rebased changes

choderalab · Aug 26, 2024 · 529f31b · 529f31b
1 parent b7412d6
commit 529f31b
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Showing 3 changed files with 3 additions and 53 deletions.
diff --git a/notebooks/klifs_pocket.ipynb b/notebooks/klifs_pocket.ipynb
@@ -27,14 +27,6 @@
     "from missense_kinase_toolkit.databases.kinase_schema import KLIFSPocket"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "3c9af9b5-d7c4-428c-9745-f147448b81b0",
-   "metadata": {},
-   "source": [
-    "## Assess AA conservation of KLIFS pocket"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -49,7 +41,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "27513e9e",
+   "id": "3c9af9b5-d7c4-428c-9745-f147448b81b0",
    "metadata": {},
    "source": [
     "## Assess AA conservation of KLIFS pocket"
@@ -505,45 +497,6 @@
    "outputs": [],
    "source": []
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "87272c61-aa0b-40a1-a743-d09ef7c21bc6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "list_KLIFSPocket[0].list_"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 16,
-   "id": "c1d90201-3c58-4bf0-a848-d2e527e7f70f",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "0"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "sum([i is None for i in asdict(list_KLIFSPocket[0])[\"list_substring_idxs\"]])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "85c07198-e4b1-4927-bfe9-d36df52a8071",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/src/missense_kinase_toolkit/databases/colors.py b/src/missense_kinase_toolkit/databases/colors.py
@@ -186,7 +186,7 @@ def map_single_letter_aa_to_color(aa, dict_color):
             "-": "#BEA06E",
         },
         "DICT_ANNOTATION" : {
-
+            
             "A"         :       "#C8C8C8",
             "R, K"      :       "#145AFF",
             "N, Q"      :       "#00DCDC",

diff --git a/src/missense_kinase_toolkit/databases/klifs.py b/src/missense_kinase_toolkit/databases/klifs.py
@@ -1,6 +1,5 @@
 import numpy as np
 import logging
-from dataclasses import dataclass
 
 from bravado.client import SwaggerClient
 
@@ -326,8 +325,6 @@ def iterate_klifs_alignment(
 
     Parameters
     ----------
-    klifs_index : int
-        Index of KLIFS region (e.g. "I") in keys of dict_klifs
     string_uniprot : str
         UniProt canonical sequence
     string_klifs : str
@@ -347,7 +344,7 @@ def iterate_klifs_alignment(
                     will be the same as list_klifs_substr_actual if no concatenation necessary to find a single exact match
             list_substring_idxs : list[list[int | None]]
                 List of indices in UniProt sequence where KLIFS region starts
-
+        
     """
     list_klifs_region = []
     list_klifs_substr_actual = []