├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── assets ├── models │ └── conditional │ │ ├── config.json │ │ ├── logs │ │ └── lightning_logs │ │ │ └── version_0 │ │ │ ├── hparams.yaml │ │ │ └── metrics.csv │ │ ├── models │ │ └── best_by_valid │ │ │ └── epoch=805-step=93496.ckpt │ │ ├── training_args.json │ │ ├── training_mean_angles.json │ │ ├── training_mean_distances.json │ │ ├── training_mean_offset.json │ │ └── training_std_angles.json └── overview.png ├── configs ├── conditional.json ├── minimal_conditional.json ├── minimal_unconditional.json └── wandb │ └── wandb.json ├── data ├── cremp │ ├── test.csv │ ├── test │ │ └── .gitkeep │ ├── train.csv │ └── train │ │ └── .gitkeep └── tetrapeptides │ ├── E.C.T.S.pickle │ ├── E.V.E.D.pickle │ ├── E.V.S.S.pickle │ ├── E.V.T.C.pickle │ ├── F.A.S.T.pickle │ ├── F.C.C.T.pickle │ ├── F.F.C.K.pickle │ ├── F.F.F.F.pickle │ ├── F.G.A.T.pickle │ ├── F.K.T.L.pickle │ ├── F.T.K.E.pickle │ ├── F.V.T.T.pickle │ ├── H.A.K.S.pickle │ ├── H.H.K.G.pickle │ ├── H.H.L.H.pickle │ ├── H.K.K.S.pickle │ ├── H.L.D.T.pickle │ ├── H.L.K.S.pickle │ ├── H.S.G.A.pickle │ ├── H.T.G.S.pickle │ ├── K.E.E.V.pickle │ ├── K.K.S.A.pickle │ ├── K.T.T.E.pickle │ ├── K.V.G.G.pickle │ ├── L.D.C.E.pickle │ ├── L.V.E.D.pickle │ ├── T.C.T.A.pickle │ ├── T.S.V.C.pickle │ ├── T.V.S.D.pickle │ ├── V.G.D.C.pickle │ ├── W.A.E.L.pickle │ ├── W.F.V.E.pickle │ ├── W.G.T.Y.pickle │ ├── W.S.F.H.pickle │ ├── W.V.E.E.pickle │ ├── W.V.V.C.pickle │ ├── Y.A.K.V.pickle │ ├── Y.D.S.Y.pickle │ ├── Y.E.A.D.pickle │ ├── Y.E.E.D.pickle │ ├── Y.E.T.D.pickle │ ├── Y.G.H.Y.pickle │ ├── Y.G.S.K.pickle │ ├── Y.K.A.D.pickle │ ├── Y.K.F.E.pickle │ ├── Y.S.C.A.pickle │ ├── Y.T.D.T.pickle │ ├── Y.T.V.K.pickle │ ├── Y.Y.F.E.pickle │ └── Y.Y.S.Y.pickle ├── environment.yaml ├── pyproject.toml ├── ringer ├── __init__.py ├── compute_metrics.py ├── data │ ├── __init__.py │ ├── macrocycle.py │ └── noised.py ├── eval.py ├── models │ ├── __init__.py │ ├── bert_for_diffusion.py │ └── components │ │ ├── __init__.py │ │ ├── attention.py │ │ ├── embeddings.py │ │ └── output.py ├── reconstruct.py ├── sidechain_reconstruction │ ├── __init__.py │ ├── data │ │ └── reconstruction_data.pickle │ ├── reconstruction.py │ └── transforms.py ├── train.py └── utils │ ├── __init__.py │ ├── chem.py │ ├── data │ └── amino_acids.csv │ ├── data_loading.py │ ├── evaluation.py │ ├── featurization.py │ ├── internal_coords.py │ ├── losses.py │ ├── peptides.py │ ├── plotting.py │ ├── reconstruction.py │ ├── sampling.py │ ├── utils.py │ └── variance_schedules.py ├── scripts ├── aggregate_metrics.py ├── compute_metrics_single.py └── reconstruct_single.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Genentech/ringer/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: 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