- Python script to lookup pKa value from local database (~7,300 records) and from Pubchem using: CAS number, SMILES, InChI, InChIKey, IUPAC name.
- Most of the records (~6,900) in the current database is from JCheminform Mansouri et. al.
- The data is provide in this repo here.
- If record is found on Pubchem but not in local database, the record will be added into the local database for faster access in the future
- Python 3.6+
- Python libraries:
- PubChemPy
- requests
- pandas
- tinyDB
The following is a snippet of search_pka.py
db = TinyDB('data/tinydb_db.json', sort_keys=True, indent=4,
storage=CachingMiddleware(JSONStorage)) # Using caching for faster performance
try:
identifiers = [
'64-19-7', # acetic acid >>> pKa = 4.76 at 25 °C
'2950-43-8', # Hydroxylamine-O-sulfonic acid, no result
'InChI=1S/C6H6S/c7-6-4-2-1-3-5-6/h1-5,7H', # thiophenol
'C1=CC=C(C=C1)O', # phenol >>> pKa = 9.9
]
for identifier in identifiers:
print('Searching for pKa of structure with identifier: {}'.format(identifier))
result = search_pka(identifier=identifier, database=db)
pprint(result)
except Exception as error:
print(error)
finally:
# Close database to write to disk
db.close()Result:
Searching for pKa of structure with identifier: 64-19-7
[
{
"Canonical_SMILES": "CC(=O)O",
"IUPAC_Name": "acetic acid",
"InChI": "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)",
"InChIKey": "QTBSBXVTEAMEQO-UHFFFAOYSA-N",
"Isomeric_SMILES": "CC(=O)O",
"Pubchem_CID": "176",
"Substance_CASRN": "64-19-7",
"pKa": "4.76 at 25 °C",
"reference": "Serjeant, E.P., Dempsey B.; Ionisation Constants of Organic Acids in Aqueous Solution. International Union of Pure and Applied Chemistry (IUPAC). IUPAC Chemical Data Series No. 23, 1979. New York, New York: Pergamon Press, Inc., p. 989",
"source": "Pubchem"
}
]
Searching for pKa of structure with identifier: 2950-43-8
null
Searching for pKa of structure with identifier: InChI=1S/C6H6S/c7-6-4-2-1-3-5-6/h1-5,7H
[
{
"Canonical_SMILES": "SC1C=CC=CC=1",
"DSSTox_Structure_Id": "DTXCID906811",
"InChI": "InChI=1S/C6H6S/c7-6-4-2-1-3-5-6/h1-5,7H",
"InChIKey": "RMVRSNDYEFQCLF-UHFFFAOYSA-N",
"Original_SMILES": "SC1(=CC=CC=C1)",
"Original_Source_ID": "17763",
"Salt_Solvent_(Concatenate)": "?",
"Structure_Formula": "C6H6S",
"Structure_SMILES": "SC1=CC=CC=C1",
"Substance_CASRN": "108-98-5",
"Substance_Name": "Benzenethiol",
"Substance_Type": "Single Compound",
"basicOrAcidic": "acidic",
"group": "SH",
"method": "mean from 6",
"pKa": "6.37",
"solvent": "H2O",
"source": "https://doi.org/10.1186/s13321-019-0384-1",
"temp": "23",
"type": "a1/apparent"
},
{
"Canonical_SMILES": "C1=CC=C(C=C1)S",
"IUPAC_Name": "benzenethiol",
"InChI": "InChI=1S/C6H6S/c7-6-4-2-1-3-5-6/h1-5,7H",
"InChIKey": "RMVRSNDYEFQCLF-UHFFFAOYSA-N",
"Isomeric_SMILES": "C1=CC=C(C=C1)S",
"Pubchem_CID": "7969",
"Substance_CASRN": "108-98-5",
"pKa": "6.62",
"reference": "Serjeant, E.P., Dempsey B.; Ionisation Constants of Organic Acids in Aqueous Solution. International Union of Pure and Applied Chemistry (IUPAC). IUPAC Chemical Data Series No. 23, 1979. New York, New York: Pergamon Press, Inc., p. 165",
"source": "Pubchem"
}
]
Searching for pKa of structure with identifier: C1=CC=C(C=C1)O
[
{
"Canonical_SMILES": "C1=CC=C(C=C1)O",
"IUPAC_Name": "phenol",
"InChI": "InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H",
"InChIKey": "ISWSIDIOOBJBQZ-UHFFFAOYSA-N",
"Isomeric_SMILES": "C1=CC=C(C=C1)O",
"Pubchem_CID": "996",
"Substance_CASRN": "108-95-2",
"pKa": "9.99 @ 25 °C",
"reference": "Lide, D.R. (ed.). CRC Handbook of Chemistry and Physics. 83rd ed. Boca Raton, Fl: CRC Press Inc.,
2002-2003., p. 8-49",
"source": "Pubchem"
}
]- Using CAS number:
>>> cas_nr = '64-19-7' # acetic acid >>> pKa = 4.76 at 25 °C
>>> print(pka_lookup_pubchem(cas_nr))
>>> # print(pka_lookup_pubchem(cas_nr, 'cas')) # give same result
{
"Canonical_SMILES": "CC(=O)O",
"IUPAC_Name": "acetic acid",
"InChI": "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)",
"InChIKey": "QTBSBXVTEAMEQO-UHFFFAOYSA-N",
"Isomeric_SMILES": "CC(=O)O",
"Pubchem_CID": "176",
"Substance_CASRN": "64-19-7",
"pKa": "4.76 at 25 °C",
"reference": "Serjeant, E.P., Dempsey B.; Ionisation Constants of Organic Acids in Aqueous Solution. International Union of Pure and Applied Chemistry (IUPAC). IUPAC Chemical Data Series No. 23, 1979. New York, New York: Pergamon Press, Inc., p. 989",
"source": "Pubchem"
}- Using SMILES string:
>>> smiles_string = 'OC1=CC=CC=C1' # phenol
>>> print(pka_lookup_pubchem(smiles_string))
>>> # print(pka_lookup_pubchem(smiles_string, 'smiles')) # give same result
{
"Canonical_SMILES": "C1=CC=C(C=C1)O",
"IUPAC_Name": "phenol",
"InChI": "InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H",
"InChIKey": "ISWSIDIOOBJBQZ-UHFFFAOYSA-N",
"Isomeric_SMILES": "C1=CC=C(C=C1)O",
"Pubchem_CID": "996",
"Substance_CASRN": "108-95-2",
"pKa": "9.99 @ 25 °C",
"reference": "Lide, D.R. (ed.). CRC Handbook of Chemistry and Physics. 83rd ed. Boca Raton, Fl: CRC Press Inc., 2002-2003., p. 8-49",
"source": "Pubchem"
}- Using InChI string:
>>> inchi_string = 'InChI=1S/C6H6S/c7-6-4-2-1-3-5-6/h1-5,7H' # thiophenol
>>> print(pka_lookup_pubchem(inchi_string))
>>> # print(pka_lookup_pubchem(inchi_string, 'inchi')) # give same result
{
"Canonical_SMILES": "C1=CC=C(C=C1)S",
"IUPAC_Name": "benzenethiol",
"InChI": "InChI=1S/C6H6S/c7-6-4-2-1-3-5-6/h1-5,7H",
"InChIKey": "RMVRSNDYEFQCLF-UHFFFAOYSA-N",
"Isomeric_SMILES": "C1=CC=C(C=C1)S",
"Pubchem_CID": "7969",
"Substance_CASRN": "108-98-5",
"pKa": "6.62",
"reference": "Serjeant, E.P., Dempsey B.; Ionisation Constants of Organic Acids in Aqueous Solution. International Union of Pure and Applied Chemistry (IUPAC). IUPAC Chemical Data Series No. 23, 1979. New York, New York: Pergamon Press, Inc., p. 165",
"source": "Pubchem"
}- Using InChIKey string:
>>> inchikey_string = 'OKKJLVBELUTLKV-UHFFFAOYSA-N' # methanol
>>> print(pka_lookup_pubchem(inchikey_string))
>>> # print(pka_lookup_pubchem(inchikey_string, "inchikey")) # give same result
{
"Canonical_SMILES": "CO",
"IUPAC_Name": "methanol",
"InChI": "InChI=1S/CH4O/c1-2/h2H,1H3",
"InChIKey": "OKKJLVBELUTLKV-UHFFFAOYSA-N",
"Isomeric_SMILES": "CO",
"Pubchem_CID": "887",
"Substance_CASRN": "67-56-1",
"pKa": "15.3",
"reference": "Serjeant, E.P., Dempsey B.; Ionisation Constants of Organic Acids in Aqueous Solution. International Union of Pure and Applied Chemistry (IUPAC). IUPAC Chemical Data Series No. 23, 1979. New York, New York: Pergamon Press, Inc., p. 989",
"source": "Pubchem"
}When getting None as the result, you can turn on debug mode by adding suffix -d to your python running code to get more info. For example:
# Running 'src/pka_lookup_pubchem.py' for CAS: 75-46-7 (trifluoromethane)
$ python src/pka_lookup_pubchem.py -d
Searching for pKa of structure with identifier: 75-46-7
Traceback (most recent call last):
File "<path-to-file>\src\pka_lookup_pubchem.py", line 181, in pka_lookup_pubchem
raise RuntimeError('pKa not found in Pubchem.')
RuntimeError: pKa not found in Pubchem.- Errors include:
RuntimeError('pKa not found in Pubchem.'): compound exists on Pubchem but there is no pKa value.RuntimeError('Compound not found in Pubchem.'): compound cannot be found in Pubchem.ValueError('This is not an exact match on Pubchem!'): when searching on Pubchem return some result but it is not an exact match.
See here for details.