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May 2, 2022 08:38
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Here's a python function that goes from search string (like "human albumin") and returns a pdb file using @rcsbPDB's top result.
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| import requests | |
| import tempfile | |
| def get_pdb(query_string): | |
| url = "https://search.rcsb.org/rcsbsearch/v1/query" | |
| query = { | |
| "query": { | |
| "type": "terminal", | |
| "service": "full_text", | |
| "parameters": {"value": query_string}, | |
| }, | |
| "return_type": "entry", | |
| } | |
| r = requests.post(url, json=query) | |
| if "result_set" in r.json() and len(r.json()["result_set"]) > 0: | |
| pdbid = r.json()["result_set"][0]["identifier"] | |
| print('Fetched PDB', pdbid) | |
| url = f"https://files.rcsb.org/download/{pdbid}.pdb" | |
| pdb = requests.get(url) | |
| tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb") | |
| tmp.write(pdb.text.encode()) | |
| return tmp | |
| return None |
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