How to download zinc-22 using rsync

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Ok, you can try this

rsync -Larv --include='*/'  --include='[a-z]/H[01]?*-*db2.tgz' --exclude='sets' --exclude='*' --verbose rsync://<?> .

(all on one line)

where <?> is d g h i k l m n o p q r s t u v x 
n is 50% of the database
x is 25%
g is "informer set" 

This will get you all molecules in the "?" layer of ZINC-22. with the db2 format. If you want sdf, mol2 or pdbqt, just change db2 into the relevant one.

We recommended starting with < H20 (thus H[01]? above) . Once you have up to H19, add H20, H21 progressively. Each is typically 50% bigger than the previous one. H25 and H26 together are more than 60% of the database. You can do a lot of productive docking with H13-H16 (fragment-like) and H17-H19 (small lead like).


The layers have no meaning, other than they allow us to prepare the database independently in steps. If you want only a subset, then you could try using the 3D tranche browser in to make a precise selection. 

I hope this helps.