Can this skill help with 3D molecular modeling?

Yes, it provides implementation patterns for 3D coordinate generation, conformer embedding, and geometry optimization using force fields like MMFF94.

How does it handle chemical similarity?

The skill includes methods for generating circular (Morgan) fingerprints and calculating Tanimoto, Dice, and Cosine similarity metrics between molecules.

What is the RDKit skill for Claude Code?

It is a specialized skill that provides Claude with the best practices and code patterns for the RDKit library, a industry-standard toolkit for cheminformatics.

Does it support large chemical datasets?

Yes, it provides patterns for batch processing using SDMolSupplier and ForwardSDMolSupplier for efficient memory management with large SDF files.

Should I use RDKit or datamol?

This skill suggests using RDKit for advanced control, custom sanitization, and specialized algorithms, while recommending datamol for simpler, standard workflows.

RDKit Cheminformatics Toolkit

Name: RDKit Cheminformatics Toolkit
Author: Activer007

byActiver007

数据科学与机器学习

Provides specialized guidance for molecular analysis, structural manipulation, and chemical property calculation using RDKit.

关于

The RDKit skill equips Claude with the domain-specific expertise required for advanced cheminformatics workflows. It offers precise implementation patterns for molecular parsing (SMILES, SDF, InChI), property descriptors, fingerprinting, and substructure searching. This skill is particularly valuable for drug discovery, computational chemistry, and bioinformatics research, enabling Claude to assist in generating 3D coordinates, optimizing conformers, and modeling chemical reactions with high scientific accuracy.

主要功能

Fingerprinting and Tanimoto similarity analysis
Advanced molecular sanitization and valence validation
Molecular I/O for SMILES, SDF, MOL, and InChI formats
Descriptor calculation (MW, LogP, TPSA, and Lipinski's Rules)
3D coordinate generation and force field optimization (UFF/MMFF)
0 GitHub stars

使用场景

Automating high-throughput screening for drug-likeness
Building and querying chemical databases using substructure search
Generating 3D conformers for molecular docking simulations

关于

主要功能

Fingerprinting and Tanimoto similarity analysis
Advanced molecular sanitization and valence validation
Molecular I/O for SMILES, SDF, MOL, and InChI formats
Descriptor calculation (MW, LogP, TPSA, and Lipinski's Rules)
3D coordinate generation and force field optimization (UFF/MMFF)
0 GitHub stars

使用场景

Automating high-throughput screening for drug-likeness
Building and querying chemical databases using substructure search
Generating 3D conformers for molecular docking simulations