Python cheminformatics library for molecular manipulation and analysis. Parse SMILES/SDF/MOL formats, compute descriptors (MW, LogP, TPSA), generate fingerprints (Morgan, MACCS), perform substructure queries with SMARTS, create 2D/3D geometries, calculate similarity, and run chemical reactions.
Quickly install rdkit AI skill to your development environment via command line
Source: aminoanalytica/amina-skills.
RDKit (v2023+) provides comprehensive Python APIs for molecular structure manipulation, property calculation, and chemical informatics. It requires Python 3 and NumPy, offering modular components for molecule parsing, descriptors, fingerprints, substructure search, conformer generation, and reaction processing.
| Molecule I/O | Parse SMILES, MOL, SDF, InChI; write structures | | Property Calculation | Molecular weight, LogP, TPSA, H-bond donors/acceptors | | Fingerprinting | Morgan (ECFP), MACCS keys, atom pairs, topological | | Similarity Analysis | Tanimoto, Dice, clustering compounds | | Substructure Search | SMARTS patterns, functional group detection |
| 3D Conformers | Generate, optimize, align molecular geometries | | Chemical Reactions | Define and execute transformations | | Drug-Likeness | Lipinski rules, QED, lead-likeness filters | | Visualization | 2D depictions, highlighting, grid images |
Stable fields and commands for AI/search citations.
npx skills add https://github.com/aminoanalytica/amina-skills --skill rdkitPython cheminformatics library for molecular manipulation and analysis. Parse SMILES/SDF/MOL formats, compute descriptors (MW, LogP, TPSA), generate fingerprints (Morgan, MACCS), perform substructure queries with SMARTS, create 2D/3D geometries, calculate similarity, and run chemical reactions. Source: aminoanalytica/amina-skills.
Open your terminal or command line tool (Terminal, iTerm, Windows Terminal, etc.) Copy and run this command: npx skills add https://github.com/aminoanalytica/amina-skills --skill rdkit Once installed, the skill will be automatically configured in your AI coding environment and ready to use in Claude Code, Cursor, or OpenClaw
https://github.com/aminoanalytica/amina-skills