rdkit

Calculate molecular descriptors and generate fingerprints from SMILES using RDKit.

Updated Mar 10, 2026

Search Tags:#drug discovery #cheminformatics #substructure search #fingerprints #rdkit #molecular descriptors

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill rdkit-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: rdkit
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/rdkit
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill rdkit-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a powerful and comprehensive toolkit for cheminformatics tasks, enabling detailed analysis, manipulation, and generation of molecular structures and properties.

Core Features & Use Cases

Molecular Analysis: Calculate descriptors (MW, LogP, TPSA), generate fingerprints (Morgan, MACCS), and perform substructure searches.
Structure Generation: Create 2D and 3D coordinates, handle chemical reactions, and visualize molecules.
Use Case: In drug discovery, use RDKit to screen large compound libraries for molecules similar to a known active compound, or to predict drug-likeness properties.

Quick Start

Use the rdkit skill to calculate the molecular weight and LogP for the SMILES string 'CCO'.

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 LogP and TPSA from a SMILES string?▼

Molecular descriptor calculation from SMILES strings involves parsing the chemical structure and computing properties like LogP and TPSA. This Skill handles descriptor calculation using RDKit to evaluate drug-likeness properties for computational chemistry workflows.

Can I perform substructure searches across a compound library for drug discovery?▼

Yes, substructure searching is supported for drug discovery workflows. You can screen large compound libraries by defining a query substructure and identifying matching molecules, enabling similarity-based screening to find compounds similar to a known active compound.

What's the best way to generate molecular fingerprints for cheminformatics analysis?▼

Generating molecular fingerprints for cheminformatics analysis involves encoding molecular structures into numerical bit vectors. This Skill supports Morgan and MACCS fingerprint generation, allowing you to represent molecules for similarity comparisons and screening tasks.

Do I need RDKit installed to calculate 2D and 3D molecular coordinates?▼

RDKit installation is required for all functionalities including 2D and 3D coordinate generation. This Skill depends entirely on the RDKit library to perform structure generation, coordinate calculation, and molecular manipulation.

How do I handle chemical reactions and visualize molecules in computational chemistry workflows?▼

Handling chemical reactions and visualizing molecules involves parsing reaction SMARTS and generating structural depictions. This Skill supports reaction handling and molecule visualization using RDKit capabilities for computational chemistry structure generation tasks.