improving some formatting

OpenFreeEnergy · Oct 8, 2024 · 6989a63 · 6989a63
1 parent 5556cfc
commit 6989a63
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/showcase/openfe_showcase.ipynb b/showcase/openfe_showcase.ipynb
@@ -155,7 +155,7 @@
     "id": "e9a7f137"
    },
    "source": [
-    "## The dataset: Alchemical transformations of TYK2 ligands\n",
+    "## 1.1. The dataset: Alchemical transformations of TYK2 ligands\n",
     "\n",
     "Here we explore how OpenFE can be used to build a network of alchemical transformations between the TYK2 ligands.\n",
     "\n",
@@ -190,22 +190,22 @@
     "id": "0870f84e"
    },
    "source": [
-    "### The plan\n",
+    "## 1.2. The plan\n",
     "\n",
     "Here is what we will achieve in this notebook and what software toolchains are\n",
     "used along the way.\n",
     " \n",
     "\n",
     "| **Actions**                    | **Software**                                                |\n",
-    "|:------------------------------:|:-----------------------------------------------------------:|\n",
+    "|:------------------------------|:-----------------------------------------------------------|\n",
     "| Create OpenFE Molecules        | OpenFE  RDKit                                            |\n",
     "| Create Network                 | OpenFE  Lomap, Networkx                                  |\n",
     "| Visualise Network              | OpenFE  NetworkX, RDKit, Matplotlib                      |\n",
     "| Create ligand topologies       | OpenFE interface - OpenFF tk                             |\n",
     "| Create hybrid OpenMM topology  | OpenFE interface - OpenMMTools (eventually - ex Perses)  |\n",
     "| Create Lambda Protocol         | OpenFE interface - OpenMMTools (eventually - ex Perses)  |\n",
-    "| Setup and run RBFE calculation | OpenFE interface - OpenMM + OpenMMTools                  |\n",
-    "| Analysis RBFE calculation      | OpenFE interface - PyMBAR + OpenMMTools                  |"
+    "| Set up and run RBFE calculation | OpenFE interface - OpenMM + OpenMMTools                  |\n",
+    "| Analyze RBFE calculation      | OpenFE interface - PyMBAR + OpenMMTools                  |"
    ]
   },
   {
@@ -403,10 +403,10 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fe2a416a-618a-44fa-ab79-c2a6e8ec7333",
+   "id": "140f4e46-a58b-425d-b9cf-ab62078fc050",
    "metadata": {},
    "source": [
-    "We can also visualize the atom mappings by invoking the individual OpenFE AtomMapping objects directly.\n",
+    "We can also visualize the atom mappings by invoking the individual OpenFE `AtomMapping` objects directly.\n",
     "\n",
     "Unique atoms between each mapping are shown in red, and atoms which are mapped but undergo element changes are shown in blue. Bonds which either involve atoms that are unique or undergo element changes are highlighted in red."
    ]