Hi Jason,
Thanks for the info.
That's exactly what I want. I want to download the compound in any format
(smiles/mol/sdf) for which I only have the Substance ID.
Sundar
On Fri, Dec 1, 2017 at 8:06 PM, Jason Biggs <jasondbi...@gmail.com> wrote:
> Sundar,
> What you do will depend on whether you have an SID or a CID number. Read
> https://pubchemblog.ncbi.nlm.nih.gov/2014/06/19/what-
> is-the-difference-between-a-substance-and-a-compound-in-pubchem/ for more
> info.
>
> In PubChem terminology, a *substance* is a chemical sample description
>> provided by a single source and a *compound* is a normalized chemical
>> structure representation found in one or more contributed *substances*.
>
>
> And looking at the pages for a few random substances, it doesn't list the
> same kind of information that you'll find on a compound page. So what you
> need is to get a list of associated compounds for a given substance ID.
>
> https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sid/
> 123061/cids/JSON?cids_type=all
>
> Leave off the cids_type=all if you only want one compound. For the SID in
> your query, it doesn't even have a compound, so it returns a message
> stating so.
>
> Jason
>
> Jason Biggs
>
>
> On Fri, Dec 1, 2017 at 5:33 PM, Sundar <jubilantsun...@gmail.com> wrote:
>
>> 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/14420
>> 5334/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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>>>>>
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>>>>>
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>>>>
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>>
>
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