typed-smiles renders SMILES strings as clean 2D molecular diagrams in Typst. It uses a small Rust/WASM plugin for parsing and layout, then draws the result with CeTZ.

The package is meant for chemistry notes, reaction schemes, reports, and teaching material where you want molecules to live directly in your Typst source instead of copying diagrams from a separate editor.

Basic molecule drawing

Start by importing smiles. Pass a SMILES string and the package will draw the skeletal structure.

#import "@preview/typed-smiles:0.2.0": smiles

#table(
  columns: (1fr, 1fr, 1fr, 1fr),
  gutter: 0em,
  row-gutter: 0em,
  align: center + horizon,
  stroke: 0.4pt + rgb("#d8d8d8"),

  [*Ethanol*],
  [*Alanine*],
  [*Chlorobenzene*],
  [*Furan*],

  [#smiles("CCO")],
  [#smiles("CC(N)C(=O)O")],
  [#smiles("ClC1=CC=CC=C1")],
  [#smiles("C1=CC=CO1")],
)

Scaling

Use scale to enlarge or shrink a diagram while keeping bond length, atom label size, and bond stroke balanced. You can still override bond-length, font-size, or bond-stroke individually when a figure needs manual tuning. Here is the same molecule drawn at three sizes:

#table(
  columns: (1fr, 1fr, 1fr),
  gutter: 0em,
  row-gutter: 0em,
  align: center + horizon,
  stroke: 0.4pt + rgb("#d8d8d8"),

  [*Small*],
  [*Default*],
  [*Large*],

  [#smiles("C1=CC=CC=C1", scale: 0.8)],
  [#smiles("C1=CC=CC=C1")],
  [#smiles("C1=CC=CC=C1", scale: 1.4)],
)

Hydrogens and labels

By default, typed-smiles follows the usual skeletal drawing convention: hydrogens on heteroatoms are shown, while carbon hydrogens stay implicit. This means ordinary SMILES such as CC(N)C(=O)O produces the expected NH2 and OH labels without bracket syntax. Use show-all-h: true when you also want carbon hydrogens, bracket syntax for explicit hydrogens, and {label} for custom upright group labels. Use {label|style} to color a label and its bonds by element symbol or named color. Atom labels can also use a custom typeface with font.

#table(
  columns: (1fr, 1fr, 1fr, 1fr, 1fr),
  gutter: 0em,
  row-gutter: 0em,
  align: center + horizon,
  stroke: 0.4pt + rgb("#d8d8d8"),

  [*Default hetero H*],
  [*All H*],
  [*Explicit bracket H*],
  [*Colored label*],
  [*Custom font*],

  [#smiles("CC(N)C(=O)O")],
  [#smiles("CCO", show-all-h: true)],
  [#smiles("[NH3]")],
  [#smiles("{PPh3|P}C=O")],
  [#smiles("CCN", font: "Libertinus Serif")],
)

Chemical formulas and equations

typed-smiles re-exports ce from chemformula, so the same import can handle ordinary formulas and text-based chemical equations. It also accepts font and font-size for local formula styling; use a math-capable font for formulas and equations. This is useful for salts, small inorganic species, conditions, and equations where a full molecular diagram would be unnecessary.

#import "@preview/typed-smiles:0.2.0": ce

#table(
  columns: (1fr, 1fr),
  gutter: 0em,
  row-gutter: 0em,
  align: center + horizon,
  stroke: 0.4pt + rgb("#d8d8d8"),

  [#stack(spacing: 0.35cm, strong[Formula], ce("H2SO4"))],
  [#stack(spacing: 0.35cm, strong[Ions], ce("(NH4)2SO4"))],
  [#stack(spacing: 0.35cm, strong[Combustion], ce("CH4 + 2O2 -> CO2 + 2H2O"))],
  [#stack(spacing: 0.35cm, strong[Equilibrium], ce("N2 + 3H2 <=> 2NH3"))],
)

Reaction schemes

For structural reaction schemes, use reaction, rxn-arrow, and mol. These helpers let you combine SMILES-based molecule diagrams with ce() formulas, plus signs, labels, and arrow conditions in one layout.

#import "@preview/typed-smiles:0.2.0": smiles, ce, rxn-arrow, mol, reaction

#stack(
  spacing: 1cm,
  stack(
    spacing: 0.4cm,
    align(center, strong[Fischer esterification]),
    align(center, reaction(
      mol(smiles("CC(=O)O"), label: text(size: 8pt)[acetic acid]),
      [+],
      mol(smiles("CCO"), label: text(size: 8pt)[ethanol]),
      rxn-arrow(above: ce("H+"), below: [heat]),
      mol(smiles("CCOC(=O)C"), label: text(size: 8pt)[ethyl acetate]),
      [+],
      ce("H2O"),
    )),
  ),
  stack(
    spacing: 0.4cm,
    align(center, strong[Electrophilic aromatic bromination]),
    align(center, reaction(
      mol(smiles("C1=CC=CC=C1"), label: text(size: 8pt)[benzene]),
      rxn-arrow(above: ce("Br2"), below: ce("FeBr3")),
      mol(smiles("BrC1=CC=CC=C1"), label: text(size: 8pt)[bromobenzene]),
    )),
  ),
)

Multi-step mechanisms

Reaction arrows can point right, left, up, or down. This lets you write compact wrap-around schemes without manually placing every molecule.

#stack(
  spacing: 1.2em,
  align(center, strong[Bromination, nitration, and reduction sequence]),
  align(center, reaction(
    mol(smiles("C1=CC=CC=C1"), label: text(size: 8pt)[1]),
    rxn-arrow(above: ce("Br2"), below: ce("FeBr3")),
    mol(smiles("BrC1=CC=CC=C1"), label: text(size: 8pt)[A]),
    rxn-arrow(dir: "down", above: ce("HNO3"), below: ce("H2SO4")),
    mol(smiles("BrC1=CC(=CC=C1)[N+](=O)[O-]"), label: text(size: 8pt)[B]),
    rxn-arrow(dir: "left", above: ce("Fe"), below: ce("HCl")),
    mol(smiles("BrC1=CC(=CC=C1)N"), label: text(size: 8pt)[C]),
  )),
)

Stereochemistry and drawing extensions

typed-smiles treats SMILES stereochemistry as chemistry: [C@H] and [C@@H] mark tetrahedral centers, while / and \ describe cis/trans geometry around double bonds. For intentionally manual drawings, use typed-smiles extensions: !w forces a solid wedge and !h forces a hashed wedge on the following single bond. Bracket atoms such as [N] remain real SMILES bracket atoms; use {N} for a literal label.

#table(
  columns: (1fr, 1fr, 1fr, 1fr),
  gutter: 0em,
  row-gutter: 0em,
  align: center + horizon,
  stroke: 0.4pt + rgb("#d8d8d8"),

  [*Manual wedge*],
  [*Manual hash*],
  [*Tetrahedral @@*],
  [*trans alkene*],

  [#smiles("C!wN")],
  [#smiles("C!hN")],
  [#smiles("N[C@@H](C)C(=O)O")],
  [#smiles("F/C=C/F")],
)

API

#smiles(smiles-str, scale, bond-length, font-size, font, bond-stroke, color, rotation, show-all-h)

Renders a SMILES string as a 2D skeletal molecular diagram.

Explicit bond-length, font-size, and bond-stroke values override the corresponding value derived from scale.

typed-smiles extensions inside smiles-str:

#ce(chem, font: none, font-size: none, ..args)

Re-exports chemformula’s ch function as ce. Passes through the usual chemformula arguments and adds optional font and font-size arguments for local formula styling. Formula fonts should support math rendering.

#rxn-arrow(above, below, dir)

Creates an arrow for #reaction.

#mol(content, label: none)

Wraps a molecule or formula with an optional centered label below it.

#reaction(gap-h, gap-v, ..items)

Lays out molecules, formulas, plus signs, and rxn-arrow values in a reaction scheme. Directional arrows move the placement cursor, so multi-line schemes can be written as a single sequence.

SMILES support

The package uses the smiles-parser crate for parsing.

Current limitations:

• Aromatic lowercase atoms are not parsed by smiles-parser 0.4. Use Kekule forms such as C1=CC=CC=C1 instead of c1ccccc1.
• Tetrahedral @/@@ and alkene //\ stereochemistry are depicted for common acyclic cases, but the package does not compute or validate R/S or E/Z descriptors.
• Allene, square-planar, trigonal-bipyramidal, octahedral, and complex ring stereochemistry are not yet supported.
• Bridged bicyclics may have atom overlap; template matching is not implemented.
• Implicit hydrogen counts use a simple standard-valence model.

Building

# Run native Rust tests
cargo test --manifest-path plugin/Cargo.toml

# Build the WASM plugin used by Typst
./build.sh

# Compile the visual test document
typst compile --root . tests/test.typ tests/test.pdf

Architecture

SMILES string -> Rust WASM plugin -> JSON layout -> CeTZ drawing in Typst

The Rust plugin handles parsing and 2D coordinates. The Typst layer is a thin renderer plus reaction-scheme helpers.

License

MIT