LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
docs/Makefile
docs/README.md
docs/make.bat
docs/requirements.txt
docs/source/changelog.rst
docs/source/citation.rst
docs/source/conf.py
docs/source/contributing.rst
docs/source/index.rst
docs/source/license.rst
docs/source/_static/favicon.ico
docs/source/_static/css/custom.css
docs/source/_static/images/surfacia_logo.png
docs/source/api/core.rst
docs/source/api/descriptors.rst
docs/source/api/index.rst
docs/source/api/ml.rst
docs/source/api/utils.rst
docs/source/api/visualization.rst
docs/source/commands/index.rst
docs/source/commands/ml_analysis.rst
docs/source/commands/mol_drawer.rst
docs/source/commands/mol_viewer.rst
docs/source/commands/rerun_gaussian.rst
docs/source/commands/shap_viz.rst
docs/source/commands/utilities.rst
docs/source/commands/workflow.rst
docs/source/descriptors/electronic_properties.rst
docs/source/descriptors/index.rst
docs/source/descriptors/size_and_shape.rst
docs/source/descriptors/surface_analysis.rst
docs/source/examples/basic_molecules.rst
docs/source/examples/complex_systems.rst
docs/source/examples/custom_workflows.rst
docs/source/examples/index.rst
docs/source/examples/machine_learning.rst
docs/source/getting_started/basic_concepts.rst
docs/source/getting_started/index.rst
docs/source/getting_started/installation.rst
docs/source/getting_started/quick_start.rst
docs/source/integrations/index.rst
docs/source/integrations/mcp_server.rst
docs/source/integrations/mcp_server_zh.rst
docs/source/tutorials/advanced_analysis.rst
docs/source/tutorials/basic_workflow.rst
docs/source/tutorials/custom_descriptors.rst
docs/source/tutorials/index.rst
docs/source/tutorials/machine_learning.rst
docs/source/user_guide/advanced_usage.rst
docs/source/user_guide/best_practices.rst
docs/source/user_guide/index.rst
docs/source/user_guide/troubleshooting.rst
docs/source/user_guide/workflows.rst
surfacia/__init__.py
surfacia/cli.py
surfacia.egg-info/PKG-INFO
surfacia.egg-info/SOURCES.txt
surfacia.egg-info/dependency_links.txt
surfacia.egg-info/entry_points.txt
surfacia.egg-info/requires.txt
surfacia.egg-info/top_level.txt
surfacia/benchmark/__init__.py
surfacia/benchmark/descriptor_matrices.py
surfacia/core/__init__.py
surfacia/core/descriptors.py
surfacia/core/gaussian.py
surfacia/core/multiwfn.py
surfacia/core/rerun_gaussian.py
surfacia/core/smi2xyz.py
surfacia/core/workflow.py
surfacia/core/xtb_opt.py
surfacia/features/__init__.py
surfacia/features/atom_properties.py
surfacia/features/fragment_match.py
surfacia/features/loffi.py
surfacia/mcp/__init__.py
surfacia/mcp/server.py
surfacia/mcp/shap_launcher.py
surfacia/mcp/tooling.py
surfacia/mcp/utils.py
surfacia/ml/__init__.py
surfacia/ml/chem_ml_analyzer_v2.py
surfacia/utils/__init__.py
surfacia/utils/chem_utils.py
surfacia/utils/file_utils.py
surfacia/utils/mol_properties.py
surfacia/visualization/__init__.py
surfacia/visualization/debug_multiwfn.py
surfacia/visualization/interactive_shap_viz.py
surfacia/visualization/mol_drawer.py
surfacia/visualization/mol_viewer.py
surfacia/visualization/surface_calc.py