Perform molecular analysis and property prediction using the RDKit library.
npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-rdkit
Please help me install this Agent Skill. Skill: lib-rdkit Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/lib-rdkit Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-rdkit
This Skill empowers users to perform complex cheminformatics tasks, from molecular manipulation and property calculation to similarity searching and substructure analysis, directly within their workflow.
Calculate the molecular weight and LogP for the molecule represented by the SMILES string 'CCO'.
High-intent search queries and answers about installing and using this skill.
Calculate molecular descriptors like LogP and TPSA from SMILES strings by reading the molecule and computing its properties using RDKit functions. This provides key drug discovery parameters directly within your workflow.
Perform substructure searching across a molecular library by defining chemical patterns with SMARTS and matching them against your loaded molecules. This identifies specific chemotypes and active compounds efficiently.
Generate molecular fingerprints like Morgan or MACCS and calculate similarity scores to compare drug candidates. This enables structural similarity screening against known active compounds for drug discovery.
Read and write molecules from formats like SMILES, SDF, and MOL using RDKit's molecular I/O capabilities. This allows seamless loading and saving of chemical structures for downstream analysis.
Using RDKit for cheminformatics tasks requires a Python environment with the RDKit library installed. This setup is necessary to execute scripts for descriptor calculation, fingerprinting, and 2D/3D coordinate generation.
SMARTS pattern matching works by defining flexible chemical queries to find specific substructures within molecules. It enables targeted screening for structural features across datasets loaded from SDF or SMILES formats.
wuyoscarGenerate RDKit-ready SDF catalogs with potency and pharmacology metadata from validated SMILES.
pradyumnasagarCalculate molecular fingerprints and physicochemical descriptors from SMILES using RDKit.
SologaCalculate molecular descriptors and generate fingerprints from SMILES strings.
galeepAutomate molecular modeling and medicinal chemistry workflows through a Python API.
