xyz2graph

A Python package for converting XYZ molecular files into interactive 3D visualizations and NetworkX graphs.

Try it live 🚀

Features

• Interactive 3D molecular visualization using Plotly
• NetworkX graph conversion for analysis
• Command-line interface

Installation

pip install xyz2graph

Requirements

• Python 3.8+
• Dependencies: NumPy, Plotly, NetworkX

Quick Start

from xyz2graph import MolGraph

# Create molecular graph and read XYZ file
mg = MolGraph()
mg.read_xyz('molecule.xyz')

# Convert to NetworkX graph
G = mg.to_networkx()

# Generate interactive 3D visualization
fig = mg.to_plotly()
fig.show()

Command Line

# Save visualization as HTML
xyz2graph molecule.xyz

# Specify output file
xyz2graph molecule.xyz --output viz.html

# Open directly in browser
xyz2graph molecule.xyz --browser

Help & Discussion

🪲 Report a bug
✨ Request a feature

Documentation

Read the documentation for guides, API reference, and examples.

Contributing

Contributions are welcome! Please see the Contributing Guide for guidelines.

Citation

If you use xyz2graph in your research, please cite:

@misc{zotko2018xyz2graph,
  author       = {Zotko, Mykola},
  title        = {xyz2graph: Molecular Structure Visualization},
  year         = {2018},
  publisher    = {GitHub},
  url          = {https://github.com/zotko/xyz2graph}
}