File "/home/misha/anaconda3/lib/python3.6/site-packages/abpytools/core/chain.py", line 71, in load_from_string
new_chain.load()
File "/home/misha/anaconda3/lib/python3.6/site-packages/abpytools/core/chain.py", line 92, in load
self.load()
File "/home/misha/anaconda3/lib/python3.6/site-packages/abpytools/core/chain.py", line 101, in load
self.hydrophobicity_matrix = self.ab_hydrophobicity_matrix()
File "/home/misha/anaconda3/lib/python3.6/site-packages/abpytools/core/chain.py", line 217, in ab_hydrophobicity_matrix
sequence=self._sequence)
File "/home/misha/anaconda3/lib/python3.6/site-packages/abpytools/core/chain.py", line 434, in calculate_hydrophobicity_matrix
else 0 for x in whole_sequence])
File "/home/misha/anaconda3/lib/python3.6/site-packages/abpytools/core/chain.py", line 434, in <listcomp>
else 0 for x in whole_sequence])
KeyError: 'X'
We've got an error while stopping in post-mortem: <class 'KeyboardInterrupt'>
Error is thrown in code below:
def calculate_hydrophobicity_matrix(whole_sequence, numbering, aa_hydrophobicity_scores, sequence):
# instantiate numpy array (whole sequence includes all the amino acid positions of the VH/VL,
# even the ones
# that aren't occupied -> these will be filled with zeros
# hydrophobicity_matrix = np.zeros(len(whole_sequence))
# #
# # # iterate through each position
# for i, position in enumerate(whole_sequence):
#
# if position in numbering:
# position_in_data = numbering.index(position)
# hydrophobicity_matrix[i] = aa_hydrophobicity_scores[sequence[position_in_data]]
# return hydrophobicity_matrix
# same thing as above but in a comprehension list
return np.array([aa_hydrophobicity_scores[sequence[numbering.index(x)]] if x in numbering
else 0 for x in whole_sequence])
seems that your "comprehension list" approach contains a bug
Error is thrown in code below:
seems that your "comprehension list" approach contains a bug