1
$\begingroup$

I'm trying to access the ZINC15 and ZINC20 databases but I've been at it the whole morning and I can not figure out how to do it. I am not that experienced with programming so maybe there's something obvious I'm missing.

If I try to download larger chunks of data from here, I get all these weird file formats I don't know what to do with. And their website doesn't really have a clear documentation for the API.

Any tips, please ? Thank you in advance !

Update with answer: Nobody really said anything for a while here and in the meantime I found this YouTube video that has a method of downloading the data through powershell. I'm not entirely sure how "formal" thi is but it worked. Hope this helps any programming newbies out there looking for answers.

$\endgroup$
1
  • $\begingroup$ You can certainly add your own answer to your question with the powershell version. $\endgroup$ Commented Dec 23, 2022 at 16:18

1 Answer 1

3
$\begingroup$

It's not too hard. One of the "formats" from ZINC is a script to use curl or wget or Windows PowerShell to download chunks (tranches) of the molecules in the formats you specify.

If you go to ZINC 20 Tranches you can configure what you want along the top (e.g., I chose 3D representations, standard reactivity, wait OK, .. etc.) You can also select or deselect from the table to pick molecular weight or logP fractions.

Then, when you've picked what you want, click on the download button.

Screenshot of ZINC20 Tranch Selection indicating download button

This brings up a new screen with the list of tranches and a place to pick:

  • the molecular format you want (e.g., SMILES, AutoDock, Mol2, or SDF) in gzip-compressed
  • the download type (e.g. curl, wget, or PowerShell commands, etc.)

screenshot of tranch download options

This gives a file like this (in curl syntax):

curl --remote-time --fail --create-dirs -o AA/AAML/AAAAML.xaa.mol2.gz http://files.docking.org/3D/AA/AAML/AAAAML.xaa.mol2.gz
curl --remote-time --fail --create-dirs -o AA/AAMM/AAAAMM.xaa.mol2.gz http://files.docking.org/3D/AA/AAMM/AAAAMM.xaa.mol2.gz
curl --remote-time --fail --create-dirs -o AA/AAMN/AAAAMN.xaa.mol2.gz http://files.docking.org/3D/AA/AAMN/AAAAMN.xaa.mol2.gz
# …

There's more on the ZINC wiki although some may be out-of-date.

$\endgroup$
1
  • $\begingroup$ Thanks for the answer ! I updated the post just now with a Youtube video I found that shows the powershell way of doing this. I found it recently by complete accident while looking up something else. Now I have two ways of doing it ! Excellent ! $\endgroup$
    – apvn
    Commented Dec 22, 2022 at 8:21

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.