Fix path to H2O dimer coordinates to work locally and with colab.

website/examples/promolecule_nci.ipynb

@@ -13,6 +13,43 @@
     "The `promolecule` module in QC-AtomDB constructs approximate molecular (promolecular) properties as linear combinations  of atomic properties. This allows for the fast calculation of the reduced density gradient for large molecular systems. The following examples show how to calculate several molecular properties. As model systems the water molecule dimer will be used:\n",
     "\n",
     "<img src=\"images/h2o_dimer.png\" alt=\"drawing\" style=\"width: 300px;\"/>\n",
+    "\n",
+    "\n",
+    "## Install dependencies and download example files\n",
+    "\n",
+    "To run this notebook in Google Colab, the AtomDB, IOData and Grid libraries need to be installed. This can be done by uncommenting and running the next cell."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# # Install packages in Google Colab. \n",
+    "# # Don't run this cell if packages/data is already in your environment\n",
+    "# ! pip install git+https://github.com/theochem/iodata.git\n",
+    "# ! pip install git+https://github.com/theochem/grid.git\n",
+    "# ! python -m pip install git+https://github.com/theochem/AtomDB.git\n",
+    "\n",
+    "# # Download the example files\n",
+    "# import os\n",
+    "# from urllib.request import urlretrieve\n",
+    "\n",
+    "# fpath = \"data/\"\n",
+    "# if not os.path.exists(fpath):\n",
+    "#     os.makedirs(fpath, exist_ok=True)\n",
+    "\n",
+    "# urlretrieve(\n",
+    "#     \"https://raw.githubusercontent.com/theochem/AtomDB/refs/heads/master/website/examples/data/h2o_dimer.xyz\",\n",
+    "#     os.path.join(fpath, \"h2o_dimer.xyz\")\n",
+    "#     )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "\n",
     "## Loading the water dimer data:\n",
     "\n",
@@ -28,6 +65,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "Package 'qc-AtomDB' is not installed.\n",
       "Atomic numbers dimer:\n",
       " [8. 8. 1. 1. 1. 1.]\n",
       "Atomic coordinates dimer:\n",
@@ -53,7 +91,7 @@
     "from importlib_resources import files\n",
     "\n",
     "# Load the H2O dimer from a .xyz file\n",
-    "data_file=files(atomdb).joinpath('../website/examples/data/h2o_dimer.xyz')\n",
+    "data_file= 'data/h2o_dimer.xyz'\n",
     "mol_data = iodata.load_one(data_file)\n",
     "\n",
     "atnums = mol_data.atcorenums\n",