Unable to get 3D structures for some molecules using Pubchempy about pubchempy

[khoivan88]

Hi, if you look a bit closer on pubchem, you will find out that your compound is a hydrochloride salt and the 3D structure is not of the salt but the free base (CID 139856)
Screenshot here:

If you want to dig a little deeper, pubchempy.get_compounds('13985','cid',record_type = '3d') is just an just a call to this URL: (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/13985/JSON?record_type=3d). If you browse that URL using your favorite browser, you would get a 'no record found').

I hope this helps!

[ffzffz08]

Hi, if you look a bit closer on pubchem, you will find out that your compound is a hydrochloride salt and the 3D structure is not of the salt but the free base (CID 139856)
Screenshot here:

If you want to dig a little deeper, pubchempy.get_compounds('13985','cid',record_type = '3d') is just an just a call to this URL: (https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/13985/JSON?record_type=3d). If you browse that URL using your favorite browser, you would get a 'no record found').

I hope this helps!

Hi:
Thanks a lot! That answers my question - not only about this very molecule but about all others. I did have a vague impression that those 'should have 3D structures but could not be located by Pubchempy' molecules are salts.
I was also reading your answer for another post (you are really contributing a lot to the community - thanks! ). Pubchem mark the relationship between the salt and its free base as 'parent compound'. Since you were able to retrive pKa using your script, I could probably modify that code (with your permission of course) and retrive the parent compound as well.

[khoivan88]

Hi @ffzffz08 ,

Thank you very much for your kind words. I am glad that some would find my answers helpful :) .

And yes, please modify my code any way you want, I believe I have at least MIT license on there so you can modify it anyway you desire. I have not use pubchempy to retrieve 'parent' compound before but I think you would figure it out one way or another :)

Best of luck and let us know if you have any questions :D!