Individual skill
rdkit
Guides use of RDKit (Python) for reading and writing SMILES, MOL/SDF, and InChI, computing descriptors (MW, LogP, TPSA), generating Morgan/MACCS/atom-pair fingerprints, running SMARTS substructure searches, applying reaction SMARTS, and building 2D/3D coordinates with ETKDG. Use when parsing or sanitizing molecules that fail default sanitization, calculating Tanimoto similarity or clustering compounds, filtering libraries by substructure, embedding and optimizing conformers, or computing Murcko scaffolds and molecule hashes. Use when fine-grained control over sanitization or algorithms is needed. For simpler standard workflows, use datamol instead, which wraps RDKit.
plugins/KalarisLabs/research-agent-skills/skills/rdkit/SKILL.md
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- Last checked
- Nov 4, 2026
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- Nov 6, 2026
- License
- Apache-2.0
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SKILL.mdcore · 6,690 bytesSKILL.mdcore · 6,690 bytesSKILL.mdcore · 6,690 bytesreferences/api_reference.mddoc · 17,491 bytesreferences/core_capabilities.mddoc · 15,446 bytesreferences/descriptors_reference.mddoc · 11,814 bytesreferences/smarts_patterns.mddoc · 8,143 bytesreferences/workflows_and_best_practices.mddoc · 5,313 bytesscripts/molecular_properties.pyruns · 7,344 bytesscripts/similarity_search.pyruns · 9,529 bytesscripts/substructure_filter.pyruns · 12,337 bytes
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# RDKit Cheminformatics Toolkit
## Overview
RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks.
**Current baseline (checked 2026-06-07):** RDKit **2026.03.3** is the latest GitHub/PyPI release (`rdkit` 2026.3.3 on PyPI). Official installation docs continue to recommend conda-forge for most users, while cross-platform PyPI wheels are published under the `rdkit` package name. `rdkit-pypi` is the old PyPI package name and should only appear when maintaining legacy environments.
## Installation and Setup
Use `uv` when installing into an existing Python environment:
```bash
uv pip install rdkit