I wish to download the natural products from ZINC database (https://zinc.docking.org) with wget command:
wget 'https://zinc.docking.org/substances/subsets/natural-products.mol2?count=all'
but some message comes out before the download is finished:
--2020-03-21 09:44:41-- https://zinc.docking.org/substances/subsets/natural-products.mol2?count=all Resolving zinc.docking.org (zinc.docking.org)... 169.230.26.43 Connecting to zinc.docking.org (zinc.docking.org)|169.230.26.43|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [chemical/x-mol2] Saving to: ‘natural-products.mol2?count=all’ [ ] 743,110 10.5KB/s in 67s 2020-03-21 09:45:52 (10.8 KB/s) - Read error at byte 743110 (Success).Retrying. --2020-03-21 09:45:53-- (try: 2) https://zinc.docking.org/substances/subsets/natural-products.mol2?count=all Connecting to zinc.docking.org (zinc.docking.org)|169.230.26.43|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [chemical/x-mol2] Saving to: ‘natural-products.mol2?count=all’ [ ] 0 --.-K/s in 0s Cannot write to ‘natural-products.mol2?count=all’ (Success).
Only a small part of the expected file is downloaded. I have tried to add some options of wget such as "--timeout==", etc, but nothing works.
Then I try to use curl to download the file:
curl -O 'https://zinc.docking.org/substances/subsets/natural- products.mol2?count=all' > natural-products.mol2
This also downloads a small part of the expected file but gives an error information:
curl: (18) transfer closed with outstanding read data remaining
Is it caused by network failure or the library itself? Could you help me solve the problem and download the complete file? I will appreciate any help.
To download a library in 2D, use the tranche browser by clicking on Tranches in the navigation bar. Across the top of the page the following tools are available:
- Representation selector: 2D or 3D
- Reactivity selector: Anodyne, Clean, Mild, Reactive, Unstable. Default Mild (ZINC12 default)
Please note: curation of patterns is ongoing and will change in the coming months. In particular, the Reactive and Unstable annotations have not yet been properly curated
- Purchasability selector: In Stock, Agent, On Demand, Boutique, Annotated. Default On Demand (ZINC12 default).
Reactivity and purchasability are by default cumulative selectors. To select compounds that are only a the specified level, toggle the exclusive option at the bottom of each popup.
- pH : only applies in 3D
- Charge: only applies in 3D
- Predefined subsets: rapid selection of common subsets. Looks like a 3x3 array.
- Download button, when all other choices have been made. Options are:
- format: SMILES or txt.
- method: curl, wget, urls. default is raw URLs.
- To select just "lead like" compounds, use the predefined subsets selector, which looks like a 3x3 array of dots.
- Click on the download tool (top right). Default is mild reactivity (includes aldhydes, michael acceptors and PAINS). Default purchasability is On demand, as it was in ZINC12.
- Click on Download.
Note: This downloads a script which allows you to get the molecules. The script must be run to get the molecules.
We hope this has given you some idea of how to get started with ZINC15. Good luck!
Source : http://wiki.docking.org/index.php/ZINC15:Getting_started
Hello Joseph Schapira,
Thank you for your explanation.
I download a csh script (usual.mol.csh, http://zinc12.docking.org/db/byvendor/acdiscnp/usual.mol2.csh) from zinc 12. I think I can download the mol2 file for natural products provided by the AnalytiCon Discovery NP (http://zinc12.docking.org/browse/catalogs/natural-products).
This csh script reads:
#!/bin/csh -f
# usual.mol2.csh from http://zinc.docking.org
# Run this script to download ZINC
# Requires curl (default) or wget, http://wget.docking.org
#
# Thus, to run this script
# using curl, do: csh usual.mol2.csh
# using wget, do: csh usual.mol2.csh wget
#
setenv base http://zinc.docking.org/db/byvendor/acdiscnp
setenv fn .zinc.$$
cat 0) then
wget --base=$base -i < $fn
else
foreach i (`cat $fn`)
curl --url $base/$i -o $i
end
endif
rm -f $fn
# File created on Sun Feb 17 14:59:41 PST 2013
# This is the end of the csh script.
My shell is bash rather than csh. Could you tell me how to rewrite this csh script into a bash one? Thank you again
Best regards.
Thanks, Joseph Schapira, for your valuable inputs. My question is after downloading large datasets from ZINC, how to stratify these ligand sets according to Lipinski Rule of five? Are there any available tools for that?
Thanks in advance
Hi, you can use this article
Article ZINC 15 - ligand discovery for everyone
- Badges
- Science topic
- Similar topics
- Filing