update notebook

nglviewer · Nov 23, 2024 · f8215fb · f8215fb
1 parent 98415dd
commit f8215fb
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Showing 8 changed files with 163 additions and 601 deletions.
diff --git a/examples/notebooks/export_image.ipynb b/examples/notebooks/export_image.ipynb
diff --git a/examples/notebooks/mdtraj.ipynb b/examples/notebooks/mdtraj.ipynb
diff --git a/examples/notebooks/multiple_ligand_view.ipynb b/examples/notebooks/multiple_ligand_view.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,62 +13,58 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
+      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
+      "100  9810  100  9810    0     0  68409      0 --:--:-- --:--:-- --:--:-- 68601\n",
+      "curl: (6) Could not resolve host: 5ht3ligs.sdf\n"
+     ]
+    },
     {
      "data": {
       "text/plain": [
-       "[<Structure 22 atoms; 1 residues; 24 bonds; NOT parametrized>,\n",
-       " <Structure 24 atoms; 1 residues; 26 bonds; NOT parametrized>,\n",
-       " <Structure 25 atoms; 1 residues; 28 bonds; NOT parametrized>,\n",
-       " <Structure 26 atoms; 1 residues; 29 bonds; NOT parametrized>]"
+       "[<Structure 22 atoms; 1 residues; 24 bonds; NOT parameterized>,\n",
+       " <Structure 24 atoms; 1 residues; 26 bonds; NOT parameterized>,\n",
+       " <Structure 25 atoms; 1 residues; 28 bonds; NOT parameterized>,\n",
+       " <Structure 26 atoms; 1 residues; 29 bonds; NOT parameterized>]"
       ]
      },
-     "execution_count": 34,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "# !wget https://raw.githubusercontent.com/rdkit/rdkit/master/rdkit/Chem/Subshape/test_data/5ht3ligs.sdf\n",
+    "!curl https://raw.githubusercontent.com/rdkit/rdkit/master/rdkit/Chem/Subshape/test_data/5ht3ligs.sdf -O 5ht3ligs.sdf\n",
     "parms = pmd.rdkit.from_sdf('5ht3ligs.sdf') # require parmed, rdkit\n",
     "parms"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6b05d49d9cea423c82989ef4161359f7",
+       "model_id": "74b824240097468d9ee5abd7add17658",
        "version_major": 2,
        "version_minor": 0
       },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>VBox</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
       "text/plain": [
        "VBox(children=(NGLWidget(), IntSlider(value=0, max=3)))"
       ]
      },
+     "execution_count": 11,
      "metadata": {},
-     "output_type": "display_data"
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -87,39 +83,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
     "for p in parms:\n",
     "    view.add_structure(nv.ParmEdTrajectory(p))\n",
     "view.show_only([0])"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 45,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "[(None, None), (None, None), (None, None), (None, None)]"
-      ]
-     },
-     "execution_count": 45,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "[(view[i].clear(), view[i].add_licorice()) for i in range(4)]"
-   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -133,9 +109,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.1"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/examples/notebooks/protein_mutation_pdb4amber.ipynb b/examples/notebooks/protein_mutation_pdb4amber.ipynb
diff --git a/examples/notebooks/representations_and_selection_language.ipynb b/examples/notebooks/representations_and_selection_language.ipynb
diff --git a/examples/notebooks/show_rosetta.ipynb b/examples/notebooks/show_rosetta.ipynb
diff --git a/examples/notebooks/trajectory_2.ipynb b/examples/notebooks/trajectory_2.ipynb
diff --git a/examples/notebooks/using_two_screens.ipynb b/examples/notebooks/using_two_screens.ipynb