Converting molecule name to SMILES?

Question

I was just wondering, is there any way to convert IUPAC or common molecular names to SMILES? I want to do this without having to manually convert every single one utilizing online systems. Any input would be much appreciated!

For background, I am currently working with python and RDkit, so I wasn't sure if RDkit could do this and I was just unaware. My current data is in the csv format.

Thank you!

Answer 1

RDKit cant convert names to SMILES. Chemical Identifier Resolver can convert names and other identifiers (like CAS No) and has an API so you can convert with a script.

from urllib.request import urlopen
from urllib.parse import quote

def CIRconvert(ids):
    try:
        url = 'http://cactus.nci.nih.gov/chemical/structure/' + quote(ids) + '/smiles'
        ans = urlopen(url).read().decode('utf8')
        return ans
    except:
        return 'Did not work'

identifiers  = ['3-Methylheptane', 'Aspirin', 'Diethylsulfate', 'Diethyl sulfate', '50-78-2', 'Adamant']

for ids in identifiers :
    print(ids, CIRconvert(ids))

Output

3-Methylheptane CCCCC(C)CC
Aspirin CC(=O)Oc1ccccc1C(O)=O
Diethylsulfate CCO[S](=O)(=O)OCC
Diethyl sulfate CCO[S](=O)(=O)OCC
50-78-2 CC(=O)Oc1ccccc1C(O)=O
Adamant Did not work

Answer 2

OPSIN (https://opsin.ch.cam.ac.uk/) is another solution for name2structure conversion.

It can be used by installing the cli, or via https://github.com/gorgitko/molminer

(OPSIN is used by the RDKit KNIME nodes also)