cosmol-viewer 0.2.19

Molecular visualization tools

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 an interactive viewer in a native window or notebook canvas.
• scene.save_image(path, ...) / scene.to_png(...) / scene.display(...): render the scene directly to a static PNG at any requested resolution. This is independent of any viewer and does not use notebook JavaScript or browser canvas readback.
• scene.set_camera_view(...) / scene.rotate_camera(...): set the reproducible camera used by both static exports and newly created viewers.
• viewer.update(scene): push incremental changes after Viewer.render() (real-time / streaming use-cases).
• Animation: An Animation object containing frames and settings.
• Animation(interval, loops, interpolate): stores precomputed frames and playback settings.
• Viewer.play(animation, width, height): 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 interpolate mode 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)

scene.set_camera_view(azimuth=35, elevation=20, distance=32, fov=18)
scene.save_image("rendered_scene.png", width=1600, height=1000)
viewer = Viewer.render(scene, width=800, height=500)

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

In a notebook, use a static PNG display when you do not need interaction:

scene.display(width=1200, height=800)
scene.display(width=1200, height=800, background="transparent")

For static exports, omit background to use the scene background, pass a color such as "#ffffff" or [255, 255, 255], or use "transparent" for a PNG with a transparent background.

2. Animation playback with Viewer.play

from cosmol_viewer import Scene, Viewer, Molecule, Animation

anim = Animation(interval=0.05, loops=-1, interpolate=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

3. Protein cartoon rendering

from cosmol_viewer import Protein, Scene, Viewer

mmcif_data = open("protein.cif", "r", encoding="utf-8").read()
protein = Protein.from_mmcif(mmcif_data).centered().rainbow_residues()

scene = Scene()
scene.add_shape_with_id("protein", protein)

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

Protein.from_mmcif() and Protein.from_pdb() parse backbone atoms and use the Rust core to assign secondary structure before rendering a ChimeraX-style cartoon ribbon mesh. Use .rainbow_residues() for ChimeraX-style residue rainbow coloring, or .color("#10ACBF") for a uniform cartoon color.

more examples can be found in the examples folder:

cd cosmol_viewer
python .\examples\render_protein.py

Documentation

Please check out our documentation at here.

---

Contact

For any questions, issues, or suggestions, please contact [e-mail] or open an issue in the repository. We will review and address them as promptly as possible.