Parse, standardize, and analyze molecular structures with RDKit via Python.
npx skills add https://github.com/Yezez9/Research-Agent --skill datamol-yezez9
Please help me install this Agent Skill. Skill: datamol Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/datamol Command: npx skills add https://github.com/Yezez9/Research-Agent --skill datamol-yezez9
This Skill simplifies complex molecular operations for drug discovery and cheminformatics, making it easier to analyze, manipulate, and understand chemical structures.
Load molecules from 'compounds.sdf', standardize them, and compute their molecular weight and logP.
High-intent search queries and answers about installing and using this skill.
This Skill processes batch molecular operations by wrapping RDKit to parse SMILES, standardize molecules, and generate ECFP fingerprints. It computes molecular descriptors like weight and logP, then clusters similar compounds to identify diverse structural groups for drug discovery workflows.
Molecule standardization normalizes chemical structures by parsing SMILES and converting formats like SDF to ensure consistent descriptor calculation. This Skill wraps RDKit to execute these cheminformatics operations, preparing a clean dataset for accurate property computation and clustering.
Yes, this Skill supports batch processing and remote file access via fsspec to load compound libraries, generate ECFP fingerprints, and cluster molecules by structural similarity. It outputs diverse structural groups, enabling efficient analysis of large drug candidate datasets.
No, this Skill provides a Pythonic interface wrapping RDKit for 3D conformer generation and visualization without requiring direct RDKit setup. It manages the cheminformatics operations internally, allowing you to focus on molecular analysis and drug discovery workflows.
Load molecules from an SDF file, apply molecule standardization, and run descriptor calculation functions to compute molecular weight and logP. This Skill wraps RDKit to execute these standard cheminformatics workflows, outputting calculated properties for batch analysis of drug candidates.
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