molecode

molecode is a Chemistry & materials skill for AI agents, published by AtomFlow-AI in the MoleCode repository on GitHub. Skillspace rates molecode C (72/100) and it passed the safety scan; the rating is based on static analysis only.

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…

Grade

C

Quality

72 / 100

Safety

Passed

GitHub stars

293

Unproven: rated by static analysis only, not yet compared head-to-head.

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