├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── antifold ├── __init__.py ├── _anarci │ └── ImmunoPDB.py ├── antiscripts.py ├── esm │ ├── __init__.py │ ├── constants.py │ ├── data.py │ ├── inverse_folding │ │ ├── __init__.py │ │ ├── features.py │ │ ├── gvp_encoder.py │ │ ├── gvp_modules.py │ │ ├── gvp_transformer.py │ │ ├── gvp_transformer_encoder.py │ │ ├── gvp_utils.py │ │ ├── multichain_util.py │ │ ├── transformer_decoder.py │ │ ├── transformer_layer.py │ │ └── util.py │ ├── modules.py │ ├── multihead_attention.py │ ├── pretrained.py │ └── rotary_embedding.py ├── esm_multichain_util_custom.py ├── esm_util_custom.py ├── if1_dataset.py └── main.py ├── data ├── antibody_antigen.csv ├── antibody_antigen │ └── 3hfm.pdb ├── example_pdbs.csv ├── mini.csv ├── nanobody.csv ├── nanobody │ ├── 8oi2_imgt.pdb │ └── nanobody_antigen_9hzj_imgt.pdb └── pdbs │ ├── 6y1l_imgt.pdb │ ├── 8ee8_imgt.pdb │ └── C143_immunebuilder.pdb ├── environment.yml ├── images └── colab-badge.svg ├── index.html ├── models └── .gitkeep ├── notebook.ipynb ├── notebooks └── LOGO.ipynb ├── output ├── antibody_antigen │ ├── 3hfm_HL.csv │ ├── 3hfm_HLY.csv │ └── log.txt ├── antifold │ ├── 6y1l_imgt_HL.csv │ └── log.txt ├── esmif1 │ ├── 6y1l_imgt_HL.csv │ └── log.txt ├── example_pdbs │ ├── 6y1l_imgt.csv │ ├── 6y1l_imgt.fasta │ ├── 6y1l_imgt_HL.csv │ ├── 6y1l_imgt_HL.fasta │ ├── 8ee8_imgt.csv │ ├── 8ee8_imgt.fasta │ ├── 8ee8_imgt_DC.csv │ ├── 8ee8_imgt_DC.fasta │ ├── C143_immunebuilder.csv │ ├── C143_immunebuilder.fasta │ ├── C143_immunebuilder_HL.csv │ ├── C143_immunebuilder_HL.fasta │ └── log.txt ├── single_pdb │ ├── 6y1l_imgt.csv │ ├── 6y1l_imgt.fasta │ └── log.txt └── untested │ └── 3hfm_HLY.csv ├── requirements.txt ├── run_example.sh ├── setup.py ├── test ├── antibody_antigen.sh ├── default.sh ├── nanobody_antigen.sh └── tests.sh └── tox.ini /.gitignore: -------------------------------------------------------------------------------- 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