cannot import name 'filter_backbone' from 'biotite.structure'

[minhphi1712]

I have attempted to run evodiff with Biotite multiple times, but I am still encountering the same issue. Could you please assist me in resolving this problem? I would greatly appreciate your help. Thank you in advance!

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[18], [line 1](vscode-notebook-cell:?execution_count=18&line=1)
----> [1](vscode-notebook-cell:?execution_count=18&line=1) from evodiff.conditional_generation import inpaint_simple 
      [3](vscode-notebook-cell:?execution_count=18&line=3) sequence = 'DQTERTVRSFEGRRTAPYLDSRNVLTIGYGHLLNRPGANKSWEGRLTSALPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI'
      [4](vscode-notebook-cell:?execution_count=18&line=4) start_idx = 20

File /opt/anaconda3/lib/python3.12/site-packages/evodiff/conditional_generation.py:8
      [6](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/evodiff/conditional_generation.py:6) import torch
      [7](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/evodiff/conditional_generation.py:7) import os
----> [8](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/evodiff/conditional_generation.py:8) import esm.inverse_folding
      [9](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/evodiff/conditional_generation.py:9) from evodiff.utils import Tokenizer, run_omegafold, clean_pdb, run_tmscore #, wrap_dr_bert, read_dr_bert_output
     [10](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/evodiff/conditional_generation.py:10) import pathlib

File /opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:6
      [1](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:1) # Copyright (c) Facebook, Inc. and its affiliates.
      [2](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:2) #
      [3](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:3) # This source code is licensed under the MIT license found in the
      [4](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:4) # LICENSE file in the root directory of this source tree.
----> [6](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:6) from . import gvp_transformer
      [7](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:7) from . import util
      [8](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/__init__.py:8) from . import multichain_util

File /opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/gvp_transformer.py:16
     [12](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/gvp_transformer.py:12) from scipy.spatial import transform
...
---> [12](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/util.py:12) from biotite.structure import filter_backbone
     [13](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/util.py:13) from biotite.structure import get_chains
     [14](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/lib/python3.12/site-packages/esm/inverse_folding/util.py:14) from biotite.sequence import ProteinSequence

ImportError: cannot import name 'filter_backbone' from 'biotite.structure' (/opt/anaconda3/lib/python3.12/site-packages/biotite/structure/__init__.py)
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?13948ed6-d3e8-485a-a3ad-21e5f2822ace) or open in a [text editor](command:workbench.action.openLargeOutput?13948ed6-d3e8-485a-a3ad-21e5f2822ace). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

[codeamt]

I'm not 100% positive but the issue might be associated with Python and PyTorch/dependency version incompatibilities. I notice you are using a conda environment (Python 3.12). The example notebook suggests using Python 3.8. Maybe try downgrading either Python or PyTorch to see if this helps. (Not a repo contributor, but working through the code myself.)