Getting the list of monomers from PDB

all_mon_from_pdbj.py

import json
import urllib
import requests
def req(query):
  url = "https://pdbj.org/rest/newweb/search/sql?q=" + urllib.parse.quote(query)
  raw = urllib.request.urlopen(url).read()
  return json.loads(raw)["results"]

# [(pdb_id, monomer_id), ...]
all_mon = req("SELECT distinct pdbid,id FROM chem_comp")
json.dump(all_mon, open("./pdb_all_mon.json", "w"))

all_res = dict(req("SELECT pdbid, ls_d_res_high FROM refine"))
mons = {} # {monomer_id: [(pdb_id, resolution), ...]}
for p, m in all_mon:
  res = all_res.get(p)
  if res is None: res = float("inf")
  mons.setdefault(m, []).append((p, res))
for m in mons:
  mons[m].sort(key=lambda x: x[1])
json.dump(mons, open("./pdb_all_mon_res.json", "w"))