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HWaymentSteele / AF_Cluster

Predict multiple protein conformations using sequence clustering and AlphaFold2.
MIT License
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import error in AF_cluster colab notebook #12

Open palvinaveen opened 8 months ago

palvinaveen commented 8 months ago

Hi, while executing the colab notebook following error is coming ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/init.py) could you help me out why it cannot import SCOPData in colab notebook. ImportError: cannot import name 'SCOPData' from 'Bio Data

ImportError Traceback (most recent call last) in <cell line: 17>() 15 16 from alphafold.model import model, config, data ---> 17 from alphafold.data import parsers, pipeline 18 from alphafold.common import protein 19

2 frames /content/alphafold/alphafold/data/mmcif_parsing.py in 22 from absl import logging 23 from Bio import PDB ---> 24 from Bio.Data import SCOPData 25 26 # Type aliases:

ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/init.py)

Thank you Best Naveen

hiyata commented 8 months ago

Hi @palvinaveen the package is depreciated, but I was able to solve this by uninstalling biopython and reinstalling an older version. I made two cells.

First:

!pip uninstall biopython

Next:

!pip install http://biopython.org/DIST/biopython-1.81.tar.gz

Restart the runtime when prompted and then the cell should run!

AhmedHassanin-IPB commented 7 months ago

I did the same with older version of biopython==1.78, and now is working.