├── .flake8 ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── THIRD_PARTY_NOTICES.txt ├── environment.yml ├── esm ├── __init__.py ├── axial_attention.py ├── constants.py ├── data.py ├── esmdynamic │ ├── __init__.py │ ├── dynamic_module.py │ ├── esmdynamic.py │ ├── predict.py │ ├── pretrained.py │ └── training │ │ ├── __init__.py │ │ ├── convert_csv_to_torch.py │ │ ├── data_reader.py │ │ ├── loss.py │ │ └── train.py ├── esmfold │ └── v1 │ │ ├── __init__.py │ │ ├── categorical_mixture.py │ │ ├── esmfold.py │ │ ├── misc.py │ │ ├── pretrained.py │ │ ├── tri_self_attn_block.py │ │ └── trunk.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 ├── model │ ├── esm1.py │ ├── esm2.py │ └── msa_transformer.py ├── modules.py ├── multihead_attention.py ├── pretrained.py ├── rotary_embedding.py └── version.py ├── examples ├── README.md ├── contact_prediction.ipynb ├── data │ ├── 1a3a_1_A.a3m │ ├── 1xcr_1_A.a3m │ ├── 5ahw_1_A.a3m │ ├── P62593.fasta │ ├── UniRef50_E9K9Y4.a3m │ ├── UniRef50_UPI0003108055.a3m │ ├── UniRef50_UPI0003674933.a3m │ ├── few_proteins.fasta │ ├── hhblits_uniclust_2017_10_1a3a_1_A.a3m │ ├── hhblits_uniclust_2017_10_1xcr_1_A.a3m │ ├── hhblits_uniclust_2017_10_5ahw_1_A.a3m │ └── some_proteins.fasta ├── esm2_infer_fairscale_fsdp_cpu_offloading.py ├── esm_structural_dataset.ipynb ├── esmdynamic │ ├── OsSWEET2b_esmdynamic_contact_map.npy │ ├── cv_selection_pipeline.ipynb │ ├── esmdynamic.ipynb │ ├── example.csv │ └── example.fasta ├── inverse_folding │ ├── README.md │ ├── data │ │ ├── 4uv3.cif │ │ ├── 4uv3.pdb │ │ ├── 5YH2.cif │ │ ├── 5YH2.pdb │ │ ├── 5YH2_mutated_seqs.fasta │ │ └── example.json │ ├── illustration.png │ ├── notebook.ipynb │ ├── notebook_multichain.ipynb │ ├── output │ │ ├── 5YH2_mutated_seqs_scores.csv │ │ └── sampled_sequences.fasta │ ├── sample_sequences.py │ └── score_log_likelihoods.py ├── sup_variant_prediction.ipynb └── variant-prediction │ ├── README.md │ ├── __init__.py │ ├── data │ ├── BLAT_ECOLX_1_b0.5.a3m │ ├── BLAT_ECOLX_Ranganathan2015.csv │ ├── BLAT_ECOLX_Ranganathan2015_labeled.csv │ ├── BLAT_ECOLX_Ranganathan2015_labeled_masked.csv │ ├── aggregated_rho.csv │ ├── aggregated_rho_round3.csv │ └── rho_pp.csv │ ├── mutation_data.bib │ └── predict.py ├── hubconf.py ├── model_scheme.png ├── pyproject.toml ├── scripts ├── atlas │ ├── README.md │ └── v0 │ │ ├── full │ │ ├── bins.txt │ │ ├── foldseekdb.txt │ │ ├── foldseekdb │ │ │ ├── tm_.40_.50_plddt_.40_.50.txt │ │ │ ├── tm_.40_.50_plddt_.50_.60.txt │ │ │ ├── tm_.40_.50_plddt_.60_.70.txt │ │ │ ├── tm_.40_.50_plddt_.70_.80.txt │ │ │ ├── tm_.40_.50_plddt_.80_.90.txt │ │ │ ├── tm_.40_.50_plddt_.90_1.txt │ │ │ ├── tm_.40_.50_plddt_0_.40.txt │ │ │ ├── tm_.50_.60_plddt_.40_.50.txt │ │ │ ├── tm_.50_.60_plddt_.50_.60.txt │ │ │ ├── tm_.50_.60_plddt_.60_.70.txt │ │ │ ├── tm_.50_.60_plddt_.70_.80.txt │ │ │ ├── tm_.50_.60_plddt_.80_.90.txt │ │ │ ├── tm_.50_.60_plddt_.90_1.txt │ │ │ ├── tm_.50_.60_plddt_0_.40.txt │ │ │ ├── tm_.60_.70_plddt_.40_.50.txt │ │ │ ├── tm_.60_.70_plddt_.50_.60.txt │ │ │ ├── tm_.60_.70_plddt_.60_.70.txt │ │ │ ├── tm_.60_.70_plddt_.70_.80.txt │ │ │ ├── tm_.60_.70_plddt_.80_.90.txt │ │ │ ├── tm_.60_.70_plddt_.90_1.txt │ │ │ ├── tm_.60_.70_plddt_0_.40.txt │ │ │ ├── tm_.70_.80_plddt_.40_.50.txt │ │ │ ├── tm_.70_.80_plddt_.50_.60.txt │ │ │ ├── tm_.70_.80_plddt_.60_.70.txt │ │ │ ├── tm_.70_.80_plddt_.70_.80.txt │ │ │ ├── tm_.70_.80_plddt_.80_.90.txt │ │ │ ├── tm_.70_.80_plddt_.90_1.txt │ │ │ ├── tm_.70_.80_plddt_0_.40.txt │ │ │ ├── tm_.80_.90_plddt_.50_.60.txt │ │ │ ├── tm_.80_.90_plddt_.60_.70.txt │ │ │ ├── tm_.80_.90_plddt_.70_.80.txt │ │ │ ├── tm_.80_.90_plddt_.80_.90.txt │ │ │ ├── tm_.80_.90_plddt_.90_1.txt │ │ │ ├── tm_.90_1_plddt_.70_.80.txt │ │ │ ├── tm_.90_1_plddt_.80_.90.txt │ │ │ ├── tm_.90_1_plddt_.90_1.txt │ │ │ ├── tm_0_.40_plddt_.40_.50.txt │ │ │ ├── tm_0_.40_plddt_.50_.60.txt │ │ │ ├── tm_0_.40_plddt_.60_.70.txt │ │ │ ├── tm_0_.40_plddt_.70_.80.txt │ │ │ ├── tm_0_.40_plddt_.80_.90.txt │ │ │ ├── tm_0_.40_plddt_.90_1.txt │ │ │ └── tm_0_.40_plddt_0_.40.txt │ │ ├── tarballs.txt │ │ └── tarballs │ │ │ ├── tm_.40_.50_plddt_.40_.50.txt │ │ │ ├── tm_.40_.50_plddt_.50_.60.txt │ │ │ ├── tm_.40_.50_plddt_.60_.70.txt │ │ │ ├── tm_.40_.50_plddt_.70_.80.txt │ │ │ ├── tm_.40_.50_plddt_.80_.90.txt │ │ │ ├── tm_.40_.50_plddt_.90_1.txt │ │ │ ├── tm_.40_.50_plddt_0_.40.txt │ │ │ ├── tm_.50_.60_plddt_.40_.50.txt │ │ │ ├── tm_.50_.60_plddt_.50_.60.txt │ │ │ ├── tm_.50_.60_plddt_.60_.70.txt │ │ │ ├── tm_.50_.60_plddt_.70_.80.txt │ │ │ ├── tm_.50_.60_plddt_.80_.90.txt │ │ │ ├── tm_.50_.60_plddt_.90_1.txt │ │ │ ├── tm_.50_.60_plddt_0_.40.txt │ │ │ ├── tm_.60_.70_plddt_.40_.50.txt │ │ │ ├── tm_.60_.70_plddt_.50_.60.txt │ │ │ ├── tm_.60_.70_plddt_.60_.70.txt │ │ │ ├── tm_.60_.70_plddt_.70_.80.txt │ │ │ ├── tm_.60_.70_plddt_.80_.90.txt │ │ │ ├── tm_.60_.70_plddt_.90_1.txt │ │ │ ├── tm_.60_.70_plddt_0_.40.txt │ │ │ ├── tm_.70_.80_plddt_.40_.50.txt │ │ │ ├── tm_.70_.80_plddt_.50_.60.txt │ │ │ ├── tm_.70_.80_plddt_.60_.70.txt │ │ │ ├── tm_.70_.80_plddt_.70_.80.txt │ │ │ ├── tm_.70_.80_plddt_.80_.90.txt │ │ │ ├── tm_.70_.80_plddt_.90_1.txt │ │ │ ├── tm_.70_.80_plddt_0_.40.txt │ │ │ ├── tm_.80_.90_plddt_.50_.60.txt │ │ │ ├── tm_.80_.90_plddt_.60_.70.txt │ │ │ ├── tm_.80_.90_plddt_.70_.80.txt │ │ │ ├── tm_.80_.90_plddt_.80_.90.txt │ │ │ ├── tm_.80_.90_plddt_.90_1.txt │ │ │ ├── tm_.90_1_plddt_.70_.80.txt │ │ │ ├── tm_.90_1_plddt_.80_.90.txt │ │ │ ├── tm_.90_1_plddt_.90_1.txt │ │ │ ├── tm_0_.40_plddt_.40_.50.txt │ │ │ ├── tm_0_.40_plddt_.50_.60.txt │ │ │ ├── tm_0_.40_plddt_.60_.70.txt │ │ │ ├── tm_0_.40_plddt_.70_.80.txt │ │ │ ├── tm_0_.40_plddt_.80_.90.txt │ │ │ ├── tm_0_.40_plddt_.90_1.txt │ │ │ └── tm_0_.40_plddt_0_.40.txt │ │ └── highquality_clust30 │ │ 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