├── .gitignore ├── LICENSE ├── README.md ├── assess_packing.py ├── config ├── dataset │ ├── bc40.yaml │ └── top2018.yaml ├── experiment │ ├── pippack_ipmp.yaml │ ├── pippack_ipmp_finetune.yaml │ ├── pippack_ipmp_ipa.yaml │ └── pippack_mpnn.yaml ├── inference.yaml ├── inference_ensemble.yaml ├── model │ ├── pippack.yaml │ └── pippack_finetune.yaml └── train.yaml ├── data ├── bc40_dataset.py ├── extract_targets_from_full_targets.py ├── features.py ├── featurizer.py ├── make_pdb_dir_for_benchmark.py ├── protein.py ├── residue_constants.py ├── rigid_utils.py ├── stereo_chemical_props.txt └── top2018_dataset.py ├── ensembled_inference.py ├── env └── pippack_env.yaml ├── eval ├── compute_clashscore.py ├── eval_rotamers.py ├── rosetta_packer.py └── rosetta_sc_min.py ├── images ├── pippack_architecture.pdf └── pippack_architecture.png ├── inference.py ├── model ├── loss.py ├── modules.py ├── optim.py └── resampling.py ├── model_weights ├── pippack_model_1_ckpt.pt ├── pippack_model_1_config.pickle ├── pippack_model_2_ckpt.pt ├── pippack_model_2_config.pickle ├── pippack_model_3_ckpt.pt ├── pippack_model_3_config.pickle ├── proteinipmp_000_ckpt.pt └── proteinmpnn_000_ckpt.pt ├── notebooks └── PIPPack.ipynb ├── proteinmpnn ├── model_utils.py ├── rigid_utils.py ├── testing.py ├── training.py └── utils.py ├── scripts ├── run_assessment.sh ├── run_clashscore.sh ├── run_ensemble.sh ├── run_inference.sh ├── run_proteinmpnn_testing.sh ├── run_proteinmpnn_training.sh ├── run_rosetta_packer.sh ├── run_rosetta_sc_min.sh ├── run_rotamer_eval.sh └── run_training.sh ├── train.py └── utils ├── train_utils.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kuhlman-Lab/PIPPack/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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