update notebook

nglviewer · Nov 28, 2024 · 0ae26f3 · 0ae26f3
1 parent addc8ea
commit 0ae26f3
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Showing 3 changed files with 82 additions and 47 deletions.
diff --git a/examples/notebooks/export_image.ipynb b/examples/notebooks/export_image.ipynb
diff --git a/examples/notebooks/multiple_ligand_view.ipynb b/examples/notebooks/multiple_ligand_view.ipynb
@@ -2,9 +2,22 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "0f5e3dc3cacc4876b00d08657b55e16f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "import nglview as nv\n",
     "import parmed as pmd\n",
@@ -13,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -22,7 +35,7 @@
      "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",
+      "100  9810  100  9810    0     0  38981      0 --:--:-- --:--:-- --:--:-- 39083\n",
       "curl: (6) Could not resolve host: 5ht3ligs.sdf\n"
      ]
     },
@@ -35,7 +48,7 @@
        " <Structure 26 atoms; 1 residues; 29 bonds; NOT parameterized>]"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -48,21 +61,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "74b824240097468d9ee5abd7add17658",
+       "model_id": "a46aed66f3a3465dbcccd21b90a9c872",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
        "VBox(children=(NGLWidget(), IntSlider(value=0, max=3)))"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -75,15 +88,15 @@
     "def show_one_ligand(change):\n",
     "    val = change['new']\n",
     "    view.show_only([val])\n",
-    "    \n",
+    "\n",
     "slider.observe(show_one_ligand, 'value')\n",
     "\n",
     "VBox([view, slider])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +108,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -109,7 +122,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/xray.ipynb b/examples/notebooks/xray.ipynb
@@ -2,18 +2,26 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "xray_fn: ../../../ngl/data//JMJD2DA-x336_event2.ccp4.gz\n",
+      "pdb_fn: ../../../ngl/data//JMJD2DA-x336_event2.pdb\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f0deeaadf3f24712a5d957adf407b6a6",
-       "version_major": "2",
-       "version_minor": "0"
+       "model_id": "4563540fbcc24d34ba0a2f75d28a7456",
+       "version_major": 2,
+       "version_minor": 0
       },
       "text/plain": [
-       "A Jupyter Widget"
+       "NGLWidget(background='black')"
       ]
      },
      "metadata": {},
@@ -24,9 +32,11 @@
     "import nglview\n",
     "\n",
     "view = nglview.NGLWidget()\n",
-    "data_dir = '../ngl/data/'\n",
+    "data_dir = '../../../ngl/data/'\n",
     "pdb_fn = data_dir + '/JMJD2DA-x336_event2.pdb'\n",
     "xray_fn = data_dir + '/JMJD2DA-x336_event2.ccp4.gz'\n",
+    "print('xray_fn:', xray_fn)\n",
+    "print('pdb_fn:', pdb_fn)\n",
     "view.add_component(xray_fn)\n",
     "view.add_component(pdb_fn)\n",
     "view.background = 'black'\n",
@@ -37,7 +47,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 7,
    "metadata": {
     "collapsed": true
    },
@@ -48,7 +58,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 8,
    "metadata": {
     "collapsed": true
    },
@@ -68,7 +78,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -82,7 +92,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,