megane 0.4.0

A fast, beautiful molecular viewer

megane

Spectacles for atomistic data.

1M+ atoms at 60fps. Visual pipelines. Jupyter, browser, React, VSCode.

Docs · Getting Started · PyPI · npm

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Features

• 1M+ Atoms at 60fps — Billboard impostor rendering scales from small molecules to massive complexes in real time. InstancedMesh for small systems auto-switches to GPU-accelerated billboard impostors for large systems. Stream XTC trajectories over WebSocket.
• Runs Everywhere — Jupyter widget, CLI server, React component, and VSCode extension. Rust-based PDB, GRO, XYZ, MOL, CIF, XTC, LAMMPS, and ASE .traj parsers shared between Python (PyO3) and browser (WASM) — parse once, run anywhere.
• Visual Pipeline Editor — Build visualization workflows by wiring nodes or let the AI generator build them from natural language. 11 node types with 7 typed data channels flowing through color-coded edges. Load multiple structures with layer-based rendering to compare systems side by side.
• Embed & Integrate — Control the viewer from Plotly via ipywidgets events. Embed in MDX / Next.js docs. React to frame_change, selection_change, and measurement events. Use the framework-agnostic renderer from Vue, Svelte, or vanilla JS.

Scale

megane renders over 1 million atoms at 60fps in the browser. Small systems get high-quality InstancedMesh spheres and cylinders; large systems automatically switch to GPU-accelerated billboard impostors. No desktop app, no plugin — just a browser tab.

Trajectory streaming works over WebSocket via a binary protocol. Load an XTC file and scrub through thousands of frames in real time, without reading everything into memory.

Anywhere

One codebase, every environment.

Environment	How	Install
Jupyter	anywidget inline viewer	pip install megane
Browser	megane serve local server	pip install megane
React	<MeganeViewer /> component	npm install megane-viewer
VSCode	Custom editor for .pdb, .gro, .xyz, .mol, .sdf, .cif	Extension

The secret: PDB, GRO, XYZ, MOL, CIF, XTC, LAMMPS, and ASE .traj parsers are written in Rust and compiled to both PyO3 (Python) and WASM (browser). Parse once, run anywhere.

Visual Pipelines

Wire nodes to build visualization workflows — no code required.

11 node types across 5 categories: load data (structure, trajectory, streaming, vector), process (filter, modify), overlay (bonds, labels, polyhedra, vectors), and display in a 3D viewport.

7 typed data channels — particle, bond, cell, label, mesh, trajectory, vector — flow through color-coded edges. Only matching types can connect.

Pipelines serialize to JSON, so you can save, share, and version-control your visualization recipes.

Integrate

megane is not a walled garden. It fits into your existing workflow.

Plotly — Click a point on a Plotly FigureWidget to jump to a trajectory frame. Use megane's on_event("frame_change") callback to update Plotly markers in sync.

MDX / Next.js — Drop <MeganeViewer /> or <Viewport /> into your .mdx documentation. WASM parsing works out of the box with a one-line webpack config.

ipywidgets — React to frame_change, selection_change, and measurement events. Compose megane with any widget in the Jupyter ecosystem.

Framework-agnostic — MoleculeRenderer is a plain Three.js class. Mount it in Vue, Svelte, or a vanilla <div>.

Installation

Python

pip install megane

npm (for React embedding)

npm install megane-viewer

Quick Start

Jupyter Notebook

from megane import Pipeline, LoadStructure, AddBonds, Viewport, MolecularViewer

# Build a pipeline
pipe = Pipeline()
s = pipe.add_node(LoadStructure("protein.pdb"))
bonds = pipe.add_node(AddBonds(source="distance"))
v = pipe.add_node(Viewport())
pipe.add_edge(s.out.particle, bonds.inp.particle)
pipe.add_edge(s.out.particle, v.inp.particle)
pipe.add_edge(bonds.out.bond, v.inp.bond)

# Display in notebook
viewer = MolecularViewer()
viewer.set_pipeline(pipe)
viewer

CLI (Docker)

docker build -t megane .
docker run --rm -p 8080:8080 megane

Open http://localhost:8080 in your browser.

To view your own files, mount them into the container:

docker run --rm -p 8080:8080 -v ./mydata:/data megane \
  megane serve /data/protein.pdb --port 8080 --no-browser

React

import { MeganeViewer, parseStructureFile } from "megane-viewer";

function App() {
  const [snapshot, setSnapshot] = useState(null);

  const handleUpload = async (file: File) => {
    const result = await parseStructureFile(file);
    setSnapshot(result.snapshot);
  };

  return <MeganeViewer snapshot={snapshot} mode="local" /* ... */ />;
}

Supported File Formats

Format	Extension	Description
PDB	.pdb	Protein Data Bank
GRO	.gro	GROMACS structure file
XYZ	.xyz	Cartesian coordinate format
MOL/SDF	.mol, .sdf	MDL Molfile (V2000)
XTC	.xtc	GROMACS compressed trajectory
CIF	.cif	Crystallographic Information File
LAMMPS data	.data, .lammps	LAMMPS data file
ASE .traj	.traj	ASE trajectory (ULM binary format)
LAMMPS dump	.lammpstrj	LAMMPS dump trajectory

Development

Prerequisites

• Python 3.10+
• Node.js 22+
• Rust (for building the parser)
• wasm-pack (for building WASM bindings)
• uv

Setup

git clone https://github.com/hodakamori/megane.git
cd megane

# Install wasm-pack (if not already installed)
cargo install wasm-pack

# Python
uv sync --extra dev

# Node.js
npm install
npm run build

Running megane serve

After setup, build and install the package, then start the server:

maturin develop --release
megane serve protein.pdb

Development Mode

# Terminal 1: Vite dev server
npm run dev

# Terminal 2: Python backend
uv run megane serve protein.pdb --dev --no-browser

Tests

uv run pytest              # Python tests
npm test                   # TypeScript unit tests
cargo test -p megane-core  # Rust tests
make test-all              # All tests

Project Structure

src/                     TypeScript frontend
  renderer/              Three.js rendering (impostor, mesh, shaders)
  protocol/              Binary protocol decoder + web workers
  parsers/               WASM-based file parsers (PDB, GRO, XYZ, MOL, CIF, XTC, LAMMPS, .traj)
  logic/                 Bond / label / vector source logic
  components/            React UI components
  hooks/                 Custom React hooks
  stream/                WebSocket client
crates/                  Rust workspace
  megane-core/           Core parsers and bond inference
  megane-python/         PyO3 Python extension
  megane-wasm/           WASM bindings (wasm-bindgen)
python/megane/           Python backend
  parsers/               PDB / XTC parsers
  pipeline.py            Pipeline builder (NetworkX-style DAG)
  protocol.py            Binary protocol encoder
  server.py              FastAPI WebSocket server
  widget.py              anywidget Jupyter widget
tests/                   Tests (Python, TypeScript, E2E)

License

MIT