rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
npx skills add LeonChaoX/qinyan-academic-skills --skill rdkit --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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. ## Core Capabilities ### 1. Molecular I/O and Creation **Reading Molecules:** Read molecular structures from various formats: ```python from rdkit import Chem # From SMILES strings mol = Chem.MolFromSmiles('Cc1ccccc1') # Returns Mol object or None # From MOL files mol = Chem.MolFromMolFile('path/to/file.mol') # From MOL blocks (string data) mol = Chem.MolFromMolBlock(mol_block_string) # From InChI mol = Chem.MolFromInchi('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H') ``` **Writing Molecules:** Convert molecules to text representations: ```python # To canonical SMILES smiles = Chem.MolToSmiles(mol) # To MOL block mol_block = Chem.MolToMolBlock(mol) # To InChI inchi = Chem.MolToInchi(mol) ``` **Batch Processing:** For processing multip
- Overview
- Core Capabilities
- 1. Molecular I/O and Creation
- 2. Molecular Sanitization and Validation
- 3. Molecular Analysis and Properties
- 4. Molecular Descriptors and Properties
- 5. Fingerprints and Molecular Similarity
- 6. Substructure Searching and SMARTS
- 7. Chemical Reactions
- 8. 2D and 3D Coordinate Generation
- 9. Molecular Visualization
- 10. Molecular Modification
- 11. Working with Molecular Hashes and Standardization
- 12. Pharmacophore and 3D Features
What does the rdkit skill do?
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill rdkit --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.