Interactive Molecular Transformation App

This is a Streamlit web application for visualizing and transforming molecular structures interactively. Users can select different molecules, apply transformations, and visualize the results in 3D.

Features

• Molecule Selection: Choose from a variety of molecules such as O3, CH4, O2, H2O, CO2, NH3, and CH3CH2OCH3.
• Transformations: Rotate, translate, or swap atom positions in the molecule.
• Calculation Functions: Apply built-in calculations such as DeepPot_SE and DimnetPlus, or add your own custom functions.
• Custom Functions: Users can add custom functions by either writing code directly or uploading a Python file.
• 3D Visualization: View the transformed molecular structure in an interactive 3D plot using py3Dmol.

Usage

1. Access the application:

   • You can open the app directly using this website link.
   • Or, start the application locally by running the command:

     streamlit run app.py

2. Use the sidebar to:

   • Select a molecule from a list of options (e.g., CH₄, O₂, H₂O).
   • Adjust transformation parameters:
     • Adjust rotation (degrees), translation, and atom swapping using sliders.
   • Choose a descriptor:
     • Select from built-in options like DeepPot_SE and DimnetPlus.
     • Or, add your own custom function:
       • Write Code: Enter your function directly in the provided text area.
       • Upload File: Upload a .py file containing your custom function (e.g., a function named custom_function).

3. View the results:

   • Transformed Positions: See the updated atomic positions displayed in a data table.
   • Calculation Results: View the results as 2D heatmaps, generated based on the selected calculation function.
   • 3D Molecular Visualization: Interact with the 3D molecular model to explore different views and gain insights into the structure.

License

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

Contributing

Feel free to fork this project, create issues, and submit pull requests. Contributions are always welcome!

Acknowledgements

• Streamlit
• ASE (Atomic Simulation Environment)
• py3Dmol

Contact

For questions or suggestions, contact [email protected] or create an issue on this repository.