├── .gitignore ├── ACKNOWLEDGEMENTS ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── LICENSE_MODEL ├── README.md ├── assets ├── 7ftv_A.cif ├── 8cny_A.cif ├── 8g8r_A.cif ├── 8i85_A.cif └── intro.png ├── configs ├── __init__.py ├── base_empty.yaml ├── base_eval.yaml ├── base_train.yaml ├── callbacks │ ├── default.yaml │ ├── model_checkpoint.yaml │ └── model_summary.yaml ├── data │ ├── apo.yaml │ ├── cameo22.yaml │ ├── casp14.yaml │ ├── codnas.yaml │ ├── pdb.yaml │ ├── pdb_sp.yaml │ ├── pdb_sp_afesm.yaml │ └── pdb_sp_afesme.yaml ├── experiment │ ├── test.yaml │ ├── train.yaml │ ├── train_fsdp.yaml │ └── train_plddt.yaml ├── extras │ └── default.yaml ├── hydra │ └── default.yaml ├── logger │ └── tensorboard.yaml ├── model │ ├── architecture │ │ ├── default.yaml │ │ ├── foldingdit_1.1B.yaml │ │ ├── foldingdit_1.6B.yaml │ │ ├── foldingdit_100M.yaml │ │ ├── foldingdit_360M.yaml │ │ ├── foldingdit_3B.yaml │ │ ├── foldingdit_700M.yaml │ │ └── plddt_module.yaml │ ├── default.yaml │ ├── processor │ │ ├── default.yaml │ │ └── protein_processor.yaml │ ├── sampler │ │ └── euler_maruyama.yaml │ └── simplefold.yaml ├── paths │ └── default.yaml └── trainer │ ├── default.yaml │ └── fsdp.yaml ├── pyproject.toml ├── sample.ipynb └── src └── simplefold ├── __init__.py ├── boltz_data_pipeline ├── __init__.py ├── const.py ├── crop │ ├── __init__.py │ ├── boltz.py │ ├── cropper.py │ └── slice.py ├── feature │ ├── __init__.py │ ├── featurizer.py │ ├── pad.py │ └── symmetry.py ├── filter │ ├── __init__.py │ ├── dynamic │ │ ├── __init__.py │ │ ├── date.py │ │ ├── filter.py │ │ ├── max_residues.py │ │ ├── resolution.py │ │ ├── size.py │ │ └── subset.py │ └── static │ │ ├── __init__.py │ │ ├── filter.py │ │ ├── ligand.py │ │ └── polymer.py ├── parse │ ├── __init__.py │ ├── a3m.py │ ├── csv.py │ ├── fasta.py │ ├── schema.py │ └── yaml.py ├── tokenize │ ├── __init__.py │ ├── boltz_protein.py │ └── tokenizer.py ├── types.py └── write │ ├── __init__.py │ ├── mmcif.py │ ├── pdb.py │ ├── utils.py │ └── writer.py ├── cli.py ├── datasets ├── __init__.py ├── test_datamodule.py └── train_datamodule.py ├── evaluation ├── analyze_folding.py ├── analyze_two_state.py └── two_state_utils │ ├── plot.py │ ├── protein_residues.py │ └── tm_ens.py ├── inference.py ├── model ├── __init__.py ├── flow.py ├── mlx │ ├── __init__.py │ ├── architecture.py │ ├── blocks.py │ ├── confidence_module.py │ ├── esm_modules.py │ ├── esm_multihead_attention.py │ ├── esm_network.py │ ├── esm_rotary_embedding.py │ ├── layers.py │ ├── pos_embed.py │ └── sampler.py ├── simplefold.py └── torch │ ├── __init__.py │ ├── architecture.py │ ├── blocks.py │ ├── confidence_module.py │ ├── layers.py │ ├── pos_embed.py │ └── sampler.py ├── process_mmcif.py ├── process_structure.py ├── processor └── protein_processor.py ├── test.py ├── train.py ├── train_fsdp.py ├── utils ├── __init__.py ├── boltz_utils.py ├── datamodule_utils.py ├── esm_utils.py ├── fasta_utils.py ├── instantiators.py ├── logging_utils.py ├── 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