[Zinc-fans] Download large set of predefined molecules

Julian julimoxx at gmail.com
Tue Jan 29 08:04:02 PST 2013

Dear ZINC fans,
I have large sets (~ 100.000 molecules) of ligands that I know by ZINC-ID
and want to download.

I know that I can upload my list and download my molecules as sdf but this
is incredibly slow. What can I do to speed it up (significantly). I have
also tried to download it through our server via command line with the
following little script

wget "http://zinc.docking.org/results?zinc.id= ZINC ID + ZINC ID + ZINC ID
+ &page.format=sdf&filter.representation=usual&filter.purchasability=purchasable"

But when I added all my ZINC ID I got an error that the URI is too large.

What could I do? My prefered solution would be by command line.

Thank you very much,
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