Analyze and manipulate molecular structures with RDKit cheminformatics operations.
npx skills add https://github.com/jimmc414/Kosmos --skill rdkit-jimmc414
Please help me install this Agent Skill. Skill: rdkit Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/rdkit Command: npx skills add https://github.com/jimmc414/Kosmos --skill rdkit-jimmc414
This Skill empowers chemists and researchers by providing a powerful toolkit for molecular analysis, manipulation, and visualization, streamlining cheminformatics workflows.
Use the rdkit skill to calculate the molecular weight and LogP for the SMILES string 'CCO'.
High-intent search queries and answers about installing and using this skill.
Calculate molecular descriptors by parsing SMILES strings to compute physicochemical properties like LogP, TPSA, molecular weight, and hydrogen bond donor/acceptor counts. This streamlines cheminformatics workflows for drug discovery.
You can perform substructure searches using SMARTS patterns to identify specific chemical substructures across molecular datasets. This allows you to filter drug candidates and retain only molecules matching your desired structural features.
Generate Morgan or MACCS fingerprints from molecular structures and calculate their similarity scores to facilitate molecular screening and clustering. This helps identify promising drug candidates by comparing structural features.
Yes, this approach supports reading, writing, sanitizing, and modifying molecular structures from various formats including SDF, MOL, and SMILES. This enables fine-grained control over molecular data manipulation in computational chemistry workflows.
Generate 2D depictions and 3D conformers by creating molecular visualizations with customizable options from your input structures. This allows you to visually inspect the most promising drug candidates during your drug discovery research.
You can evaluate drug candidates by calculating Lipinski's Rule of Five parameters such as molecular weight, LogP, and hydrogen bond donors/acceptors. This allows you to quickly filter lists of drug candidates and visualize the most promising ones.
jasrajtulsiParse and standardize molecular structures for cheminformatics workflows.
pradyumnasagarCalculate molecular fingerprints and physicochemical descriptors from SMILES using RDKit.
InternScienceOptimize drug molecule LogP, QED, and solubility through iterative SMILES edits.
tondevrelBuild, manipulate, and analyze atomic structures for atomistic simulations.
