{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"name":"python","version":"3.6.6","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"},"kaggle":{"accelerator":"none","dataSources":[],"dockerImageVersionId":28755,"isInternetEnabled":false,"language":"python","sourceType":"notebook","isGpuEnabled":false}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"# This Python 3 environment comes with many helpful analytics libraries installed\n# It is defined by the kaggle/python Docker image: https://github.com/kaggle/docker-python\n# For example, here's several helpful packages to load\n\nimport numpy as np # linear algebra\nimport pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)\n\n# Input data files are available in the read-only \"../input/\" directory\n# For example, running this (by clicking run or pressing Shift+Enter) will list all files under the input directory\n\nimport os\nfor dirname, _, filenames in os.walk('/kaggle/input'):\n    for filename in filenames:\n        print(os.path.join(dirname, filename))\n\n# You can write up to 20GB to the current directory (/kaggle/working/) that gets preserved as output when you create a version using \"Save & Run All\" \n# You can also write temporary files to /kaggle/temp/, but they won't be saved outside of the current session\n\n# Use the kagglehub client library to attach Kaggle resources like competitions, datasets, and models to your session\n# Learn more about kagglehub: https://github.com/Kaggle/kagglehub/blob/main/README.md\n\nimport kagglehub\n# kagglehub.dataset_download('<owner>/<dataset-slug>')","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!pip install biopython","metadata":{"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"from Bio import SeqIO\nimport os\n\n# Step 1: Read protein IDs from FASTA\nprotein_ids = []\nfasta_path = \"/kaggle/input/competitions/cafa-5-protein-function-prediction/Train/train_sequences.fasta\"\n\nfor record in SeqIO.parse(fasta_path, \"fasta\"):\n    parts = record.id.split(\"|\")\n\n    if len(parts) >= 2:\n        protein_id = parts[1]\n    else:\n        protein_id = record.id\n\n    protein_ids.append(protein_id)\nprotein_ids = set(protein_ids)   ","metadata":{"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"pdb_dir = \"/kaggle/input/notebooks/pradippokhrel77/cafa-5-alpha-fold/pdbs\"\n\navailable_pdb_ids = set()\n\nfor file in os.listdir(pdb_dir):\n    if file.endswith(\".pdb\"):\n        protein_id = os.path.splitext(file)[0]\n        available_pdb_ids.add(protein_id)\n\nmissing_proteins = protein_ids - available_pdb_ids\nprint(\"Missing count:\", len(missing_proteins))\n\nwith open(\"/kaggle/working/missing_proteins.txt\", \"w\") as f:\n    for pid in missing_proteins:\n        f.write(pid + \"\\n\")","metadata":{"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"protein_ids = missing_proteins","metadata":{"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"import requests\nimport os\n\nos.makedirs(\"pdbs\", exist_ok=True)\n\nfor pid in protein_ids:\n    api_url = f\"https://alphafold.ebi.ac.uk/api/prediction/{pid}\"\n    r = requests.get(api_url)\n\n    if r.status_code != 200:\n        print(f\"Not found in API: {pid}\")\n        continue\n\n    data = r.json()\n\n    # safest: take first model\n    pdb_url = data[0][\"pdbUrl\"]\n\n    print(\"Downloading:\", pdb_url)\n\n    pdb_data = requests.get(pdb_url)\n\n    if pdb_data.status_code == 200:\n        with open(f\"pdbs/{pid}.pdb\", \"wb\") as f:\n            f.write(pdb_data.content)\n        print(\"Downloaded:\", pid)\n    else:\n        print(\"Failed download:\", pid)","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}