rdkit
Category: chemistry-and-drug-discovery · License: BSD-3-Clause license · Version: 1.3 · Includes scripts
Tags: cheminformatics, RDKit, SMILES, molecular descriptors, fingerprints, drug discovery
When to use it
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.Example requests
Ask your agent in plain language, for example:- “Chem.MolFromSmiles keeps returning None for my nitro-containing SMILES. How do I find out what’s wrong and still load the molecule?”
- “I have compounds.sdf with about 40k molecules from a vendor. I need to keep only those containing a carboxylic acid but no primary amine, then write the hits to a new SDF with their MW, cLogP and TPSA as properties. Some records fail to parse. Can you write the script?”
- “I’ve got a list of ~2,000 screening hits and want to group them into structural clusters, then pick one representative from each cluster. The distance cutoff matters to me and I want to control how the fingerprints are built.”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole chemistry-and-drug-discovery category with /plugin install chemistry-and-drug-discovery@research-agent-skills.