xyzrender

name	xyzrender
version	1.0.0
description	Publication-quality molecular graphics. Render molecular structures as SVG, PNG, PDF, and animated GIF from XYZ, mol/SDF, MOL2, PDB, SMILES, CIF, cube files, or quantum chemistry output.
homepage	https://github.com/aligfellow/xyzrender
metadata	{"category":"visualization","tags":["chemistry","molecular-graphics","svg","gif","xyz","quantum-chemistry","分子可视化","molecule visualization","渲染分子","render molecule","xyz渲染","xyz render","分子出图","molecular graphics"]}

xyzrender - Publication-Quality Molecular Graphics

Render molecular structures as publication-quality SVG, PNG, PDF, and animated GIF from XYZ files and quantum chemistry input/output.

Installation

# Using uv (recommended)
uv tool install xyzrender

# Using pip
pip install xyzrender

Quick Start

Command Line

# Basic rendering (outputs SVG by default)
xyzrender molecule.xyz

# Specify output format
xyzrender molecule.xyz -o molecule.png

# Rotation GIF
xyzrender molecule.xyz --gif-rot -o movie.gif

Python API

from xyzrender import load, render, render_gif

mol = load("molecule.xyz")
render(mol, output="output.svg")
render_gif("molecule.xyz", gif_rot="y", output="movie.gif")

Key Features

• Automatic detection: Bond orders, aromaticity, TS bonds, NCI interactions
• Multiple formats: SVG, PNG, PDF, GIF
• Styling presets: default, flat, paton (PyMOL-like)
• Annotations: atom indices, bond measurements, custom labels
• Surfaces: MO, density, ESP, NCI from cube files

Common Use Cases

# Publication figure
xyzrender molecule.xyz --config paton -o paper.svg

# Rotating molecule
xyzrender molecule.xyz --gif-rot -o rotating.gif

# Transition state
xyzrender ts.out --ts --gif-ts -o ts_animation.gif

# With vdW surface
xyzrender molecule.xyz --vdw --gif-rot -o vdw.gif

Citation

A.S. Goodfellow* and B.N. Nguyen, J. Chem. Theory Comput., 2026, DOI: 10.1021/acs.jctc.5c02073