What file formats does the RDKit skill support?

It supports a wide range of formats including SMILES, SDF, MOL blocks, and InChI, along with batch processing for large files.

Can I use this for drug-likeness screening?

Yes, it provides methods to calculate Lipinski's Rule of Five parameters like Molecular Weight, LogP, H-bond donors, and acceptors.

How does RDKit handle chemical reactions?

It uses Reaction SMARTS to define transformations, allowing for automated product generation, atom mapping, and reaction similarity analysis.

Does it support 3D coordinate generation?

Yes, it includes guidance for generating 3D conformers using ETKDG and optimizing them with UFF or MMFF94 force fields.

RDKit Cheminformatics

Name: RDKit Cheminformatics
Author: Microck

byMicrock

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Data Science & ML

Provides comprehensive cheminformatics capabilities for molecular analysis, property calculation, and 3D coordinate generation.

The RDKit skill equips Claude with advanced cheminformatics expertise for pharmaceutical research, computational chemistry, and molecular data processing. It enables fine-grained control over molecular I/O (SMILES, SDF, InChI), structure validation, property calculation (LogP, TPSA), fingerprinting for similarity searches, substructure matching using SMARTS, and the generation of 2D/3D coordinates for visualization and modeling. It is the ideal tool for developers and researchers automating drug discovery workflows and chemical data analysis.

Key Features

01Calculation of chemical descriptors like LogP, MW, and TPSA

02Chemical reaction modeling and atom mapping

03Molecular I/O for SMILES, SDF, MOL, and InChI formats

04Substructure searching and SMARTS pattern matching

052D and 3D coordinate generation with force field optimization

0681 GitHub stars

Use Cases

01Automating drug-likeness screening and Rule of Five validation

02Generating molecular visualizations and conformer ensembles

03Processing large chemical datasets for virtual screening

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills rdkit

For use in Claude.ai and ChatGPT

Download Skill