{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"name":"python","version":"3.12.12","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"},"kaggle":{"accelerator":"none","dataSources":[{"sourceType":"competition","sourceId":118765,"databundleVersionId":16320058},{"sourceType":"datasetVersion","sourceId":15547929,"datasetId":9947354,"databundleVersionId":16476993},{"sourceType":"datasetVersion","sourceId":15548425,"datasetId":9947636,"databundleVersionId":16477514},{"sourceType":"datasetVersion","sourceId":15531080,"datasetId":9936502,"databundleVersionId":16458773},{"sourceType":"datasetVersion","sourceId":10855324,"datasetId":6742586,"databundleVersionId":11219268},{"sourceType":"kernelVersion","sourceId":305681400}],"dockerImageVersionId":31259,"isInternetEnabled":false,"language":"python","sourceType":"notebook","isGpuEnabled":false}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"markdown","source":"### This notebook is part of the 3rd place solution for the Stanford RNA 3D Folding Part 2 competition. This code was executed locally, not on Kaggle.","metadata":{}},{"cell_type":"code","source":"import os\nimport sys\nimport shutil\nsys.version","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-04-08T20:59:29.60929Z","iopub.execute_input":"2026-04-08T20:59:29.609738Z","iopub.status.idle":"2026-04-08T20:59:29.627042Z","shell.execute_reply.started":"2026-04-08T20:59:29.60968Z","shell.execute_reply":"2026-04-08T20:59:29.624817Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"shutil.copy2('/kaggle/input/usalign/USalign', '/kaggle/working/USalign')\nos.chmod('/kaggle/working/USalign', 0o755)","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-04-08T20:59:29.630559Z","iopub.execute_input":"2026-04-08T20:59:29.631511Z","iopub.status.idle":"2026-04-08T20:59:29.680143Z","shell.execute_reply.started":"2026-04-08T20:59:29.631441Z","shell.execute_reply":"2026-04-08T20:59:29.678863Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!mkdir ~/python-packages\n!cp -r /kaggle/input/datasets/stefanstefanov/srna3d2-rnapro-tbm ~/python-packages/srna3d2-rnapro-tbm","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-04-08T20:59:29.681506Z","iopub.execute_input":"2026-04-08T20:59:29.682065Z","iopub.status.idle":"2026-04-08T20:59:30.722275Z","shell.execute_reply.started":"2026-04-08T20:59:29.681967Z","shell.execute_reply":"2026-04-08T20:59:30.720753Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"for local_package_name in ['srna3d2-rnapro-tbm']:\n    local_package_path = os.path.expanduser(f'~/python-packages/{local_package_name}')\n    os.environ['PYTHONPATH'] = os.environ.get('PYTHONPATH', '') + os.pathsep + local_package_path\n    sys.path.append(local_package_path)","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-04-08T20:59:30.724096Z","iopub.execute_input":"2026-04-08T20:59:30.724496Z","iopub.status.idle":"2026-04-08T20:59:30.731733Z","shell.execute_reply.started":"2026-04-08T20:59:30.724448Z","shell.execute_reply":"2026-04-08T20:59:30.730346Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!python -m srna3d.scripts.train_tmscore_lightgbm_model \\\n    --train-csv /kaggle/input/datasets/stefanstefanov/srna3d2-tmscore-dataset/tm_score_dataset.csv \\\n    --seed 1337 \\\n    --n-folds 3 \\\n    --n-trials 200 \\\n    --output-dir /kaggle/working/","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-04-08T20:59:30.733131Z","iopub.execute_input":"2026-04-08T20:59:30.73343Z","iopub.status.idle":"2026-04-08T21:00:48.765405Z","shell.execute_reply.started":"2026-04-08T20:59:30.733403Z","shell.execute_reply":"2026-04-08T21:00:48.764402Z"}},"outputs":[],"execution_count":null}]}