xyz2graph 3.2.0

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

xyz2graph

A lightweight Python package for reading XYZ files and creating interactive molecular visualizations. Convert molecular structures into 3D visualizations using Plotly or analyze them as NetworkX graphs.

Features

• Read and parse XYZ molecular structure files
• Generate interactive 3D molecular visualizations using Plotly
• Convert molecular structures to NetworkX graphs for analysis
• Command-line interface for quick visualizations

Documentation

Full documentation is available at https://zotko.github.io/xyz2graph

Installation

pip install xyz2graph

Requirements

• Python 3.8+
• NumPy
• Plotly
• NetworkX

Usage

Basic Usage

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()

Command Line

# Save visualization as HTML
xyz2graph molecule.xyz

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

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

Examples

Example XYZ files can be found in the examples directory.

Contributing

I welcome contributions! Please see the CONTRIBUTING.md file for guidelines on how to make contributions to this project.

License

This project is licensed under the ISC License - see the LICENSE file for details.

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}
}