├── NeuralMD ├── __init__.py ├── dataloaders │ └── dataloader_MISATO.py ├── datasets │ ├── MISATO │ │ ├── __init__.py │ │ ├── common.py │ │ ├── dataset_MISATO_semi_flexible.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── atoms_name_map_for_pdb.pickle │ │ │ ├── atoms_residue_map.pickle │ │ │ ├── atoms_type_map.pickle │ │ │ └── peptides.txt │ ├── __init__.py │ └── periodic_table.csv ├── evaluation.py └── models │ ├── FrameNetComplexEnergy_01_semi_flexible.py │ ├── FrameNetComplex_01_semi_flexible.py │ ├── FrameNetLigand_01.py │ ├── FrameNetProtein_01_semi_flexible.py │ ├── FrameNet_support.py │ └── __init__.py ├── README.md ├── data ├── MISATO │ ├── step_01_atom_mapping_illustration.py │ ├── step_02_subsample.py │ ├── step_03_general_analysis.py │ └── step_04_plot.py └── README.md ├── examples ├── main_MISATO_multi_traj_DenoisingLD.py ├── main_MISATO_multi_traj_GNNMD.py ├── main_MISATO_multi_traj_NeuralMD.py ├── main_MISATO_multi_traj_VerletMD.py ├── 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