.editorconfig
.gitignore
CITATION.cff
LICENSE
MANIFEST.in
MDTerp_SPIB_ntl9.ipynb
MDTerp_SPIB_villin.ipynb
MDTerp_VAMPNets.ipynb
MDTerp_blackbox.ipynb
README.md
mkdocs.yml
ntl9.pdb
pyproject.toml
requirements.txt
requirements_dev.txt
villin.pdb
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/docs-build.yml
.github/workflows/docs.yml
.github/workflows/installation.yml
.github/workflows/macos.yml
.github/workflows/pypi.yml
.github/workflows/ubuntu.yml
.github/workflows/windows.yml
MDTerp/__init__.py
MDTerp/base.py
MDTerp/checkpoint.py
MDTerp/final_analysis.py
MDTerp/init_analysis.py
MDTerp/models.py
MDTerp/neighborhood.py
MDTerp/parallel.py
MDTerp/utils.py
MDTerp/visualization.py
MDTerp.egg-info/PKG-INFO
MDTerp.egg-info/SOURCES.txt
MDTerp.egg-info/dependency_links.txt
MDTerp.egg-info/entry_points.txt
MDTerp.egg-info/requires.txt
MDTerp.egg-info/top_level.txt
docs/MDTerp.md
docs/MDTerp_logo.png
docs/changelog.md
docs/contributing.md
docs/faq.md
docs/final_analysis.md
docs/index.md
docs/init_analysis.md
docs/installation.md
docs/neighborhood.md
docs/usage.md
docs/utils.md
docs/visualization.md
docs/examples/MDTerp_script_SPIB_ntl9.txt
docs/examples/MDTerp_script_SPIB_villin.txt
docs/examples/MDTerp_script_VAMPNets.txt
docs/examples/MDTerp_script_blackbox.txt
docs/overrides/main.html
docs/plans/2026-03-16-mdterp-v2-design.md
docs/plans/2026-03-16-mdterp-v2-implementation.md
tests/__init__.py
tests/test_MDTerp.py