COSMol-viewer

A high-performance molecular viewer for Python and Rust, powered by a unified Rust core. It supports both in-notebook visualization and native desktop rendering, with smooth playback for scientific animations.

COSMol-viewer is a compact, cross-platform renderer for molecular and geometric scenes. Unlike purely notebook-bound solutions such as py3Dmol, COSMol-viewer runs everywhere:

• Native desktop window (Python or Rust) via egui
• Jupyter / IPython notebook via WASM backend
• Rust applications

All implementations share the same Rust rendering engine, ensuring consistent performance and visual output.

Quick concepts

• Scene: container for shapes (molecules, proteins, spheres, etc.).
• Viewer.render(scene, ...): create a static viewer bound to a canvas (native or notebook). Good for static visualization.
• viewer.update(scene): push incremental changes after Viewer.render() (real-time / streaming use-cases).
• Animation: An Animation object containing frames and settings.
• Viewer.play(animation, interval, loops, width, height, smooth): recommended for precomputed animations and demonstrations. The viewer takes care of playback timing and looping.

Why prefer play for demos?

• Single call API (hand off responsibility to the viewer).
• Built-in timing & loop control.
• Optional smooth interpolation between frames for visually pleasing playback even when input frame rate is low.

Why keep update?

• update is ideal for real-time simulations, MD runs, or streaming data where frames are not precomputed. It provides strict fidelity (no interpolation) and minimal latency.

Usage

python

See examples in Google Colab.

Install with pip install cosmol-viewer

1. Static molecular rendering

from cosmol_viewer import Molecule, Scene, Viewer

mol_data = open("molecule.sdf", "r", encoding="utf-8").read()

mol = Molecule.from_sdf(mol_data).centered()

scene = Scene()

scene.set_scale(1.0)

scene.add_shape_with_id("molecule", mol)

viewer = Viewer.render(scene, width=800, height=500)

viewer.save_image("screenshot.png")

print("Press Any Key to exit...", end='', flush=True)
_ = input()  # Keep the viewer open until you decide to close

2. Animation playback with Viewer.play

from cosmol_viewer import Scene, Viewer, Molecule, Animation

anim = Animation(interval=0.05, loops=-1, smooth=False)
for i in range(1, 10):
    with open(f"frames/frame_{i}.sdf", "r") as f:
        mol = Molecule.from_sdf(f.read())

    scene = Scene()
    scene.add_shape(mol)
    anim.add_frame(scene)

Viewer.play(anim, width=800, height=500) # loops=-1 for infinite repeat

more examples can be found in the examples folder:

cd cosmol_viewer
python .\examples\render_protein.py

Rust

Install with cargo add cosmol_viewer

see examples in examples folder:

cd cosmol_viewer
cargo run --example render_protein

Documentation

Please check out our documentation at here.

Contact

For any questions, issues, or suggestions, please contact wjt@cosmol.org or open an issue in the repository. We will review and address them as promptly as possible.