add rna_tools/rna_pdb_fetch_header.py

rna_tools/rna_pdb_fetch_header.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+
+"""
+from __future__ import print_function
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    #parser.add_argument('-', "--", help="", default="")
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument("file", help="", default="", nargs='+')
+    return parser
+
+import requests
+
+def fetch_pdb_header(pdb_id):
+    """
+    Fetches the header information for a given PDB ID using the RCSB PDB GraphQL API.
+
+    :param pdb_id: The PDB ID to query.
+    :return: A dictionary containing the header information or an error message.
+    """
+    # Define the GraphQL query
+    query = """
+    query getPDBHeader($id: String!) {
+      entry(entry_id: $id) {
+        rcsb_id
+        struct {
+          title
+        }
+        exptl {
+          method
+        }
+        rcsb_accession_info {
+          deposit_date
+          initial_release_date
+        }
+        citation {
+          title
+          rcsb_authors
+          year
+          pdbx_database_id_DOI
+        }
+      }
+    }
+    """
+
+    # Define the variables
+    variables = {"id": pdb_id}
+
+    # API endpoint
+    url = "https://data.rcsb.org/graphql"
+    headers = {"Content-Type": "application/json"}
+
+    try:
+        # Send the POST request
+        response = requests.post(url, json={"query": query, "variables": variables}, headers=headers)
+        response.raise_for_status()  # Raise HTTPError for bad responses (4xx and 5xx)
+        data = response.json()
+
+        # Return the data or error
+        if "data" in data:
+            return data["data"]
+        else:
+            return {"error": "No data returned. Check the PDB ID or API response."}
+
+    except requests.exceptions.RequestException as e:
+        return {"error": str(e)}
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    if list != type(args.file):
+        args.file = args.file
+
+    for pdb_id in [f.replace('.pdb', '').replace('.cif', '') for f in args.file]:
+        header_info = fetch_pdb_header(pdb_id)
+        title = header_info.get('entry', {}).get('struct', {}).get('title', 'Title not found')
+        # Print the extracted title
+        print(pdb_id, title)

setup.py

@@ -19,6 +19,7 @@
              'rna_tools/rna_standardize.py',
              'rna_tools/rna_pdb_inspect.py',
              'rna_tools/rna_cif2pdb.py',
+             'rna_tools/rna_pdb_fetch_header.py',             
 
              'rna_tools/tools/misc/rna_tools_which.py',
              'rna_tools/tools/misc/rna_tools_demo.py',