├── Dockerfile ├── LICENSE ├── README.md ├── alphaflow ├── config.py ├── data │ ├── data_modules.py │ ├── data_pipeline.py │ ├── feature_pipeline.py │ ├── inference.py │ └── input_pipeline.py ├── model │ ├── __init__.py │ ├── alphafold.py │ ├── esmfold.py │ ├── input_stack.py │ ├── layers.py │ ├── tri_self_attn_block.py │ ├── trunk.py │ └── wrapper.py └── utils │ ├── diffusion.py │ ├── logging.py │ ├── loss.py │ ├── misc.py │ ├── parsing.py │ ├── protein.py │ └── tensor_utils.py ├── assets ├── 12l_md_templates.md └── 6uof_A_animation.gif ├── predict.py ├── scripts ├── add_msa_info.py ├── analyze_ensembles.py ├── cluster_chains.py ├── download_atlas.sh ├── mmseqs_query.py ├── mmseqs_search.py ├── mmseqs_search_helper.py ├── prep_atlas.py ├── print_analysis.py └── unpack_mmcif.py ├── splits ├── atlas.csv ├── atlas_test.csv ├── atlas_train.csv ├── atlas_val.csv ├── cameo2022.csv ├── pdb_test.csv └── pdb_test.json └── train.py /Dockerfile: 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