Remove atom mapping CLI stuff

openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb

@@ -808,9 +808,7 @@
    "source": [
     "### The OpenFE CLI\n",
     "\n",
-    "The OpenFE toolkit also has a command line interface which we plan to add several convenience methods to.\n",
-    "\n",
-    "For now functionality is limited to atom mapping, but it will be expanded upon as the project grows."
+    "The OpenFE toolkit also has a command line interface which we plan to add several convenience methods to."
    ]
   },
   {
@@ -862,46 +860,6 @@
     "!openfe --help"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 15,
-   "id": "363f9691",
-   "metadata": {
-    "colab": {
-     "base_uri": "https://localhost:8080/"
-    },
-    "id": "363f9691",
-    "outputId": "b20a66f8-c14f-490e-d761-3b5c01677c13"
-   },
-   "outputs": [],
-   "source": [
-    "### Fully remove this since this CLI command is not exposed to the user?\n",
-    "# # Get an atom mapping using the CLI\n",
-    "\n",
-    "# !openfe atommapping --mapper LomapAtomMapper --mol inputs/benzene.sdf --mol inputs/styrene.sdf"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 16,
-   "id": "3b0dc398",
-   "metadata": {
-    "colab": {
-     "base_uri": "https://localhost:8080/",
-     "height": 317
-    },
-    "id": "3b0dc398",
-    "outputId": "cec53cce-2f7a-4e0c-98af-fb31cc57c62d"
-   },
-   "outputs": [],
-   "source": [
-    "### Fully remove this since this CLI command is not exposed to the user?\n",
-    "# We can also directly visualise the mapping\n",
-    "# !openfe atommapping --mapper LomapAtomMapper --mol inputs/benzene.sdf --mol inputs/styrene.sdf --output test.png\n",
-    "\n",
-    "# Image('test.png')"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "5d609a0a",