├── Dockerfile ├── LICENSE ├── README.md ├── contacts_to_distograms.py ├── deepspeed_config.json ├── environment.yml ├── imgs ├── T1064_pred.png └── of_banner.png ├── lib └── openmm.patch ├── make_ihm.py ├── notebooks └── OpenFold.ipynb ├── openfold ├── __init__.py ├── config.py ├── config_crosslinks.py ├── data │ ├── __init__.py │ ├── data_modules.py │ ├── data_modules_xl.py │ ├── data_pipeline.py │ ├── data_transforms.py │ ├── errors.py │ ├── feature_pipeline.py │ ├── input_pipeline.py │ ├── mmcif_parsing.py │ ├── msa_subsampling.py │ ├── parsers.py │ ├── templates.py │ ├── tools │ │ ├── __init__.py │ │ ├── hhblits.py │ │ ├── hhsearch.py │ │ ├── jackhmmer.py │ │ ├── kalign.py │ │ └── utils.py │ └── xl_subsampling.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 │ ├── __init__.py │ ├── argparse.py │ ├── callbacks.py │ ├── checkpointing.py │ ├── chunk_utils.py │ ├── exponential_moving_average.py │ ├── feats.py │ ├── import_weights.py │ ├── kernel │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ └── attention_core.cpython-37.pyc │ ├── attention_core.py │ └── csrc │ │ ├── compat.h │ │ ├── softmax_cuda.cpp │ │ ├── softmax_cuda_kernel.cu │ │ └── softmax_cuda_stub.cpp │ ├── logger.py │ ├── loss.py │ ├── lr_schedulers.py │ ├── rigid_utils.py │ ├── seed.py │ ├── superimposition.py │ ├── suppress_output.py │ ├── tensor_utils.py │ ├── trace_utils.py │ └── validation_metrics.py ├── predict_with_crosslinks.py ├── preprocessing_distributions.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_data.sh ├── download_mgnify.sh ├── download_mmseqs_dbs.sh ├── download_openfold_params_gdrive.sh ├── download_openfold_params_huggingface.sh ├── download_pdb70.sh ├── download_pdb_mmcif.sh ├── download_small_bfd.sh ├── download_uniclust30.sh ├── download_uniref30.sh ├── download_uniref90.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 ├── test_set ├── CDK │ ├── crosslinks │ │ ├── 1h01_xl.csv │ │ ├── 1h01_xl.pt │ │ ├── 2bpm_xl.csv │ │ ├── 2bpm_xl.pt │ │ ├── mixture.csv │ │ └── mixture.pt │ ├── fasta │ │ └── CDK.fasta │ ├── features │ │ └── CDK_neff10.pkl.gz │ └── predictions │ │ ├── CDK_neff10_1h01_xl_model_5_ptm.pdb │ │ └── CDK_neff10_2bpm_xl_model_5_ptm.pdb └── membrane │ ├── crosslinks │ ├── 1a3a_D.pt │ ├── 1bxw_A.pt │ ├── 1c5k_A.pt │ ├── 1fep_A.pt │ ├── 1grl_G.pt │ ├── 1i78_B.pt │ ├── 1igw_D.pt │ ├── 1lv7_A.pt │ ├── 1pb1_A.pt │ ├── 1qfg_A.pt │ ├── 2f1m_D.pt │ ├── 2grx_A.pt │ ├── 2guf_A.pt │ ├── 2hdi_A.pt │ ├── 2hqs_H.pt │ ├── 2j1n_C.pt │ ├── 2qcu_B.pt │ ├── 2qzs_A.pt │ ├── 3bp3_B.pt │ ├── 3tch_A.pt │ ├── 4jne_B.pt │ ├── 4rhb_C.pt │ ├── 4yah_X.pt │ ├── 5d0o_A.pt │ ├── 5d0o_B.pt │ ├── 5j43_E.pt │ ├── 6bpn_A.pt │ 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