[pre-commit.ci] auto fixes from pre-commit.com hooks

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missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py

@@ -6,12 +6,12 @@
 from pydantic import BaseModel, ValidationError, constr, model_validator
 from typing_extensions import Self
 
+from missense_kinase_toolkit.databases import klifs
 from missense_kinase_toolkit.databases.kincore import (
     align_kincore2uniprot,
     extract_pk_fasta_info_as_dict,
 )
 from missense_kinase_toolkit.databases.utils import get_repo_root
-from missense_kinase_toolkit.databases import klifs
 
 logger = logging.getLogger(__name__)
 
@@ -154,7 +154,7 @@ class KinaseInfo(BaseModel):
     Pfam: Pfam | None
     KinCore: KinCore | None
     bool_offset: bool = True
-    KLIFS2UniProt: dict[str, int] | None  = None
+    KLIFS2UniProt: dict[str, int] | None = None
 
     # https://docs.pydantic.dev/latest/examples/custom_validators/#validating-nested-model-fields
     @model_validator(mode="after")
@@ -185,30 +185,27 @@ def validate_uniprot_length(cls, values):
                     "UniProt sequence length does not match Pfam protein length."
                 )
         return values
-    
+
     @model_validator(mode="after")
     def generate_klifs2uniprot_dict(self) -> Self:
         """Generate dictionary mapping KLIFS to UniProt indices."""
 
         if self.KinCore is not None:
-            kd_idx = (self.KinCore.start-1, self.KinCore.end-1)
+            kd_idx = (self.KinCore.start - 1, self.KinCore.end - 1)
         else:
             kd_idx = (None, None)
 
         if self.KLIFS is not None and self.KLIFS.pocket_seq is not None:
             temp_obj = klifs.KLIFSPocket(
-                uniprotSeq = self.UniProt.canonical_seq,
-                klifsSeq = self.KLIFS.pocket_seq,
-                idx_kd = kd_idx,
-                offset_bool = self.bool_offset
+                uniprotSeq=self.UniProt.canonical_seq,
+                klifsSeq=self.KLIFS.pocket_seq,
+                idx_kd=kd_idx,
+                offset_bool=self.bool_offset,
             )
 
             if temp_obj.list_align is not None:
                 self.KLIFS2UniProt = dict(
-                    zip(
-                        klifs.LIST_KLIFS_REGION,
-                        temp_obj.list_align
-                    )
+                    zip(klifs.LIST_KLIFS_REGION, temp_obj.list_align)
                 )
 
         return self

missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/klifs.py

@@ -1,7 +1,7 @@
 import logging
 import re
-from itertools import chain
 from dataclasses import dataclass, field
+from itertools import chain
 
 import numpy as np
 from Bio import Align
@@ -139,12 +139,15 @@
 
 LIST_KLIFS_REGION = list(
     chain(
-        *[[f"{key}:{i}" for i in range(val["start"], val["end"] + 1)] \
-          for key, val in DICT_POCKET_KLIFS_REGIONS.items()]
+        *[
+            [f"{key}:{i}" for i in range(val["start"], val["end"] + 1)]
+            for key, val in DICT_POCKET_KLIFS_REGIONS.items()
+        ]
     )
 )
 """list[str]: List of string of all KLIFS pocket regions in format region:idx."""
 
+
 class KLIFS(SwaggerAPIClient):
     """Class to interact with the KLIFS API."""
 
@@ -327,6 +330,7 @@ class KLIFSPocket:
         List of final alignments to UniProt sequence
 
     """
+
     uniprotSeq: str
     klifsSeq: str
     idx_kd: tuple[int | None, int | None]
@@ -475,7 +479,6 @@ def select_correct_alignment(
         else:
             alignment = alignments[list_idx[0]]
 
-
         return self.return_idx_of_alignment_match(alignment)
 
     def align_klifs_pocket_to_uniprot_seq(
@@ -713,12 +716,9 @@ def iterate_klifs_alignment(
                             i + start_global for i in list_global
                         ]
 
-    def generate_alignment_list(
-        self,
-        bool_offset: bool
-    ) -> list[str | None]:
+    def generate_alignment_list(self, bool_offset: bool) -> list[str | None]:
         """Generate and validate alignment list.
-        
+
         Parameters
         ----------
         bool_offset : bool
@@ -731,8 +731,7 @@ def generate_alignment_list(
         """
         list_align = []
         for list_idx, list_seq in zip(
-            self.list_substring_idxs,
-            self.list_klifs_substr_actual
+            self.list_substring_idxs, self.list_klifs_substr_actual
         ):
             if list_idx is not None and len(list_idx) == 1:
                 if bool_offset:
@@ -744,7 +743,7 @@ def generate_alignment_list(
                         list_align.append(None)
                     else:
                         list_align.append(temp_idx)
-                        temp_idx+=1
+                        temp_idx += 1
             elif list_idx is None:
                 list_align.extend([None] * len(list_seq))
             else:
@@ -757,7 +756,7 @@ def generate_alignment_list(
                             list_align.append(list_idx[idx] + 1)
                         else:
                             list_align.append(list_idx[idx])
-                        idx+=1
+                        idx += 1
 
         for idx, i in enumerate(list_align):
             if i is not None:
@@ -778,5 +777,5 @@ def generate_alignment_list(
                         f"KLIFS: {self.klifsSeq[idx]}\n"
                     )
                     return None
-        
+
         self.list_align = list_align