alphabase 1.2.2__tar.gz → 1.2.4__tar.gz

{alphabase-1.2.2/alphabase.egg-info → alphabase-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: alphabase
-Version: 1.2.2
+Version: 1.2.4
 Summary: An infrastructure Python package of the AlphaX ecosystem
 Home-page: https://github.com/MannLabs/alphabase
 Author: Mann Labs
@@ -37,6 +37,8 @@ Requires-Dist: regex
 Requires-Dist: dask
 Requires-Dist: dask_expr
 Requires-Dist: pyahocorasick
+Requires-Dist: pyteomics
+Requires-Dist: lxml
 Requires-Dist: pywin32; sys_platform == "win32"
 Provides-Extra: development-stable
 Requires-Dist: jupyter; extra == "development-stable"
@@ -44,7 +46,6 @@ Requires-Dist: twine; extra == "development-stable"
 Requires-Dist: bumpversion; extra == "development-stable"
 Requires-Dist: pipdeptree; extra == "development-stable"
 Requires-Dist: ipykernel; extra == "development-stable"
-Requires-Dist: nbdev; extra == "development-stable"
 Requires-Dist: pyteomics; extra == "development-stable"
 Requires-Dist: scikit-learn; extra == "development-stable"
 Requires-Dist: matplotlib; extra == "development-stable"
@@ -69,13 +70,14 @@ Requires-Dist: regex; extra == "development-stable"
 Requires-Dist: pydivsufsort; extra == "development-stable"
 Requires-Dist: pyahocorasick; extra == "development-stable"
 Requires-Dist: pytest; extra == "development-stable"
+Requires-Dist: pre-commit==3.7.0; extra == "development-stable"
+Requires-Dist: nbmake==1.5.3; extra == "development-stable"
 Provides-Extra: development
 Requires-Dist: jupyter; extra == "development"
 Requires-Dist: twine; extra == "development"
 Requires-Dist: bumpversion; extra == "development"
 Requires-Dist: pipdeptree; extra == "development"
 Requires-Dist: ipykernel; extra == "development"
-Requires-Dist: nbdev; extra == "development"
 Requires-Dist: pyteomics; extra == "development"
 Requires-Dist: scikit-learn; extra == "development"
 Requires-Dist: matplotlib; extra == "development"
@@ -100,6 +102,8 @@ Requires-Dist: regex; extra == "development"
 Requires-Dist: pydivsufsort; extra == "development"
 Requires-Dist: pyahocorasick; extra == "development"
 Requires-Dist: pytest; extra == "development"
+Requires-Dist: pre-commit; extra == "development"
+Requires-Dist: nbmake; extra == "development"
 Provides-Extra: stable
 Requires-Dist: numba; extra == "stable"
 Requires-Dist: numpy; extra == "stable"
@@ -116,6 +120,8 @@ Requires-Dist: regex; extra == "stable"
 Requires-Dist: dask; extra == "stable"
 Requires-Dist: dask_expr; extra == "stable"
 Requires-Dist: pyahocorasick; extra == "stable"
+Requires-Dist: pyteomics; extra == "stable"
+Requires-Dist: lxml; extra == "stable"
 
 # AlphaBase
 
@@ -315,6 +321,20 @@ For an even more interactive participation, check out the
 [discussions](https://github.com/MannLabs/alphabase/discussions) and the
 [the Contributors License Agreement](misc/CLA.md).
 
+### Notes for developers
+#### pre-commit hooks
+It is highly recommended to use the provided pre-commit hooks, as the CI pipeline enforces all checks therein to
+pass in order to merge a branch.
+
+The hooks need to be installed once by
+```bash
+pre-commit install
+```
+You can run the checks yourself using:
+```bash
+pre-commit run --all-files
+```
+
 ------------------------------------------------------------------------
 
 ## Changelog

{alphabase-1.2.2 → alphabase-1.2.4}/README.md

@@ -196,6 +196,20 @@ For an even more interactive participation, check out the
 [discussions](https://github.com/MannLabs/alphabase/discussions) and the
 [the Contributors License Agreement](misc/CLA.md).
 
+### Notes for developers
+#### pre-commit hooks
+It is highly recommended to use the provided pre-commit hooks, as the CI pipeline enforces all checks therein to
+pass in order to merge a branch.
+
+The hooks need to be installed once by
+```bash
+pre-commit install
+```
+You can run the checks yourself using:
+```bash
+pre-commit run --all-files
+```
+
 ------------------------------------------------------------------------
 
 ## Changelog

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphabase"
-__version__ = "1.2.2"
+__version__ = "1.2.4"
 __license__ = "Apache"
 __description__ = "An infrastructure Python package of the AlphaX ecosystem"
 __author__ = "Mann Labs"

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/cli.py

@@ -1,2 +1,2 @@
 def run(*args, **kwargs):
-    pass
+    pass

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/constants/_const.py

@@ -3,21 +3,16 @@ import numpy as np
 
 from alphabase.yaml_utils import load_yaml
 
-CONST_FILE_FOLDER = os.path.join(
-    os.path.dirname(__file__),
-    "const_files"
-)
+CONST_FILE_FOLDER = os.path.join(os.path.dirname(__file__), "const_files")
 
-common_const_dict:dict = load_yaml(
+common_const_dict: dict = load_yaml(
     os.path.join(CONST_FILE_FOLDER, "common_constants.yaml")
 )
 
-# Only applied in peak and fragment dataframes to save RAM. 
+# Only applied in peak and fragment dataframes to save RAM.
 # Using float32 still keeps 0.1 ppm precision in any value range.
 # Default float dtype is "float64" for value calculation and other senarios.
-PEAK_MZ_DTYPE:np.dtype = np.dtype(
-    common_const_dict["PEAK_MZ_DTYPE"]
-).type
-PEAK_INTENSITY_DTYPE:np.dtype = np.dtype(
+PEAK_MZ_DTYPE: np.dtype = np.dtype(common_const_dict["PEAK_MZ_DTYPE"]).type
+PEAK_INTENSITY_DTYPE: np.dtype = np.dtype(
     common_const_dict["PEAK_INTENSITY_DTYPE"]
-).type
+).type

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/constants/aa.py

@@ -5,30 +5,30 @@ import typing
 
 from alphabase.yaml_utils import load_yaml
 
-from alphabase.constants.element import (
-    calc_mass_from_formula, 
-    MASS_H2O, parse_formula,
-    reset_elements
+from alphabase.constants.atom import (
+    calc_mass_from_formula,
+    MASS_H2O,
+    parse_formula,
+    reset_elements,
 )
 
 from alphabase.constants._const import CONST_FILE_FOLDER
 
 # We use all 128 ASCII code to represent amino acids for flexible extensions in the future.
-# The amino acid masses are stored in 128-lengh array :py:data:`AA_ASCII_MASS`. 
+# The amino acid masses are stored in 128-lengh array :py:data:`AA_ASCII_MASS`.
 # If an ASCII code is not in `AA_Formula`, the mass will be set as a large value to disable MS search.
-AA_Formula:dict = load_yaml(
-    os.path.join(CONST_FILE_FOLDER, 'amino_acid.yaml')
-)
+AA_Formula: dict = load_yaml(os.path.join(CONST_FILE_FOLDER, "amino_acid.yaml"))
 #: AA mass array with ASCII code, mass of 'A' is AA_ASCII_MASS[ord('A')]
-AA_ASCII_MASS:np.ndarray = np.ones(128)*1e8
+AA_ASCII_MASS: np.ndarray = np.ones(128) * 1e8
 
 #: 128-len AA dataframe
-AA_DF:pd.DataFrame = pd.DataFrame()
+AA_DF: pd.DataFrame = pd.DataFrame()
 
 # AA formula to formula dict of dict. For example: {'K': {'C': n, 'O': m, ...}}
-AA_Composition:dict = {}
+AA_Composition: dict = {}
+
 
-def replace_atoms(atom_replace_dict:typing.Dict):
+def replace_atoms(atom_replace_dict: typing.Dict):
     for aa, formula in list(AA_Formula.items()):
         atom_comp = dict(parse_formula(formula))
         for atom_from, atom_to in atom_replace_dict.items():
@@ -37,58 +37,66 @@ def replace_atoms(atom_replace_dict:typing.Dict):
                 del atom_comp[atom_from]
         AA_Formula[aa] = "".join([f"{atom}({n})" for atom, n in atom_comp.items()])
 
-def reset_AA_mass()->np.ndarray:
+
+def reset_AA_mass() -> np.ndarray:
     """AA mass in np.array with shape (128,)"""
     global AA_ASCII_MASS
     for aa, chem in AA_Formula.items():
         AA_ASCII_MASS[ord(aa)] = calc_mass_from_formula(chem)
     return AA_ASCII_MASS
+
+
 reset_AA_mass()
 
+
 def reset_AA_df():
     global AA_DF
     AA_DF = pd.DataFrame()
-    AA_DF['aa'] = [chr(aa) for aa in range(len(AA_ASCII_MASS))]
-    AA_DF['formula'] = ['']*len(AA_ASCII_MASS)
+    AA_DF["aa"] = [chr(aa) for aa in range(len(AA_ASCII_MASS))]
+    AA_DF["formula"] = [""] * len(AA_ASCII_MASS)
     aa_idxes = []
     formulas = []
     for aa, formula in AA_Formula.items():
         aa_idxes.append(ord(aa))
         formulas.append(formula)
-    AA_DF.loc[aa_idxes, 'formula'] = formulas
-    AA_DF['mass'] = AA_ASCII_MASS
+    AA_DF.loc[aa_idxes, "formula"] = formulas
+    AA_DF["mass"] = AA_ASCII_MASS
     return AA_DF
+
+
 reset_AA_df()
 
+
 def reset_AA_Composition():
     global AA_Composition
     AA_Composition = {}
     for aa, formula, mass in AA_DF.values:
-        AA_Composition[aa] = dict(
-            parse_formula(formula)
-        )
+        AA_Composition[aa] = dict(parse_formula(formula))
     return AA_Composition
+
+
 reset_AA_Composition()
 
-def reset_AA_atoms(atom_replace_dict:typing.Dict = {}):
+
+def reset_AA_atoms(atom_replace_dict: typing.Dict = {}):
     reset_elements()
     replace_atoms(atom_replace_dict)
     reset_AA_mass()
     reset_AA_df()
     reset_AA_Composition()
 
-def update_an_AA(aa:str, formula:str):
+
+def update_an_AA(aa: str, formula: str):
     aa_idx = ord(aa)
-    AA_DF.loc[aa_idx,'formula'] = formula
+    AA_DF.loc[aa_idx, "formula"] = formula
     AA_ASCII_MASS[aa_idx] = calc_mass_from_formula(formula)
-    AA_DF.loc[aa_idx,'mass'] = AA_ASCII_MASS[aa_idx]
+    AA_DF.loc[aa_idx, "mass"] = AA_ASCII_MASS[aa_idx]
     AA_Formula[aa] = formula
     AA_Composition[aa] = dict(parse_formula(formula))
 
-def calc_AA_masses(
-    sequence: str
-)->np.ndarray:
-    '''
+
+def calc_AA_masses(sequence: str) -> np.ndarray:
+    """
     Parameters
     ----------
     sequence : str
@@ -98,13 +106,12 @@ def calc_AA_masses(
     -------
     np.ndarray
         Masses of each amino acid.
-    '''
-    return AA_ASCII_MASS[np.array(sequence,'c').view(np.int8)]
+    """
+    return AA_ASCII_MASS[np.array(sequence, "c").view(np.int8)]
 
-def calc_AA_masses_for_same_len_seqs(
-    sequence_array: np.ndarray
-)->np.ndarray:
-    '''
+
+def calc_AA_masses_for_same_len_seqs(sequence_array: np.ndarray) -> np.ndarray:
+    """
     Calculate AA masses for the array of same-len AA sequences.
 
     Parameters
@@ -121,17 +128,16 @@ def calc_AA_masses_for_same_len_seqs(
     -------
     ValueError
         If sequences are not with the same length.
-    '''
+    """
     return AA_ASCII_MASS[
-        # we use np.int32 here because unicode str 
+        # we use np.int32 here because unicode str
         # uses 4 bytes for a char.
-        np.array(sequence_array).view(np.int32) 
+        np.array(sequence_array).view(np.int32)
     ].reshape(len(sequence_array), -1)
 
-def calc_sequence_masses_for_same_len_seqs(
-    sequence_array: np.ndarray
-)->np.ndarray:
-    '''
+
+def calc_sequence_masses_for_same_len_seqs(sequence_array: np.ndarray) -> np.ndarray:
+    """
     Calculate sequence masses for the array of same-len AA sequences.
 
     Parameters
@@ -143,34 +149,29 @@ def calc_sequence_masses_for_same_len_seqs(
     -------
     np.ndarray
         1-D (array_size, sequence_len) array of masses.
-    
+
     Raises
     -------
     ValueError
         If sequences are not with the same length.
-    '''
-    return np.sum(
-        calc_AA_masses_for_same_len_seqs(sequence_array),
-        axis=1
-    )+MASS_H2O
+    """
+    return np.sum(calc_AA_masses_for_same_len_seqs(sequence_array), axis=1) + MASS_H2O
 
 
-def calc_AA_masses_for_var_len_seqs(
-    sequence_array: np.ndarray
-)->np.ndarray:
-    '''
+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.
 
     Parameters
     ----------
     sequence_array : np.ndarray
         Sequences with variable lengths.
-        
+
     Returns
     -------
     np.ndarray
         1D array of masses, zero values are padded to fill the max length.
-    '''
-    return AA_ASCII_MASS[
-        np.array(sequence_array).view(np.int32)
-    ].reshape(len(sequence_array), -1)
+    """
+    return AA_ASCII_MASS[np.array(sequence_array).view(np.int32)].reshape(
+        len(sequence_array), -1
+    )

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/constants/atom.py

@@ -5,26 +5,22 @@ import typing
 
 from alphabase.yaml_utils import load_yaml
 
-from alphabase.constants._const import (
-    CONST_FILE_FOLDER,
-    common_const_dict
-)
+from alphabase.constants._const import CONST_FILE_FOLDER, common_const_dict
 
-MASS_PROTON:float = common_const_dict['MASS_PROTON']
-MASS_ISOTOPE:float = common_const_dict['MASS_ISOTOPE']
+MASS_PROTON: float = common_const_dict["MASS_PROTON"]
+MASS_ISOTOPE: float = common_const_dict["MASS_ISOTOPE"]
 
-MAX_ISOTOPE_LEN:int = common_const_dict['MAX_ISOTOPE_LEN']
-EMPTY_DIST:np.ndarray = np.zeros(MAX_ISOTOPE_LEN)
+MAX_ISOTOPE_LEN: int = common_const_dict["MAX_ISOTOPE_LEN"]
+EMPTY_DIST: np.ndarray = np.zeros(MAX_ISOTOPE_LEN)
 EMPTY_DIST[0] = 1
 
+
 @numba.njit
-def truncate_isotope(
-    isotopes: np.ndarray, mono_idx: int
-)->tuple:
-    '''
-    For a given isotope distribution (intensity patterns), 
-    this function truncates the distribution by top 
-    `MAX_ISOTOPE_LEN` neighbors those contain the monoisotopic 
+def truncate_isotope(isotopes: np.ndarray, mono_idx: int) -> tuple:
+    """
+    For a given isotope distribution (intensity patterns),
+    this function truncates the distribution by top
+    `MAX_ISOTOPE_LEN` neighbors those contain the monoisotopic
     peak pointed by `mono_idx`.
 
     Parameters
@@ -36,34 +32,39 @@ def truncate_isotope(
     mono_idx : int
 
         Monoisotopic peak position (index) in the isotope patterns
-            
+
     Returns
     -------
     int
-    
+
         the new position of `mono_idx`
 
     int
-    
+
         the start position of the truncated isotopes
 
     int
-    
+
         the end position of the truncated isotopes
-    '''
+    """
     trunc_start = mono_idx - 1
     trunc_end = mono_idx + 1
-    while trunc_start >= 0 and trunc_end < len(isotopes) and (trunc_end-trunc_start-1)<MAX_ISOTOPE_LEN:
+    while (
+        trunc_start >= 0
+        and trunc_end < len(isotopes)
+        and (trunc_end - trunc_start - 1) < MAX_ISOTOPE_LEN
+    ):
         if isotopes[trunc_end] >= isotopes[trunc_start]:
             trunc_end += 1
         else:
             trunc_start -= 1
-    if trunc_end-trunc_start-1 < MAX_ISOTOPE_LEN:
+    if trunc_end - trunc_start - 1 < MAX_ISOTOPE_LEN:
         if trunc_start == -1:
             trunc_end = MAX_ISOTOPE_LEN
         elif trunc_end == len(isotopes):
-            trunc_start = len(isotopes)-MAX_ISOTOPE_LEN-1
-    return mono_idx-trunc_start-1, trunc_start+1, trunc_end
+            trunc_start = len(isotopes) - MAX_ISOTOPE_LEN - 1
+    return mono_idx - trunc_start - 1, trunc_start + 1, trunc_end
+
 
 #: chemical element information in dict defined by `nist_element.yaml`
 CHEM_INFO_DICT = {}
@@ -72,25 +73,24 @@ CHEM_INFO_DICT = {}
 CHEM_MONO_MASS = {}
 
 #: {element: np.ndarray of abundance distribution}
-CHEM_ISOTOPE_DIST:numba.typed.Dict = numba.typed.Dict.empty(
-    key_type=numba.types.unicode_type,
-    value_type=numba.types.float64[:]
+CHEM_ISOTOPE_DIST: numba.typed.Dict = numba.typed.Dict.empty(
+    key_type=numba.types.unicode_type, value_type=numba.types.float64[:]
 )
 
 #: {element: int (mono position)}
-CHEM_MONO_IDX:numba.typed.Dict = numba.typed.Dict.empty(
-    key_type=numba.types.unicode_type,
-    value_type=numba.types.int64
+CHEM_MONO_IDX: numba.typed.Dict = numba.typed.Dict.empty(
+    key_type=numba.types.unicode_type, value_type=numba.types.int64
 )
 
-MASS_H:int = None
-MASS_C:int = None
-MASS_O:int = None
-MASS_N:int = None
-MASS_H2O:int = None #raise errors if the value is not reset
-MASS_NH3:int = None
+MASS_H: int = None
+MASS_C: int = None
+MASS_O: int = None
+MASS_N: int = None
+MASS_H2O: int = None  # raise errors if the value is not reset
+MASS_NH3: int = None
+
 
-def update_atom_infos(new_atom_info:typing.Dict):
+def update_atom_infos(new_atom_info: typing.Dict):
     """
     Args:
         atom_dict (Dict): Example, replacing N with 15N
@@ -104,14 +104,14 @@ def update_atom_infos(new_atom_info:typing.Dict):
 
     reset_elements()
 
-def reset_elements():
 
+def reset_elements():
     global MASS_C, MASS_H, MASS_O, MASS_N
     global MASS_H2O, MASS_NH3
 
     for elem, items in CHEM_INFO_DICT.items():
-        isotopes = np.array(items['abundance'])
-        masses = np.array(items['mass'])
+        isotopes = np.array(items["abundance"])
+        masses = np.array(items["mass"])
         _sort_idx = np.argsort(masses)
         masses = masses[_sort_idx]
         isotopes = isotopes[_sort_idx]
@@ -139,18 +139,19 @@ def reset_elements():
 
             CHEM_ISOTOPE_DIST[elem] = _isos[start:end]
             CHEM_MONO_IDX[elem] = _mono_idx
-    
-    MASS_C = CHEM_MONO_MASS['C']
-    MASS_H = CHEM_MONO_MASS['H']
-    MASS_N = CHEM_MONO_MASS['N']
-    MASS_O = CHEM_MONO_MASS['O']
-    MASS_H2O = CHEM_MONO_MASS['H']*2 + CHEM_MONO_MASS['O']
-    MASS_NH3 = CHEM_MONO_MASS['H']*3 + CHEM_MONO_MASS['N']
-
-def load_elem_yaml(yaml_file:str):
-    '''Load built-in or user-defined element yaml file. Default yaml is: 
-        os.path.join(_base_dir, 'nist_element.yaml')
-    '''
+
+    MASS_C = CHEM_MONO_MASS["C"]
+    MASS_H = CHEM_MONO_MASS["H"]
+    MASS_N = CHEM_MONO_MASS["N"]
+    MASS_O = CHEM_MONO_MASS["O"]
+    MASS_H2O = CHEM_MONO_MASS["H"] * 2 + CHEM_MONO_MASS["O"]
+    MASS_NH3 = CHEM_MONO_MASS["H"] * 3 + CHEM_MONO_MASS["N"]
+
+
+def load_elem_yaml(yaml_file: str):
+    """Load built-in or user-defined element yaml file. Default yaml is:
+    os.path.join(_base_dir, 'nist_element.yaml')
+    """
     global CHEM_INFO_DICT
     global CHEM_MONO_MASS
     global CHEM_ISOTOPE_DIST
@@ -160,52 +161,42 @@ def load_elem_yaml(yaml_file:str):
 
     CHEM_MONO_MASS = {}
     CHEM_ISOTOPE_DIST = numba.typed.Dict.empty(
-        key_type=numba.types.unicode_type,
-        value_type=numba.types.float64[:]
+        key_type=numba.types.unicode_type, value_type=numba.types.float64[:]
     )
-    
+
     CHEM_MONO_IDX = numba.typed.Dict.empty(
-        key_type=numba.types.unicode_type,
-        value_type=numba.types.int64
+        key_type=numba.types.unicode_type, value_type=numba.types.int64
     )
 
     reset_elements()
 
-load_elem_yaml(
-    os.path.join(CONST_FILE_FOLDER,
-        'nist_element.yaml'
-    )
-)
 
-def parse_formula(
-    formula:str
-)->list:
-    '''
-    Given a formula (str, e.g. `H(1)C(2)O(3)`), 
+load_elem_yaml(os.path.join(CONST_FILE_FOLDER, "nist_element.yaml"))
+
+
+def parse_formula(formula: str) -> list:
+    """
+    Given a formula (str, e.g. `H(1)C(2)O(3)`),
     it generates `[('H', 2), ('C', 2), ('O', 1)]`
-    '''
-    if not formula: return []
-    items = [item.split('(') for item in 
-        formula.strip(')').split(')')
-    ]
+    """
+    if not formula:
+        return []
+    items = [item.split("(") for item in formula.strip(")").split(")")]
     return [(elem, int(n)) for elem, n in items]
 
 
-def calc_mass_from_formula(formula:str):
-    '''
+def calc_mass_from_formula(formula: str):
+    """
     Calculates the mass of the formula`
 
     Parameters
     ----------
     formula : str
         e.g. `H(1)C(2)O(3)`
-    
+
     Returns
     -------
     float
         mass of the formula
-    '''
-    return np.sum([
-        CHEM_MONO_MASS[elem]*n 
-        for elem, n in parse_formula(formula)
-    ])
+    """
+    return np.sum([CHEM_MONO_MASS[elem] * n for elem, n in parse_formula(formula)])

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/constants/const_files/amino_acid.yaml

@@ -30,11 +30,11 @@ X: 'C(1000000)'
 Y: 'C(9)H(9)N(1)O(2)S(0)'
 Z: 'C(1000000)'
 # Any other ASCII chars could be the placeholders for future usage.
-# For example: 
+# For example:
 # phospho site-specific search (only lower case 'sty' can be modified)
 # s is S
 s: 'C(3)H(5)N(1)O(2)S(0)'
 # t is T
 t: 'C(4)H(8)N(1)O(5)P(1)'
 # y is Y
-y: 'C(9)H(9)N(1)O(2)S(0)'
+y: 'C(9)H(9)N(1)O(2)S(0)'

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/constants/const_files/common_constants.yaml

@@ -2,7 +2,7 @@ MASS_PROTON: 1.007276467 #https://physics.nist.gov/cgi-bin/cuu/Value?arp|search_
 MASS_ISOTOPE: 1.0033
 MAX_ISOTOPE_LEN: 10
 MOBILITY:
-  # 1059.62245 is the estimated constant coef in 
+  # 1059.62245 is the estimated constant coef in
   # Mason Schamp equation of Burker.
   CCS_IM_COEF: 1059.62245
   # 28 is the mass of N(2), the default gas in IM bruker
@@ -10,4 +10,4 @@ MOBILITY:
 
 # Only applied in peak/fragment dataframes to save RAM
 PEAK_MZ_DTYPE: float32
-PEAK_INTENSITY_DTYPE: float32
+PEAK_INTENSITY_DTYPE: float32

{alphabase-1.2.2 → alphabase-1.2.4}/alphabase/constants/const_files/protease.yaml

@@ -40,4 +40,4 @@ trypsin_not_p:  '([KR](?=[^P]))'
 trypsin:  '([KR])'
 trypsin/p:  '([KR])'
 non-specific:  '()'
-no-cleave: '_'
+no-cleave: '_'