all unique compound structure (SMILES) of PubChem Database
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
2 answers
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
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