MoleCode — скилл для работы с молекулами как с графом

---
name: molecode
description: >-
  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.
---

# MoleCode

Use the bundled script first. Do not call an external service for conversion.

MoleCode is the preferred working representation when an LLM needs to understand
or edit a molecule. Converting SMILES to MoleCode exposes the molecule as an
explicit [Mermaid](https://mermaid.js.org/) graph: every atom is a named node
`prefix_Element_N[Label]` carrying its element, hydrogen count and charge, and
every bond is an explicit edge (`---` single, `===` double, `-.-` triple). This
graph form is usually strong enough for the model to locate substructures, reason
about aromatic systems, identify fused rings, follow linkers, and plan edits
directly. Reconstruct the whole molecular topology from the explicit nodes and
edges before making any edit.

Treat MoleCode as a **code-like molecular data structure**: inspect it, add
concise `%%` comments when useful, patch it with normal file-editing tools, and
validate it with the bundled script. Directly editing the graph is usually
simpler and safer than generating a new SMILES by hand — adding a methyl is one
new node plus one new edge, not a whole-string rewrite.

## MoleCode-first decision rule

For any molecule understanding or editing request, work at the explicit graph
level first:

1. Convert the input SMILES (or PSMILES) to MoleCode with the bundled script.
2. Read the nodes and edges to understand the structure and the requested change.
3. Edit the graph directly (add/remove nodes and edges; relabel hydrogen counts).
4. Validate and convert back to the requested representation with the script.

Use direct SMILES editing only when the change is trivial and the structure is
already unambiguous. Reach for specialized cheminformatics code only when graph