├── .codecov.yml ├── .gitattributes ├── .github ├── pull_request_template.md └── workflows │ └── CI.yaml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools └── conda-envs │ └── test_env.yaml ├── docs ├── Makefile ├── README.md ├── _static │ └── README.md ├── _templates │ ├── README.md │ ├── custom-class-template.rst │ └── custom-module-template.rst ├── api.rst ├── conf.py ├── index.rst ├── installation.rst ├── intro_to_MTFEP.ipynb ├── make.bat └── requirements.yaml ├── pyproject.toml ├── readthedocs.yml ├── setup.cfg └── tfep ├── __init__.py ├── analysis ├── __init__.py ├── bootstrap.py └── estimator.py ├── app ├── __init__.py ├── base.py ├── cartesianmaf.py └── mixedmaf.py ├── io ├── __init__.py ├── dataset │ ├── __init__.py │ ├── dict.py │ ├── merged.py │ └── traj.py ├── log.py └── sampler.py ├── loss.py ├── nn ├── __init__.py ├── conditioners │ ├── __init__.py │ ├── conditioner.py │ └── made.py ├── dynamics │ ├── __init__.py │ └── egnn.py ├── embeddings │ ├── __init__.py │ ├── mafembed.py │ └── radial.py ├── flows │ ├── __init__.py │ ├── autoregressive.py │ ├── centroid.py │ ├── continuous.py │ ├── maf.py │ ├── oriented.py │ ├── partial.py │ ├── pca.py │ └── sequential.py ├── graph.py ├── masked.py └── transformers │ ├── __init__.py │ ├── affine.py │ ├── mixed.py │ ├── moebius.py │ ├── quatprod.py │ ├── sos.py │ ├── spline.py │ └── transformer.py ├── potentials ├── __init__.py ├── ase.py ├── base.py ├── gromacs.py ├── mimic.py ├── openmm.py ├── psi4.py └── tblite.py ├── py.typed ├── tests ├── __init__.py ├── analysis │ └── test_bootstrap.py ├── app │ ├── __init__.py │ ├── test_cartesianmaf.py │ ├── test_maps.py │ └── test_mixedmaf.py ├── data │ ├── README.md │ ├── amber │ │ ├── amber.in │ │ └── water.prmtop │ ├── auxiliary.xvg │ ├── benzoic_acid.npz │ ├── chloro-fluoromethane.pdb │ └── mimic │ │ ├── README.md │ │ ├── acetone.itp │ │ ├── acetone.top │ │ ├── cpmd.inp │ │ ├── equilibrated-forces-gromacs-only.trr │ │ ├── equilibrated.gro │ │ ├── gmx_to_cpmd_atom_indices.json │ │ ├── gromacs-only.mdp │ │ ├── gromacs.mdp │ │ ├── index.ndx │ │ ├── mimic-forces-gromacs-only.trr │ │ └── mimic.pdb ├── io │ ├── __init__.py │ ├── test_dataset_dict.py │ ├── test_dataset_merged.py │ ├── test_dataset_traj.py │ ├── test_log.py │ └── test_sampler.py ├── nn │ ├── __init__.py │ ├── conditioners │ │ ├── __init__.py │ │ └── test_made.py │ ├── dynamics │ │ └── test_egnn.py │ ├── embeddings │ │ ├── __init__.py │ │ ├── test_mafembed.py │ │ └── test_radial.py │ ├── flows │ │ ├── __init__.py │ │ ├── test_centroid.py │ │ ├── test_continuous.py │ │ ├── test_maf.py │ │ ├── test_oriented.py │ │ ├── test_partial.py │ │ └── test_pca.py │ ├── test_graph.py │ ├── test_masked.py │ └── transformers │ │ ├── __init__.py │ │ ├── test_affine.py │ │ ├── test_mixed.py │ │ ├── test_moebius.py │ │ ├── test_quatprod.py │ │ ├── test_sos.py │ │ └── test_spline.py ├── potentials │ ├── __init__.py │ ├── test_ase.py │ ├── test_base.py │ ├── test_gromacs.py │ ├── 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