How To Use Rsync: Difference between revisions

From DISI
Jump to navigation Jump to search
(Created page with "== How to download zinc-22 using rsync == 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...")
 
mNo edit summary
Line 1: Line 1:
== How to download zinc-22 using rsync ==
== New Notes ==
=== List Available Directories for Download ===
<source>
rsync --list-only rsync://files.docking.org
</source>
 
== Old Notes ==
=== How To Download ZINC-22 Using Rsync ===


Ok, you can try this
Ok, you can try this

Revision as of 20:17, 4 October 2024

New Notes

List Available Directories for Download

rsync --list-only rsync://files.docking.org

Old Notes

How To Download ZINC-22 Using Rsync

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.