xyz2graph 3.0.3

Package for reading of .xyz files and constructing of molecular graphs from atomic coordinates.

xyz2graph

A lightweight Python package for reading XYZ files and creating interactive molecular visualizations. Convert molecular structures into 3D visualizations using Plotly or analyze them as NetworkX graphs.

Features

• Read and parse XYZ molecular structure files
• Generate interactive 3D molecular visualizations using Plotly
• Convert molecular structures to NetworkX graphs for analysis
• Command-line interface for quick visualizations

Installation

pip install xyz2graph

Requirements

• Python 3.8+
• NumPy
• NetworkX
• Plotly

Usage

Python API

from xyz2graph import MolGraph
from plotly.offline import plot

# Create molecular graph and read XYZ file
mg = MolGraph()
mg.read_xyz('molecule.xyz')

print(mg)  # e.g., "MolGraph(H20: 3 atoms, 2 bonds)"
print(mg.formula())  # e.g., "H20"

# Generate interactive 3D visualization
fig = mg.to_plotly()
plot(fig)

# Convert to NetworkX graph for analysis
G = mg.to_networkx()

Jupyter Notebook

from xyz2graph import MolGraph
from plotly.offline import init_notebook_mode, iplot

# Initialize Plotly for notebook
init_notebook_mode(connected=True)

# Create and display molecular visualization
mg = MolGraph()
mg.read_xyz('molecule.xyz')
fig = mg.to_plotly()
iplot(fig)

Command Line Interface

Quickly visualize molecules from XYZ files:

# Save visualization as HTML
xyz2graph molecule.xyz

# Specify output file
xyz2graph molecule.xyz --output visualization.html

# Open directly in browser
xyz2graph molecule.xyz --browser

Customization

Customize atomic properties for visualization:

mg = MolGraph()

# Customize atomic radius
mg.set_element_radius('C', 0.75)

# Customize element color
mg.set_element_color('O', 'red')

# Set default color for unlisted elements
mg.set_default_color('pink')

Examples

Example XYZ files can be found in the examples directory.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use xyz2graph in your research, please cite:

@misc{xyz2graph,
  author       = {Zotko, Mykola},
  title        = {xyz2graph: Molecular Structure Visualization},
  year         = {2018},
  publisher    = {GitHub},
  url          = {https://github.com/zotko/xyz2graph}
}