megane 0.1.1

A fast, beautiful molecular viewer

megane

Desktop-grade molecular visualization. Right in your browser.

Docs · Getting Started · PyPI · npm

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Features

• 1M+ atoms at 60fps — Billboard impostor rendering with WebGL handles massive protein complexes in real time
• Jupyter, CLI, React — Use as a Jupyter widget, serve from the command line, or embed the React component in your own app
• Rust + WASM — PDB, GRO, XYZ, MOL, and XTC parsers in Rust, shared between Python (PyO3) and browser (WASM)
• Trajectory streaming — Stream XTC trajectories over WebSocket in real time, scrub through thousands of frames
• Atom selection & measurement — Select 2–4 atoms to measure distances, angles, or dihedral angles
• Adaptive rendering — High-quality InstancedMesh for small systems, auto-switches to Billboard Impostor for large systems

Installation

Python

pip install megane

npm (for React embedding)

npm install megane-viewer

Quick Start

Jupyter Notebook

import megane

viewer = megane.MolecularViewer()
viewer.load("protein.pdb")
viewer  # display in cell

# With trajectory
viewer.load("protein.pdb", xtc="trajectory.xtc")
viewer.frame_index = 50

CLI

megane serve protein.pdb
megane serve protein.pdb --xtc trajectory.xtc
megane serve  # upload from 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

Development

Prerequisites

• Python 3.10+
• Node.js 18+
• Rust (for building the parser)
• uv

Setup

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

# Python
uv sync --extra dev

# Node.js
npm install
npm run build

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, XTC)
  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
  protocol.py            Binary protocol encoder
  server.py              FastAPI WebSocket server
  widget.py              anywidget Jupyter widget
tests/                   Tests (Python, TypeScript, E2E)

License

MIT