zinc-downloader

Reproducible and scriptable downloader for ZINC tranches. zincdl allows reconstruction of ZINC tranche codes from property subsets, retrieval of corresponding download URLs, and batch file download from the public ZINC repository.

Relevant links

• ZINC tranche browser (ZINC20) – where tranches are browsable
• ZINC static files – source of downloadable tranche data
• ZINC Wiki – background on tranche organization

⚠️ Note zincdl is an independent open-source utility for ZINC data access, and not affiliated with or maintained by the Irwin Lab @ UCSF. This tool only automates access to publicly available ZINC files and does not redistribute any data. Please avoid excessive parallel downloads.

🔧 Installation

$ pip install zincdl

Usage

You can generate tranche codes and corresponding URLs for arbitrary property selections, and optionally download them. Note: using predefined subsets (via subset in generate_urls or --subset in CLI) yields the highest chance of successful downloads.

Python API

from zincdl import generate_urls
from zincdl.download import download_tranches

# Generate tranche URLs from an MW × logP region
urls = generate_urls(
    mw=[300, 325],
    logp=[2, 3],
    fmt="mol2",
)

print(urls)
# [
#   'https://files2.docking.org/3D/CD/EBRN/CDEBRN.xaa.mol2.gz',
#   'https://files2.docking.org/3D/CF/EBRN/CFEBRN.xaa.mol2.gz',
#   ...
# ]

# Download into a local directory
download_tranches(urls, out_dir="my_zinc")

CLI

# Show help
zincdl --help

# Preview tranche URLs (no download)
zincdl --mw 300,325 --logp 2,3 --fmt smi

# Download predefined subsets
zincdl --subset fragments --fmt mol2 --download --out-dir downloads/fragments
zincdl --subset leadlike --fmt smi --download --out-dir downloads/leadlike

# Include charge, pH, and reactivity filters
zincdl --subset druglike --charge 1 --fmt sdf --download --out-dir downloads/druglike_cationic

Citation

Please cite ZINC20 when using downloaded data:

Irwin, J. J.; Tang, K. G.; Young, J.; Dandarchuluun, C.; Wong, B. R.; Khurelbaatar, M.; Moroz, Y. S.; Mayfield, J.; Sayle, R. A. ZINC20 — A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J. Chem. Inf. Model. 2020, 60, 6065–6073. https://doi.org/10.1021/acs.jcim.0c00675