Drug Sniffer can be used with any collection of molecules as its database. However, we provide two databases for users who do not wish to bring their own. The first, an extremely small database, just a few dozen molecules, exists for testing purposes. It can be found at examples/small-db. The second is much, much larger (about 450GB decompressed). This database is available for download as a split ZIP file from

Specifically, the full database is available for download with the following steps in a shell environment :

# download a collection of 166 files representing the complete database. This will create
# a new directory in your current working directory called molecule-files/
$ mkdir molecule_db
$ cd molecule_db
$ wget --accept-regex "ds_" -nH -np -r

# merge all those files into a single zip file, then unzip it
$ zip -F molecule-files/ --out
$ unzip

# clean up
$ rm -rf molecule-files/

Once extracted, you can point Drug Sniffer at the location using the molecule_db parameter. That will be the path to (and including) the molecule_db directory described above.