rdkit

Parse SMILES and SDF files and calculate molecular descriptors.

8|Updated Jan 13, 2026

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

Ready to run

npx skills add https://github.com/hxk622/TokenDance --skill rdkit-hxk622

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: rdkit
Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/chemistry/rdkit
Command: npx skills add https://github.com/hxk622/TokenDance --skill rdkit-hxk622

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill empowers chemists and researchers to analyze, manipulate, and understand molecular structures and properties programmatically, accelerating drug discovery and materials science.

Core Features & Use Cases

Molecular Analysis: Calculate descriptors (MW, LogP, TPSA), generate fingerprints, and perform substructure searches.
Structure Manipulation: Read/write various molecular formats (SMILES, SDF, MOL), generate 2D/3D coordinates, and handle chemical reactions.
Use Case: Screen a library of compounds for drug-likeness by calculating Lipinski's Rule of Five parameters and TPSA for each molecule.

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 MW and LogP from a SMILES string?▼

To calculate molecular descriptors from a SMILES string, you can parse the molecular structure and compute properties such as MW, LogP, and TPSA programmatically. This allows rapid screening of compounds for drug-likeness using Lipinski's Rule of Five parameters.

What is the best way to parse and convert molecular file formats like SDF and MOL?▼

The best way to parse and convert molecular file formats like SDF and MOL is by using a cheminformatics toolkit that reads and writes these structures natively. This enables seamless structure manipulation and data extraction for computational chemistry workflows.

Can I generate 2D and 3D molecular coordinates programmatically for my compound library?▼

Yes, you can generate 2D and 3D molecular coordinates programmatically. By parsing SMILES or SDF inputs, the cheminformatics toolkit computes spatial coordinates, facilitating molecular modeling and structural visualization for drug discovery research.

How do I perform substructure searching and fingerprint generation for molecular analysis?▼

To perform substructure searching and fingerprint generation for molecular analysis, you can use cheminformatics functions that encode structural motifs into fingerprints. This enables rapid similarity screening and identification of specific chemical substructures within a compound library.

Does this cheminformatics toolkit support handling and processing chemical reactions?▼

Yes, this cheminformatics toolkit supports handling and processing chemical reactions. It enables you to parse reaction SMILES, manipulate reactant and product structures, and integrate reaction workflows into computational chemistry and drug discovery pipelines.

How do I screen a compound library for drug-likeness using computational chemistry tools?▼

To screen a compound library for drug-likeness using computational chemistry tools, calculate Lipinski's Rule of Five parameters and TPSA for each molecule. This involves parsing SMILES strings and computing molecular descriptors to evaluate absorption and permeability.