MoleCode

Use for deterministic molecule understanding, graph-level editing, generation, and validation with MoleCode — an explicit Mermaid graph in which every atom and bond is a typed, named node/edge. Converting SMILES to MoleCode exposes the molecule as explicit atoms, hydrogen counts, bonds, bond orders, stereochemistry (R/S, E/Z), aromatic/ring systems, functional groups, and linkers, so an agent can locate substructures and plan edits far more reliably than from linear SMILES. Trigger when the task is to understand or edit a molecular structure, replace a functional group, add/delete/substitute atoms, close or fuse rings, change a linker or scaffold, count atoms/elements, check formula/connectivity/ valence, design a molecule under constraints, or convert between SMILES and MoleCode. Also covers polymers (PSMILES repeat units) and Markush structures (variable R-groups). Prefer MoleCode graph inspection and editing before hand-writing SMILES; the bundled script provides the conversion and validation API.