Molecular Visualization Python Packages

proteinmotion

Animate proteins, DNA, and RNA in Python with a Manim-inspired API, native GPU rendering, and Blender EEVEE.

hofmann

Ball-and-stick crystal structure viewer for Python. Publication-quality vector output (SVG, PDF) and trajectory animations (GIF, MP4) via matplotlib, with ASE and pymatgen interoperability.

vmol

A simple X11 molecular viewer

ammolite

Visualize structure data from Biotite with PyMOL

plotlymol

Interactive 3D molecular visualization in Python — ball-and-stick, VDW, orbital rendering, and a Dash GUI. Built on Plotly and RDKit.

refua-notebook

Jupyter and IPython extension for interactive Refua visualizations of ADMET profiles, 2D and 3D molecules, and fold results.

xyzsdf

Align a 3D molecular structure to the viewing direction of its 2D SDF depiction

molecular-string-renderer

A python utility for rendering 2D molecular graph images given a string representation (SMILES, SELFIES)