{"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.12.12"},"kaggle":{"accelerator":"none","dataSources":[{"sourceId":118765,"databundleVersionId":15231210,"sourceType":"competition"},{"sourceId":731240,"sourceType":"modelInstanceVersion","modelInstanceId":557082,"modelId":569638}],"dockerImageVersionId":31234,"isInternetEnabled":false,"language":"python","sourceType":"notebook","isGpuEnabled":false},"papermill":{"default_parameters":{},"duration":2354.045049,"end_time":"2026-01-13T06:54:44.524542","environment_variables":{},"exception":null,"input_path":"__notebook__.ipynb","output_path":"__notebook__.ipynb","parameters":{},"start_time":"2026-01-13T06:15:30.479493","version":"2.6.0"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"# Move all necessary files\n!cp -r /kaggle/input/rnabaselinemodel/other/default/1/* /kaggle/working/\nimport sys \nsys.path.append('/kaggle/working/RNABaselineModel.py')","metadata":{"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"import pandas as pd\nimport numpy as np\nfrom scipy.spatial.transform import Rotation as _Rot\nimport random as _rnd\nfrom Bio import pairwise2 as _pw2\nfrom Bio.Seq import Seq as _Seq\nimport time as _time\nfrom scipy.spatial import distance_matrix as _distmat\nfrom tqdm.auto import tqdm\nfrom RNABaselineModel import RNABaselineModel \nimport warnings\nwarnings.filterwarnings(\"ignore\")","metadata":{"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# =========================\n# USAGE\n# =========================\n\nmodel = RNABaselineModel(\n    n_preds=5,\n    pool=60,\n    rel_len_cap=0.3,\n    log_every=20000,     # reduce to print less (e.g., 1000)\n    verbose=False       # set False for quiet mode\n)\n\nmodel.load_data(\n    train_seq_path=\"/kaggle/input/stanford-rna-3d-folding-2/train_sequences.csv\",\n    valid_seq_path=\"/kaggle/input/stanford-rna-3d-folding-2/validation_sequences.csv\",\n    test_seq_path=\"/kaggle/input/stanford-rna-3d-folding-2/test_sequences.csv\",\n    train_lbl_path=\"/kaggle/input/stanford-rna-3d-folding-2/train_labels.csv\",\n    valid_lbl_path=\"/kaggle/input/stanford-rna-3d-folding-2/validation_labels.csv\",\n)\n\nmodel.build_banks()\n\nsubmission_df = model.make_submission_csv(out_path=\"submission.csv\")\n\nsubmission_df.head()\n","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}