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

.. code-block:: text

   surfacia extract-features



   options:
     -h, --help
       show this help message and exit
     -i, --input INPUT (required)
       Input CSV file
     --mode MODE (required)
       Feature extraction mode: 1=element, 2=fragment, 3=LOFFI
       choices: 1, 2, 3
     --element ELEMENT
       Target element for mode 1 (e.g., S, N, O)
     --xyz1 XYZ1
       Fragment XYZ file for mode 2
     --threshold THRESHOLD
       Surface analysis threshold (default: 0.001)

   Examples:
     # Extract features in Mode 1 (element-specific)
     surfacia extract-features -i ./Surfacia*/FullOption2.csv --mode 1 --element S

     # Extract features in Mode 2 (fragment-specific)
     surfacia extract-features -i ./Surfacia*/FullOption2.csv --mode 2 --xyz1 fragment.xyz

     # Extract features in Mode 3 (LOFFI comprehensive)
     surfacia extract-features -i ./Surfacia*/FullOption2.csv --mode 3

     # Use custom threshold for surface analysis
     surfacia extract-features -i ./Surfacia*/FullOption2.csv --mode 1 --element N --threshold 0.002
