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Graylab / IgFold

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
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Error: AbNumber not installed. Please install AbNumber to use renumbering #35

Open suhailislam opened 1 year ago

suhailislam commented 1 year ago

We have installed IgFold (RedHat 7) following the instructions on GitHub and Anaconda Python 3.9.13. Testing with below example from Git. abnumber is definitely installed (works: python -c 'import abnumber'). However running (python ig-test.py) below we get error "Error: AbNumber not installed. Please install AbNumber to use renumbering".

igtest.py

from igfold import IgFoldRunner sequences = { "H": "QVQLQESGGGLVQAGGSLTLSCAVSGLTFSNYAMGWFRQAPGKEREFVAAITWDGGNTYYTDSVKGRFTISRDNAKNTVFLQMNSLKPEDTAVYYCAAKLLGSSRYELALAGYDYWGQGTQVTVS" } pred_pdb = "my_nanobody.pdb" igfold = IgFoldRunner() igfold.fold( pred_pdb, # Output PDB file sequences=sequences, # Nanobody sequence do_refine=False, # Refine the antibody structure with PyRosetta do_renum=True, # Renumber predicted antibody structure (Chothia) )

Thank you

yshen25 commented 7 months ago

@suhailislam I hade the same issue and fixed it by upgrading numpy and pandas. The error message is misleading. The line of code that caused error is if do_renum: try: from igfold.utils.abnumber_ import renumber_pdb except: exit("AbNumber not installed. Please install AbNumber to use renumbering.") The real issue is at the bottom of chain of imports: from pandas.compat.numpy import is_numpy_dev as _is_numpy_dev As the real error message indicates, the real issue is that the pandas version doesn't match the numpy version.