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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데이터 과학 및 ML

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

소개

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.

주요 기능

Calculation of chemical descriptors like LogP, MW, and TPSA
Chemical reaction modeling and atom mapping
Molecular I/O for SMILES, SDF, MOL, and InChI formats
Substructure searching and SMARTS pattern matching
2D and 3D coordinate generation with force field optimization
81 GitHub stars

사용 사례

Automating drug-likeness screening and Rule of Five validation
Generating molecular visualizations and conformer ensembles
Processing large chemical datasets for virtual screening

소개

주요 기능

Calculation of chemical descriptors like LogP, MW, and TPSA
Chemical reaction modeling and atom mapping
Molecular I/O for SMILES, SDF, MOL, and InChI formats
Substructure searching and SMARTS pattern matching
2D and 3D coordinate generation with force field optimization
81 GitHub stars

사용 사례

Automating drug-likeness screening and Rule of Five validation
Generating molecular visualizations and conformer ensembles
Processing large chemical datasets for virtual screening