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google-deepmind / alphafold

Open source code for AlphaFold 2.
Apache License 2.0
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ImportError: cannot import name 'SCOPData' from 'Bio.Data' #885

Open lx19930 opened 10 months ago

lx19930 commented 10 months ago

When using ColabFold an error occured when importing packages: ImportError: cannot import name 'SCOPData' from 'Bio.Data' image

yamule commented 10 months ago

I think issues about ColabFold can be discussed in https://twitter.com/sokrypton/status/1553733908189028353 If my understanding of the conversation on the server is correct, (I am not using ColabFold so much) ・The issue has been fixed in the latest version. ・Or installing Biopython as version 1.81 will also fix the issue.

scw0101001 commented 10 months ago

I guess your Biopython version < 1.78, just try Biopython version >= 1.78.

PIGGS-BOSON commented 9 months ago

Hi I am new to codes but I would like to use Alphafold to predict some of my proteins. I met the same problem. I used the same software online and tried to run a "pip install biopython==1.81" on VSCode terminal on my computer, but nothing changed. This error information is still given. What should I do?

yamule commented 9 months ago

I used the same software online and tried to run a "pip install biopython==1.81" on VSCode terminal on my computer, but nothing changed.

Is your VSCode terminal attached to online environment? If it isn't, nothing will affect to the online software (Colab).

Google How to pip install Google Colab.

(The Colab notebook may insist restarting the runtime after pip.)

sherryliu987 commented 9 months ago

If you're struggling to install AlphaFold locally, feel free to try https://www.tamarind.bio/alphafold, a website which offers a no-code interface for bioinformatics tools including protein structure prediction with AlphaFold for free.

psp3dcg commented 5 months ago

Hi I am new to codes but I would like to use Alphafold to predict some of my proteins. I met the same problem. I used the same software online and tried to run a "pip install biopython==1.81" on VSCode terminal on my computer, but nothing changed. This error information is still given. What should I do?

I changed biopython version from 1.83 to 1.79 and it worked. Maybe you can install biopython=1.79 and see what happens.

firsc commented 1 month ago

Biopython has deprecated SCOPData in favor of PDBData since 1.82 (see warning in SCOPData.py).

If you don't want to stay at Biopython 1.81 or lower, simply change the line from Bio.Data import SCOPData to from Bio.Data import PDBData inside alphafold/data/mmcif_parsing.py