[ase-users] Potential Pubchem API Integration

[Jakob Blomqvist]

I think it would be a very useful feature.

Jakob Blomqvist
Faculty of Technology and Society
Malmo University
+46 40 6657751
jakob.blomqvist at mau.se

On Aug 9, 2019 21:59, Ben Comer via ase-users <ase-users at listserv.fysik.dtu.dk> wrote:
Hello all,

I've noticed that ASE has a very limited number of molecules that can be
easily made into an atoms object. An easy fix for this could be to
integrate a restful API to a chemical database to query and pull in
structures from the internet. Pubchem
(https://pubchem.ncbi.nlm.nih.gov/) might make sense for this, since it
does not require an API key to access. We could just use the requests
library to access molecules by name (or anything else, like cid fro
example.) Some code to access the API would be a fairly short putt, we
might make something like this:

from io import StringIO
from ase.io import read
import requests


def pubchem(name):
     r =
requests.get("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{}/sdf".format(name))
     f_like = StringIO(r.text)
     atoms = read(f_like, format = 'sdf')
     return atoms

atoms = pubchem('ammonia')
print(atoms)


Just an idea, what do you guys think?


Thanks,

Ben Comer


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