├── .gitignore ├── LICENSE ├── README.md ├── citation.bib ├── environment.yml ├── notebooks ├── data_usage.ipynb ├── data_usage.py ├── feature_generation.ipynb └── feature_generation.py ├── project ├── datasets │ ├── DB5 │ │ ├── README │ │ ├── db5_dgl_data_module.py │ │ └── db5_dgl_dataset.py │ ├── DIPS │ │ └── filters │ │ │ ├── buried_surface_over_500.txt │ │ │ ├── nmr_res_less_3.5.txt │ │ │ ├── seq_id_less_30.txt │ │ │ └── size_over_50.0.txt │ ├── EVCoupling │ │ ├── evcoupling_heterodimer_list.txt │ │ ├── final │ │ │ └── stub │ │ ├── group_files.py │ │ └── interim │ │ │ └── stub │ ├── analysis │ │ ├── analyze_experiment_types_and_resolution.py │ │ ├── analyze_feature_correlation.py │ │ └── analyze_interface_waters.py │ └── builder │ │ ├── add_new_feature.py │ │ ├── annotate_idr_residues.py │ │ ├── collect_dataset_statistics.py │ │ ├── compile_casp_capri_dataset_on_andes.sh │ │ ├── compile_db5_dataset_on_andes.sh │ │ ├── compile_dips_dataset_on_andes.sh │ │ ├── compile_evcoupling_dataset_on_andes.sh │ │ ├── convert_complexes_to_graphs.py │ │ ├── create_hdf5_dataset.py │ │ ├── download_missing_pruned_pair_pdbs.py │ │ ├── extract_raw_pdb_gz_archives.py │ │ ├── generate_hhsuite_features.py │ │ ├── generate_psaia_features.py │ │ ├── impute_missing_feature_values.py │ │ ├── launch_parallel_slurm_jobs_on_andes.sh │ │ ├── log_dataset_statistics.py │ │ ├── make_dataset.py │ │ ├── partition_dataset_filenames.py │ │ ├── postprocess_pruned_pairs.py │ │ ├── prune_pairs.py │ │ ├── psaia_chothia.radii │ │ ├── psaia_config_file_casp_capri.txt │ │ ├── psaia_config_file_db5.txt │ │ ├── psaia_config_file_dips.txt │ │ ├── psaia_config_file_evcoupling.txt │ │ ├── psaia_hydrophobicity.hpb │ │ └── psaia_natural_asa.asa └── utils │ ├── constants.py │ ├── modules.py │ ├── training_constants.py │ ├── training_utils.py │ └── utils.py ├── setup.cfg └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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