Does this skill help with drug-likeness analysis?

Yes, it provides tools to calculate all necessary descriptors for Lipinski's Rule of Five, including molecular weight, LogP, and hydrogen bond donor/acceptor counts.

How does RDKit handle chemical reactions?

It utilizes Reaction SMARTS to define chemical transformations, allowing you to run reactants through specific reaction rules to generate sanitized product sets.

When should I use RDKit instead of Datamol?

Use RDKit when you need fine-grained control, custom sanitization rules, specialized algorithms, or advanced substructure search features that go beyond standard workflows.

Can RDKit generate 3D structures for molecules?

Yes, RDKit can generate 3D coordinates using the ETKDG method and optimize those geometries using force fields like UFF or MMFF94.

What molecular formats does the RDKit skill support?

The RDKit skill supports a wide range of formats including SMILES, SDF, MOL files, InChI, and MOL blocks for both reading and writing molecular data.

RDKit Cheminformatics

Name: RDKit Cheminformatics
Author: K-Dense-AI

byK-Dense-AI

•

2,188

Data Science & ML

Performs advanced molecular analysis, manipulation, and chemical informatics tasks using the RDKit toolkit.

About

This skill provides deep integration with the RDKit library to enable sophisticated cheminformatics workflows within Claude. It offers comprehensive guidance for parsing molecular formats like SMILES and SDF, calculating physicochemical descriptors, performing substructure searches with SMARTS, and generating 3D conformations. Ideal for researchers and developers in drug discovery or computational chemistry, it bridges the gap between natural language intent and complex chemical programming, ensuring best practices in sanitization, molecular representation, and reaction simulation.

Key Features

Calculation of physicochemical descriptors like LogP, TPSA, and molecular weight
Molecular I/O and creation from SMILES, SDF, InChI, and MOL formats
2,188 GitHub stars
Substructure searching and complex chemical reaction simulation via SMARTS
2D/3D coordinate generation, conformer analysis, and molecular visualization
Advanced molecular sanitization, validation, and chemistry problem detection

Use Cases

Automated chemical data cleaning and molecular standardization pipelines
Drug discovery and virtual screening of molecular libraries
Generating 3D molecular structures and conformers for computational modeling

About

Key Features

Calculation of physicochemical descriptors like LogP, TPSA, and molecular weight
Molecular I/O and creation from SMILES, SDF, InChI, and MOL formats
2,188 GitHub stars
Substructure searching and complex chemical reaction simulation via SMARTS
2D/3D coordinate generation, conformer analysis, and molecular visualization
Advanced molecular sanitization, validation, and chemistry problem detection

Use Cases

Automated chemical data cleaning and molecular standardization pipelines
Drug discovery and virtual screening of molecular libraries
Generating 3D molecular structures and conformers for computational modeling