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xyz2graph\n\n[![PyPI version](https://img.shields.io/pypi/v/xyz2graph.svg)](https://pypi.org/project/xyz2graph/)\n[![Python Version](https://img.shields.io/pypi/pyversions/xyz2graph.svg)](https://pypi.org/project/xyz2graph/)\n[![License](https://img.shields.io/github/license/zotko/xyz2graph.svg)](https://github.com/zotko/xyz2graph/blob/master/LICENSE)\n[![Documentation](https://img.shields.io/badge/docs-mkdocs-blue)](https://zotko.github.io/xyz2graph)\n[![DOI](https://zenodo.org/badge/144382005.svg)](https://doi.org/10.5281/zenodo.14569337)\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/zotko/xyz2graph/main?urlpath=%2Fdoc%2Ftree%2Fbinder%2Fxyz2graph.ipynb)\n\n\n[![PyPI Downloads](https://static.pepy.tech/badge/xyz2graph/month)](https://pepy.tech/projects/xyz2graph)\n[![GitHub Stars](https://img.shields.io/github/stars/zotko/xyz2graph)](https://github.com/zotko/xyz2graph/stargazers)\n[![GitHub Forks](https://img.shields.io/github/forks/zotko/xyz2graph)](https://github.com/zotko/xyz2graph/network/members)\n\n[![Stand With Ukraine](https://raw.githubusercontent.com/vshymanskyy/StandWithUkraine/main/badges/StandWithUkraine.svg)](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\nTry 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)\n\n## Features\n\n- [Interactive 3D molecular visualization using Plotly](https://zotko.github.io/xyz2graph/demo)\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\nimport numpy as np\nfrom xyz2graph import MolGraph\n\n# Create molecular graph and read XYZ file\nmg = MolGraph()\nmg.read_xyz('molecule.xyz')\n\n# Generate interactive 3D visualization\nfig = mg.to_plotly()\nfig.show()\n\n# Convert to NetworkX graph\nG = mg.to_networkx()\n\nG.nodes[0]\n# Output: {'element': 'C', 'xyz': (0.1718396797, 1.4440789224, 0.2473852864)}\n\nG.edges[(0, 1)]\n# Output: {'length': np.float64(1.49623)}\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 \u0026 Discussion\n\n🪲 [Report a bug](https://github.com/zotko/xyz2graph/issues)  \n✨ [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\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://www.buymeacoffee.com/mykola_zotko\"\u003e\n    \u003cimg src=\"https://www.buymeacoffee.com/assets/img/custom_images/yellow_img.png\" alt=\"Buy Me A Coffee\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzotko%2Fxyz2graph","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzotko%2Fxyz2graph","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzotko%2Fxyz2graph/lists"}