https://github.com/zotko/xyz2graph

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
https://github.com/zotko/xyz2graph

3d-plot atomic-coordinates chemical-structures chemistry chemoinformatics computational-chemistry data-visualization molecular-graph molecular-modeling molecule molecule-visualization networkx plotly scientific-computing xyz-files xyz-reader

Last synced: 17 days ago
JSON representation

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

• Host: GitHub
• URL: https://github.com/zotko/xyz2graph
• Owner: zotko
• License: isc
• Created: 2018-08-11T12:05:10.000Z (over 6 years ago)
• Default Branch: main
• Last Pushed: 2025-03-10T21:41:27.000Z (about 1 month ago)
• Last Synced: 2025-03-28T17:08:16.476Z (24 days ago)
• Topics: 3d-plot, atomic-coordinates, chemical-structures, chemistry, chemoinformatics, computational-chemistry, data-visualization, molecular-graph, molecular-modeling, molecule, molecule-visualization, networkx, plotly, scientific-computing, xyz-files, xyz-reader
• Language: Python
• Homepage:
• Size: 7.61 MB
• Stars: 85
• Watchers: 1
• Forks: 23
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
# xyz2graph

[![PyPI version](https://img.shields.io/pypi/v/xyz2graph.svg)](https://pypi.org/project/xyz2graph/)

[![Python Version](https://img.shields.io/pypi/pyversions/xyz2graph.svg)](https://pypi.org/project/xyz2graph/)

[![License](https://img.shields.io/github/license/zotko/xyz2graph.svg)](https://github.com/zotko/xyz2graph/blob/master/LICENSE)

[![Documentation](https://img.shields.io/badge/docs-mkdocs-blue)](https://zotko.github.io/xyz2graph)

[![DOI](https://zenodo.org/badge/144382005.svg)](https://doi.org/10.5281/zenodo.14569337)

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/zotko/xyz2graph/main?urlpath=%2Fdoc%2Ftree%2Fbinder%2Fxyz2graph.ipynb)

[![PyPI Downloads](https://static.pepy.tech/badge/xyz2graph/month)](https://pepy.tech/projects/xyz2graph)

[![GitHub Stars](https://img.shields.io/github/stars/zotko/xyz2graph)](https://github.com/zotko/xyz2graph/stargazers)

[![GitHub Forks](https://img.shields.io/github/forks/zotko/xyz2graph)](https://github.com/zotko/xyz2graph/network/members)

[![Stand With Ukraine](https://raw.githubusercontent.com/vshymanskyy/StandWithUkraine/main/badges/StandWithUkraine.svg)](https://stand-with-ukraine.pp.ua)

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

Try it live 🚀: [Binder](https://mybinder.org/v2/gh/zotko/xyz2graph/main?urlpath=%2Fdoc%2Ftree%2Fbinder%2Fxyz2graph.ipynb) | [GESIS Notebooks](https://notebooks.gesis.org/binder/v2/gh/zotko/xyz2graph/main?urlpath=%2Fdoc%2Ftree%2Fbinder%2Fxyz2graph.ipynb)

## Features

- [Interactive 3D molecular visualization using Plotly](https://zotko.github.io/xyz2graph/demo)

- NetworkX graph conversion for analysis

- Command-line interface

## Installation

```bash

pip install xyz2graph

```

## Requirements

- Python 3.8+

- Dependencies: NumPy, Plotly, NetworkX

## Quick Start

```python

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

```bash

# 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](https://zotko.github.io/xyz2graph) for guides, API reference, and examples.

## Help & Discussion

🪲 [Report a bug](https://github.com/zotko/xyz2graph/issues)  

✨ [Request a feature](https://github.com/zotko/xyz2graph/discussions)

## Contributing

Contributions are welcome! Please see the [Contributing Guide](https://github.com/zotko/xyz2graph/tree/main/CONTRIBUTING.md) for guidelines.

## Citation

If you use xyz2graph in your research, please cite:

```bibtex

@misc{zotko2018xyz2graph,

  author       = {Zotko, Mykola},

  title        = {xyz2graph: Molecular Structure Visualization},

  year         = {2018},

  publisher    = {GitHub},

  url          = {https://github.com/zotko/xyz2graph}

}

```