clean up alchemical network planning

cookbook/create_alchemical_network.ipynb

@@ -23,6 +23,16 @@
     "[Alchemical Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.AlchemicalNetwork.html"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "a052ba0b",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-info\">\n",
+    "This notebook creates an Hybrid Topology RBFE AlchemicalNetwork as an example. For other protocol types, see our step-by-step tutorials on running <a href=https://docs.openfree.energy/en/stable/tutorials/septop_tutorial.html>SepTop RBFE</a> and <a href=https://docs.openfree.energy/en/stable/tutorials/abfe_tutorial.html>ABFE</a> calculations.\n",
+    "</div>\n"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "471531a1-a351-413b-b147-794f9af4e0f8",
@@ -57,8 +67,6 @@
    "source": [
     "import openfe\n",
     "import rdkit.Chem\n",
-    "from openff.units import unit\n",
-    "from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol\n",
     "\n",
     "ligand_network = openfe.ligand_network_planning.generate_minimal_spanning_network(\n",
     "    ligands=[\n",
@@ -90,6 +98,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol\n",
+    "\n",
     "protocol = RelativeHybridTopologyProtocol(RelativeHybridTopologyProtocol.default_settings())"
    ]
   },
@@ -115,6 +125,8 @@
    },
    "outputs": [],
    "source": [
+    "from openff.units import unit\n",
+    "\n",
     "solvent = openfe.SolventComponent(\n",
     "    ion_concentration=0.15 * unit.molar\n",
     ")\n",
@@ -131,36 +143,6 @@
     "## Create the Alchemical Network"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "8b2f6271-3c89-4cd6-8283-e617d535b910",
-   "metadata": {},
-   "source": [
-    "### Automatically"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "cc13516d-92b6-44ac-a3eb-20e7f9e00631",
-   "metadata": {},
-   "source": [
-    "The `LigandNetwork.to_rbfe_alchemical_network()` method makes constructing alchemical networks for relative binding free energy calculations very simple: "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "733dee64-d23a-4eb0-87cf-c03065b8d2a6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "alchemical_network_auto = ligand_network.to_rbfe_alchemical_network(\n",
-    "    solvent=solvent,\n",
-    "    protein=protein,\n",
-    "    protocol=protocol,\n",
-    ")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "35774b4f-83e7-4235-960b-aa591e20e016",
@@ -174,14 +156,14 @@
    "id": "0da5558b-3894-4c11-aafd-e4478972e161",
    "metadata": {},
    "source": [
-    "If your needs are not catered to by the above method, you can instead loop over the `LigandNetwork` edges and manually create the `Transformation` objects for each of them. This gives you full control over the entire network. For more information, see [Under the Hood]:\n",
+    "To create an `AlchemicalNetwork` loop over the `LigandNetwork` edges and manually create the `Transformation` objects for each of them. This gives you full control over the entire network. For more information, see [Under the Hood]:\n",
     "\n",
     "[Under the Hood]: https://docs.openfree.energy/en/stable/cookbook/under_the_hood.html"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "c49f36b1-c3c1-425e-b1de-24da25ed01c3",
    "metadata": {},
    "outputs": [],
@@ -201,7 +183,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "id": "77d71229-5dcc-40cf-a9ae-0724a7327578",
    "metadata": {},
    "outputs": [],
@@ -232,8 +214,7 @@
     "            stateB=system_b,\n",
     "            mapping=mapping,\n",
     "            protocol=protocol,\n",
-    "            # Using the same name as to_rbfe_alchemical_network()\n",
-    "            name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n",
+    "            name=f\"rbfe_{system_a.name}_{system_b.name}\"\n",
     "        )\n",
     "    \n",
     "        transformations.append(transformation)\n"
@@ -249,39 +230,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 9,
    "id": "fc6cac68-bdcd-4d51-b4e1-f9bb7169c6f6",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<AlchemicalNetwork-130d122e6027d856bebe9a480b35f363>"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "alchemical_network = openfe.AlchemicalNetwork(transformations)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "b623d82e-1069-4c69-81af-ccc795ba5690",
-   "metadata": {},
-   "source": [
-    "We can confirm that this produces identical results to the previous strategy:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 8,
-   "id": "c9baa54c-513a-486a-a06a-fd8fd5d19fa5",
-   "metadata": {
-    "slideshow": {
-     "slide_type": ""
-    },
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "assert alchemical_network == ligand_network.to_rbfe_alchemical_network(\n",
-    "    solvent=solvent,\n",
-    "    protein=protein,\n",
-    "    protocol=protocol,\n",
-    ")"
+    "alchemical_network = openfe.AlchemicalNetwork(transformations)\n",
+    "alchemical_network"
    ]
   },
   {
@@ -314,7 +280,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "id": "2da4dafb-20d6-4ce7-ab83-4690528097d6",
    "metadata": {
     "slideshow": {
@@ -359,7 +325,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.13.15"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {