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

.. code-block:: text

   surfacia workflow



   options:
     -h, --help
       show this help message and exit
     -i, --input INPUT (required)
       Initial CSV file with SMILES
     --resume
       Resume workflow from existing calculations (smart continuation)
     --skip-xtb
       Skip XTB optimization
     --test-samples TEST_SAMPLES
       Test samples for ML analysis
     --keywords KEYWORDS
       Gaussian keywords
     --charge CHARGE
       Molecular charge
     --multiplicity MULTIPLICITY
       Spin multiplicity
     --nproc NPROC
       Number of processors
     --memory MEMORY
       Memory allocation
     --extract-mode EXTRACT_MODE
       Feature extraction mode: 1=element-specific, 2=fragment-specific, 3=LOFFI comprehensive (default: 3)
       choices: 1, 2, 3
     --extract-element EXTRACT_ELEMENT
       Target element for mode 1 (e.g., S, N, O)
     --extract-xyz1 EXTRACT_XYZ1
       Fragment XYZ file for mode 2
     --extract-threshold EXTRACT_THRESHOLD
       Surface analysis threshold for mode 2 (default: 0.001)
     --max-features MAX_FEATURES
       Maximum features for ML
     --stepreg-runs STEPREG_RUNS
       Number of stepwise regression runs
     --initial-features INITIAL_FEATURES
       Comma-separated initial features for stepwise regression
     --train-test-split TRAIN_TEST_SPLIT
       Train/test split ratio
     --shap-fit-threshold SHAP_FIT_THRESHOLD
       SHAP R2 threshold for feature recommendation
     --no-generate-fitting
       Disable generation of fitting plots for manual mode
     --epoch EPOCH
       Number of epochs
     --cores CORES
       Number of CPU cores
     --api-key API_KEY
       ZhipuAI API key for SHAP visualization
     --port PORT
       Port for SHAP visualization server
     --host HOST
       Host for SHAP visualization server

   Examples:
     # Complete workflow with default settings
     surfacia workflow -i molecules.csv

     # Resume workflow (smart continuation from existing calculations)
     surfacia workflow -i molecules.csv --resume

     # Skip XTB optimization step
     surfacia workflow -i molecules.csv --skip-xtb

     # Custom Gaussian settings
     surfacia workflow -i molecules.csv --keywords "# B3LYP/6-31G* opt freq" --nproc 64

     # Include test samples for ML analysis
     surfacia workflow -i molecules.csv --test-samples "1,5,10,15,20"

     # Custom ML parameters
     surfacia workflow -i molecules.csv --max-features 8 --stepreg-runs 5 --epoch 128

   Pipeline Steps:
     1. SMILES → XYZ conversion
     2. XTB geometry optimization (optional)
     3. Gaussian input generation
     4. Gaussian calculations (most time-consuming)
     5. Multiwfn analysis
     6. Feature extraction
     7. Machine learning analysis
     8. Interactive SHAP visualization

   Resume Mode:
     - Automatically detects completed .fchk files
     - Reruns failed calculations only
     - Skips to feature extraction if all calculations are complete
     - Saves significant computation time
