fix py3dmol save snippet

chemosim-lab · Sep 3, 2023 · 40ac0ea · 40ac0ea
1 parent b76bbb5
commit 40ac0ea
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Showing 4 changed files with 34 additions and 44 deletions.
diff --git a/docs/notebooks/docking.ipynb b/docs/notebooks/docking.ipynb
@@ -757,15 +757,9 @@
     "\n",
     "The advantage of using a count fingerprint in that case is that it will automatically select the interaction occurence with the shortest distance for a more intuitive visualization.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "\n",
+    "```python\n",
     "from IPython.display import Javascript\n",
     "\n",
     "Javascript(\n",
@@ -776,9 +770,10 @@
     "    a.download = \"prolif-3d.png\"\n",
     "    a.click()\n",
     "    a.remove()\n",
-    "\"\"\"\n",
+    "    \"\"\"\n",
     "    % view.uniqueid\n",
-    ")"
+    ")\n",
+    "```"
    ]
   }
  ],

diff --git a/docs/notebooks/md-ligand-protein.ipynb b/docs/notebooks/md-ligand-protein.ipynb
@@ -637,15 +637,9 @@
     "\n",
     "The advantage of using a count fingerprint in that case is that it will automatically select the interaction occurence with the shortest distance for a more intuitive visualization.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "\n",
+    "```python\n",
     "from IPython.display import Javascript\n",
     "\n",
     "Javascript(\n",
@@ -656,9 +650,10 @@
     "    a.download = \"prolif-3d.png\"\n",
     "    a.click()\n",
     "    a.remove()\n",
-    "\"\"\"\n",
+    "    \"\"\"\n",
     "    % view.uniqueid\n",
-    ")"
+    ")\n",
+    "```"
    ]
   }
  ],

diff --git a/docs/notebooks/md-protein-protein.ipynb b/docs/notebooks/md-protein-protein.ipynb
@@ -184,6 +184,16 @@
     ":::"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    ":::{admonition} Advanced usage\n",
+    "If you would like to ignore backbone interactions in the analysis, head over to the\n",
+    "corresponding section of the advanced tutorial: {ref}`notebooks/advanced:Ignoring the protein backbone`\n",
+    ":::"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -637,15 +647,9 @@
    "source": [
     "As in the lignetwork plot, you can hover atoms and interactions to display more information.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "\n",
+    "```python\n",
     "from IPython.display import Javascript\n",
     "\n",
     "Javascript(\n",
@@ -656,9 +660,10 @@
     "    a.download = \"prolif-3d.png\"\n",
     "    a.click()\n",
     "    a.remove()\n",
-    "\"\"\"\n",
+    "    \"\"\"\n",
     "    % view.uniqueid\n",
-    ")"
+    ")\n",
+    "```"
    ]
   },
   {

diff --git a/docs/notebooks/pdb.ipynb b/docs/notebooks/pdb.ipynb
@@ -441,15 +441,9 @@
     "\n",
     "The advantage of using a count fingerprint in that case is that it will automatically select the interaction occurence with the shortest distance for a more intuitive visualization.\n",
     "\n",
-    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "Once you're satisfied with the orientation, you can export the view as a PNG image with the following snippet:\n",
+    "\n",
+    "```python\n",
     "from IPython.display import Javascript\n",
     "\n",
     "Javascript(\n",
@@ -460,9 +454,10 @@
     "    a.download = \"prolif-3d.png\"\n",
     "    a.click()\n",
     "    a.remove()\n",
-    "\"\"\"\n",
+    "    \"\"\"\n",
     "    % view.uniqueid\n",
-    ")"
+    ")\n",
+    "```"
    ]
   }
  ],