Multiple ModuleNotFoundError
kierandidi opened this issue · 1 comments
Hi,
similar to issue 22, when I want to run the script af2_metrics.py, I get the following ModuleNotFoundError:
Traceback (most recent call last):
File "/home/kieran/RFDesign/hallucination/tests/../../scripts/af2_metrics.py", line 34, in <module>
from alphafold.common import protein
File "/home/kieran/RFDesign/scripts/../hallucination/models/alphafold/alphafold/common/protein.py",
line 20, in <module>
from Bio.PDB import PDBParser
ModuleNotFoundError: No module named 'Bio'
I also had the tree error from issue 22 before, but this one popped up after I installed tree.
I solved it by running pip install biopython, but for reproducibility, it might be useful to include biopython in the environment file.
After that got another one:
File "/home/kieran/RFDesign/hallucination/tests/../../scripts/af2_metrics.py", line 35, in <module>
from alphafold.data import pipeline
File "/home/kieran/RFDesign/scripts/../hallucination/models/alphafold/alphafold/data/pipeline.py",
line 19, in <module>
from absl import logging
ModuleNotFoundError: No module named 'absl'
Fixed this one via pip install absl-py. If I am correct this was not included in the .yaml file either right?
A third one:
Traceback (most recent call last):
File "/home/kieran/RFDesign/hallucination/tests/../../scripts/af2_metrics.py", line 37, in <module>
from alphafold.model import data
File "/home/kieran/RFDesign/scripts/../hallucination/models/alphafold/alphafold/model/data.py", line 20, in <module>
from alphafold.model import utils
File "/home/kieran/RFDesign/scripts/../hallucination/models/alphafold/alphafold/model/utils.py", line 21, in <module>
import haiku as hk
ModuleNotFoundError: No module named 'haiku'
After that quite a few others came up (fixes listed below):
- pip install dm-haiku
- pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
(from: https://github.com/google/jax#installation) - pip install ml-collections
- pip install tensorflow
- conda install -c conda-forge pdbfixer
- pip install torch
Currently I get the error ModuleNotFoundError: No module named 'simtk.openmm.app.internal'.
Before I continue down the rabbit hole: did I miss some installation files here or are these dependencies just not documented?
All the best,
Kieran