I am also having issues with this line could this be checked into? i tried using jupyter notebooks and google colab but still couldn't get around it
results = align(complexes, method=METHODS["mda"])
this is the error i keep getting when i run the code
AttributeError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_2872/2813988720.py in
----> 1 results = align(complexes, method=METHODS["mda"])
~\anaconda3\envs\introductiontopython\lib\site-packages\opencadd\structure\superposition\api.py in align(structures, method, **kwargs)
40 results = []
41 for mobile in mobiles:
---> 42 result = aligner.calculate([reference, mobile])
43 results.append(result)
44
~\anaconda3\envs\introductiontopython\lib\site-packages\opencadd\structure\superposition\engines\base.py in calculate(self, structures, *args, **kwargs)
29 """
30 assert len(structures) == 2
---> 31 return self._calculate(structures, *args, **kwargs)
32
33 def _calculate(self, structures, *args, **kwargs):
~\anaconda3\envs\introductiontopython\lib\site-packages\opencadd\structure\superposition\engines\mda.py in _calculate(self, structures, *args, **kwargs)
117
118 # Get matching atoms
--> 119 selection, alignment = self.matching_selection(*structures)
120 ref_atoms = ref_universe.select_atoms(selection["reference"])
121 mobile_atoms = mob_universe.select_atoms(selection["mobile"])
~\anaconda3\envs\introductiontopython\lib\site-packages\opencadd\structure\superposition\engines\mda.py in matching_selection(self, reference, mobile)
176 fasta["ref"], fasta["mob"], *_empty = alignment.get_gapped_sequences()
177 fasta.write("temp.fasta")
--> 178 selection = fasta2select(
179 "temp.fasta",
180 ref_resids=ref_resids,
~\anaconda3\envs\introductiontopython\lib\site-packages\opencadd\structure\superposition\sequences.py in fasta2select(fastafilename, ref_resids, ref_segids, target_resids, target_segids, backbone_selection)
115
116 """
--> 117 protein_gapped = Bio.Alphabet.Gapped(Bio.Alphabet.IUPAC.protein)
118 with open(fastafilename) as fasta:
119 alignment = Bio.AlignIO.read(fasta, "fasta", alphabet=protein_gapped)
AttributeError: module 'Bio' has no attribute 'Alphabet'