├── README.md ├── data.py ├── engine_train.py ├── environment.yml ├── example ├── 1gl5.fasta ├── 1gl5_af │ ├── 1gl5_double.csv │ └── 1gl5_single.csv ├── 1gl5_esm │ ├── 1gl5_double.csv │ └── 1gl5_single.csv └── 1gl5_msa │ └── 1gl5.a3m ├── figs └── model.jpeg ├── main_train.py ├── metrics.py ├── misc.py ├── modeling ├── backbone.py ├── criterion.py ├── module.py ├── mutate_everything.py └── utils.py ├── openfold ├── .github │ └── workflows │ │ ├── docker-image.yml │ │ └── undefined_names.yml ├── .gitignore ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── README.md ├── deepspeed_config.json ├── environment.yml ├── imgs │ └── of_banner.png ├── lib │ └── openmm.patch ├── notebooks │ ├── OpenFold.ipynb │ └── environment.yml ├── openfold │ ├── __init__.py │ ├── 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 │ └── utils │ │ ├── __init__.py │ │ ├── argparse.py │ │ ├── callbacks.py │ │ ├── checkpointing.py │ │ ├── chunk_utils.py │ │ ├── exponential_moving_average.py │ │ ├── feats.py │ │ ├── import_weights.py │ │ ├── kernel │ │ ├── __init__.py │ │ ├── attention_core.py │ │ └── csrc │ │ │ ├── compat.h │ │ │ ├── softmax_cuda.cpp │ │ │ ├── softmax_cuda_kernel.cu │ │ │ └── softmax_cuda_stub.cpp │ │ ├── logger.py │ │ ├── loss.py │ │ ├── lr_schedulers.py │ │ ├── precision_utils.py │ │ ├── rigid_utils.py │ │ ├── script_utils.py │ │ ├── seed.py │ │ ├── superimposition.py │ │ ├── suppress_output.py │ │ ├── tensor_utils.py │ │ ├── trace_utils.py │ │ └── validation_metrics.py ├── run_pretrained_openfold.py ├── scripts │ ├── activate_conda_env.sh │ ├── alignment_db_scripts │ │ ├── create_alignment_db.py │ │ └── unify_alignment_db_indices.py │ ├── build_deepspeed_config.py │ ├── colabfold_search.sh │ ├── convert_of_weights_to_jax.py │ ├── data_dir_to_fasta.py │ ├── deactivate_conda_env.sh │ ├── download_alphafold_dbs.sh │ ├── download_alphafold_params.sh │ ├── download_bfd.sh │ ├── download_cameo.py │ ├── download_colabfold_envdb.sh │ ├── download_mgnify.sh │ ├── download_mmseqs_dbs.sh │ ├── download_openfold_params.sh │ ├── download_openfold_params_gdrive.sh │ ├── download_openfold_params_huggingface.sh │ ├── download_pdb70.sh │ ├── download_pdb_mmcif.sh │ ├── download_roda_pdbs.sh │ ├── download_small_bfd.sh │ ├── download_uniclust30.sh │ ├── download_uniref30.sh │ ├── download_uniref90.sh │ ├── flatten_roda.sh │ ├── generate_alphafold_feature_dict.py │ ├── generate_chain_data_cache.py │ ├── generate_mmcif_cache.py │ ├── install_hh_suite.sh │ ├── install_third_party_dependencies.sh │ ├── precompute_alignments.py │ ├── precompute_alignments_mmseqs.py │ ├── prep_mmseqs_dbs.sh │ ├── prep_proteinnet_msas.py │ ├── run_unit_tests.sh │ ├── slurm_scripts │ │ └── run_uniclust30_search.sh │ ├── unpack_proteinnet.py │ ├── utils.py │ ├── vars.sh │ └── zero_to_fp32.py ├── setup.py ├── tests │ ├── __init__.py │ ├── compare_utils.py │ ├── config.py │ ├── data_utils.py │ ├── test_data_pipeline.py │ ├── test_data_transforms.py │ ├── test_embedders.py │ ├── test_evoformer.py │ ├── test_feats.py │ ├── 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