Update functionalities

notebooks/Peptide_mapper_fileupload_voila.ipynb

@@ -27,7 +27,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8fc73c7604984da9a36481ccc7addf1d",
+       "model_id": "9f67753b9bdf4d0d8b2d27e80d22db65",
        "version_major": 2,
        "version_minor": 0
       },
@@ -36,10 +36,18 @@
      "metadata": {},
      "output_type": "display_data"
     },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/paddy/venvs/ptm/lib/python3.12/site-packages/nglview/__init__.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
+      "  import pkg_resources\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6bc63bf29ccf4ca5893cd08a94f03e67",
+       "model_id": "a7825ffbd74f4b8685711c2f343b36fb",
        "version_major": 2,
        "version_minor": 0
       },
@@ -698,7 +706,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

notebooks/Peptide_mapper_scop3p_voila.ipynb

@@ -20,10 +20,22 @@
    "id": "aa78e88b-1eef-4df2-8783-67208e8b13c0",
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/paddy/venvs/ptm/lib/python3.12/site-packages/b2bTools/singleSeq/PSPer/Constants.py:18: UserWarning: \n",
+      "PSPer can only run if HMMER is installed.\n",
+      "Please install it from http://hmmer.org on your computer, and refer to this installation in the\n",
+      "   b2bTools/python/b2bTools/singleSeq/PSPer/Constant.py\n",
+      "file by pointing the hmmbuild_bin and hmmscan_bin variables at the binaries.\n",
+      "  warnings.warn(\"\"\"\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "4e75c608a90244d89518e2e499dc4af8",
+       "model_id": "2b623049f1d54b8fae909e4d4a703f24",
        "version_major": 2,
        "version_minor": 0
       },
@@ -33,18 +45,16 @@
      "output_type": "display_data"
     },
     {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f48174f10d6746b4b0bbfe8f2e96bfa3",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(HTML(value='<b>Scop3P → AlphaFold → NGLView peptide mapper</b><br>Enter accession → Load → (opt…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'pkg_resources'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mModuleNotFoundError\u001b[39m                       Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[1]\u001b[39m\u001b[32m, line 12\u001b[39m\n\u001b[32m      8\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m urllib.error \u001b[38;5;28;01mimport\u001b[39;00m HTTPError, URLError\n\u001b[32m      9\u001b[39m \u001b[38;5;28;01mimport\u001b[39;00m re\n\u001b[32m     10\u001b[39m \n\u001b[32m     11\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m IPython.display \u001b[38;5;28;01mimport\u001b[39;00m display, clear_output\n\u001b[32m---> \u001b[39m\u001b[32m12\u001b[39m \u001b[38;5;28;01mimport\u001b[39;00m nglview \u001b[38;5;28;01mas\u001b[39;00m nv\n\u001b[32m     13\u001b[39m \n\u001b[32m     14\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m pathlib \u001b[38;5;28;01mimport\u001b[39;00m Path\n\u001b[32m     15\u001b[39m \n",
+      "\u001b[36mFile \u001b[39m\u001b[32m~/venvs/ptm/lib/python3.12/site-packages/nglview/__init__.py:12\u001b[39m\n\u001b[32m      9\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01m.\u001b[39;00m\u001b[34;01mutils\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m js_utils, widget_utils\n\u001b[32m     10\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01m.\u001b[39;00m\u001b[34;01mwidget\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m NGLWidget, write_html\n\u001b[32m---> \u001b[39m\u001b[32m12\u001b[39m \u001b[38;5;28;01mimport\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mpkg_resources\u001b[39;00m\n\u001b[32m     14\u001b[39m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[32m     15\u001b[39m     __version__ = pkg_resources.get_distribution(\u001b[33m\"\u001b[39m\u001b[33mnglview\u001b[39m\u001b[33m\"\u001b[39m).version\n",
+      "\u001b[31mModuleNotFoundError\u001b[39m: No module named 'pkg_resources'"
+     ]
     }
    ],
    "source": [
@@ -624,7 +634,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,