xyz2graph

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

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# xyz2graph

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

[Try it live](https://mybinder.org/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 3.9+
- 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/categories/ideas)

## Contributing

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

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