cosmol-viewer 0.1.5.dev6

Molecular visualization tools

COSMol-viewer

A high-performance molecular viewer for Python and Rust, backed by Rust. Supports both static rendering and smooth animation playback — including inside Jupyter notebooks.

A compact, high-performance renderer for molecular and scientific shapes with two usage patterns:

• Static rendering + update — push individual scene updates from your application or simulation.
• Play (recommended for demonstrations & smooth playback) — precompute frames and hand the sequence to the viewer to play back with optional interpolation (smooth).

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Quick concepts

• Scene: container for shapes (molecules, spheres, lines, 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 (real-time / streaming use-cases).
• Viewer.play(frames, 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.

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Installation

pip install cosmol-viewer

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Quick Start

See examples in Google Colab.

1. Static molecular rendering

from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules

with open("molecule.sdf", "r") as f:
    sdf = f.read()
    mol = Molecules(parse_sdf(sdf)).centered()

scene = Scene()
scene.scale(0.1)
scene.add_shape(mol, "mol")

viewer = Viewer.render(scene, width=600, height=400)

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, parse_sdf, Molecules
import time

interval = 0.033   # ~30 FPS

frames = []

for i in range(1, 10):
    with open(f"frames/frame_{i}.sdf", "r") as f:
        sdf = f.read()
        mol = Molecules(parse_sdf(sdf)).centered()

    scene = Scene()
    scene.scale(0.1)
    scene.add_shape(mol, "mol")

    frames.append(scene)

Viewer.play(frames, interval=interval, loops=1, width=600, height=400, smooth=True)

Documentation

For API reference and advanced usage, please see the latest documentation.