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rdkit

Analyze molecular structures and calculate properties via the RDKit Python API.

Updated May 17, 2026
Search Tags:#cheminformatics#substructure search#RDKit#molecular analysis#chemical reaction
One-click install
npx skills add https://github.com/galeep/plugin-place --skill rdkit-galeep
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: rdkit
Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-cheminformatics-drug-discovery/skills/rdkit
Command: npx skills add https://github.com/galeep/plugin-place --skill rdkit-galeep

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a comprehensive toolkit for cheminformatics tasks, enabling users to analyze and manipulate molecular structures, calculate properties, and perform substructure searches and chemical reactions.

Core Features & Use Cases

  • Molecular I/O and Creation: Read and write molecular structures in various formats, including SMILES, MOL, and InChI.
  • Molecular Analysis: Calculate molecular properties like molecular weight, logP, TPSA, and more.
  • Substructure Searching: Perform substructure searches using SMARTS patterns.
  • Chemical Reactions: Define and run chemical reactions using SMARTS patterns.
  • Use Case: Imagine you have a set of molecules and you want to identify those that can potentially form a specific type of chemical bond. Use this Skill to define the reaction and search for matches within your molecule set.

Quick Start

Use the rdkit skill to calculate the molecular weight of the molecule with SMILES '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 properties like molecular weight and logP from a SMILES string?▼

To calculate molecular properties like molecular weight and logP, you can use a cheminformatics toolkit to read the SMILES string and compute the values directly. This approach supports analyzing molecular structures to derive properties such as TPSA and molecular weight.

How do I perform substructure searching using SMARTS patterns across a set of molecules?▼

Substructure searching using SMARTS patterns is performed by reading your molecular structures and defining the SMARTS pattern to match. This allows you to identify specific structural motifs within a set of molecules efficiently.

Can I simulate chemical reactions using SMARTS patterns to identify reactive molecules?▼

Yes, you can simulate chemical reactions by defining them with SMARTS patterns. This allows you to identify molecules within a set that can potentially form specific chemical bonds and generate the resulting products.

What molecular I/O formats are supported for reading and writing chemical structures?▼

Supported molecular I/O formats include SMILES, MOL, and InChI. You can read and write molecular structures using these formats to integrate chemical data into your analysis workflow.

Do I need to install RDKit to execute molecular analysis and manipulation tasks?▼

Yes, you need RDKit installed to perform operations on molecular structures. This dependency is required to execute the underlying cheminformatics tasks such as molecular I/O, property calculation, and reaction simulation.

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