coot-rdkit

What problem does it solve?

This Skill enables RDKit molecular manipulation and visualization inside Coot's Python environment, helping researchers streamline ligand editing, structure validation, and 2D diagram generation directly within their modeling workflow.

Core Features & Use Cases

• RDKit molecule creation from Coot monomers: Convert monomer codes to RDKit molecules for analysis and editing.
• Atom substitution and structural modifications: Perform targeted atom replacements within RDKit molecules to explore design options.
• 2D structure regeneration and visualization: Generate clean 2D coordinates and SVG diagrams for inspection and reporting.
• Use Case: A structural biologist needs to modify a bound ligand and generate a publication-ready 2D diagram from within Coot without exporting intermediate files.

Quick Start

Load a monomer from Coot, convert it to an RDKit molecule, perform an atom substitution, regenerate 2D coordinates, and render an SVG diagram.