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Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
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zotko/xyz2graph
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A Python package to convert XYZ molecular files into NetworkX graphs with interactive 3D visualization using Plotly.
- Interactive 3D molecular visualization using Plotly
- NetworkX graph conversion for analysis
- Command-line interface
pip install xyz2graph
- Python 3.8+
- Dependencies: NumPy, Plotly, NetworkX
importnumpyasnpfromxyz2graphimportMolGraph# Create molecular graph and read XYZ filemg=MolGraph()mg.read_xyz('molecule.xyz')# Generate interactive 3D visualizationfig=mg.to_plotly()fig.show()# Convert to NetworkX graphG=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)}
# Save visualization as HTMLxyz2graph molecule.xyz# Specify output filexyz2graph molecule.xyz --output viz.html# Open directly in browserxyz2graph molecule.xyz --browser
Read thedocumentation for guides, API reference, and examples.
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Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
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