Multiple ModuleNotFoundError

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

RosettaCommons / RFDesign

Multiple ModuleNotFoundError #33