Does it support 3D structure generation?

Absolutely. The skill includes guidance for generating 3D coordinates, embedding multiple conformers, and optimizing geometries using UFF or MMFF force fields.

How is this different from the datamol skill?

While datamol is a high-level wrapper for simpler workflows, the RDKit skill provides fine-grained control for advanced algorithms, custom sanitization, and specialized chemical logic.

Can I use this skill to calculate drug-likeness?

Yes, it provides functions to calculate descriptors such as Molecular Weight, LogP, TPSA, and H-bond counts required for Lipinski's Rule of Five.

What molecular formats does this skill support?

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

RDKit Cheminformatics

Name: RDKit Cheminformatics
Author: Activer007

byActiver007

0•

Data Science & ML

Performs advanced molecular analysis, property calculation, and structural manipulation for cheminformatics workflows.

The RDKit skill provides Claude with specialized capabilities for handling chemical data, ranging from basic SMILES parsing to complex 3D coordinate generation. It enables researchers and developers to automate tasks such as calculating molecular descriptors like LogP and TPSA, performing substructure searches using SMARTS, and modeling chemical reactions. By integrating these industry-standard cheminformatics tools, this skill streamlines the process of drug discovery, computational chemistry, and large-scale molecular dataset management.

Key Features

01Substructure searching and SMARTS pattern matching

02Chemical reaction modeling and molecular fingerprinting

030 GitHub stars

04Comprehensive descriptor calculation including Lipinski's Rule of Five

052D and 3D coordinate generation with conformer embedding

06Molecular I/O for SMILES, SDF, MOL, and InChI formats

Use Cases

01Automating drug-likeness screening and chemical property filtering

02Large-scale chemical library analysis and substructure identification

03Generating 3D molecular structures for computational docking simulations

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills rdkit

For use in Claude.ai and ChatGPT

Download Skill