├── .env.example ├── .github ├── PULL_REQUEST_TEMPLATE.md ├── codecov.yml ├── dependabot.yml ├── release-drafter.yml └── workflows │ ├── code-quality-main.yaml │ ├── code-quality-pr.yaml │ ├── publish.yaml │ ├── release-drafter.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .project-root ├── .vscode └── launch.json ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── alphafold3_pytorch ├── __init__.py ├── app.py ├── cli.py ├── common │ ├── amino_acid_constants.py │ ├── biomolecule.py │ ├── dna_constants.py │ ├── ligand_constants.py │ ├── mmcif_metadata.py │ ├── paper_constants.py │ └── rna_constants.py ├── data │ ├── __init__.py │ ├── atom_datamodule.py │ ├── chemical │ │ ├── A.cif │ │ ├── ALA.cif │ │ ├── ARG.cif │ │ ├── ASN.cif │ │ ├── ASP.cif │ │ ├── C.cif │ │ ├── CYS.cif │ │ ├── DA.cif │ │ ├── DC.cif │ │ ├── DG.cif │ │ ├── DT.cif │ │ ├── G.cif │ │ ├── GLN.cif │ │ ├── GLU.cif │ │ ├── GLY.cif │ │ ├── HIS.cif │ │ ├── ILE.cif │ │ ├── LEU.cif │ │ ├── LYS.cif │ │ ├── MET.cif │ │ ├── PHE.cif │ │ ├── PRO.cif │ │ ├── SER.cif │ │ ├── THR.cif │ │ ├── TRP.cif │ │ ├── TYR.cif │ │ ├── U.cif │ │ └── VAL.cif │ ├── data_pipeline.py │ ├── kalign.py │ ├── life.py │ ├── mmcif_parsing.py │ ├── mmcif_writing.py │ ├── mocks.py │ ├── msa_pairing.py │ ├── msa_parsing.py │ ├── pdb_datamodule.py │ ├── template_parsing.py │ └── weighted_pdb_sampler.py ├── eval.py ├── models │ ├── __init__.py │ ├── alphafold3_module.py │ └── components │ │ ├── __init__.py │ │ ├── alphafold3.py │ │ ├── attention.py │ │ ├── callbacks │ │ ├── ema.py │ │ └── lr_monitor.py │ │ ├── inputs.py │ │ ├── nlm.py │ │ └── plm.py ├── train.py └── utils │ ├── __init__.py │ ├── data_utils.py │ ├── instantiators.py │ ├── logging_utils.py │ ├── model_utils.py │ ├── pylogger.py │ ├── rich_utils.py │ ├── tensor_typing.py │ └── utils.py ├── configs ├── __init__.py ├── callbacks │ ├── default.yaml │ ├── ema.yaml │ ├── last_model_checkpoint.yaml │ ├── learning_rate_monitor.yaml │ ├── model_checkpoint.yaml │ ├── model_summary.yaml │ ├── none.yaml │ └── rich_progress_bar.yaml ├── data │ ├── atom.yaml │ └── pdb.yaml ├── debug │ ├── default.yaml │ ├── fdr.yaml │ ├── limit.yaml │ ├── overfit.yaml │ └── profiler.yaml ├── environment │ ├── default.yaml │ ├── lightning.yaml │ ├── slurm.yaml │ └── torch_elastic.yaml ├── eval.yaml ├── experiment │ ├── af3_fine_tuning_1.yaml │ ├── af3_fine_tuning_2.yaml │ ├── af3_initial_training.yaml │ ├── af3_overfitting_e1.yaml │ ├── af3_overfitting_e16.yaml │ └── af3_overfitting_e8.yaml ├── extras │ └── default.yaml ├── hparams_search │ └── pdb_optuna.yaml ├── hydra │ └── default.yaml ├── local │ └── .gitkeep ├── logger │ ├── aim.yaml │ ├── comet.yaml │ ├── csv.yaml │ ├── many_loggers.yaml │ ├── mlflow.yaml │ ├── neptune.yaml │ ├── tensorboard.yaml │ └── wandb.yaml ├── model │ └── alphafold3.yaml ├── paths │ └── default.yaml ├── strategy │ ├── ddp.yaml │ ├── ddp_spawn.yaml │ ├── deepspeed.yaml │ ├── default.yaml │ ├── fsdp.yaml │ └── optimized_ddp.yaml ├── train.yaml └── trainer │ ├── cpu.yaml │ ├── ddp.yaml │ ├── ddp_sim.yaml │ ├── deepspeed.yaml │ ├── default.yaml │ ├── fsdp.yaml │ ├── gpu.yaml │ └── mps.yaml ├── containers ├── Pawsey_PyTorch_ROCm_Dockerfile ├── Pawsey_PyTorch_ROCm_Source_Dockerfile └── PyTorch_ROCm_Source_Dockerfile ├── contibuting.sh ├── data ├── afdb_data │ └── data_caches │ │ └── uniprot_to_pdb_id_mapping.dat ├── ccd_data │ └── components_smiles.json ├── pdb_data │ ├── data_caches │ │ ├── msa │ │ │ └── train_msas │ │ │ │ ├── 209d-assembly1C_protein.a3m │ │ │ │ ├── 721p-assembly1A_protein.a3m │ │ │ │ ├── 721p-assembly1B_protein.a3m │ │ │ │ ├── 7a4d-assembly1A_protein.a3m │ │ │ │ ├── 7a4d-assembly1B_protein.a3m │ │ │ │ ├── 7a4d-assembly1C_protein.a3m │ │ │ │ ├── 7a4d-assembly1D_protein.a3m │ │ │ │ ├── 7a4d-assembly1E_protein.a3m │ │ │ │ └── 7a4d-assembly1F_protein.a3m │ │ └── template │ │ │ └── train_templates │ │ │ ├── 209d-assembly1C_protein_pdball_230102_db.m8 │ │ │ ├── 721p-assembly1A_protein_pdball_230102_db.m8 │ │ │ ├── 721p-assembly1B_protein_pdball_230102_db.m8 │ │ │ ├── 7a4d-assembly1A_protein_pdball_230102_db.m8 │ │ │ ├── 7a4d-assembly1B_protein_pdball_230102_db.m8 │ │ │ ├── 7a4d-assembly1C_protein_pdball_230102_db.m8 │ │ │ ├── 7a4d-assembly1D_protein_pdball_230102_db.m8 │ │ │ ├── 7a4d-assembly1E_protein_pdball_230102_db.m8 │ │ │ └── 7a4d-assembly1F_protein_pdball_230102_db.m8 │ └── train_mmcifs │ │ ├── 21 │ │ └── 721p-assembly1.cif │ │ ├── 09 │ │ └── 209d-assembly1.cif │ │ └── a4 │ │ └── 7a4d-assembly1.cif └── test │ ├── afdb_data │ ├── data_caches │ │ ├── train │ │ │ ├── 1a00_A │ │ │ │ ├── a3m │ │ │ │ │ ├── bfd_uniclust_hits.a3m │ │ │ │ │ ├── mgnify_hits.a3m │ │ │ │ │ └── uniref90_hits.a3m │ │ │ │ └── hhr │ │ │ │ │ └── pdb70_hits.hhr │ │ │ ├── 1a02_F │ │ │ │ ├── a3m │ │ │ │ │ ├── bfd_uniclust_hits.a3m │ │ │ │ │ ├── mgnify_hits.a3m │ │ │ │ │ └── uniref90_hits.a3m │ │ │ │ └── hhr │ │ │ │ │ └── pdb70_hits.hhr │ │ │ ├── 1a0g_A │ │ │ │ ├── a3m │ │ │ │ │ ├── bfd_uniclust_hits.a3m │ │ │ │ │ ├── mgnify_hits.a3m │ │ │ │ │ └── uniref90_hits.a3m │ │ │ │ └── hhr │ │ │ │ │ └── pdb70_hits.hhr │ │ │ ├── 1a2y_B │ │ │ │ ├── a3m │ │ │ │ │ ├── bfd_uniclust_hits.a3m │ │ │ │ │ ├── mgnify_hits.a3m │ │ │ │ │ └── uniref90_hits.a3m │ │ │ │ └── hhr │ │ │ │ │ └── pdb70_hits.hhr │ │ │ └── 1a3p_A │ │ │ │ ├── a3m │ │ │ │ ├── bfd_uniclust_hits.a3m │ │ │ │ ├── mgnify_hits.a3m │ │ │ │ └── uniref90_hits.a3m │ │ │ │ └── hhr │ │ │ │ └── pdb70_hits.hhr │ │ └── uniprot_to_pdb_id_mapping.dat │ └── mmcifs │ │ └── P01112 │ │ └── AF-P01112-F1-model_v4.cif │ └── pdb_data │ ├── data_caches │ ├── clusterings │ │ ├── interface_cluster_mapping.csv │ │ ├── ligand_chain_cluster_mapping.csv │ │ ├── nucleic_acid_chain_cluster_mapping.csv │ │ ├── peptide_chain_cluster_mapping.csv │ │ └── protein_chain_cluster_mapping.csv │ ├── msa │ │ └── msas │ │ │ ├── 209d-assembly1C_protein.a3m │ │ │ ├── 721p-assembly1A_protein.a3m │ │ │ ├── 721p-assembly1B_protein.a3m │ │ │ ├── 7a4d-assembly1A_protein.a3m │ │ │ ├── 7a4d-assembly1B_protein.a3m │ │ │ ├── 7a4d-assembly1C_protein.a3m │ │ │ ├── 7a4d-assembly1D_protein.a3m │ │ │ ├── 7a4d-assembly1E_protein.a3m │ │ │ └── 7a4d-assembly1F_protein.a3m │ └── template │ │ └── templates │ │ ├── 209d-assembly1C_protein_pdball_230102_db.m8 │ │ ├── 721p-assembly1A_protein_pdball_230102_db.m8 │ │ ├── 721p-assembly1B_protein_pdball_230102_db.m8 │ │ ├── 7a4d-assembly1A_protein_pdball_230102_db.m8 │ │ ├── 7a4d-assembly1B_protein_pdball_230102_db.m8 │ │ ├── 7a4d-assembly1C_protein_pdball_230102_db.m8 │ │ ├── 7a4d-assembly1D_protein_pdball_230102_db.m8 │ │ ├── 7a4d-assembly1E_protein_pdball_230102_db.m8 │ │ └── 7a4d-assembly1F_protein_pdball_230102_db.m8 │ └── mmcifs │ ├── 21 │ └── 721p-assembly1.cif │ ├── 09 │ └── 209d-assembly1.cif │ └── a4 │ └── 7a4d-assembly1.cif ├── docs └── alphafold3-supplementary.pdf ├── environment.yaml ├── img └── alphafold3.png ├── install-nim.sh ├── pyproject.toml ├── scripts ├── cluster_pdb_test_mmcifs.py ├── cluster_pdb_train_mmcifs.py ├── cluster_pdb_val_mmcifs.py ├── distillation_data_download.sh ├── filter_pdb_test_mmcifs.py ├── filter_pdb_train_mmcifs.py ├── filter_pdb_val_mmcifs.py ├── generate_id.py ├── reduce_uniprot_ids_to_pdb.py ├── reduce_uniprot_predictions_to_pdb.py └── slurm │ ├── hellbender │ ├── af3_initial_training.sh │ ├── af3_overfitting_e16.sh │ └── af3_single_gpu_initial_training.sh │ └── pawsey │ ├── af3_4_node_initial_training.sh │ ├── af3_fine_tuning_1.sh │ ├── af3_fine_tuning_2.sh │ ├── af3_initial_training.sh │ ├── af3_overfitting_experiment_e1.sh │ ├── af3_overfitting_experiment_e16.sh │ ├── af3_overfitting_experiment_e8.sh │ ├── af3_single_gpu_initial_training.sh │ ├── rocm-5.7-torch-distributed-gpu-test.sh │ ├── rocm-6.2-torch-distributed-gpu-test.sh │ └── torch-distributed-gpu-test.py └── tests ├── __init__.py ├── conftest.py ├── helpers ├── __init__.py ├── package_available.py ├── run_if.py └── run_sh_command.py ├── test_alphafold3.py ├── test_cli.py ├── test_configs.py ├── 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