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MIDIfactory / AlphaFastPPi

Fast AlphaFold-Multimer based pipeline for Protein-Protein Interaction (PPI) screening
GNU General Public License v3.0
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Cannot import get_run_alphafold, while running AlphaFastPPI.py #1

Closed soderling-lab closed 4 months ago

soderling-lab commented 4 months ago

We are having some trouble running AlphaFastPPI.py, I have the alphafold databases installed, and the monomer objects created with create_individual_features.py. However, I am consistently encountering this error:

(AlphaFastPPi) a05-ppXXXXXX@a05-duke01:~/AlphaFastPPi$ python AlphaFastPPi.py --mode all_vs_all -l proteins.txt -d alphafold_non_docker/ -m alphapulldown/output -o ppitoutput
2024-06-18 15:33:46.988600: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Traceback (most recent call last):
  File "/home/a05-ppXXXXXX/AlphaFastPPi/AlphaFastPPi.py", line 15, in <module>
    from alphapulldown.utils import get_run_alphafold
ImportError: cannot import name 'get_run_alphafold' from 'alphapulldown.utils' (/home/a05-ppXXXXXX/AlphaFastPPi/alphapulldown/utils/__init__.py)

Even with the Python path set: /home/a05-ppXXXXXX/AlphaFastPPi

I have moved the necessary folders into AlphaFastPPi, so I am not sure where the problem could be

(AlphaFastPPi) a05-ppXXXXXX@a05-duke01:~/AlphaFastPPi$ ls
AlphaFastPPi.py  AlphaPPI.png  LICENSE      README.md  alphafold_non_docker  alphapulldown.zip  manuals       setup.cfg  soderlinglab
AlphaLink2       ColabFold     MANIFEST.in  alphafold  alphapulldown         docker             proteins.txt  setup.py   test
(AlphaFastPPi) a05-ppXXXXXX@a05-duke01:~/AlphaFastPPi$

I appreciate help! Thank you.