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missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py

@@ -1,8 +1,8 @@
 from enum import Enum, StrEnum
-from pydantic import BaseModel, constr
+
 import numpy as np
 import pandas as pd
-
+from pydantic import BaseModel, constr
 
 LIST_PFAM_KD = [
     "Protein kinase domain",
@@ -70,9 +70,9 @@ class Family(Enum):
     Null = None
 
 
-KinaseDomainName = StrEnum("KinaseDomainName", 
-                           {"KD" + str(idx + 1): kd \
-                            for idx, kd in enumerate(LIST_PFAM_KD)})
+KinaseDomainName = StrEnum(
+    "KinaseDomainName", {"KD" + str(idx + 1): kd for idx, kd in enumerate(LIST_PFAM_KD)}
+)
 
 
 class KinHub(BaseModel):
@@ -93,6 +93,7 @@ class UniProt(BaseModel):
 
 class KLIFS(BaseModel):
     """Pydantic model for KLIFS information."""
+
     gene_name: str
     name: str
     full_name: str
@@ -105,6 +106,7 @@ class KLIFS(BaseModel):
 
 class Pfam(BaseModel):
     """Pydantic model for Pfam information."""
+
     domain_name: KinaseDomainName
     start: int
     end: int
@@ -126,6 +128,7 @@ class KinaseInfo(BaseModel):
 
 class CollectionKinaseInfo(BaseModel):
     """Pydantic model for kinase information."""
+
     kinase_dict: dict[str, KinaseInfo]
 
 
@@ -156,12 +159,12 @@ def concatenate_source_dataframe(
     # columns to include in the final dataframe
     if col_pfam_include is None:
         col_pfam_include = [
-            "name", 
+            "name",
             "start",
             "end",
             "protein_length",
             "pfam_accession",
-            "in_alphafold"
+            "in_alphafold",
         ]
 
     # list of Pfam domains to include
@@ -171,13 +174,12 @@ def concatenate_source_dataframe(
     # set indices to merge columns
     kinhub_df_merge = kinhub_df.set_index(col_kinhub_merge)
     uniprot_df_merge = uniprot_df.set_index(col_uniprot_merge)
-    klifs_df_merge = klifs_df.set_index(col_klifs_merge)    
+    klifs_df_merge = klifs_df.set_index(col_klifs_merge)
     pfam_df_merge = pfam_df.set_index(col_pfam_merge)
 
     # filter Pfam dataframe for KD domains and columns to include
     df_pfam_kd = pfam_df_merge.loc[
-        pfam_df_merge["name"].isin(LIST_PFAM_KD), 
-        col_pfam_include
+        pfam_df_merge["name"].isin(LIST_PFAM_KD), col_pfam_include
     ]
 
     # rename "name" column in Pfam so doesn't conflict with KLIFS name
@@ -188,17 +190,12 @@ def concatenate_source_dataframe(
 
     # concat dataframes
     df_merge = pd.concat(
-        [
-            kinhub_df_merge,
-            uniprot_df_merge,
-            klifs_df_merge,
-            df_pfam_kd
-        ],
+        [kinhub_df_merge, uniprot_df_merge, klifs_df_merge, df_pfam_kd],
         join="outer",
-        axis=1
-    ).reset_index()    
+        axis=1,
+    ).reset_index()
 
-    return df_merge    
+    return df_merge
 
 
 def is_not_valid_string(str_input: str) -> bool:
@@ -208,12 +205,9 @@ def is_not_valid_string(str_input: str) -> bool:
         return False
 
 
-def convert_to_group(
-    str_input: str, 
-    bool_list: bool = True
-) -> list[Group]:
+def convert_to_group(str_input: str, bool_list: bool = True) -> list[Group]:
     """Convert KinHub group to Group enum.
-    
+
     Parameters
     ----------
     str_input : str
@@ -234,7 +228,7 @@ def convert_to_group(
 
 def convert_str2family(str_input: str) -> Family:
     """Convert string to Family enum.
-    
+
     Parameters
     ----------
     str_input : str
@@ -259,7 +253,7 @@ def convert_to_family(
     bool_list: bool = True,
 ) -> Family:
     """Convert KinHub family to Family enum.
-    
+
     Parameters
     ----------
     str_input : str
@@ -284,20 +278,18 @@ def create_kinase_models_from_df(
     # create KinHub model
     dict_kinase_models = {}
 
-    for _, row in df.iterrows(): 
-        # create KinHub model           
+    for _, row in df.iterrows():
+        # create KinHub model
         kinhub = KinHub(
             kinase_name=row["Kinase Name"],
             manning_name=row["Manning Name"].split(", "),
             xname=row["xName"].split(", "),
             group=convert_to_group(row["Group"]),
-            family=convert_to_family(row["Family"])
+            family=convert_to_family(row["Family"]),
         )
 
         # create UniProt model
-        uniprot = UniProt(
-            canonical_seq=row["canonical_sequence"]
-        )
+        uniprot = UniProt(canonical_seq=row["canonical_sequence"])
 
         # create KLIFS model
         if is_not_valid_string(row["family"]):
@@ -315,7 +307,7 @@ def create_kinase_models_from_df(
                 family=convert_to_family(row["family"], bool_list=False),
                 iuphar=row["iuphar"],
                 kinase_id=row["kinase_ID"],
-                pocket_seq=pocket
+                pocket_seq=pocket,
             )
 
         # create Pfam model
@@ -328,7 +320,7 @@ def create_kinase_models_from_df(
                 end=row["end"],
                 protein_length=row["protein_length"],
                 pfam_accession=row["pfam_accession"],
-                in_alphafold=row["in_alphafold"]
+                in_alphafold=row["in_alphafold"],
             )
 
         # create KinaseInfo model
@@ -338,9 +330,9 @@ def create_kinase_models_from_df(
             KinHub=kinhub,
             UniProt=uniprot,
             KLIFS=klifs,
-            Pfam=pfam
+            Pfam=pfam,
         )
 
         dict_kinase_models[row["HGNC Name"]] = kinase_info
 
-    return dict_kinase_models
+    return dict_kinase_models