key capabilities
- 2D Molecular Depictions
- Property Calculation (e.g., logP, molecular weight)
- Chemical Reaction Handling
Example prompts
- "Generate a 2D depiction of aspirin."
- "Calculate the molecular weight of caffeine."
- "Predict the products of reacting benzene with chlorine in the presence of iron(III) chloride."
Tips & gotchas
- Requires familiarity with chemical structure representation (e.g., SMILES, MOL files).
- RDKit can be computationally intensive for complex molecules or large datasets.
Tags
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