Difference between revisions of "Rsyncing zinc15"

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Let's say, you are in folder /ZINC15DB, which contains your 3D database (named as 3D), and you want to sync only *.db2.gz files from CA-tranche, then:  
 
Let's say, you are in folder /ZINC15DB, which contains your 3D database (named as 3D), and you want to sync only *.db2.gz files from CA-tranche, then:  
 
  rsync -L  -a --progress --prune-empty-dirs --include="*/" --include="CA[ABCE][A-D][RM][LMNOP].*.db2.gz" --exclude="*" rsync://files.docking.org/ZINC-3D/CA 3D
 
  rsync -L  -a --progress --prune-empty-dirs --include="*/" --include="CA[ABCE][A-D][RM][LMNOP].*.db2.gz" --exclude="*" rsync://files.docking.org/ZINC-3D/CA 3D
 +
 +
 +
# special subsets. e.g.  metabolites, biogenic
 +
 +
For instance, to get all metabolites in PDBQT format:
 +
rsync -L -a --progress --prune-empty-dirs --include="*/" --include="*.pdbqt.gz" --exclude="*" rsync://files.docking.org/ZINC-special/metabolites zinc
 +
To get all biogenic in SDF format
 +
rsync -L -a --progress --prune-empty-dirs --include="*/" --include="*.sdf.gz" --exclude="*" rsync://files.docking.org/ZINC-special/biogenic zinc
 +
To get all aggregators in DB2 format
 +
rsync -L -a --progress --prune-empty-dirs --include="*/" --include="*.db.gz" --exclude="*" rsync://files.docking.org/ZINC-special/aggregators zinc
 +
To get SMILES and other details:
 +
wget http://files.docking.org/special/current/biogenic/biogenic.info.txt.gz
 +
http://files.docking.org/special/current/metabolites/metabolites.info.txt.gz
 +
http://files.docking.org/special/current/aggregators/aggregators.info.txt.gz

Latest revision as of 09:00, 6 November 2019

A few examples below: This is how you set up a ZINC Mirror. I am looking at you Uppsala, Beijing, and Kiev.

  1. what is available?
rsync --list-only rsync://files.docking.org
  1. download 2D
rsync -L  -a --progress  --include="[ABCDEFG][A-G]*.smi" --exclude="[HIJK]*" rsync://files.docking.org/ZINC-2D/ zinc
  1. download 3D
rsync -L  -a --progress  --include="[ABCDEFG][A-G]*.db2.gz" --exclude="[HIJK]*" rsync://files.docking.org/ZINC-3D/  zinc
  1. Example (download 3D):

Let's say, you are in folder /ZINC15DB, which contains your 3D database (named as 3D), and you want to sync only *.db2.gz files from CA-tranche, then:

rsync -L  -a --progress --prune-empty-dirs --include="*/" --include="CA[ABCE][A-D][RM][LMNOP].*.db2.gz" --exclude="*" rsync://files.docking.org/ZINC-3D/CA 3D


  1. special subsets. e.g. metabolites, biogenic

For instance, to get all metabolites in PDBQT format:

rsync -L -a --progress --prune-empty-dirs --include="*/" --include="*.pdbqt.gz" --exclude="*" rsync://files.docking.org/ZINC-special/metabolites zinc

To get all biogenic in SDF format

rsync -L -a --progress --prune-empty-dirs --include="*/" --include="*.sdf.gz" --exclude="*" rsync://files.docking.org/ZINC-special/biogenic zinc

To get all aggregators in DB2 format

rsync -L -a --progress --prune-empty-dirs --include="*/" --include="*.db.gz" --exclude="*" rsync://files.docking.org/ZINC-special/aggregators zinc

To get SMILES and other details:

wget http://files.docking.org/special/current/biogenic/biogenic.info.txt.gz
http://files.docking.org/special/current/metabolites/metabolites.info.txt.gz
http://files.docking.org/special/current/aggregators/aggregators.info.txt.gz