├── .gitignore ├── .idea ├── .gitignore ├── .name ├── enzyme-stability.iml ├── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── misc.xml ├── modules.xml └── vcs.xml ├── LICENSE ├── README.md ├── analysis ├── SSM.py ├── bootstrap.py ├── custom_inference.py ├── rosetta_RaSP_metrics.py └── thermompnn_benchmarking.py ├── cache.py ├── config.yaml ├── data_all ├── testing │ ├── fireprot_HF.csv │ ├── fireprot_test.csv │ ├── mega_test.csv │ ├── myoglobin_clean.csv │ ├── s669_clean_dir.csv │ ├── ssym-5fold_clean_dir.csv │ └── ssym-5fold_clean_inv.csv └── training │ ├── fireprot_train.csv │ ├── fireprot_val.csv │ ├── mega_train.csv │ └── mega_val.csv ├── dataset_splits ├── fireprot_clusters.tsv ├── fireprot_splits.pkl ├── mega_splits.pkl ├── megascale_clusters.tsv ├── megascale_vs_fireprot_homologues.m8 └── s669_vs_megascale_homologues.m8 ├── datasets.py ├── environment.yaml ├── examples ├── 2OCJ.pdb ├── ThermoMPNN_inference_2OCJ.csv ├── inference.sh └── train.sh ├── images ├── PDF │ └── thermoMPNN_scheme.pdf └── SVG │ └── thermoMPNN_scheme.svg ├── local.yaml ├── model_utils.py ├── models └── thermoMPNN_default.pt ├── preprocessing ├── 1_clean_fireprot_dataset.py ├── 2_seqalign_fireprot_dataset.py ├── 3_add_metadata_fireprot_dataset.py ├── 4_consolidate_pH_entries.py ├── download_pdb.py ├── split_fireprot.ipynb └── split_megascale.ipynb ├── protein_mpnn_utils.py ├── train_thermompnn.py ├── transfer_model.py └── vanilla_model_weights ├── v_48_002.pt ├── v_48_010.pt ├── v_48_020.pt └── v_48_030.pt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kuhlman-Lab/ThermoMPNN/HEAD/.gitignore -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- 1 | # Default ignored files 2 | /shelf/ 3 | /workspace.xml 4 | 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