License¶

Surfacia is released under the MIT License.

MIT License¶

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Third-Party Licenses¶

Surfacia includes or depends on several third-party libraries and tools. Below are the licenses for these dependencies:

Core Dependencies¶

NumPy

License: BSD 3-Clause License
Copyright: NumPy Developers
Used for: Numerical computations and array operations

SciPy

License: BSD 3-Clause License
Copyright: SciPy Developers
Used for: Scientific computing and optimization

Pandas

License: BSD 3-Clause License
Copyright: Pandas Development Team
Used for: Data manipulation and analysis

Matplotlib

License: Python Software Foundation License
Copyright: Matplotlib Development Team
Used for: Data visualization and plotting

Scikit-learn

License: BSD 3-Clause License
Copyright: Scikit-learn Developers
Used for: Machine learning algorithms and tools

SHAP

License: MIT License
Copyright: Scott Lundberg
Used for: Model interpretability and feature importance

Visualization Dependencies¶

Plotly

License: MIT License
Copyright: Plotly, Inc.
Used for: Interactive visualizations and dashboards

Dash

License: MIT License
Copyright: Plotly, Inc.
Used for: Web-based interactive applications

Bokeh

License: BSD 3-Clause License
Copyright: Bokeh Development Team
Used for: Interactive web visualizations

Development Dependencies¶

Pytest

License: MIT License
Copyright: Pytest Development Team
Used for: Testing framework

Sphinx

License: BSD 2-Clause License
Copyright: Sphinx Team
Used for: Documentation generation

Black

License: MIT License
Copyright: Python Software Foundation
Used for: Code formatting

Flake8

License: MIT License
Copyright: Flake8 Team
Used for: Code linting and style checking

Optional Dependencies¶

RDKit

License: BSD 3-Clause License
Copyright: RDKit Contributors
Used for: Chemical informatics and molecular handling

OpenEye Toolkits (Optional)

License: Commercial/Academic License
Copyright: OpenEye Scientific Software
Used for: Advanced molecular processing (requires separate license)

Gaussian (External)

License: Commercial License
Copyright: Gaussian, Inc.
Used for: Quantum chemistry calculations (requires separate license)

License Compatibility¶

All included dependencies are compatible with the MIT License under which Surfacia is distributed. Users should be aware of the following:

Open Source Components¶

All core functionality relies on open-source libraries
No restrictions on commercial or academic use
Full source code availability and modification rights

Commercial Components¶

Some optional features may require commercial software licenses
Gaussian integration requires a valid Gaussian license
OpenEye Toolkits require appropriate licensing for commercial use

Academic Use¶

All features are available for academic research
Some commercial tools offer academic licenses
Educational use is fully supported under the MIT License

Attribution Requirements¶

When using Surfacia in publications or derivative works, please:

Cite the Software: Include appropriate citations to Surfacia
Acknowledge Dependencies: Credit the underlying libraries used
Include License Notice: Maintain the MIT License notice in distributions
Respect Third-Party Terms: Follow licensing terms of dependencies

Citation Information¶

If you use Surfacia in your research, please cite:

@software{surfacia2024,
  title={Surfacia: A Comprehensive Molecular Surface Analysis Tool},
  author={Surfacia Development Team},
  year={2024},
  url={https://github.com/sym823808458/Surfacia},
  license={MIT}
}

Contributing¶

By contributing to Surfacia, you agree that your contributions will be licensed under the same MIT License. This ensures:

Open Access: All contributions remain freely available
Compatibility: Consistent licensing across the project
Flexibility: Users can freely use, modify, and distribute
Attribution: Contributors are acknowledged appropriately

License Updates¶

The Surfacia development team reserves the right to:

Update dependency licenses as libraries evolve
Add new optional dependencies with compatible licenses
Clarify licensing terms for better understanding
Maintain compatibility with open-source principles

For questions about licensing, please contact the development team or consult the project repository for the most current information.

Disclaimer¶

This license information is provided for convenience and may not be complete or current. Users should verify licensing terms independently, especially for commercial applications or when using optional commercial dependencies.

The Surfacia development team makes no warranties regarding the accuracy or completeness of this license information and disclaims any liability for licensing-related issues arising from the use of this software.