| Name | xyz2graph JSON |
| Version |
3.5.0
JSON |
| download |
| home_page | None |
| Summary | Package for reading of .xyz files and constructing of molecular graphs from atomic coordinates. |
| upload_time | 2025-02-27 16:01:14 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | ISC License
Copyright (c) 2018 Mykola Zotko
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
PERFORMANCE OF THIS SOFTWARE. |
| keywords |
chemistry
molecular-graphs
visualization
xyz-files
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# xyz2graph
[](https://pypi.org/project/xyz2graph/)
[](https://pypi.org/project/xyz2graph/)
[](https://github.com/zotko/xyz2graph/blob/master/LICENSE)
[](https://zotko.github.io/xyz2graph)
[](https://doi.org/10.5281/zenodo.14569337)
[](https://pepy.tech/projects/xyz2graph)
[](https://github.com/zotko/xyz2graph/stargazers)
[](https://github.com/zotko/xyz2graph/network/members)
[](https://stand-with-ukraine.pp.ua)
A Python package to convert XYZ molecular files into NetworkX graphs with interactive 3D visualization using Plotly.
<a href="https://zotko.github.io/xyz2graph/demo" target="_blank">Try it live 🚀</a>
## Features
- Interactive 3D molecular visualization using Plotly
- NetworkX graph conversion for analysis
- Command-line interface
## Installation
```bash
pip install xyz2graph
```
## Requirements
- Python 3.8+
- Dependencies: NumPy, Plotly, NetworkX
## Quick Start
```python
from xyz2graph import MolGraph
# Create molecular graph and read XYZ file
mg = MolGraph()
mg.read_xyz('molecule.xyz')
# Convert to NetworkX graph
G = mg.to_networkx()
# Generate interactive 3D visualization
fig = mg.to_plotly()
fig.show()
```
## 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}
}
```
<p align="center">
<a href="https://www.buymeacoffee.com/mykola_zotko">
<img src="https://www.buymeacoffee.com/assets/img/custom_images/yellow_img.png" alt="Buy Me A Coffee">
</a>
</p>
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"description": "# xyz2graph\n\n[](https://pypi.org/project/xyz2graph/)\n[](https://pypi.org/project/xyz2graph/)\n[](https://github.com/zotko/xyz2graph/blob/master/LICENSE)\n[](https://zotko.github.io/xyz2graph)\n[](https://doi.org/10.5281/zenodo.14569337)\n\n[](https://pepy.tech/projects/xyz2graph)\n[](https://github.com/zotko/xyz2graph/stargazers)\n[](https://github.com/zotko/xyz2graph/network/members)\n\n[](https://stand-with-ukraine.pp.ua)\n\nA Python package to convert XYZ molecular files into NetworkX graphs with interactive 3D visualization using Plotly.\n\n<a href=\"https://zotko.github.io/xyz2graph/demo\" target=\"_blank\">Try it live \ud83d\ude80</a>\n\n## Features\n\n- Interactive 3D molecular visualization using Plotly\n- NetworkX graph conversion for analysis\n- Command-line interface\n\n## Installation\n\n```bash\npip install xyz2graph\n```\n\n## Requirements\n\n- Python 3.8+\n- Dependencies: NumPy, Plotly, NetworkX\n\n## Quick Start\n\n```python\nfrom xyz2graph import MolGraph\n\n# Create molecular graph and read XYZ file\nmg = MolGraph()\nmg.read_xyz('molecule.xyz')\n\n# Convert to NetworkX graph\nG = mg.to_networkx()\n\n# Generate interactive 3D visualization\nfig = mg.to_plotly()\nfig.show()\n```\n\n## Command Line\n\n```bash\n# Save visualization as HTML\nxyz2graph molecule.xyz\n\n# Specify output file\nxyz2graph molecule.xyz --output viz.html\n\n# Open directly in browser\nxyz2graph molecule.xyz --browser\n```\n\n## Documentation\n\nRead the [documentation](https://zotko.github.io/xyz2graph) for guides, API reference, and examples.\n\n## Help & Discussion\n\n\ud83e\udeb2 [Report a bug](https://github.com/zotko/xyz2graph/issues) \n\u2728 [Request a feature](https://github.com/zotko/xyz2graph/discussions)\n\n## Contributing\n\nContributions are welcome! Please see the [Contributing Guide](https://github.com/zotko/xyz2graph/tree/main/CONTRIBUTING.md) for guidelines.\n\n## Citation\n\nIf you use xyz2graph in your research, please cite:\n\n```bibtex\n@misc{zotko2018xyz2graph,\n author = {Zotko, Mykola},\n title = {xyz2graph: Molecular Structure Visualization},\n year = {2018},\n publisher = {GitHub},\n url = {https://github.com/zotko/xyz2graph}\n}\n```\n\n<p align=\"center\">\n <a href=\"https://www.buymeacoffee.com/mykola_zotko\">\n <img src=\"https://www.buymeacoffee.com/assets/img/custom_images/yellow_img.png\" alt=\"Buy Me A Coffee\">\n </a>\n</p>\n",
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