Analyze and manipulate molecules with RDKit for cheminformatics workflows.
npx skills add https://github.com/ovachiever/droid-tings --skill rdkit
Please help me install this Agent Skill. Skill: rdkit Source: https://github.com/ovachiever/droid-tings/tree/main/skills/rdkit Command: npx skills add https://github.com/ovachiever/droid-tings --skill rdkit
RDKit enables fine-grained molecular analysis, including I/O, descriptor calculations, fingerprinting, substructure searches, and 2D/3D generation for drug discovery workflows.
Analyze a SMILES string to compute MW, LogP, and fingerprint, then search for a substructure pattern.
High-intent search queries and answers about installing and using this skill.
RDKit computes molecular descriptors directly from SMILES input. Parse the SMILES string into a molecule object, then call descriptor functions to extract MW, LogP, TPSA, hydrogen bond donors/acceptors, and rotatable bond counts for drug discovery and property analysis.
Yes. RDKit generates Morgan, MACCS, and RDKit fingerprints from molecule objects. These fingerprints enable fast similarity comparisons between compounds for lead optimization and compound library screening.
RDKit performs substructure matching using SMARTS patterns. Define a SMARTS query pattern, then search against molecule objects to identify and locate functional groups, enabling targeted chemical discovery and structural analysis.
RDKit reads and writes SMILES, MOL, SDF, and InChI formats. It converts between these formats seamlessly, supports batch I/O for large compound libraries, and handles multiple molecules in SDF and SMILES files.
RDKit generates both 2D and 3D coordinates for molecular structures. After parsing molecules, apply coordinate generation functions to prepare structures for visualization, docking studies, or computational chemistry workflows.
RDKit offers automatic or configurable sanitization during molecule parsing. Sanitization validates chemical structure correctness, assigns bond orders, and prepares molecules for downstream analysis, with options to relax constraints for non-standard inputs.
silversteinConvert SMILES or RDKit molecules into numeric feature vectors for machine learning.
mkurmanCompute molecular descriptors, fingerprints, and substructure patterns with RDKit.
JosephWoodallCompute molecular descriptors, fingerprints, and substructure searches with RDKit in Python.
dralkhAutomate molecular modeling and medicinal-chemistry workflows via a Python API.
