How to download zinc-22 using rsync: Difference between revisions
(asdf) |
m (asdf) |
||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
Ok, you can try this | Ok, you can try this | ||
rsync -Larv --include='*/' --include='[a-z]/H[01]?*-*db2.tgz' --exclude='sets' --exclude='*' --verbose rsync://files.docking.org/ZINC22-3D/zinc-22<?> . | |||
(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 cartblanche22.docking.org to make a precise selection. | |||
I hope this helps. | I hope this helps. | ||
Latest revision as of 21:10, 3 August 2022
Ok, you can try this
rsync -Larv --include='*/' --include='[a-z]/H[01]?*-*db2.tgz' --exclude='sets' --exclude='*' --verbose rsync://files.docking.org/ZINC22-3D/zinc-22<?> .
(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 cartblanche22.docking.org to make a precise selection.
I hope this helps.