A command line tool for downloading 3D structures of small chemical molecules from http://zinc.docking.org.
An input file is just a simple 1-column text file of ZINC codes, e.g.,
ZINC08714378
ZINC59339553
ZINC67643437
ZINC05481096
By executing the following line, all ZINC codes from an input file ids.txt are queried and
the molecular structures are downloaded as individual files or a multi-structure file.
For example, a single multi-structure SDF file is created by executing the following code:
> python zinc_downloader.py -i ./ids.txt -o ./zinc.sdf --filetype sdf
Downloading ZINC Molecules
0% 100%
[#### ] | ETA[sec]: 31.431 | Item ID: ZINC54810967
The PDB Info Table tool was tested in Python 3.4 and Python 2.7. The required packages
beautifulsoup4>=4.4.0
lxml>=3.4.4
PyPrind>=2.9.3
can be downloaded and installed via pip
pip install -r requirements.txt
> python zinc_downloader.py -h
usage: zinc_downloader.py [-h] [-i INPUT] [-o OUTPUT_FILE] [-d OUTPUT_DIR]
[-f FILETYPE] [-v]
A command line tool for downloading 3D structures of small chemical molecules from http://zinc.docking.org.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
One-column text file with ZINC codes
-o OUTPUT_FILE, --output_file OUTPUT_FILE
Filename for creating a single output file
-d OUTPUT_DIR, --output_dir OUTPUT_DIR
Directory name for saving multiple output files
-f FILETYPE, --filetype FILETYPE
Filetype set(['smiles', 'sdf', 'flexibase', 'mol2']), default=mol2
-v, --version show program's version number and exit
Example run:
./zinc_downloader.py -i ./examples/ids.txt -o ./examples/1file.mol2
Example input file:
ZINC08714378
ZINC59339553
ZINC67643437
[...]
- v1.0 2015-09-05