From c6aafccfef899d88c94c1a18683a4231067b22f8 Mon Sep 17 00:00:00 2001
From: Shyue Ping Ong <shyuep@gmail.com>
Date: Fri, 28 Jun 2024 11:39:50 -0700
Subject: [PATCH] Fix pybel import.

---
 notebooks/2013-01-01-Basic functionality.ipynb     |  4 ++--
 ... Reaction Energies with the Materials API.ipynb |  6 +++---
 notebooks/2013-01-01-Molecule.ipynb                | 14 +++++++-------
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/notebooks/2013-01-01-Basic functionality.ipynb b/notebooks/2013-01-01-Basic functionality.ipynb
index 49891aa..bfc5125 100644
--- a/notebooks/2013-01-01-Basic functionality.ipynb	
+++ b/notebooks/2013-01-01-Basic functionality.ipynb	
@@ -490,9 +490,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb b/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb
index 34fb3e6..9fe40cd 100644
--- a/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb	
+++ b/notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb	
@@ -91,7 +91,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3.10.5 64-bit",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -105,7 +105,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.11.8"
   },
   "vscode": {
    "interpreter": {
@@ -114,5 +114,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/2013-01-01-Molecule.ipynb b/notebooks/2013-01-01-Molecule.ipynb
index b973be7..753a65b 100644
--- a/notebooks/2013-01-01-Molecule.ipynb
+++ b/notebooks/2013-01-01-Molecule.ipynb
@@ -215,23 +215,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
      "ename": "ModuleNotFoundError",
-     "evalue": "No module named 'pybel'",
+     "evalue": "No module named 'openbabel'",
      "output_type": "error",
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-8-15cbf4a933be>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mpymatgen\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mio\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbabel\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mBabelMolAdaptor\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mpybel\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpb\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0ma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBabelMolAdaptor\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmol\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;31m# Create a pybel.Molecule, which simplifies a lot of access\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mpm\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mMolecule\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopenbabel_mol\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'pybel'"
+      "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mopenbabel\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m pybel \u001b[38;5;28;01mas\u001b[39;00m pb\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpymatgen\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mbabel\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m BabelMolAdaptor\n\u001b[1;32m      4\u001b[0m a \u001b[38;5;241m=\u001b[39m BabelMolAdaptor(mol)\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'openbabel'"
      ]
     }
    ],
    "source": [
-    "import pybel as pb\n",
+    "from openbabel import pybel as pb\n",
     "from pymatgen.io.babel import BabelMolAdaptor\n",
     "\n",
     "a = BabelMolAdaptor(mol)\n",
@@ -363,9 +363,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }