import logging
import requests
from functools import lru_cache
pubchem_url = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug'
logger = logging.getLogger(__name__)
[docs]@lru_cache(maxsize=5000)
def get_inchi_key(pubchem_cid):
"""Return the InChIKey for a given PubChem CID.
Parameters
----------
pubchem_cid : str
The PubChem CID whose InChIKey should be returned.
Returns
-------
str
The InChIKey corresponding to the PubChem CID.
"""
url = '%s/compound/cid/%s/property/InChIKey/TXT' % \
(pubchem_url, pubchem_cid)
res = requests.get(url)
if res.status_code != 200:
logger.error('Could not retrieve InChIKey for %s' % pubchem_cid)
return None
return res.text.strip()
[docs]@lru_cache(maxsize=5000)
def get_json_record(pubchem_cid):
"""Return the JSON record of a given PubChem CID.
Parameters
----------
pubchem_cid : str
The PubChem CID whose record should be returned.
Returns
-------
dict
The record deserialized from JSON.
"""
url = (pubchem_url + '_view/data/compound/%s/JSON/') % pubchem_cid
res = requests.get(url)
return res.json()
[docs]def get_preferred_compound_ids(pubchem_cid):
"""Return a list of preferred CIDs for a given PubChem CID.
Parameters
----------
pubchem_cid : str
The PubChem CID whose preferred CIDs should be returned.
Returns
-------
list of str
The list of preferred CIDs for the given CID. If there are no
preferred CIDs for the given CID then an empty list is returned.
"""
record = get_json_record(pubchem_cid)
sections = record['Record']['Section']
pref_ids = set()
for section in sections:
if section['TOCHeading'] == 'Preferred Compound':
for pref_cpd in section['Information']:
pref_ids |= set(pref_cpd['Value']['Number'])
pref_ids = sorted([str(pid) for pid in pref_ids])
return pref_ids