notebooks clean up

.binder/environment.yml

@@ -27,6 +27,6 @@ dependencies:
   - python
   - rdkit
   - typing_extensions
-  - gufe>=0.9.4
+  - gufe>=1.4.1
   - openfe~=1.2
   - py3dmol

abfe_tutorial/python_tutorial.ipynb → abfe_tutorial/abfe_tutorial.ipynb

@@ -25,11 +25,13 @@
   {
    "cell_type": "markdown",
    "id": "f9154ba7",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
    "source": [
-    "# 0. Setup for Google Colab\n",
+    "## 0. Setup for Google Colab\n",
     "\n",
-    "If you are running this example in Google Colab, run the following cells to setup the environment. If you are running this notebook locally, skip down to `1. Overview`"
+    "If you are running this example in Google Colab, run the following cells to setup the environment. If you are running this notebook locally, skip down to `1. Loading the ligand`"
    ]
   },
   {
@@ -45,7 +47,7 @@
     "if \"COLAB_RELEASE_TAG\" in os.environ:\n",
     "    !pip install -q condacolab\n",
     "    import condacolab\n",
-    "    condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
+    "    condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0a0-Linux-x86_64.sh\")"
    ]
   },
   {
@@ -73,17 +75,6 @@
     "        break"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "fc97de03",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%matplotlib inline\n",
-    "import openfe"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "2fea29c3",
@@ -96,6 +87,17 @@
     "This can be loaded using the `SDMolSupplier` class from rdkit and passed to openfe."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "fc97de03",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import openfe"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -131,9 +133,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/gufe/components/explicitmoleculecomponent.py:93: UserWarning: Partial charges have been provided, these will preferentially be used instead of generating new partial charges\n",
-      "  warnings.warn(wmsg)\n",
-      "Generating charges: 100%|█████████████████████████| 1/1 [00:00<00:00,  1.79it/s]\n"
+      "Generating charges: 100%|█████████████████████████| 1/1 [00:00<00:00,  1.53it/s]\n"
      ]
     }
    ],
@@ -231,33 +231,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 10,
    "id": "c31c712b-4844-477b-8aa4-ded6f0c8ca5f",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
-      "\n",
-      "Due to the on going maintenance burden of keeping command line application\n",
-      "wrappers up to date, we have decided to deprecate and eventually remove these\n",
-      "modules.\n",
-      "\n",
-      "We instead now recommend building your command line and invoking it directly\n",
-      "with the subprocess module.\n",
-      "  warnings.warn(\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "from openfe.protocols.openmm_afe import AbsoluteBindingProtocol"
+    "from openfe.protocols.openmm_afe import AbsoluteBindingProtocol;"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 11,
    "id": "fb839094",
    "metadata": {},
    "outputs": [],
@@ -267,7 +251,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 12,
    "id": "8b99f77f-c70c-436d-b4eb-fb462a4b043e",
    "metadata": {
     "scrolled": true
@@ -443,7 +427,7 @@
       "                        'host_max_distance': <Quantity(3, 'nanometer')>,\n",
       "                        'host_min_distance': <Quantity(1, 'nanometer')>,\n",
       "                        'host_selection': 'backbone',\n",
-      "                        'rmsf_cutoff': <Quantity(1, 'nanometer')>},\n",
+      "                        'rmsf_cutoff': <Quantity(0.1, 'nanometer')>},\n",
       " 'solvent_equil_output_settings': {'checkpoint_interval': <Quantity(250.0, 'picosecond')>,\n",
       "                                   'checkpoint_storage_filename': 'checkpoint.chk',\n",
       "                                   'equil_npt_structure': 'equil_npt_structure.pdb',\n",
@@ -550,7 +534,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 13,
    "id": "55067780-d228-4661-8c1e-5cb0217fd2dc",
    "metadata": {},
    "outputs": [],
@@ -577,7 +561,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 14,
    "id": "23f6322b-0336-4aa9-b9d0-ebe533dc5753",
    "metadata": {},
    "outputs": [],
@@ -611,7 +595,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 15,
    "id": "1231fad8-b37d-4008-a851-5ad546386286",
    "metadata": {},
    "outputs": [],
@@ -635,7 +619,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 16,
    "id": "b69efbcd-b888-4afc-a33e-01860889f408",
    "metadata": {},
    "outputs": [],
@@ -683,7 +667,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 17,
    "id": "44ba94ca",
    "metadata": {},
    "outputs": [],
@@ -718,7 +702,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 18,
    "id": "6dbedb47-46b9-4c22-ad74-a580174a359c",
    "metadata": {},
    "outputs": [],
@@ -729,7 +713,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 19,
    "id": "be690ef1-3243-4114-b56f-5babbb660af6",
    "metadata": {
     "scrolled": true
@@ -738,10 +722,10 @@
    "source": [
     "# Finally we can run the simulations\n",
     "path = pathlib.Path('./abfe_results')\n",
-    "path.mkdir()\n",
     "\n",
-    "# Execute the DAG\n",
     "# Commented out since this would be too expensive to run in this notebook.\n",
+    "# path.mkdir()\n",
+    "# Execute the DAG\n",
     "# dag_results = execute_DAG(dag, scratch_basedir=path, shared_basedir=path, n_retries=3)"
    ]
   },
@@ -782,7 +766,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 20,
    "id": "d0f6b8fb-dde2-442a-b641-3160a70e2f84",
    "metadata": {},
    "outputs": [],
@@ -803,7 +787,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 21,
    "id": "847b5663-2e6c-4cb2-aa9d-39d132fcff3d",
    "metadata": {},
    "outputs": [],
@@ -844,7 +828,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 22,
    "id": "f62f69a1-09c0-4a4a-9b37-9663b51a75ac",
    "metadata": {},
    "outputs": [],
@@ -862,7 +846,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 23,
    "id": "3b459b28-a4dc-4fa9-a961-b106c45d79ce",
    "metadata": {},
    "outputs": [
@@ -875,7 +859,7 @@
        " 'pint_unit_registry': 'openff_units'}"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 23,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -909,7 +893,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.12.10"
   }
  },
  "nbformat": 4,