rdkit

Analyze and manipulate molecules with RDKit for cheminformatics workflows.

52|6|Updated Nov 24, 2025

Search Tags:#cheminformatics #fingerprints #substructure #descriptors #rdkit

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill rdkit

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: rdkit
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/rdkit
Command: npx skills add https://github.com/ovachiever/droid-tings --skill rdkit

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit, and includes scripts (resource) and references (resource) components.

What problem does it solve?

RDKit enables fine-grained molecular analysis, including I/O, descriptor calculations, fingerprinting, substructure searches, and 2D/3D generation for drug discovery workflows.

Core Features & Use Cases

Molecular I/O: Read/write SMILES, MOL, SDF; convert to SMILES, InChI.
Descriptors & properties: MW, LogP, TPSA, HBD/HBA, rotatable bonds.
Fingerprints: Morgan/ECFP, MACCS, RDKit fingerprints for similarity.
Substructure search: SMARTS pattern matching for functional group discovery.
Generation & drawing: 2D/3D coordinate setup and visualization.

Quick Start

Analyze a SMILES string to compute MW, LogP, and fingerprint, then search for a substructure pattern.

Frequently Asked Questions about rdkit

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I calculate molecular descriptors like molecular weight and LogP from a SMILES string?▼

RDKit computes molecular descriptors directly from SMILES input. Parse the SMILES string into a molecule object, then call descriptor functions to extract MW, LogP, TPSA, hydrogen bond donors/acceptors, and rotatable bond counts for drug discovery and property analysis.

Can I generate fingerprints for molecular similarity searches?▼

Yes. RDKit generates Morgan, MACCS, and RDKit fingerprints from molecule objects. These fingerprints enable fast similarity comparisons between compounds for lead optimization and compound library screening.

How do I search for functional groups or substructures in molecules?▼

RDKit performs substructure matching using SMARTS patterns. Define a SMARTS query pattern, then search against molecule objects to identify and locate functional groups, enabling targeted chemical discovery and structural analysis.

What file formats does RDKit support for molecular input and output?▼

RDKit reads and writes SMILES, MOL, SDF, and InChI formats. It converts between these formats seamlessly, supports batch I/O for large compound libraries, and handles multiple molecules in SDF and SMILES files.

Can I generate 2D and 3D coordinates for molecule visualization?▼

RDKit generates both 2D and 3D coordinates for molecular structures. After parsing molecules, apply coordinate generation functions to prepare structures for visualization, docking studies, or computational chemistry workflows.

Does RDKit handle molecule sanitization automatically?▼

RDKit offers automatic or configurable sanitization during molecule parsing. Sanitization validates chemical structure correctness, assigns bond orders, and prepares molecules for downstream analysis, with options to relax constraints for non-standard inputs.