all unique compound structure (SMILES) of PubChem Database

Question

[ajingnk]

Hi everyone,

I want to get all unique compound structures of PubChem Database. I have download SDF file for PubChem, but it is 45G after gzip. If I convert all SDF file to SMILES, that won't be easy... Is there any way to retrieve all SMILES for the whole PubChem?

Thanks,
Jing

Answer 1

[ajingnk]

In case someone also needs it, PubChem has InCHI data for all compound.

The FTP InCHI data can be downloaded from the following FTP directory: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-InChI-Key.gz

Answer 2

[gbrault]

109,485,000 smiles in this file 2/17/2021