[ase-users] [EXTERNAL] Potential Pubchem API Integration

[Hermes, Eric]

I really like this idea. Please consider creating a MR on gitlab.

I would think this functionality should go in ase.data. It looks like ase.data.isotopes does something similar with physics.nist.gov to get isotope information, so ASE connecting to NIST isn't completely unheard of.

The function should probably also return a list of Atoms objects, since pubchem will provide multiple conformers. We may also want to improve the "sdf" parser so that it stores PUBCHEM_MMFF94_PARTIAL_CHARGES in arrays['initial_charges'].

It also looks like the URL needs to have "?record_type=3d" at the end, otherwise everything gets squashed into the xy-plane.
-- 
Eric Hermes
Postdoctoral Researcher
Sandia National Laboratories

On 8/9/19, 13:01, "ase-users-bounces at listserv.fysik.dtu.dk on behalf of Ben Comer via ase-users" <ase-users-bounces at listserv.fysik.dtu.dk on behalf of 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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