Fix to the notebook, as previously it wasnt able to read mol v2

Author: cm-beilstein

INCHI-1-DOC/Notebooks/Molecular_inorganics/Geometries/molsimplify_test_v1.ipynb

@@ -20,20 +20,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "32069b9b",
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
     "import molSimplify\n",
-    "\n",
+    "from openbabel import openbabel\n",
     "from molSimplify.Classes import mol3D"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "604aa4ca",
    "metadata": {},
    "outputs": [
@@ -70,6 +70,7 @@
    ],
    "source": [
     "#Example with one file\n",
+    "#this seems to work only with mol v2\n",
     "\n",
     "filename = \"./data/cis_platin.mol\"\n",
     "complex_mol = mol3D()\n",
@@ -79,7 +80,80 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
+   "id": "f0f589b8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "filename = \"./data/cis_platin.mol\"\n",
+    "\n",
+    "test_mol = openbabel.OBMol()\n",
+    "\n",
+    "# Create an OBConversion object\n",
+    "obConversion = openbabel.OBConversion()\n",
+    "\n",
+    "# Set the input format ('mol') and output format ('xyz')\n",
+    "obConversion.SetInFormat(\"mol\")\n",
+    "obConversion.SetOutFormat(\"xyz\")\n",
+    "\n",
+    "if not obConversion.ReadFile(test_mol, filename):\n",
+    "    print(\"Error: Could not read the mol file.\")\n",
+    "else:\n",
+    "    xyz_string = obConversion.WriteString(test_mol)\n",
+    "\n",
+    "    complex_mol = mol3D()\n",
+    "    complex_mol.readfromstring(xyz_string)\n",
+    "    print(complex_mol.get_geometry_type())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cf526836",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "directory = './data'\n",
+    "\n",
+    "absolute_file_paths = [os.path.abspath(os.path.join(directory, f)) for f in os.listdir(directory) if os.path.isfile(os.path.join(directory, f)) and \"mol\" in f and not \"xyz\" in f]\n",
+    "\n",
+    "tmp_mol = openbabel.OBMol()\n",
+    "\n",
+    "# Create an OBConversion object\n",
+    "obConversion = openbabel.OBConversion()\n",
+    "\n",
+    "# Set the input format ('mol') and output format ('xyz')\n",
+    "obConversion.SetInFormat(\"mol\")\n",
+    "obConversion.SetOutFormat(\"xyz\")\n",
+    "\n",
+    "for cur_fn in absolute_file_paths:\n",
+    "    \n",
+    "    complex_mol = mol3D()\n",
+    "\n",
+    "    try:\n",
+    "        print(\"----------------------\")\n",
+    "        print(cur_fn)\n",
+    "        \n",
+    "        if not obConversion.ReadFile(tmp_mol, filename):\n",
+    "            print(\"Error: Could not read the mol file.\")\n",
+    "        else:        \n",
+    "            xyz_string = obConversion.WriteString(test_mol)\n",
+    "            \n",
+    "            complex_mol = mol3D()\n",
+    "            complex_mol.readfromstring(xyz_string)\n",
+    "            \n",
+    "            geo_dict = complex_mol.get_geometry_type()\n",
+    "            if \"geometry\" in geo_dict:\n",
+    "                print(geo_dict[\"geometry\"])\n",
+    "    except Exception as ex:\n",
+    "        # pass\n",
+    "        print(\"error\", str(ex))\n",
+    "        \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "id": "55927958",
    "metadata": {},
    "outputs": [
@@ -103,6 +177,8 @@
     }
    ],
    "source": [
+    "#works only with mol v2\n",
+    "\n",
     "directory = './data'\n",
     "\n",
     "absolute_file_paths = [os.path.abspath(os.path.join(directory, f)) for f in os.listdir(directory) if os.path.isfile(os.path.join(directory, f)) and \"mol\" in f and not \"xyz\" in f]\n",
@@ -121,6 +197,16 @@
     "    except Exception as ex:\n",
     "        print(\"error\", str(ex))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "facfae74",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n"
+   ]
   }
  ],
  "metadata": {