├── .DS_Store ├── .dockerignore ├── .gitignore ├── 20240226_mov.gif ├── 20240226_mov.mp4 ├── AF_multitemplate ├── abl_msa.sh ├── alphafold │ ├── __init__.py │ ├── common │ │ ├── __init__.py │ │ ├── confidence.py │ │ ├── protein.py │ │ ├── protein_test.py │ │ ├── residue_constants.py │ │ ├── residue_constants_test.py │ │ ├── stereo_chemical_props.txt │ │ └── testdata │ │ │ └── 2rbg.pdb │ ├── data │ │ ├── __init__.py │ │ ├── feature_processing.py │ │ ├── mmcif_parsing.py │ │ ├── msa_identifiers.py │ │ ├── msa_pairing.py │ │ ├── parsers.py │ │ ├── pipeline.py │ │ ├── pipeline_multimer.py │ │ ├── templates.py │ │ └── tools │ │ │ ├── __init__.py │ │ │ ├── hhblits.py │ │ │ ├── hhsearch.py │ │ │ ├── hmmbuild.py │ │ │ ├── hmmsearch.py │ │ │ ├── jackhmmer.py │ │ │ ├── kalign.py │ │ │ └── utils.py │ ├── model │ │ ├── __init__.py │ │ ├── all_atom.py │ │ ├── all_atom_multimer.py │ │ ├── all_atom_test.py │ │ ├── common_modules.py │ │ ├── config.py │ │ ├── config_cfold.py │ │ ├── data.py │ │ ├── features.py │ │ ├── folding.py │ │ ├── folding_multimer.py │ │ ├── geometry │ │ │ ├── __init__.py │ │ │ ├── rigid_matrix_vector.py │ │ │ ├── rotation_matrix.py │ │ │ ├── struct_of_array.py │ │ │ ├── test_utils.py │ │ │ ├── utils.py │ │ │ └── vector.py │ │ ├── layer_stack.py │ │ ├── layer_stack_test.py │ │ ├── lddt.py │ │ ├── lddt_test.py │ │ ├── mapping.py │ │ ├── model.py │ │ ├── modules.py │ │ ├── modules_cfold.py │ │ ├── modules_multimer.py │ │ ├── prng.py │ │ ├── prng_test.py │ │ ├── quat_affine.py │ │ ├── quat_affine_test.py │ │ ├── r3.py │ │ ├── tf │ │ │ ├── __init__.py │ │ │ ├── data_transforms.py │ │ │ ├── input_pipeline.py │ │ │ ├── protein_features.py │ │ │ ├── protein_features_test.py │ │ │ ├── proteins_dataset.py │ │ │ ├── shape_helpers.py │ │ │ ├── shape_helpers_test.py │ │ │ ├── shape_placeholders.py │ │ │ └── utils.py │ │ └── utils.py │ ├── notebooks │ │ ├── __init__.py │ │ ├── notebook_utils.py │ │ └── notebook_utils_test.py │ └── relax │ │ ├── __init__.py │ │ ├── amber_minimize.py │ │ ├── amber_minimize_test.py │ │ ├── cleanup.py │ │ ├── cleanup_test.py │ │ ├── relax.py │ │ ├── relax_test.py │ │ ├── testdata │ │ ├── model_output.pdb │ │ ├── multiple_disulfides_target.pdb │ │ ├── with_violations.pdb │ │ └── with_violations_casp14.pdb │ │ ├── utils.py │ │ └── utils_test.py ├── monomer_full_dbs.flag ├── multimer_dbs_container.flag ├── run_afsample2.py └── scripts │ ├── download_all_data.sh │ ├── download_alphafold_params.sh │ ├── download_bfd.sh │ ├── download_mgnify.sh │ ├── download_pdb70.sh │ ├── download_pdb_mmcif.sh │ ├── download_pdb_seqres.sh │ ├── download_small_bfd.sh │ ├── download_uniprot.sh │ ├── download_uniref30.sh │ └── download_uniref90.sh ├── LICENSE ├── README.md ├── docker └── Dockerfile ├── environment.yaml ├── examples └── P31133 │ ├── P31133.fasta │ ├── P31133_perturb_profile.txt │ └── msas │ ├── bfd_uniref_hits.a3m │ ├── mgnify_hits.sto │ ├── pdb_hits.hhr │ └── uniref90_hits.sto ├── notebooks ├── plotting_functions.py ├── 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