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Merged
atravitz merged 2 commits into from
Oct 23, 2025
Merged

use ligandatommapping.view_3d in examples #236

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ed90fa8
use new view_3d method
atravitz Oct 17, 2025
62f141f
Merge branch 'main' into use_view_3d_method
atravitz Oct 23, 2025
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154 changes: 85 additions & 69 deletions cookbook/ligandnetwork_vis.ipynb
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92 changes: 64 additions & 28 deletions networks/creating_networks_from_external_files.ipynb
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228 changes: 189 additions & 39 deletions openmm_rbfe/benchmark_demo.ipynb
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22 changes: 11 additions & 11 deletions openmm_septop/septop_analysis.ipynb
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Expand Up @@ -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",
Expand All @@ -80,7 +80,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"id": "7fbf1482-25ca-427b-a881-af88a983461c",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -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": {
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2 changes: 1 addition & 1 deletion openmm_septop/septop_tutorial.ipynb
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Expand Up @@ -666,7 +666,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.10"
"version": "3.13.8"
}
},
"nbformat": 4,
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6 changes: 2 additions & 4 deletions showcase/openfe_showcase.ipynb
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Expand Up @@ -487,7 +487,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"id": "bbcfd2e2-a50e-4398-85d1-f80b01597720",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -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)"
]
},
{
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