├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── casp14_pdbs ├── T1024.pdb ├── T1025.pdb ├── T1026.pdb ├── T1027.pdb ├── T1029.pdb ├── T1030.pdb ├── T1031.pdb ├── T1032.pdb ├── T1033.pdb ├── T1035.pdb ├── T1037.pdb ├── T1038.pdb ├── T1039.pdb ├── T1040.pdb ├── T1041.pdb ├── T1042.pdb ├── T1043.pdb ├── T1046s1.pdb ├── T1046s2.pdb ├── T1049.pdb ├── T1054.pdb ├── T1056.pdb ├── T1064.pdb ├── T1067.pdb ├── T1073.pdb ├── T1074.pdb ├── T1079.pdb ├── T1080.pdb ├── T1082.pdb ├── T1090.pdb └── T1099.pdb ├── config ├── lm │ ├── generation.yaml │ ├── model │ │ ├── gpt_1.7k_df_1.yaml │ │ ├── gpt_432_df_1.yaml │ │ ├── gpt_4k_df_1.yaml │ │ └── gpt_64k_df_1.yaml │ └── sampling │ │ └── sampling.yaml └── structure_tokenizer │ ├── data │ ├── ablation_df_1.yaml │ ├── ablation_df_2.yaml │ └── ablation_df_4.yaml │ ├── model │ ├── gnn │ │ ├── ablation_0.5k_df_1.yaml │ │ ├── ablation_1.7k_df_1.yaml │ │ ├── ablation_4k_df_1.yaml │ │ ├── ablation_4k_df_2.yaml │ │ ├── ablation_4k_df_4.yaml │ │ ├── ablation_64k_df_1.yaml │ │ ├── ablation_64k_df_2.yaml │ │ ├── ablation_64k_df_4.yaml │ │ ├── ablation_continuous_df_1.yaml │ │ ├── ablation_continuous_df_2.yaml │ │ └── ablation_continuous_df_4.yaml │ └── shared.yaml │ └── vq3d_inference.yaml ├── scripts ├── __init__.py ├── decode_tokens.py ├── gpt_generation.py ├── inference_runner.py ├── lm │ ├── generation_utils.py │ ├── gpt_layer.py │ ├── gpt_model.py │ ├── lm_types.py │ └── utils.py └── tokenize_pdb.py ├── setup.py ├── source_images ├── algorithm.png ├── reconstruction.png └── samples.png └── structure_tokenizer ├── __init__.py ├── data ├── .DS_Store ├── __init__.py ├── preprocessing.py ├── protein.py ├── protein_structure_sample.py ├── residue_constants.py ├── test_data │ └── cif_raw_data.npy └── tools │ ├── __init__.py │ ├── lddt.py │ ├── tm_score.py │ └── utils.py ├── model ├── .DS_Store ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── all_atom.cpython-38.pyc │ ├── quat_affine.cpython-38.pyc │ ├── 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