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PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
89 stars 16 forks source link

ctest failures #47

Open meh47336 opened 3 days ago

meh47336 commented 3 days ago

Hello,

I've installed all dependencies which took a while and am now on the ctest step of alphafill.

When I run ctest --test-dir build the first test is successful then the next two (run_process and validation) fail.

The cause of failure of the second test is that AlphaFill can't seem to find or load the mmcif_pdbx dictionary. I've downloaded and installed mmcif_pdbx. Then I realized from googling that mmcif_pdbx.dic is actually found in libcifpp/rsrc and I confirmed this locally.

Any idea how I can direct alphafill to the dictionary or why it's not detecting it?

Specs: Rock Linux 9.2 boost 1.78 cmake 3.30 gcc and gxx 11.3.1 make 4.4.1 mmcif-pdbx 2.0.1 libcifpp, libmcfp, and libzeep were cloned and installed today (9/17/24, so should be updated versions)

Thanks for any help,

mhekkel commented 3 days ago

Alphafill uses libcifpp. And libcifpp attempts to load the dictionary from a 'resource'. That is, if you use mrc, then this dictionary will be built in in the executable. If you do not use mrc, you will have to install libcifpp first and make sure this is done correctly. Alternatively, you can specify resource locations using an environment variable.

Please read this related documentation: https://www.hekkelman.net/libcifpp-doc/resources.html

meh47336 commented 1 day ago

I removed libcifpp and performed the installation as described on the libcifpp page. The only difference between this time and last time was using ccmake. Anyway, AlphaFill is now finding everything, is installed, and passing the tests.

Thanks!