├── .DS_Store ├── .gitattributes ├── CMakeLists.txt ├── LICENSE ├── OUTPUT_TERMS_OF_USE.md ├── README.md ├── WEIGHTS_PROHIBITED_USE_POLICY.md ├── WEIGHTS_TERMS_OF_USE.md ├── dev-requirements.txt ├── docker ├── Dockerfile └── dockerignore ├── docs ├── contributing.md ├── header.jpg ├── input.md ├── installation.md ├── known_issues.md ├── output.md └── performance.md ├── environment.yml ├── example ├── 1_extract_chains.py ├── 2_pdb2jax.py ├── 3_generate_json.py ├── 4_extract_iptm-ipae-pae-interaction.py ├── pdb │ └── bcov_v4_r4_ems_p1-15H-GBL-16H-GBL-16H_0129_0001_0001_0002_000000002_0001_0001_19_34_H_.._ems_p1-16H-GBL-16H-GABBL-16H_0045_0001_0001_0002_0001_0001_0001_0001.pdb ├── subset_data.csv └── subset_data_with_metrics.csv ├── fetch_databases.sh ├── pyproject.toml ├── requirements.txt ├── run_af3score.py └── src └── alphafold3 ├── __init__.py ├── __pycache__ ├── __init__.cpython-311.pyc ├── build_data.cpython-311.pyc └── version.cpython-311.pyc ├── build_data.py ├── common ├── __pycache__ │ ├── base_config.cpython-311.pyc │ ├── folding_input.cpython-311.pyc │ └── resources.cpython-311.pyc ├── base_config.py ├── folding_input.py ├── resources.py └── testing │ ├── __pycache__ │ └── data.cpython-311.pyc │ └── data.py ├── constants ├── __pycache__ │ ├── atom_types.cpython-311.pyc │ ├── chemical_component_sets.cpython-311.pyc │ ├── chemical_components.cpython-311.pyc │ ├── mmcif_names.cpython-311.pyc │ ├── periodic_table.cpython-311.pyc │ ├── residue_names.cpython-311.pyc │ └── side_chains.cpython-311.pyc ├── atom_types.py ├── chemical_component_sets.py ├── chemical_components.py ├── converters │ ├── __pycache__ │ │ ├── ccd_pickle_gen.cpython-311.pyc │ │ └── chemical_component_sets_gen.cpython-311.pyc │ ├── ccd_pickle_gen.py │ ├── chemical_component_sets.pickle │ └── chemical_component_sets_gen.py ├── mmcif_names.py ├── periodic_table.py ├── residue_names.py └── side_chains.py ├── cpp.cc ├── data ├── __pycache__ │ ├── featurisation.cpython-311.pyc │ ├── msa.cpython-311.pyc │ ├── msa_config.cpython-311.pyc │ ├── msa_features.cpython-311.pyc │ ├── parsers.cpython-311.pyc │ ├── pipeline.cpython-311.pyc │ ├── structure_stores.cpython-311.pyc │ ├── template_realign.cpython-311.pyc │ └── templates.cpython-311.pyc ├── 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 │ ├── __pycache__ │ ├── hmmalign.cpython-311.pyc │ ├── hmmbuild.cpython-311.pyc │ ├── hmmsearch.cpython-311.pyc │ ├── jackhmmer.cpython-311.pyc │ ├── msa_tool.cpython-311.pyc │ ├── nhmmer.cpython-311.pyc │ ├── rdkit_utils.cpython-311.pyc │ └── subprocess_utils.cpython-311.pyc │ ├── hmmalign.py │ ├── hmmbuild.py │ ├── hmmsearch.py │ ├── jackhmmer.py │ ├── msa_tool.py │ ├── nhmmer.py │ ├── rdkit_utils.py │ └── subprocess_utils.py ├── jax ├── attention │ ├── __pycache__ │ │ ├── attention.cpython-311.pyc │ │ ├── attention_base.cpython-311.pyc │ │ ├── flash_attention.cpython-311.pyc │ │ └── xla_attention.cpython-311.pyc │ ├── attention.py │ ├── attention_base.py │ ├── attention_call_arg_specs.py │ ├── flash_attention.py │ └── xla_attention.py ├── common │ ├── __pycache__ │ │ ├── array_view.cpython-311.pyc │ │ ├── precision.cpython-311.pyc │ │ └── triton_utils.cpython-311.pyc │ ├── array_view.py │ ├── precision.py │ └── triton_utils.py ├── gated_linear_unit │ ├── __pycache__ │ │ ├── block.cpython-311.pyc │ │ ├── gated_linear_unit.cpython-311.pyc │ │ ├── gated_linear_unit_base.cpython-311.pyc │ │ ├── matmul_config.cpython-311.pyc │ │ └── matmul_ext.cpython-311.pyc │ ├── block.py │ ├── gated_linear_unit.py │ ├── gated_linear_unit_base.py │ ├── matmul_config.py │ └── matmul_ext.py └── geometry │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-311.pyc │ ├── rigid_matrix_vector.cpython-311.pyc │ ├── rotation_matrix.cpython-311.pyc │ ├── struct_of_array.cpython-311.pyc │ ├── utils.cpython-311.pyc │ └── vector.cpython-311.pyc │ ├── rigid_matrix_vector.py │ ├── rotation_matrix.py │ ├── struct_of_array.py │ ├── utils.py │ └── vector.py ├── model ├── __pycache__ │ ├── confidence_types.cpython-311.pyc │ ├── confidences.cpython-311.pyc │ ├── data3.cpython-311.pyc │ ├── data_constants.cpython-311.pyc │ ├── feat_batch.cpython-311.pyc │ ├── features.cpython-311.pyc │ ├── merging_features.cpython-311.pyc │ ├── mmcif_metadata.cpython-311.pyc │ ├── model_config.cpython-311.pyc │ ├── msa_pairing.cpython-311.pyc │ ├── params.cpython-311.pyc │ ├── post_processing.cpython-311.pyc │ └── protein_data_processing.cpython-311.pyc ├── atom_layout │ ├── __pycache__ │ │ └── atom_layout.cpython-311.pyc │ └── atom_layout.py ├── components │ ├── __pycache__ │ │ ├── base_model.cpython-311.pyc │ │ ├── haiku_modules.cpython-311.pyc │ │ ├── mapping.cpython-311.pyc │ │ └── utils.cpython-311.pyc │ ├── base_model.py │ ├── haiku_modules.py │ ├── mapping.py │ └── utils.py ├── confidence_types.py ├── confidences.py ├── data3.py ├── data_constants.py ├── diffusion │ ├── __pycache__ │ │ ├── atom_cross_attention.cpython-311.pyc │ │ ├── confidence_head.cpython-311.pyc │ │ ├── diffusion_head.cpython-311.pyc │ │ ├── diffusion_transformer.cpython-311.pyc │ │ ├── distogram_head.cpython-311.pyc │ │ ├── featurization.cpython-311.pyc │ │ ├── model.cpython-311.pyc │ │ ├── modules.cpython-311.pyc │ │ └── template_modules.cpython-311.pyc │ ├── atom_cross_attention.py │ ├── confidence_head.py │ ├── diffusion_head.py │ ├── diffusion_transformer.py │ ├── distogram_head.py │ ├── featurization.py │ ├── model.py │ ├── modules.py │ └── template_modules.py ├── feat_batch.py ├── features.py ├── merging_features.py ├── mkdssp_pybind.cc ├── mkdssp_pybind.h ├── mmcif_metadata.py ├── model_config.py ├── msa_pairing.py ├── params.py ├── pipeline │ ├── __pycache__ │ │ ├── inter_chain_bonds.cpython-311.pyc │ │ ├── pipeline.cpython-311.pyc │ │ └── structure_cleaning.cpython-311.pyc │ ├── inter_chain_bonds.py │ ├── pipeline.py │ └── structure_cleaning.py ├── post_processing.py ├── protein_data_processing.py └── scoring │ ├── __pycache__ │ ├── alignment.cpython-311.pyc │ ├── covalent_bond_cleaning.cpython-311.pyc │ └── scoring.cpython-311.pyc │ ├── alignment.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 ├── __pycache__ │ ├── __init__.cpython-311.pyc │ ├── bioassemblies.cpython-311.pyc │ ├── bonds.cpython-311.pyc │ ├── chemical_components.cpython-311.pyc │ ├── mmcif.cpython-311.pyc │ ├── parsing.cpython-311.pyc │ ├── sterics.cpython-311.pyc │ ├── structure.cpython-311.pyc │ ├── structure_tables.cpython-311.pyc │ ├── table.cpython-311.pyc │ └── test_utils.cpython-311.pyc ├── 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 │ └── 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