Use the PDB REST API to get a list of PDB entries that contain a particular ligand

pdb_rest_example_get_pbids_with_ligand.py

#!/usr/bin/env python
# adapted example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
# edited to use the python 'requests' module

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

if PY3:
    import urllib.request as urllib2
else:
    import urllib2

SERVER_URL = "https://www.ebi.ac.uk/pdbe/api"

INPDB = "/pdb/compound/in_pdb"

#====================================================================#

def get_request(url, arg, pretty=False):
    full_url = "%s/%s/%s?pretty=%s" % (SERVER_URL, url, arg, str(pretty).lower())
    # e.g. for ligand ID. 'ATP' we get:
    # full_url = https://www.ebi.ac.uk/pdbe/api//pdb/compound/in_pdb/ATP?pretty=true
    print("This is the url string:\n{}".format(full_url))

    json_results = requests.get( full_url ).json() #This calls the information back from the API using the 'requests' module, and converts it to json format

    # pull out the list of PDB ids. that have this ligand ID:
    list_of_pdb_ids = json_results[arg] # 'arg' is the input ligand ID e.g. ATP

    # print out the list of PDB ids.:
    for pdb_id in range(len(list_of_pdb_ids)):
        print(list_of_pdb_ids[pdb_id])

    return(list_of_pdb_ids)

#====================================================================#

if __name__ == '__main__':
    parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument('-e', type=str, default=None, action='store', help='the ligandID')
    args = parser.parse_args()

    # If you type:
    # % python3 pdb_rest_example_get_pbids_with_ligand.py
    # You will see:
    #  usage: pdb_rest_example_get_pbids_with_ligand.py [-h] [-e E]
    #
    # optional arguments:
    #       -h, --help  show this help message and exit
    #       -e E        the ligandID

    # Note we defined at the top of the script that:
    # INPDB = "/pdb/compound/in_pdb"

    if args.e:
        response = get_request(INPDB, args.e, True)
    else:
        parser.print_help()
        sys.exit(1)

    print("FINISHED\n")

#====================================================================#