# clean2d

Builds the 2D-layout blob used by the `smilesdrawer` engine of
`MoleculeContainer.clean2d()`. Wraps smiles-drawer's layout internals and exposes a
single `$.clean2d(tree)` global that MiniRacer evaluates from Python.

## Rebuild

    npm install
    npm run build

`npm run build` bundles `src/index.js` with esbuild into
`../chython/algorithms/calculate2d/clean2d.js` (IIFE, global `$`).

## Deps

- `smiles-drawer` (pinned exact) — layout engine. Its package `exports` only expose the
  bundled dist, so `src/index.js` imports the internals directly by relative path
  (`../node_modules/smiles-drawer/src/DrawerBase.js`). Keep the version pinned: the parse
  tree below is coupled to smiles-drawer's internal `Graph` format.
- `esbuild` (dev) — the only build dependency.

## API: `$.clean2d(tree)`

`tree` is a smiles-drawer parse tree built directly on the Python side (no SMILES round
trip). Returns `[[x, y], ...]` for heavy atoms, in the same order the Python builder
created them (heavy-atom `idx` order == `graph.atomIdxToVertexId`).

### Parse-tree node schema

    {
      atom: "C",               // bare element string
      isBracket: false,
      branches: [ <node with extra `branchBond`>, ... ],
      branchCount: int,
      ringbonds: [ { bond: "-"|"="|"#", id: int }, ... ],
      ringbondCount: int,
      bond: "-"|"="|"#"|".",   // bond to `next` ("." chains disconnected components)
      next: <node> | null,
      hasNext: bool
    }

- Layout depends only on element and connectivity, so atoms are plain element strings:
  charge, isotope, hydrogen counts and aromaticity are omitted (none of them move atoms).
  Aromatic bonds are emitted as `"-"`.
- A ring closure pushes a matching `ringbond` entry (same `id`) on both endpoints.
- Implicit hydrogens are not emitted; only heavy atoms receive an `idx`.