skip nbval for uploading pdb file to dogsitescorer

teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb

@@ -9433,9 +9433,23 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If we want to detect the binding sites of a protein from a local PDB file, we should first upload the file to the *DogSiteScorer* webserver using the `upload_pdb_file` function; it returns a dummy PDB-code for the uploaded structure, which can be used in place of a valid PDB-code to submit a binding site detection job.  \n",
+    "Notice that the `submit_job` function can also take in a chain-ID to limit the detection on that specific chain, and a ligand-ID to also calculate the coverage of each detected binding site. However, the ligand-ID that *DoGSiteScorer* accepts has its own format and is not the same as the ligand-ID in the protein PDB file. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Nevertheless, it follows the following format: (ligand-ID)\\_(chain-ID)\\_(ligand-residue-ID). When implementing the `BindingSiteDetection` class, we will circumvent this by automatically generating the *DogSiteScorer* ligand-ID from the normal ligand-ID so that the user does not have to manually look up and enter the ligand-ID in this specific format. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If we want to detect the binding sites of a protein from a local PDB file, we should first upload the file to the *DogSiteScorer* webserver using the `upload_pdb_file` function; it returns a dummy PDB-code for the uploaded structure, which can be used in place of a valid PDB-code to submit a binding site detection job. For this, we will use the PDB file we downloaded earlier. \n",
     "\n",
-    "For this, we will use the PDB file we downloaded earlier:"
+    "*Note*: This process should take **about one minute** to complete. We recently experienced very long processing times, so the following line may raise `ValueError: Fetching results from DoGSiteScorer API failed`."
    ]
   },
   {
@@ -9455,27 +9469,12 @@
     }
    ],
    "source": [
+    "# NBVAL_SKIP\n",
     "example_dummy_pdb_id = dogsitescorer.upload_pdb_file(filepath=example_downloaded_protein_filepath)\n",
     "\n",
     "example_dummy_pdb_id"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Notice that the `submit_job` function can also take in a chain-ID to limit the detection on that specific chain, and a ligand-ID to also calculate the coverage of each detected binding site. However, the ligand-ID that *DoGSiteScorer* accepts has its own format and is not the same as the ligand-ID in the protein PDB file. "
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Nevertheless, it follows the following format: (ligand-ID)\\_(chain-ID)\\_(ligand-residue-ID). When implementing the `BindingSiteDetection` class, we will circumvent this by automatically generating the *DogSiteScorer* ligand-ID from the normal ligand-ID so that the user does not have to manually look up and enter the ligand-ID in this specific format. \n",
-    "\n",
-    "*Note*: This process should take **about one minute** to complete. We recently experienced very long processing times, so the following line may raise `ValueError: Fetching results from DoGSiteScorer API failed`."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 106,