Add SepTop results example

Author: hannahbaumann

openmm_septop/python_tutorial.ipynb

@@ -12,8 +12,8 @@
     "\n",
     "The relative binding free energy is obtained through a thermodynamic cycle. The ligands are transformed into each other both in solvent, giving \n",
     "$\\Delta\\Delta G$ (solvent) and in the complex, giving $\\Delta\\Delta G$ (complex), which allows calculation of the relative binding free energy, $\\Delta\\Delta G$. \n",
-    "Each ligand is represented with its own set of coordinates, meaning that the interactions of all atoms are turned off/on. Therefore, restraints are required: \n",
-    "Ligands are restrained to the protein in the complex states using orientational (Boresch-style) restraints; in the solvent states ligands are restrained to each other using a single harmonic distance restraint. Restraints are not depicted in the graphic below for simplicity.\n",
+    "Each ligand is represented with its own set of coordinates, meaning that the interactions of all atoms of one ligand are turned off while simultaneously turning on the interactions of all atoms of the other ligand. Therefore, restraints are required: \n",
+    "Ligands are restrained to the protein in the complex states using orientational (Boresch-style) restraints; in the solvent states ligands are restrained to remain apart from each other using a single harmonic distance restraint between the ligands. Restraints are not depicted in the thermodynamic cycle below for simplicity.\n",
     "\n",
     "Note: In this `Protocol`, the coulombic interactions of the molecule are fully turned off (annihilated), while the Lennard-Jones interactions are decoupled, meaning the intermolecular interactions are turned off, whilst keeping the intramolecular Lennard-Jones interactions."
    ]
@@ -84,7 +84,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Generating charges: 100%|███████████████████████| 10/10 [02:41<00:00, 16.12s/it]\n"
+      "Generating charges: 100%|███████████████████████| 10/10 [02:38<00:00, 15.87s/it]\n"
      ]
     }
    ],
@@ -112,7 +112,7 @@
    "source": [
     "## Creating the `LigandNetwork`\n",
     "\n",
-    "The first step is to create a `LigandNetwork`. Here, we will be using the same process as in the relative hybrid topology `Protocol`, including the use of a mapper which is required by the scorer. **The mappings will not be used in the `Protocol`.** This is a temporary solution until we have developed a scorer specifically for the `SepTopProtocol`.\n",
+    "The first step is to create a `LigandNetwork`. Here, we will be using the same process as in the relative hybrid topology `Protocol`, including the use of a mapper which is required by the scorer. **The mappings will not be used in the `Protocol`.** This is a temporary solution until we have developed a scorer specifically for the `SepTopProtocol`. Alternatively, the user can also manually define the edges they want to run when creating the transformations below, without creating a `LigandNetwork` first.\n",
     "\n",
     "The pipeline for creating a `LigandNetwork` can involve three components:\n",
     "\n",
@@ -329,7 +329,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 12,
    "id": "c2b3de6d-1f11-432d-82f3-9deff16c78dc",
    "metadata": {},
    "outputs": [],
@@ -344,7 +344,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 13,
    "id": "7adf42d6",
    "metadata": {},
    "outputs": [],
@@ -364,7 +364,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 14,
    "id": "44ba94ca",
    "metadata": {},
    "outputs": [],
@@ -401,7 +401,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 15,
    "id": "66666a80",
    "metadata": {},
    "outputs": [],
@@ -446,7 +446,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 16,
    "id": "d6cebd9a",
    "metadata": {},
    "outputs": [],
@@ -463,7 +463,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 17,
    "id": "b96b57a9",
    "metadata": {},
    "outputs": [
@@ -522,7 +522,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 18,
    "id": "de7d7920-b171-42fe-9b82-5ff5694d26e5",
    "metadata": {},
    "outputs": [],
@@ -531,7 +531,7 @@
     "import json\n",
     "import gufe\n",
     "\n",
-    "outfile = \"results_septop/rbfe_lig_ejm_31_lig_ejm_42.json\"\n",
+    "outfile = \"results/rbfe_lig_ejm_31_lig_ejm_42.json\"\n",
     "with open(outfile) as stream:\n",
     "    results = json.load(stream)\n",
     "    estimate = results['estimate']\n",
@@ -540,13 +540,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 19,
    "id": "0e2e0727-2c4a-4b60-947c-44504aed2eee",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'magnitude': -1.0343272142162547,\n",
+       " 'unit': 'kilocalorie_per_mole',\n",
+       " ':is_custom:': True,\n",
+       " 'pint_unit_registry': 'openff_units'}"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "estimate"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8bd82399-c523-4960-a0c1-38dbc0901b57",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {