Fixed import conflict from deprecated biotite function needed by ESM #1
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Current version of Colab notebook
stab_ESM_IF.ipynbcrashes during the first import step:`installing libs...
installing esmfold...
downloading params...
ImportError Traceback (most recent call last)
in
/usr/local/lib/python3.10/dist-packages/esm/inverse_folding/init.py in
4 # LICENSE file in the root directory of this source tree.
5
----> 6 from . import gvp_transformer
7 from . import util
8 from . import multichain_util
2 frames
/usr/local/lib/python3.10/dist-packages/esm/inverse_folding/util.py in
10 from biotite.structure.io import pdbx, pdb
11 from biotite.structure.residues import get_residues
---> 12 from biotite.structure import filter_backbone
13 from biotite.structure import get_chains
14 from biotite.sequence import ProteinSequence
ImportError: cannot import name 'filter_backbone' from 'biotite.structure' (/usr/local/lib/python3.10/dist-packages/biotite/structure/init.py)`
Looking at the Biotite API, this function was deprecated with the 1.0 (current) release. To fix this, the pip install command for biotite needs to be changed to explicitly request the old version:
os.system(f"pip install biotite==0.41")I have tested this on 10x input structures and it now seems to work as intended. Thanks for making this project open source and user-friendly!