Does it support 3D coordinate generation?

Absolutely. The skill covers 3D conformer generation using the ETKDG method and optimization using force fields like UFF and MMFF94.

How do I perform substructure searches with this skill?

The skill provides implementation details for using SMARTS (SMILES Arbitrary Target Specification) to identify specific functional groups or structural motifs within a molecule.

What chemical file formats are supported by the RDKit skill?

The RDKit skill provides guidance for reading and writing several formats including SMILES, SDF (Structure-Data File), MOL blocks, and InChI strings.

Can this skill help with drug-likeness screening?

Yes, it includes patterns for calculating Lipinski's Rule of Five descriptors such as molecular weight, LogP, and the number of hydrogen bond donors and acceptors.

RDKit Cheminformatics

Name: RDKit Cheminformatics
Author: Microck

byMicrock

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데이터 과학 및 ML

Provides comprehensive tools for molecular analysis, chemical property calculation, and 3D coordinate generation.

소개

The RDKit skill for Claude Code empowers developers and researchers to perform advanced cheminformatics tasks directly within their workflow. It offers domain-specific guidance for reading and writing molecular structures (SMILES, SDF, InChI), calculating critical descriptors like LogP and TPSA, and executing complex substructure searches using SMARTS patterns. Whether you are screening chemical libraries for drug-likeness or generating 3D conformers for computational chemistry, this skill provides the implementation patterns and best practices needed for high-precision molecular manipulation.

주요 기능

Comprehensive chemical descriptor calculations including Lipinski's Rule of Five
3D coordinate generation and conformer optimization with force fields
81 GitHub stars
Molecular I/O and batch processing for SMILES, SDF, and InChI formats
Molecular visualization and 2D depiction with substructure highlighting
Advanced substructure searching and pattern matching with SMARTS

사용 사례

Screening large chemical datasets for drug discovery and lead optimization
Automating the generation of molecular fingerprints for machine learning models
Performing chemical reaction modeling and structural similarity analysis

소개

주요 기능

Comprehensive chemical descriptor calculations including Lipinski's Rule of Five
3D coordinate generation and conformer optimization with force fields
81 GitHub stars
Molecular I/O and batch processing for SMILES, SDF, and InChI formats
Molecular visualization and 2D depiction with substructure highlighting
Advanced substructure searching and pattern matching with SMARTS

사용 사례

Screening large chemical datasets for drug discovery and lead optimization
Automating the generation of molecular fingerprints for machine learning models
Performing chemical reaction modeling and structural similarity analysis