Hi Jason,
This is great. I would really benefit from this.
At present I am looking for a way to download smiles or mol data of a few
compound which only have SIDs and CIDs.
Can we do it? I failed after trying the following,
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/sid/144205334/property/CanonicalSMILES,IsomericSMILES,InChI/JSON
Thanks,
On Fri, Dec 1, 2017 at 1:11 PM, Jason Biggs <jasondbi...@gmail.com> wrote:
> 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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