.. Generated by tools/update_cli_reference.py; do not edit.

.. code-block:: text

   surfacia shap-viz



   options:
     -h, --help
       show this help message and exit
     -i, --input INPUT (required)
       Training_Set_Detailed CSV file from ML analysis
     -x, --xyz-folder XYZ_FOLDER (required)
       Folder containing XYZ files and molecular structure files
     --test-csv TEST_CSV
       Test_Set_Detailed CSV file for test set visualization (optional)
     --api-key API_KEY
       ZhipuAI API key for AI assistant features (optional)
     --skip-surface-gen
       Skip surface PDB generation if files already exist
     --port PORT
       Port for the web server (default: 8052)
     --host HOST
       Host for the web server (default: 0.0.0.0 for all interfaces)

   Examples:
     # Basic SHAP visualization
     surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_folder

     # Include test set visualization
     surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_folder --test-csv Test_Set_Detailed.csv


     # Use AI assistant with API key
     surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_folder --api-key your_api_key

     # Custom server settings
     surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_folder --port 8080 --host localhost

   Features:
     - Interactive SHAP scatter plots
     - 3D molecular visualization with isosurfaces
     - AI-powered analysis assistant
     - Real-time molecular property exploration
