├── .gitignore ├── LICENSE ├── README.md ├── SSbuilder ├── SSBLIB.tar.gz ├── SSbuilder.py └── __init__.py ├── analysis ├── __init__.py ├── amber_minimize.py ├── cleanup.py ├── interface_analyze.xml ├── metrics.py ├── postprocess.py ├── postprocess_utils.py └── utils.py ├── config ├── base.yaml ├── docking.yaml ├── eval.yaml ├── finetune.yaml └── inference.yaml ├── data ├── __init__.py ├── all_atom.py ├── chemical.py ├── errors.py ├── igso3.py ├── parsers.py ├── pdb_data_loader.py ├── protein.py ├── r3_diffuser.py ├── residue_constants.py ├── se3_diffuser.py ├── so3_diffuser.py ├── so3_utils.py └── utils.py ├── datasets ├── PepPC-F_dataset.csv ├── PepPC_after_202201.csv ├── PepPC_before_202201.csv ├── PepPC_dataset.csv ├── README.md ├── datasets.jpg └── docking │ ├── AF2_predicted_domains │ ├── O75554.pdb │ ├── O75791.pdb │ ├── P07948.pdb │ ├── P08631.pdb │ ├── P15498.pdb │ ├── P46937.pdb │ ├── P50552.pdb │ ├── Q00013.pdb │ ├── Q14155.pdb │ ├── Q16584.pdb │ ├── Q5VV41.pdb │ ├── Q8IWW6.pdb │ ├── Q8N8S7.pdb │ ├── Q96J02.pdb │ ├── Q99469.pdb │ ├── Q9BVN2.pdb │ ├── Q9H6S3.pdb │ ├── Q9UI08.pdb │ ├── Q9UPV0.pdb │ └── Q9Y371.pdb │ ├── PBD_data_subsampled.csv │ ├── PBD_screening_metrics.csv │ └── docking_benchmark.csv ├── environment.yml ├── examples ├── DiffPepBuilder_demo.ipynb ├── DiffPepDock_demo.ipynb ├── docking_data │ ├── 7Z6F.pdb │ ├── docking_cases.json │ └── peptide_seq.fasta ├── figures │ ├── dpb_model.jpg │ └── dpd_model.jpg └── receptor_data │ ├── alk1.pdb │ └── de_novo_cases.json ├── experiments ├── __init__.py ├── preprocess_utils.py ├── process_batch_dock.py ├── process_dataset.py ├── process_receptor.py ├── run_docking.py ├── run_inference.py ├── run_postprocess.py ├── split_dataset.py ├── train.py └── utils.py ├── model ├── __init__.py ├── embedding.py ├── ipa_module.py ├── layers.py └── score_network.py ├── openfold ├── __init__.py ├── config.py ├── data │ ├── __init__.py │ ├── data_modules.py │ ├── data_pipeline.py │ ├── data_transforms.py │ ├── errors.py │ ├── feature_pipeline.py │ ├── input_pipeline.py │ ├── mmcif_parsing.py │ ├── parsers.py │ ├── templates.py │ └── tools │ │ ├── __init__.py │ │ ├── hhblits.py │ │ ├── hhsearch.py │ │ ├── jackhmmer.py │ │ ├── kalign.py │ │ └── utils.py ├── model │ ├── __init__.py │ ├── dropout.py │ ├── embedders.py │ ├── evoformer.py │ ├── heads.py │ ├── model.py │ ├── msa.py │ ├── outer_product_mean.py │ ├── pair_transition.py │ ├── primitives.py │ ├── structure_module.py │ ├── template.py │ ├── torchscript.py │ ├── triangular_attention.py │ └── triangular_multiplicative_update.py ├── np │ ├── __init__.py │ ├── protein.py │ ├── relax │ │ ├── __init__.py │ │ ├── amber_minimize.py │ │ ├── cleanup.py │ │ ├── relax.py │ │ └── utils.py │ └── residue_constants.py ├── resources │ ├── __init__.py │ └── stereo_chemical_props.txt └── utils │ ├── __init__.py │ ├── argparse.py │ ├── callbacks.py │ ├── checkpointing.py │ ├── exponential_moving_average.py │ ├── feats.py │ ├── import_weights.py │ ├── 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