michem

Michem

Draw chemical structures from SMILES or authored molecular graphs, compose automatic reaction routes, and annotate electron flow. Michem uses Chitin through a precompiled WebAssembly plugin, with an optional CeTZ canvas adapter.

Molecular structures

Ciprofloxacin and linezolid illustrate fused rings, heterocycles and stereochemistry at a shared physical drawing scale. The tinted bonds identify the piperazine and oxazolidinone rings.

#import "@preview/michem:0.1.0" as michem

#michem.compound-grid(
  michem.compound(
    "C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O",
    name: [Ciprofloxacin],
    highlights: ((bonds: ((14, 15), (15, 16), (16, 17),
      (17, 18), (18, 19), (19, 14)), color: rgb("#88c7a880")),),
  ),
  michem.compound(
    "CC(=O)NC[C@H]1CN(C(=O)O1)C2=CC(=C(C=C2)N3CCOCC3)F",
    name: [Linezolid],
    highlights: ((bonds: ((5, 6), (6, 7), (7, 8),
      (8, 10), (10, 5)), color: rgb("#6aaed680")),),
  ),
  columns: 2, gutter: 32pt,
)

Molecular structures: PubChem ciprofloxacin and PubChem linezolid.

Automatic reaction routes

Stages group participants. The template inserts plus signs, reaction arrows, conditions and names, and arranges chains, branches and joins. All participants share physical atom sizes and bond lengths; structures are not independently scaled to fit cell widths.

#import "@preview/michem:0.1.0" as michem

#michem.reaction-route(
  michem.reaction-stage("substrates",
    michem.compound("CC(=O)c1ccc(Br)cc1", name: [*1*]),
    michem.compound("OB(O)c1ccccc1", name: [*2*]),
  ),
  michem.reaction-stage("biaryl",
    michem.compound("CC(=O)c1ccc(-c2ccccc2)cc1",
      name: [*3*],
      highlights: ((bonds: ((6, 7),), color: rgb("#88c7a880")),),
    ),
  ),
  steps: (michem.reaction-step("substrates", "biaryl",
    above: [Pd(OAc)₂ / metformin],
    below: [K₂CO₃, H₂O, 100 °C],
  ),),
)

4-Bromoacetophenone (1) and phenylboronic acid (2) give 4-acetylbiphenyl (3). The coupling substrates and conditions follow the palladium/metformin Suzuki–Miyaura study. Green marks the newly formed biaryl C–C bond; this figure does not assert a yield.

Add highlights: ((bonds: ((6, 7),), color: rgb("#88c7a880")),) to a compound to highlight a bond in any route, including a peripheral product. Region dictionaries also accept atoms and radius. Atom references are zero-based SMILES parse indices, or explicit names for authored graphs. Highlighter bounds are measured before layout, and the color is painted beneath bonds and labels. Each compound's regions remain local to that occurrence.

Use layout: "circular" for a cycle. Omitted steps close the last stage back to the first. clockwise, start-angle, radius and center control the layout. Additional step reactants and products enter and leave through peripheral branches. branch-curve: "tangent-circle" is the default; "bezier" selects cubic branches. A step can override the route's curve setting.

This larger cycle is exported on a cropped standalone page, ready to place as a figure in a manuscript.

#import "@preview/michem:0.1.0" as michem

#set page(width: auto, height: auto, margin: 12pt)

#michem.reaction-route(
  michem.reaction-stage("orn", michem.compound(
    "C(C[C@@H](C(=O)O)N)CN", name: [L-Ornithine])),
  michem.reaction-stage("cit", michem.compound(
    "C(C[C@@H](C(=O)O)N)CNC(=O)N", name: [L-Citrulline])),
  michem.reaction-stage("asu", michem.compound(
    "C(C[C@@H](C(=O)O)N)CN=C(N)N[C@@H](CC(=O)O)C(=O)O",
    name: [Argininosuccinate])),
  michem.reaction-stage("arg", michem.compound(
    "C(C[C@@H](C(=O)O)N)CN=C(N)N", name: [L-Arginine])),
  layout: "circular", center: [Urea cycle],
  steps: (
    michem.reaction-step("orn", "cit", above: [OTC],
      reactants: (michem.compound("NC(=O)OP(=O)(O)O",
        name: [Carbamoyl phosphate]),),
      products: (michem.compound("OP(=O)(O)O", name: [Phosphate]),),
    ),
    michem.reaction-step("cit", "asu", above: [ASS1],
      below: [ATP → AMP + PPᵢ],
      reactants: (michem.compound("N[C@@H](CC(=O)O)C(=O)O",
        name: [L-Aspartate]),),
    ),
    michem.reaction-step("asu", "arg", above: [ASL],
      products: (michem.compound("O=C(O)/C=C/C(=O)O",
        name: [Fumarate]),),
    ),
    michem.reaction-step("arg", "orn", above: [ARG1],
      below: [H₂O],
      products: (michem.compound("NC(=O)N", name: [Urea],
        highlights: ((bonds: ((0, 1), (1, 3)),
          color: rgb("#88c7a880")),),
      ),),
    ),
  ),
)

The four enzymatic steps follow the Reactome urea cycle. Structures use neutral molecular forms for depiction; ATP/AMP/PPᵢ are shown as condition text. Transport and upstream carbamoyl-phosphate synthesis are outside this diagram.

Electron flow

Use mechanism for atom-level annotations and local electron-flow panels. Arrow endpoints, lone pairs, structures and products are authored explicitly. This local panel shows an acetone enolate attacking benzaldehyde; the second arrow moves the carbonyl π electrons onto oxygen. Optional routing searches for clear curves between the supplied endpoints.

#import "@preview/michem:0.1.0" as michem

#let enolate = michem.smiles-input("[CH2-]C(=O)C",
  positions: ((1, -0.5), (0, 0), (0, 1), (-1, -0.5)))
#michem.mechanism(
  michem.mol("enolate", enolate),
  michem.mol("aldehyde", "O=Cc1ccccc1",
    at: michem.near("enolate", side: "east", gap: 60pt)),
  michem.highlight("aldehyde", bonds: ((0, 1),),
    color: rgb("#6aaed680")),
  michem.electron-arrow(
    michem.atom-ref("enolate", 0), michem.atom-ref("aldehyde", 1),
    arc-angle: -90deg, route: "auto",
  ),
  michem.electron-arrow(
    michem.bond-ref("aldehyde", 0, 1), michem.atom-ref("aldehyde", 0),
    arc-angle: 90deg, route: "auto",
  ),
  font: "Libertinus Serif",
)

Inspecting atom indices

Enable debug to display the atom IDs used by highlights and electron-arrow references. This numbers every atom, including unlabeled skeletal carbons. For example, inspect the Suzuki product before selecting its new biaryl bond:

#import "@preview/michem:0.1.0" as michem

#michem.smiles("CC(=O)c1ccc(-c2ccccc2)cc1", style: michem.style(
  font: "Libertinus Serif",
  debug: true,
))

The new bond connects atoms 6 and 7, so its highlight uses bonds: ((6, 7),). These are two atom IDs, not a bond index. SMILES IDs start at zero in parse order; branches contribute atoms, while ring closure digits and implicit hydrogens do not. Authored molecular graphs display their atom names instead of numeric indices. Each molecular occurrence has its own IDs.

To inspect a complete reaction-route, including circular stages and peripheral participants, pass molecular-style: michem.style(debug: true). The same option works with compound-grid. In a mechanism, pass style: michem.style(debug: true) to each mol that needs inspection.

Debug is off by default. Blue ID labels follow the molecular font at 65% of its size and participate in measured bounds without changing atom positions or IDs. Dense structures may need a larger bond length for readability. Turn debug off after choosing references for the final figure.

Public interfaces

See the user guide source for signatures, coordinate systems, parameter defaults and routing limits.

Fonts and scope

Route templates default to Libertinus Serif. For individual structures, choose style: michem.style(font: "Libertinus Serif"); document set text rules do not change molecular fonts. Any selected family must be available to Typst through system fonts, the web project, or the CLI's --font-path. Documentation code uses Cascadia Code. No separate font files are bundled in the package.

Without a selected molecular font, the plugin uses bundled Noto Sans outlines. Named-font SVG exports reference the selected family, so standalone SVG viewers need that font too.

Michem does not predict reactions, infer lone-pair counts, or balance equations. Circular routes support one ring with neighboring stages. Automatic routing is bounded and can fail when no clear candidate is found. Enlarge the layout or adjust the authored geometry when necessary.

License

Michem's original code is Apache-2.0.

Copyright 2026 AshGrey.