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It looks like the issue you're having is stemming from something within the OpenCadd library? MDTraj doesn't support Perhaps you'll find an answer opening an issue there? |
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Hello Everyone,
I am learning by running some tutorials. I am supposed to run
results = align(complexes, method=METHODS["mda"])
, where complexes are PDBs structures with ligands. I am having the following error;AttributeError Traceback (most recent call last)
in <cell line: 1>()
----> 1 results = align(complexes, method=METHODS["mda"])
4 frames
/usr/local/lib/python3.10/dist-packages/opencadd/structure/superposition/sequences.py in fasta2select(fastafilename, ref_resids, ref_segids, target_resids, target_segids, backbone_selection)
113
114 """
--> 115 protein_gapped = Bio.Alphabet.Gapped(Bio.Alphabet.IUPAC.protein)
116 with open(fastafilename) as fasta:
117 alignment = Bio.AlignIO.read(fasta, "fasta", alphabet=protein_gapped)
AttributeError: module 'Bio' has no attribute 'Alphabet'
Would you please guide me, how to address this issue of alphabet?
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