charlesbeattie
commented
1 week ago I think it may be not finding the module and instead finding the local directory /app/alphafold/alphafold3
I'm not sure why that directory is there from the current docker setup.
Can you print out the output of listing the venv site-package?
docker run -it alphafold3 ls /alphafold3_venv/lib/python3.11/site-packages/alphafold3It should contain a file named cpp.cpython-311-x86_64-linux-gnu.so which is built during the pip install.
If that file is present then the run_alphafold.py is finding the directory /app/alphafold/alphafold3 instead of the one installed in the venv.
Can you remove folder alphafold3 from /app/alphafold/ in your docker image?
Augustin-Zidek
I have performed all the steps in the installation documentation. After completing build of the docker container, upon running the suggested example to test the setup I obtain the following error traceback message:
Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 39, in
from alphafold3.common import folding_input
File "/app/alphafold/alphafold3/common/folding_input.py", line 23, in
from alphafold3 import structure
File "/app/alphafold/alphafold3/structure/init.py", line 14, in
from alphafold3.structure.bioassemblies import BioassemblyData
File "/app/alphafold/alphafold3/structure/bioassemblies.py", line 18, in
from alphafold3.structure import mmcif
File "/app/alphafold/alphafold3/structure/mmcif.py", line 24, in
from alphafold3.constants import chemical_components
File "/app/alphafold/alphafold3/constants/chemical_components.py", line 20, in
from alphafold3.cpp import cif_dict
ModuleNotFoundError: No module named 'alphafold3.cpp'
I have also tried to perform the installation locally without the need to use docker, and get the same error when launching run_alphafold.py.