Foldcomp database download fails on HPC (connection error)

[ShawnGao911101]

Hi there,

I am writing to report an issue I encountered when using Foldcomp to download AlphaFold databases, and to ask for guidance on the recommended workflow in HPC environments.

I am running Foldcomp on a Linux HPC cluster where compute nodes do not have outbound internet access. When executing:

import foldcomp
foldcomp.setup("afdb_swissprot_v4")
the download fails with the following error:

httpcore.ConnectError: All connection attempts failed
httpx.ConnectError: All connection attempts failed
From the traceback, it appears that foldcomp.setup() performs an online HTTP HEAD request to check file size, which is blocked in our environment.

I would greatly appreciate your advice on the following points:

Is there an official way to manually download Foldcomp databases (e.g. on a login node or external machine) and then use them locally?

What is the expected directory structure so that Foldcomp can recognize a pre-downloaded database without calling setup()?

Is there a way to disable or bypass the online connectivity check and directly point Foldcomp to a local database path?

Do you have any recommended practices for running Foldcomp on HPC systems without internet access?

Foldcomp is extremely valuable for large-scale protein structure analysis, and we would very much like to integrate it into our local pipelines.

Thank you very much for your time and for developing such a useful tool.

Best regards,
Shang Gao
Institute of Crop Sciences,
Chinese Academy of Agricultural Sciences

[milot-mirdita]

Could you try if the latest foldcomp git commit fixes the issue for you please:

pip install "foldcomp @ git+https://github.com/steineggerlab/foldcomp.git"

Only setup and setup_async try to initiate internet connection to download something. What is (now) does is download files from: https://opendata.mmseqs.org/foldcomp, you can download these files also separately and point foldcomp to them.

The previous URL we used (that i now replaced) has known issues with China, as Cloudflare is commonly blocked.

[ShawnGao911101]

@milot-mirdita Many thanks. The amazon one works good. I'm downloading the files separately. Kind regards. -Shang

[milot-mirdita]

Does the python setup also work?

[ShawnGao911101]

Successfully built foldcomp
Installing collected packages: foldcomp
Successfully installed foldcomp-0.1.0
(base) gaoshang@slurmctld:~$ python
Python 3.13.9 | packaged by Anaconda, Inc. | (main, Oct 21 2025, 19:16:10) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import foldcomp
foldcomp.setup('c_albicans')

@milot-mirdita
works well. but quite sllow.
Nice job anyway.