Hi Jubi,
If you need the entire dataset and are not creating queries via the API, you
can download all PubChem Data via ftp here:
ftp://ftp.ncbi.nlm.nih.gov/pubchem/
Then download the SDFs, and extract out SMILES (I’ve used regular expressions
that match the appropriate data tag with good success).
Vin
University of Alabama
From: Jason Biggs [mailto:jasondbi...@gmail.com]
Sent: Friday, December 1, 2017 1:12 PM
To: Sundar <jubilantsun...@gmail.com>
Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] RDkit and Pubchem
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<mailto: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<mailto: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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