xyz2graph 3.5.1

Package for reading of .xyz files and constructing of molecular graphs from atomic coordinates.

xyz2graph

A Python package to convert XYZ molecular files into NetworkX graphs with interactive 3D visualization using Plotly.

Try it live 🚀

Features

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

Installation

pip install xyz2graph

Requirements

• Python 3.9+
• Dependencies: NumPy, Plotly, NetworkX

Quick Start

import numpy as np
from xyz2graph import MolGraph

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

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

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

G.nodes[0]
# Output: {'element': 'C', 'xyz': (0.1718396797, 1.4440789224, 0.2473852864)}

G.edges[(0, 1)]
# Output: {'length': np.float64(1.49623)}

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

Documentation

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

Help & Discussion

🪲 Report a bug
✨ Request a feature

Contributing

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