How To Use Rsync

New Notes

Functional Public Domain Names

• rsync://irwinlab1.ucsf.edu
• rsync://files2.docking.org

List Available Directories for Download

rsync --list-only rsync://files2.docking.org

How to Download

For example, I would like to only download all of the smiles from ZINC15-2D and the destination for the files will be called zinc_test

rsync -L -a -m --progress --include="*.smi" --exclude="*.*" rsync://files2.docking.org/ZINC15-2D zinc_test

Breaking down the options used:

• -L: transform symbolic links into referent file/directory
• -a: This switch puts rsync into archive mode, which preserves time stamps, performs a recursive copy, keeps all file and directory permissions, preserves owner and group information, and copies any symbolic links.
• -m: Skips empty directories
• --progress: Shows progress during file transfer
• --include=”PATTERN”: includes files that are of the same pattern as “*.smi”
• --exclude=”PATTERN”: excludes everything that isn’t “*.smi”

You can check what files you can download by excluding the destination folder and removing the “include” and “exclude” options.

You can also use "--dry-run" to simulate what you're about to download.

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://files2.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.