Updates at symposium

Author: mattwthompson

joint-demo.ipynb

@@ -7,7 +7,9 @@
    "source": [
     "# OMSF 2025 Joint Demo\n",
     "\n",
-    "https://github.com/openforcefield/joint-demo"
+    "https://github.com/openforcefield/joint-demo\n",
+    "\n",
+    "<img alt=\"omsf\" src=\"attachment:03b87689-31ee-41a9-a044-5c11e114899e.png\" width=200><img alt=\"fold\" src=\"attachment:bedf5ef4-fc7d-403d-af5b-ac2c3470483d.png\" width=200><img alt=\"omsf\" src=\"attachment:956d7d06-3d2c-4e73-bb09-e851a413b1db.png\" width=200><img alt=\"fe\" src=\"attachment:060c8458-0f1b-45e3-be85-72c9461b6267.png\" width=200><img alt=\"ff\" src=\"attachment:939ed32c-3e32-4f05-8692-029786e4f79d.png\" width=200>"
    ]
   },
   {
@@ -183,7 +185,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "b16150f4",
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "keep = predictions[mask]\n",
@@ -588,7 +592,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "7dfcf893",
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "from openff.toolkit import Molecule, Topology\n",
@@ -908,7 +914,8 @@
    "outputs": [],
    "source": [
     "from openff.toolkit.utils.ambertools_wrapper import AmberToolsToolkitWrapper\n",
-    "from openff.toolkit.utils.nagl_wrapper import NAGLToolkitWrapper"
+    "from openff.toolkit.utils.nagl_wrapper import NAGLToolkitWrapper\n",
+    "from openff.toolkit import *"
    ]
   },
   {
@@ -958,7 +965,7 @@
     "\n",
     "\n",
     "logger = logging.getLogger()\n",
-    "logger.setLevel(logging.CRITICAL)"
+    "logger.setLevel(logging.INFO)"
    ]
   },
   {
@@ -974,15 +981,48 @@
     "nagl_wrapper.assign_partial_charges(ligand_5x3, \"openff-gnn-am1bcc-0.1.0-rc.3.pt\");"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15677be4-d8c7-41c1-8262-b14e36e5d185",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from openff.toolkit.utils.toolkit_registry import toolkit_registry_manager"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "497805ed-fba3-4ef0-b897-c5be7e3dc489",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with toolkit_registry_manager(ToolkitRegistry(\n",
+    "    toolkit_precedence=[RDKitToolkitWrapper()])):\n",
+    "    nagl_wrapper.assign_partial_charges(ligand_5x3, \"openff-gnn-am1bcc-0.1.0-rc.3.pt\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7bcab571-a84b-4310-8435-52432dbb797e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with toolkit_registry_manager(ToolkitRegistry(\n",
+    "    toolkit_precedence=[OpenEyeToolkitWrapper()])):\n",
+    "    nagl_wrapper.assign_partial_charges(ligand_5x3, \"openff-gnn-am1bcc-0.1.0-rc.3.pt\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "ab4ab21e",
    "metadata": {},
    "source": [
     "## Credits\n",
     "\n",
-    "* OMSF:\n",
-    "  * Zachary Baker\n",
+    "* Zachary Baker (OMSF)\n",
     "* OpenFold:\n",
     "  * Mallory Tollefson\n",
     "  * Jennifer Wei\n",
@@ -994,6 +1034,14 @@
     "* Irfan Alibay, Alyssa Travitz, OpenFE team\n",
     "* Jeff Wagner, Josh Mitchell, OpenFF team"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3c1aaca1-9819-41bc-a95d-8b32e9e80f13",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {