import logging
from rdkit import Chem
import rdkit.Chem.rdMolDescriptors as molD
import pubchempy as pcp
import requests
from ..utils.errors import ChemMCPSearchFailError
from .pubchem import pubchem_iupac2cid, pubchem_name2cid
logger = logging.getLogger(__name__)
def pubchem_iupac2smiles(
query: str,
strict: bool = False,
) -> str:
cid = pubchem_iupac2cid(query, strict=strict) # May be a tuple in the case of multiple components in the IUPAC name
if not isinstance(cid, tuple):
cid = (cid,)
smiles = []
for single_cid in cid:
c = pcp.Compound.from_cid(single_cid)
r = c.isomeric_smiles
smiles.append(r.strip())
r = '.'.join(smiles)
return r
def pubchem_name2smiles(
query: str,
) -> str:
cid = pubchem_name2cid(query)
c = pcp.Compound.from_cid(cid)
r = c.isomeric_smiles
return r
def pubchem_smiles2cas(smi):
"""This function queries the given molecule smiles and returns cas"""
url_cid = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/{}/{}/cids/JSON"
url_data = "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{}/JSON"
try:
url_cid = url_cid.format('smiles', smi)
cid = requests.get(url_cid).json()["IdentifierList"]["CID"][0]
url_data = url_data.format(cid)
data = requests.get(url_data).json()
except (requests.exceptions.RequestException, KeyError):
raise ChemMCPSearchFailError("No Pubchem entry for the input SMILES.")
try:
for section in data["Record"]["Section"]:
if section.get("TOCHeading") == "Names and Identifiers":
for subsection in section["Section"]:
if subsection.get("TOCHeading") == "Other Identifiers":
for subsubsection in subsection["Section"]:
if subsubsection.get("TOCHeading") == "CAS":
return subsubsection["Information"][0]["Value"][
"StringWithMarkup"
][0]["String"]
except KeyError:
raise ChemMCPSearchFailError("Cannot find the CAS for the input SMILES.")
raise ChemMCPSearchFailError("Cannot find the CAS for the input SMILES.")
def pubchem_smiles2iupac(smi):
"""This function queries the given molecule smiles and returns iupac"""
c = pcp.get_compounds(smi, 'smiles')
if len(c) == 0:
parts = smi.split('.')
if len(parts) > 1:
parts_iupac = []
parts_cannot_find = []
for part in parts:
try:
iupac = pubchem_smiles2iupac(part)
except ChemMCPSearchFailError:
parts_cannot_find.append(part)
else:
parts_iupac.append(iupac)
if len(parts_cannot_find) > 0:
raise ChemMCPSearchFailError("Cannot find a matched molecule/compound for the following parts of the input SMILES: %s" % ', '.join(parts_cannot_find))
else:
r = ';'.join(parts_iupac)
else:
raise ChemMCPSearchFailError("Cannot find a matched molecule/compound. Please check the input SMILES.")
elif len(c) >= 1:
if len(c) > 1:
logger.info("There are more than one molecules/compounds that match the input SMILES. Using the first matched one.")
c = c[0]
r = c.iupac_name
if r is None or r == 'None':
raise ChemMCPSearchFailError(f"The PubChem entry (CID: {c.cid}) does not have a valid IUPAC name recorded.")
return r
def addHs(mol):
mol = Chem.rdmolops.AddHs(mol, explicitOnly=True)
return mol
def smiles2formula(smiles):
mol = Chem.MolFromSmiles(smiles, sanitize=False)
mol = addHs(mol)
formula = molD.CalcMolFormula(mol)
return formula
