Pubchem has an easy to use rest API, described here:
https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest

If you have a compound ID, you can query properties via something

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/CanonicalSMILES,IsomericSMILES,InChI/JSON


It comes back in JSON format, but you can have it return XML or plain text.

If you want an SDF file, something like

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF?record_type=3d


setting up a python function to query this shouldn't be difficult.

Jason Biggs


On Fri, Dec 1, 2017 at 12:51 PM, Sundar <jubilantsun...@gmail.com> wrote:

> I would like to download at least SMILES (great if I can also download mol
> files).
> And the same is true for Pubchem Compound ID or using Substance ID.
> Or even download the whole data set using an assay id. Anything could help.
>
> Thanks,
> Jubi
>
> On Fri, Dec 1, 2017 at 11:55 AM, Tim Dudgeon <tdudgeon...@gmail.com>
> wrote:
>
>> In what way? Given a single PubChem compound or substance ID you just
>> want to pull the smiles or molfile into RDKit?
>>
>> Tim
>> On 01/12/17 17:26, Sundar wrote:
>>
>> Hi RDkit users,
>>
>> I was wondering if RDkit has a means of downloading compounds from
>> Pubchem.
>> Also let me other ways that helps here.
>>
>> Thanks,
>> Jubi
>>
>>
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