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Notebook improvements #292

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Notebook improvements #292

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3da71e8
add a check to satisfy docstring and method name
mschwoer Jan 29, 2025
75d97a4
add a check for robustness
mschwoer Jan 29, 2025
52f1841
add some comments
mschwoer Jan 29, 2025
9bde390
improve tutorial_basic_definitions.ipynb
mschwoer Jan 29, 2025
314d521
improve unimod_to_tsv.ipynb
mschwoer Jan 29, 2025
f402481
improve link to unimod_to_tsv.ipynb
mschwoer Jan 29, 2025
a27b635
change some wordings and variable names
mschwoer Jan 30, 2025
4d01684
add content again
mschwoer Jan 30, 2025
3b1f33e
Revert "add a check to satisfy docstring and method name"
mschwoer Jan 30, 2025
6c2bc11
Revert "add a check for robustness"
mschwoer Jan 30, 2025
84db157
restore old output
mschwoer Jan 30, 2025
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4 changes: 2 additions & 2 deletions alphabase/constants/aa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ def calc_sequence_masses_for_same_len_seqs(sequence_array: np.ndarray) -> np.nda

def calc_AA_masses_for_var_len_seqs(sequence_array: np.ndarray) -> np.ndarray:
"""
We recommend to use `calc_AA_masses_for_same_len_seqs` as it is much faster.
We recommend to use `calc_AA_masses_for_same_len_seqs` as it is much faster. # TODO it's the same

Parameters
----------
Expand All @@ -175,7 +175,7 @@ def calc_AA_masses_for_var_len_seqs(sequence_array: np.ndarray) -> np.ndarray:
Returns
-------
np.ndarray
1D array of masses, zero values are padded to fill the max length.
1D array of masses, values of 1e8 are used to fill the max length.
"""
return AA_ASCII_MASS[np.array(sequence_array).view(np.int32)].reshape(
len(sequence_array), -1
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