Rsyncing zinc15: Difference between revisions
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# Example (download 3D): | # 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: | 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 --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 --delete-excluded --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 14:21, 29 April 2020
A few examples below: This is how you set up a ZINC Mirror. I am looking at you Uppsala, Beijing, and Kiev.
- what is available?
rsync --list-only rsync://files.docking.org
- download 2D
rsync -L -a --progress --include="[ABCDEFG][A-G]*.smi" --exclude="[HIJK]*" rsync://files.docking.org/ZINC-2D/ zinc
- download 3D
rsync -L -a --progress --include="[ABCDEFG][A-G]*.db2.gz" --exclude="[HIJK]*" rsync://files.docking.org/ZINC-3D/ zinc
- 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 --delete-excluded --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