Downloading PubChem raw data using rsync

PubChem raw data is hosted on the NCBI servers which provide convenient access using rsync.

Download PubChem data using a rsync command like

rsync -Pav ftp.ncbi.nlm.nih.gov::pubchem/Compound/CURRENT-Full/SDF/\*.gz pubchem/

This example command will download all current compounds in SDF format.

You can explore the PubChem directory structure by accessing the NCBI FTP server using your browser.

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