Command reference

Options are generated from surfacia.cli.build_parser. They describe the implemented CLI, not planned features. The ML engine is XGBoost regression with repeated random splits, without arbitrary classifier/algorithm or k-fold switches.

surfacia

Surfacia - Surface Atomic Chemical Interaction Analyzer

positional arguments:
  commands: smi2xyz, xtb-opt, xyz2gaussian, run-gaussian, multiwfn, extract-features, ml-analysis, shap-viz, workflow, mol-draw, mol-info, rerun-gaussian

options:
  -h, --help
    show this help message and exit

🧪 SURFACIA COMMAND OVERVIEW:

MAIN WORKFLOW:
  workflow          Complete end-to-end analysis pipeline

INDIVIDUAL STEPS:
  smi2xyz           Convert SMILES to XYZ coordinates
  xtb-opt           XTB geometry optimization
  xyz2gaussian      Generate Gaussian input files
  run-gaussian      Execute Gaussian calculations
  multiwfn          Run Multiwfn analysis on .fchk files
  extract-features  Extract atomic properties and features
  ml-analysis       Machine learning analysis with feature selection
  shap-viz          Interactive SHAP visualization with AI assistant

UTILITY TOOLS (Independent):
  mol-draw          Generate 2D molecular structure images
  mol-info          Calculate and display molecular properties
  rerun-gaussian    Rerun failed Gaussian calculations

📚 For detailed help on any command: surfacia <command> --help
🌐 Documentation: https://surfacia.readthedocs.io/zh-cn/latest/

• ml-analysis
• shap-viz
• workflow
• rerun-gaussian
• smi2xyz
• xtb-opt
• xyz2gaussian
• run-gaussian
• multiwfn
• extract-features
• mol-draw
• mol-info

Supporting information

Python interfaces · MCP integration · Read model outputs · Troubleshooting · Upgrade to 4.0.0 · Citation and contact · Release notes · License