├── LICENSE ├── README.md ├── cryo2struct.yml ├── example └── 22898 │ ├── 7KJR.fasta │ └── 7kjr.pdb ├── img ├── 22898_labels.png ├── 25855.gif ├── 25855_1.gif └── data_preparation_workflow.png ├── prediction └── src │ ├── __init__.py │ ├── config │ └── arguments.yml │ ├── cryo2struct.py │ ├── infer │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── ca_final_amino_inference_no_attn.cpython-39.pyc │ │ └── ca_final_atom_inference_no_attn.cpython-39.pyc │ ├── ca_final_amino_inference_no_attn.py │ └── ca_final_atom_inference_no_attn.py │ ├── utils │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── clustering_centroid.cpython-39.pyc │ │ ├── extract_seq_from_pdb.cpython-39.pyc │ │ ├── get_ca_from_pred_probs.cpython-39.pyc │ │ └── get_probs_cords_from_atom_amino_sec.cpython-39.pyc │ ├── clustering_centroid.py │ ├── extract_seq_from_pdb.py │ ├── get_ca_from_pred_probs.py │ └── get_probs_cords_from_atom_amino_sec.py │ └── viterbi │ ├── __pycache__ │ └── viterbi_batches.cpython-39.pyc │ ├── lightning_logs │ ├── version_0 │ │ ├── events.out.tfevents.1686545733.protein.rnet.missouri.edu.25858.0 │ │ └── hparams.yaml │ └── version_1 │ │ ├── events.out.tfevents.1686546349.protein.rnet.missouri.edu.25858.1 │ │ └── hparams.yaml │ ├── run_hmm.bash │ ├── viterbi.cpp │ ├── viterbi.so │ └── viterbi_batches.py ├── preprocessing ├── fetch_EMDB_maps.sh ├── get_amino_labels.py ├── get_atoms_label.py ├── get_ca_from_pdb.py ├── get_fasta_from_rcsb.py ├── get_normalize_map.py ├── get_pdb_from_rcsb.py ├── get_pdb_seq.py ├── get_resample_map.py ├── get_sec_stru_coil_label.py ├── get_sec_stru_helix_label.py ├── get_sec_stru_strand_label.py ├── get_secondary_pdb.py ├── grid_division.py ├── make_input_run_clustal.py ├── merge_chains_fasta.py ├── pdb2seq.pl └── run_data_preparation.bash └── validation ├── labeling_validation.py ├── normalization_validation.py ├── resampling_validation.py └── validate_mrc.py /LICENSE: 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