├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── CMakeLists.txt ├── LICENSE ├── OUTPUT_TERMS_OF_USE.md ├── README.md ├── WEIGHTS_PROHIBITED_USE_POLICY.md ├── WEIGHTS_TERMS_OF_USE.md ├── alphafold3_paper.txt ├── chat_with_gemini.txt ├── dev-requirements.txt ├── docker ├── Dockerfile └── dockerignore ├── docs ├── contributing.md ├── header.jpg ├── input.md ├── installation.md ├── known_issues.md ├── metadata_antibody_antigen.csv ├── metadata_antibody_antigen.md ├── output.md └── performance.md ├── fetch_databases.sh ├── legal ├── WEIGHTS_PROHIBITED_USE_POLICY-Bahasa-Indonesia.md ├── WEIGHTS_PROHIBITED_USE_POLICY-Espanol-Latinoamerica.md ├── WEIGHTS_PROHIBITED_USE_POLICY-Francais-Canada.md ├── WEIGHTS_PROHIBITED_USE_POLICY-Portugues-Brazil.md ├── WEIGHTS_TERMS_OF_USE-Bahasa-Indonesia.md ├── WEIGHTS_TERMS_OF_USE-Espanol-Latinoamerica.md ├── WEIGHTS_TERMS_OF_USE-Francais-Canada.md └── WEIGHTS_TERMS_OF_USE-Portugues-Brazil.md ├── pyproject.toml ├── requirements.txt ├── run_alphafold.ipynb ├── run_alphafold.py ├── run_alphafold_data_test.py ├── run_alphafold_test.py ├── screenshot.png └── src └── alphafold3 ├── __init__.py ├── build_data.py ├── common ├── base_config.py ├── folding_input.py ├── resources.py └── testing │ └── data.py ├── constants ├── atom_types.py ├── chemical_component_sets.py ├── chemical_components.py ├── converters │ ├── ccd_pickle_gen.py │ └── chemical_component_sets_gen.py ├── mmcif_names.py ├── periodic_table.py ├── residue_names.py └── side_chains.py ├── cpp.cc ├── data ├── cpp │ ├── msa_profile_pybind.cc │ └── msa_profile_pybind.h ├── featurisation.py ├── msa.py ├── msa_config.py ├── msa_features.py ├── msa_identifiers.py ├── msa_store.py ├── parsers.py ├── pipeline.py ├── structure_stores.py ├── template_realign.py ├── template_store.py ├── templates.py └── tools │ ├── hmmalign.py │ ├── hmmbuild.py │ ├── hmmsearch.py │ ├── jackhmmer.py │ ├── msa_tool.py │ ├── nhmmer.py │ ├── rdkit_utils.py │ └── subprocess_utils.py ├── jax ├── attention │ ├── attention.py │ ├── attention_base.py │ ├── attention_call_arg_specs.py │ ├── flash_attention.py │ └── xla_attention.py ├── common │ ├── array_view.py │ ├── precision.py │ └── triton_utils.py ├── gated_linear_unit │ ├── block.py │ ├── gated_linear_unit.py │ ├── gated_linear_unit_base.py │ ├── matmul_config.py │ └── matmul_ext.py └── geometry │ ├── __init__.py │ ├── rigid_matrix_vector.py │ ├── rotation_matrix.py │ ├── struct_of_array.py │ ├── utils.py │ └── vector.py ├── model ├── atom_layout │ └── atom_layout.py ├── components │ ├── haiku_modules.py │ ├── mapping.py │ └── utils.py ├── confidence_types.py ├── confidences.py ├── data3.py ├── data_constants.py ├── feat_batch.py ├── features.py ├── merging_features.py ├── mkdssp_pybind.cc ├── mkdssp_pybind.h ├── mmcif_metadata.py ├── model.py ├── model_config.py ├── msa_pairing.py ├── network │ ├── atom_cross_attention.py │ ├── confidence_head.py │ ├── diffusion_head.py │ ├── diffusion_transformer.py │ ├── distogram_head.py │ ├── evoformer.py │ ├── featurization.py │ ├── modules.py │ ├── noise_level_embeddings.py │ └── template_modules.py ├── params.py ├── pipeline │ ├── inter_chain_bonds.py │ ├── pipeline.py │ └── structure_cleaning.py ├── post_processing.py ├── protein_data_processing.py └── scoring │ ├── alignment.py │ ├── chirality.py │ ├── covalent_bond_cleaning.py │ └── scoring.py ├── parsers └── cpp │ ├── cif_dict.pyi │ ├── cif_dict_lib.cc │ ├── cif_dict_lib.h │ ├── cif_dict_pybind.cc │ ├── cif_dict_pybind.h │ ├── fasta_iterator.pyi │ ├── fasta_iterator_lib.cc │ ├── fasta_iterator_lib.h │ ├── fasta_iterator_pybind.cc │ ├── fasta_iterator_pybind.h │ ├── msa_conversion.pyi │ ├── msa_conversion_pybind.cc │ └── msa_conversion_pybind.h ├── scripts ├── copy_to_ssd.sh └── gcp_mount_ssd.sh ├── structure ├── __init__.py ├── bioassemblies.py ├── bonds.py ├── chemical_components.py ├── cpp │ ├── aggregation.pyi │ ├── aggregation_pybind.cc │ ├── aggregation_pybind.h │ ├── membership.pyi │ ├── membership_pybind.cc │ ├── membership_pybind.h │ ├── mmcif_altlocs.cc │ ├── mmcif_altlocs.h │ ├── mmcif_atom_site.pyi │ ├── mmcif_atom_site_pybind.cc │ ├── mmcif_atom_site_pybind.h │ ├── mmcif_layout.h │ ├── mmcif_layout.pyi │ ├── mmcif_layout_lib.cc │ ├── mmcif_layout_pybind.cc │ ├── mmcif_layout_pybind.h │ ├── mmcif_struct_conn.h │ ├── mmcif_struct_conn.pyi │ ├── mmcif_struct_conn_lib.cc │ ├── mmcif_struct_conn_pybind.cc │ ├── mmcif_struct_conn_pybind.h │ ├── mmcif_utils.pyi │ ├── mmcif_utils_pybind.cc │ ├── mmcif_utils_pybind.h │ ├── string_array.pyi │ ├── string_array_pybind.cc │ └── string_array_pybind.h ├── mmcif.py ├── parsing.py ├── sterics.py ├── structure.py ├── structure_tables.py ├── table.py └── test_utils.py ├── test_data ├── alphafold_run_outputs │ ├── run_alphafold_test_output_bucket_1024.pkl │ └── run_alphafold_test_output_bucket_default.pkl ├── featurised_example.json ├── featurised_example.pkl ├── miniature_databases │ ├── 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