├── .codespell-ignore.txt ├── .gitignore ├── .pre-commit-config.yaml ├── .pylintrc ├── Dockerfile ├── LICENSE.md ├── ProteinMPNN ├── LICENSE ├── README.md ├── ca_model_weights │ ├── v_48_002.pt │ ├── v_48_010.pt │ └── v_48_020.pt ├── colab_notebooks │ ├── README.md │ ├── ca_only_quickdemo.ipynb │ ├── quickdemo.ipynb │ └── quickdemo_wAF2.ipynb ├── examples │ ├── submit_example_1.sh │ ├── submit_example_2.sh │ ├── submit_example_3.sh │ ├── submit_example_3_score_only.sh │ ├── submit_example_4.sh │ ├── submit_example_4_non_fixed.sh │ ├── submit_example_5.sh │ ├── submit_example_6.sh │ ├── submit_example_7.sh │ └── submit_example_8.sh ├── helper_scripts │ ├── assign_fixed_chains.py │ ├── make_bias_AA.py │ ├── make_bias_per_res_dict.py │ ├── make_fixed_positions_dict.py │ ├── make_pos_neg_tied_positions_dict.py │ ├── make_tied_positions_dict.py │ ├── other_tools │ │ ├── make_omit_AA.py │ │ └── make_pssm_dict.py │ ├── parse_multiple_chains.py │ └── parse_multiple_chains.sh ├── inputs │ ├── PDB_complexes │ │ └── pdbs │ │ │ ├── 3HTN.pdb │ │ │ └── 4YOW.pdb │ ├── PDB_homooligomers │ │ └── pdbs │ │ │ ├── 4GYT.pdb │ │ │ └── 6EHB.pdb │ └── PDB_monomers │ │ └── pdbs │ │ ├── 5L33.pdb │ │ └── 6MRR.pdb ├── protein_mpnn_run.py ├── protein_mpnn_utils.py ├── training │ ├── LICENSE │ ├── README.md │ ├── colab_training_example.ipynb │ ├── model_utils.py │ ├── plot_training_results.ipynb │ ├── training.py │ └── utils.py └── vanilla_model_weights │ ├── v_48_002.pt │ ├── v_48_010.pt │ ├── v_48_020.pt │ └── v_48_030.pt ├── README.md ├── cg2all ├── README.md ├── cg2all.yml └── convert_backbone_to_full_atom.sh ├── config ├── base.yaml ├── data_process.yaml ├── evaluation.yaml └── inference.yaml ├── database ├── TCR.csv ├── TCR_pMHC_I.csv ├── TCR_pMHC_II.csv └── unbound_bound_tcr.csv ├── environment.yml ├── evaluation ├── __init__.py ├── eval_cg2all.py ├── eval_denovo.py ├── evaluate_tcr.py ├── residue_reindex.py └── utils │ ├── __init__.py │ ├── constants.py │ ├── directory_parser.py │ ├── metrics.py │ ├── plot.py │ └── sample_selection.py ├── experiments ├── __init__.py ├── check_forward_fn.py ├── check_score_and_reverse_fns.py ├── inference.py ├── sampler.py └── utils.py ├── framedipt ├── __init__.py ├── analysis │ ├── __init__.py │ ├── metrics.py │ └── utils.py ├── data │ ├── __init__.py │ ├── mmcif_parsing.py │ ├── parsers.py │ ├── process_pdb_dataset.py │ ├── process_pdb_files.py │ ├── transforms.py │ └── utils.py ├── diffusion │ ├── __init__.py │ ├── igso3.py │ ├── r3_diffuser.py │ ├── r3_utils.py │ ├── se3_diffuser.py │ ├── so3_diffuser.py │ └── so3_utils.py ├── model │ ├── __init__.py │ ├── ipa_pytorch.py │ ├── layers.py │ └── score_network.py ├── protein │ ├── __init__.py │ ├── align.py │ ├── all_atom.py │ ├── chemical.py │ ├── filters.py │ ├── protein.py │ ├── residue_constants.py │ └── tcr.py └── tools │ ├── __init__.py │ ├── custom_type.py │ ├── errors.py │ └── log.py ├── notebooks ├── examples.csv └── tcr_cdr3_inpainting.ipynb ├── openfold ├── config.py ├── data │ ├── __init__.py │ ├── data_modules.py │ ├── data_pipeline.py │ ├── data_transforms.py │ ├── errors.py │ ├── feature_pipeline.py │ ├── input_pipeline.py │ ├── mmcif_parsing.py │ ├── parsers.py │ ├── templates.py │ └── tools │ │ ├── __init__.py │ │ ├── hhblits.py │ │ ├── hhsearch.py │ │ ├── jackhmmer.py │ │ ├── kalign.py │ │ └── utils.py ├── model │ ├── __init__.py │ ├── dropout.py │ ├── embedders.py │ ├── evoformer.py │ ├── heads.py │ ├── model.py │ ├── msa.py │ ├── outer_product_mean.py │ ├── pair_transition.py │ ├── primitives.py │ ├── structure_module.py │ ├── template.py │ ├── torchscript.py │ ├── triangular_attention.py │ └── triangular_multiplicative_update.py ├── np │ ├── __init__.py │ ├── protein.py │ ├── relax │ │ ├── __init__.py │ │ ├── amber_minimize.py │ │ ├── cleanup.py │ │ ├── relax.py │ │ └── utils.py │ └── residue_constants.py ├── resources │ ├── __init__.py │ └── stereo_chemical_props.txt └── utils │ ├── argparse.py │ ├── callbacks.py │ ├── checkpointing.py │ ├── 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