rdkit

Name: rdkit
Availability: InStock
Author: dp-archive

Calculate molecular descriptors and generate fingerprints from SMILES strings using RDKit.

1.1k|99|Updated Feb 12, 2026

Search Tags:#drug discovery #cheminformatics #fingerprints #descriptors #rdkit #molecular analysis #computational chemistry

Ready to run

npx skills add https://github.com/dp-archive/archive --skill rdkit-dp-archive

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: rdkit
Source: https://github.com/dp-archive/archive/tree/main/seed_skills/rdkit
Command: npx skills add https://github.com/dp-archive/archive --skill rdkit-dp-archive

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a powerful 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, and perform substructure searches.
Structure Generation: Create 2D and 3D molecular coordinates, and handle chemical reactions.
Use Case: Analyze a library of drug candidates by calculating their Lipinski's Rule of Five compliance, generating Morgan fingerprints, and screening for similarity against a known active compound.

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?▼

You can calculate molecular descriptors by parsing SMILES strings and computing properties like molecular weight, LogP, and TPSA. This Skill uses RDKit to execute these cheminformatics operations directly on the input molecular structures.

What is the best way to generate Morgan fingerprints for a library of drug candidates?▼

Generating Morgan fingerprints for drug candidates involves converting molecular structures into bit vectors for similarity screening. This Skill supports fingerprint generation to analyze chemical libraries and screen them against known active compounds.

Can I perform substructure searches to screen compounds using RDKit?▼

Yes, you can perform substructure searches to identify specific chemical motifs within a library. This Skill provides comprehensive cheminformatics capabilities to execute substructure matching and screen compounds using RDKit.

Do I need to install RDKit to use this Skill for molecular analysis?▼

Yes, RDKit installation is required for all cheminformatics operations. This Skill depends on the RDKit library to execute molecular analysis, descriptor calculations, and coordinate generation.

How do I check Lipinski's Rule of Five compliance for a set of compounds?▼

Checking Lipinski's Rule of Five compliance requires calculating specific molecular descriptors such as molecular weight and LogP. This Skill computes these descriptors using RDKit to help you evaluate drug-like properties of chemical compounds.