xyz2graph
A Python package to convert XYZ molecular files into NetworkX graphs with interactive 3D visualization using Plotly.
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.
1 maintainer
Metadata
1 maintainer
Release files for xyz2graph 3.5.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| xyz2graph-3.5.1.tar.gz | 1.4 MB | With provenance | Details for xyz2graph-3.5.1.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| xyz2graph-3.5.1-py3-none-any.whl | Python 3 | none | any | Details for xyz2graph-3.5.1-py3-none-any.whl |
Total release size: 1.4 MB
Release files / xyz2graph-3.5.1.tar.gz
| Download URL | xyz2graph-3.5.1.tar.gz |
|---|---|
| Size | 1.4 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Download URL | xyz2graph-3.5.1-py3-none-any.whl |
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| Size | 21.8 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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Yes |
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twine/6.1.0 CPython/3.13.12
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Transparency logSecurity for xyz2graph 3.5.1
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Signed by GitHub Actions, verified by PyPI on May 8, 2026.
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