Merge branch 'main' into v1.7_cookbooks

Author: atravitz

cookbook/ligandnetwork_vis.ipynb

@@ -35,27 +35,27 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2025-09-01 13:22:08--  https://zenodo.org/records/17019064/files/septop_results.zip\n",
-      "Resolving zenodo.org (zenodo.org)... 188.185.43.25, 188.185.45.92, 188.185.48.194, ...\n",
-      "Connecting to zenodo.org (zenodo.org)|188.185.43.25|:443... connected.\n",
+      "--2025-10-14 20:00:18--  https://zenodo.org/records/17019064/files/septop_results.zip\n",
+      "Resolving zenodo.org (zenodo.org)... 188.185.45.92, 188.185.48.194, 188.185.43.25\n",
+      "Connecting to zenodo.org (zenodo.org)|188.185.45.92|:443... connected.\n",
       "HTTP request sent, awaiting response... 200 OK\n",
       "Length: 5974197 (5.7M) [application/octet-stream]\n",
       "Saving to: ‘septop_results.zip’\n",
       "\n",
-      "septop_results.zip  100%[===================>]   5.70M  3.05MB/s    in 1.9s    \n",
+      "septop_results.zip  100%[===================>]   5.70M   559KB/s    in 11s     \n",
       "\n",
-      "2025-09-01 13:22:11 (3.05 MB/s) - ‘septop_results.zip’ saved [5974197/5974197]\n",
+      "2025-10-14 20:00:30 (529 KB/s) - ‘septop_results.zip’ saved [5974197/5974197]\n",
       "\n",
       "Archive:  septop_results.zip\n",
-      "   creating: septop_results/\n",
-      "   creating: septop_results/results_2/\n",
+      "   creating: septop_results\n",
+      "   creating: septop_results/results_2\n",
       "  inflating: septop_results/results_2/rbfe_7a_7b.json  \n",
       "  inflating: septop_results/results_2/rbfe_1_7b.json  \n",
       "  inflating: septop_results/results_2/rbfe_1_7a.json  \n",
-      "   creating: septop_results/results_1/\n",
+      "   creating: septop_results/results_1\n",
       "  inflating: septop_results/results_1/rbfe_7a_7b.json  \n",
       "  inflating: septop_results/results_1/rbfe_1_7a.json  \n",
-      "   creating: septop_results/results_0/\n",
+      "   creating: septop_results/results_0\n",
       "  inflating: septop_results/results_0/rbfe_7a_7b.json  \n",
       "  inflating: septop_results/results_0/rbfe_1_7b.json  \n",
       "  inflating: septop_results/results_0/rbfe_1_7a.json  \n",
@@ -80,7 +80,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "7fbf1482-25ca-427b-a881-af88a983461c",
    "metadata": {},
    "outputs": [],
@@ -1183,7 +1183,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.13.8"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

networks/creating_networks_from_external_files.ipynb

@@ -23,7 +23,7 @@
    "id": "23881797-0bd3-408b-9212-ac206d46cd39",
    "metadata": {},
    "source": [
-    "<img src=\"septop_cycle.png\" width=600 height=600 />"
+    "<img src=\"septop_cycle.png\" width=600/>"
    ]
   },
   {
@@ -666,7 +666,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.10"
+   "version": "3.13.8"
   }
  },
  "nbformat": 4,

openmm_rbfe/benchmark_demo.ipynb

@@ -487,7 +487,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "bbcfd2e2-a50e-4398-85d1-f80b01597720",
    "metadata": {},
    "outputs": [
@@ -619,9 +619,7 @@
    ],
    "source": [
     "# Visualize the mapping in 3D\n",
-    "from openfe.utils import visualization_3D\n",
-    "\n",
-    "visualization_3D.view_mapping_3d(lomap_mapping, show_atomIDs=True)"
+    "lomap_mapping.view_3d(show_atomIDs=True)"
    ]
   },
   {