Molfig

Molfig is a Typst package for rendering molecular structure files in static documents.

It accepts PDB, mmCIF, and BinaryCIF input, converts structures through a CPU-side Mol*-style Model/Structure/Unit layer, exports static OBJ/STL/PLY mesh bytes, and delegates final document rendering to maquette.

Quickstart

#import "@preview/molfig:0.1.1"
#set page(width: auto, height: auto, margin: 0mm)

// Uses structural data from RCSB PDB / wwPDB.
// PDB ID: 9R1O
// PDB DOI: https://doi.org/10.2210/pdb9R1O/pdb
// Deposition authors: Petrenas, R.; Ozga, K.; Chubb, J.J.; Woolfson, D.N.
// PDB archive data files are available under CC0 1.0.
#let pdb = read("9R1O.pdb", encoding: none)

#molfig.render(
  pdb,
  format: "pdb",
  representation: "cartoon",
  assembly: "1",
  mesh-format: "obj",
  quality: "high",
  center: true,
  output-format: "svg",
  config: (
    azimuth: 35,
    elevation: 24,
    background: "",
  ),
)

The manual uses PDB entry 9R1O as its complete example. Put 9R1O.typ and 9R1O.pdb in the same directory, then compile the figure PDF:

typst compile 9R1O.typ

Rendered 9R1O Example

Structural data source: RCSB PDB / wwPDB, PDB ID 9R1O, DOI 10.2210/pdb9R1O/pdb. PDB archive data files are distributed under CC0 1.0.

Use format: "mmcif" or format: "bcif" for text mmCIF and BinaryCIF inputs. For reproducible documents, prefer explicit format, representation, assembly, alt-loc, mesh-format, and geometry quality options instead of relying on auto-detection.

Examples

The package/examples directory contains complete example sources, rendered PDFs, and their accompanying structural data files. The example data files are kept under package/examples/data, together with attribution metadata.

Features

• Inputs: PDB, text CIF/mmCIF, and BinaryCIF.
• Structure layer: Mol*-style Model/Structure/Unit concepts, assembly operators, altLoc handling, bond metadata, lookup3d/boundary summaries, secondary structure, coarse IHM spheres/gaussians, and semantic render-object metadata.
• Representations: default follows the Mol* Viewer preset, including pLDDT, QMEAN, and SB-NCBR partial-charge annotation themes before automatic size routing; cartoon is the Viewer Quick Styles Cartoon preset; spacefill is the Viewer illustrative Spacefill preset; and polymer-cartoon exposes the standalone Mol* Cartoon provider defaults. Ball-and-stick, ribbon, and backbone are also available.
• Assembly support: biological assemblies are represented as source model plus unit operators before static mesh export.
• Alternate locations: select a concrete altLoc, all altLocs, or the highest-occupancy conformer.
• Color themes: color-theme supports chain-id, element-symbol, entity-id, operator-name, plddt-confidence, qmean-score, and sb-ncbr-partial-charges. The optional theme dictionary mirrors Mol* Viewer overrides such as globalName, carbonColor, and symmetryColor; OBJ materials are forwarded to maquette.
• Outputs: OBJ, companion MTL, binary STL, and ASCII PLY.
• Rendering: render passes generated mesh bytes to maquette; render-object exposes the mesh, rendered content, and normalized metadata for advanced documents.

Public API

• render(data, ..., config: (:), width: auto, height: auto) converts and renders through maquette.
• render-object(data, ...) returns generated mesh bytes, rendered content, and metadata.
• to-obj(data, ...), to-mtl(data, ...), to-stl(data, ...), and to-ply(data, ...) return export bytes.
• info(data, ...) returns molecular and mesh-planning metadata without rendering.
• mesh-info(data, mesh-format: "obj", config: (:), ...) delegates to maquette's mesh metadata helpers for the generated mesh.
• v15-or-later() returns whether the active Typst compiler supports project-side path(...) values.

Common options include format, representation, color-theme, theme, assembly, alt-loc, block-index, block-header, quality, sphere-detail, linear-segments, radial-segments, radius-scale, atom-radius, bond-radius, ribbon-radius, ribbon-width, helix-profile, round-cap, sheet-arrow-factor, tubular-helices, infer-bonds, and center.

The data argument accepts bytes from read(..., encoding: none), inline string data for small examples, and Typst 0.15+ path values created with path("...").

Choosing A Mesh Format

• Use OBJ for the closest static Mol* exporter parity and readable diffs.
• Use STL when a downstream tool specifically requires binary triangle data.
• Use PLY when package-owned face group metadata is useful in a compact text mesh.

OBJ output can be paired with to-mtl. During render, OBJ material colors are automatically converted to maquette's materials map; entries supplied through config.materials override generated colors. OBJ and PLY preserve Molfig group or operator metadata where the format can represent it. Binary STL follows Mol* static exporter behavior and keeps the two-byte facet attribute field at zero.

Choosing A Render Format

output-format: "png" is the default and is recommended for high-poly meshes, large assemblies, and spacefill representations. Maquette rasterizes PNG output with a Z-buffer, avoiding the document-node cost of representing every visible mesh face as SVG content.

Use output-format: "svg" when vector output is important and the mesh is small or moderately sized. A large SVG render can exceed Typst's SVG node limit and fail with failed to parse SVG (nodes limit reached). If that happens, switch to PNG or reduce the mesh complexity with quality: "auto", a lower quality preset, or smaller sphere-detail, linear-segments, and radial-segments values.

Documentation

The full Molfig manual is available at package/docs/documentation.pdf. It documents:

• installation and import conventions;
• input format handling and BinaryCIF block selection;
• every public command and return shape;
• mesh, representation, assembly, altLoc, and quality options;
• maquette passthrough configuration;
• metadata fields returned by info and render-object;
• licensing, third-party notices, and example data attribution;
• troubleshooting and development commands;
• the embedded 9R1O rendering and its data source.

The manual source is package/docs/documentation.typ, and it reads the package version from package/typst.toml.

Notes And Limits

Molfig emits static presentation meshes. representation: "surface" implements the Mol* Viewer Quick Styles Molecular Surface preset on the CPU and exports the result as OBJ/STL/PLY. Gaussian volume and density/volume visuals remain outside the static export contract; the size-dependent ViewerAuto path uses a CPU Gaussian surface for Huge and Gigantic structures.

IHM coarse sphere and gaussian rows remain available as coarse model units and participate in the size-dependent ViewerAuto Gaussian-surface path.

License And Notices

Molfig project code is licensed under the MIT License. See LICENSE.

Molfig ports or adapts Mol* behavior and includes Mol*-derived reference data in the Rust/WASM implementation. Mol* is licensed under the MIT License, copyright (c) 2017 - now, Mol* contributors.

Bundled example structure files under package/examples/data are PDB archive data from RCSB PDB / wwPDB and are available under CC0 1.0. Per-file PDB IDs, DOIs, and recommended attributions are listed in package/examples/data/README.md.

See NOTICE.md and THIRD_PARTY_NOTICES.md for the full distribution notice.

Development

cd wasm-plugin
cargo fmt --check
cargo test
cargo build --release --target wasm32-unknown-unknown
cp target/wasm32-unknown-unknown/release/molfig.wasm ../package/molfig.wasm
cd ..
typst compile --root package package/docs/documentation.typ package/docs/documentation.pdf

The checked-in package/molfig.wasm should be regenerated after Rust changes that affect the Typst plugin. Regenerate package/docs/documentation.pdf after public API or documentation changes.