diff --git a/ipython/Tools/External symmetry and optical isomers.ipynb b/ipython/Tools/External symmetry and optical isomers.ipynb
index f5da0b3752..97d311fb81 100644
--- a/ipython/Tools/External symmetry and optical isomers.ipynb	
+++ b/ipython/Tools/External symmetry and optical isomers.ipynb	
@@ -19,24 +19,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "RDKit WARNING: [13:53:02] Enabling RDKit 2019.09.3 jupyter extensions\n"
-     ]
-    }
-   ],
-   "source": [
-    "from arc.molecule import Molecule\n",
-    "from arc.species import ARCSpecies\n",
-    "from IPython.display import display\n",
-    "from arc.plotter import show_sticks\n",
-    "from arc.species.converter import molecules_from_xyz, check_xyz_dict"
-   ]
+   "outputs": [],
+   "source": "from arc.molecule import Molecule\nfrom arc.species import ARCSpecies\nfrom IPython.display import display\nfrom arc.plotter import show_sticks\nfrom arc.species.converter import check_xyz_dict\nfrom arc.species.perceive import perceive_molecule_from_xyz"
   },
   {
    "cell_type": "code",
@@ -90,100 +76,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "WARNING:pint.util:Could not resolve planks_constant: UndefinedUnitError()\n",
-      "WARNING:pint.util:Could not resolve plank_constant: UndefinedUnitError()\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "SMILES:  [O]OC(c1cc(ccc1OC)C(C)C)NC(C)C\n",
-      "External symmetry:  1\n",
-      "Optical isomers:  2\n"
-     ]
-    },
-    {
-     "data": {
-      "image/png": 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-       "$3Dmolpromise.then(function() {\n",
-       "viewer_15931954791471632 = $3Dmol.createViewer($(\"#3dmolviewer_15931954791471632\"),{backgroundColor:\"white\"});\n",
-       "\tviewer_15931954791471632.addModel(\"\\n     RDKit          3D\\n\\n 40 40  0  0  0  0  0  0  0  0999 V2000\\n   -1.2234    2.3879   -0.3134 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.1480   -0.1944    2.3919 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2458   -0.4645    3.0320 O   0  0  0  0  0  1  0  0  0  0  0  0\\n   -1.7224   -1.4210    0.4870 N   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.4775   -0.8093   -0.0681 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.8681   -1.5928   -0.9629 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.3923   -0.0964    0.9409 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.8991   -1.0677    1.3827 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.2789   -2.1263   -0.8273 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2076   -3.0540   -1.2315 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.8957   -0.6518   -1.6013 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2112    3.6664   -0.9107 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.2407    0.0642   -0.1407 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1181    0.4201    0.3389 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.0655    1.6772   -0.2774 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.0265   -0.3608    0.3959 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.2687    1.3137   -0.7474 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.1360    2.1193   -0.8224 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.2890   -0.2602   -0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.8888   -1.3820   -1.4044 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2001    0.6353    0.8529 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.8237   -1.6513    1.4178 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.0633   -0.1294    1.9182 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.1290   -1.6289    1.9207 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.0030   -1.9430   -1.8689 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.1963   -2.7220   -0.8140 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.4858   -2.7261   -0.3701 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -3.1825   -3.3114   -0.8023 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2564   -3.2473   -2.3058 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.4556   -3.7105   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.6229    0.3977   -1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -3.8865   -0.8091   -1.1605 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.9707   -0.8388   -2.6762 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2250    4.0514   -0.8151 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.5186    4.3405   -0.3952 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9445    3.6090   -1.9718 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.5758   -1.7118    0.9554 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.9441   -1.3333    0.8707 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.2057    3.0841   -1.3071 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.1963    1.6777   -1.1788 H   0  0  0  0  0  0  0  0  0  0  0  0\\n  1 12  1  0\\n  1 15  1  0\\n  2  7  1  0\\n  2  3  1  0\\n  4  6  1  0\\n  4  7  1  0\\n  4 37  1  0\\n  5  8  1  0\\n  5  9  1  0\\n  5 13  1  0\\n  5 19  1  0\\n  6 10  1  0\\n  6 11  1  0\\n  6 20  1  0\\n  7 14  1  0\\n  7 21  1  0\\n  8 22  1  0\\n  8 23  1  0\\n  8 24  1  0\\n  9 25  1  0\\n  9 26  1  0\\n  9 27  1  0\\n 10 28  1  0\\n 10 29  1  0\\n 10 30  1  0\\n 11 31  1  0\\n 11 32  1  0\\n 11 33  1  0\\n 12 34  1  0\\n 12 35  1  0\\n 12 36  1  0\\n 13 17  2  0\\n 13 16  1  0\\n 14 16  2  0\\n 14 15  1  0\\n 15 18  2  0\\n 16 38  1  0\\n 17 18  1  0\\n 17 40  1  0\\n 18 39  1  0\\nM  RAD  1   3   2\\nM  END\\n\",\"sdf\");\n",
-       "\tviewer_15931954791471632.setStyle({\"stick\": {}});\n",
-       "\tviewer_15931954791471632.zoomTo();\n",
-       "viewer_15931954791471632.render();\n",
-       "});\n",
-       "</script>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "\n",
-    "if smiles is None:\n",
-    "    mol = molecules_from_xyz(check_xyz_dict(xyz))[1]\n",
-    "    smiles = mol.to_smiles()\n",
-    "\n",
-    "rmg_mol = Molecule(smiles=smiles)\n",
-    "arc_spc = ARCSpecies(label='test', smiles=smiles, xyz=xyz)\n",
-    "arc_spc.determine_symmetry()\n",
-    "\n",
-    "print('SMILES: ', smiles)\n",
-    "print('External symmetry: ', arc_spc.external_symmetry)\n",
-    "print('Optical isomers: ', arc_spc.optical_isomers)\n",
-    "\n",
-    "display(rmg_mol)\n",
-    "success = show_sticks(xyz=xyz)"
-   ]
+   "outputs": [],
+   "source": "\nif smiles is None:\n    mol = perceive_molecule_from_xyz(check_xyz_dict(xyz))\n    smiles = mol.to_smiles()\n\nrmg_mol = Molecule(smiles=smiles)\narc_spc = ARCSpecies(label='test', smiles=smiles, xyz=xyz)\narc_spc.determine_symmetry()\n\nprint('SMILES: ', smiles)\nprint('External symmetry: ', arc_spc.external_symmetry)\nprint('Optical isomers: ', arc_spc.optical_isomers)\n\ndisplay(rmg_mol)\nsuccess = show_sticks(xyz=xyz)"
   },
   {
    "cell_type": "code",
@@ -214,4 +110,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
\ No newline at end of file
diff --git a/ipython/Tools/Perceive_xyz_(xyz_to_smiles).ipynb b/ipython/Tools/Perceive_xyz_(xyz_to_smiles).ipynb
index 5eda953f57..405edb52ae 100644
--- a/ipython/Tools/Perceive_xyz_(xyz_to_smiles).ipynb
+++ b/ipython/Tools/Perceive_xyz_(xyz_to_smiles).ipynb
@@ -40,40 +40,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {
     "pycharm": {}
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "SMILES: O=CN(C)C\n"
-     ]
-    },
-    {
-     "data": {
-      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAEQAAAAmCAIAAADyTaq0AAAABmJLR0QA/wD/AP+gvaeTAAAEIklEQVRYhe2YX0haXxzAzww2agku7ZKgmMNClJoRPWQkYT30j8EeLsSgXmz25H0LX0bCRsNHhRYzGCsYc1REXHqLwLInGQZRSzB7mXIp7sqcpmn6/T3cfmXarHVvTIafp+v3fM/33M/heu459wEAoH8F3t8aeHFx0e/3c1vzXCYej3NbtzDJZJKmaa1WOzo6GolEuCp7LqPRaIaHh/f397mq+zsymcz09LRcLpdKpT6fL5lM1tXV2e32dDrNQXUAAIBoNGqxWIRCocViicfjcD94PB6tVqtSqXAcp2maCXq9Xp1O19TUtLq6yrI+yv7h9/txHFcoFLOzsyzr5hAKhYxGo0QicTgc4XDYZDJhGGa321OpFJNAkmRtbW1/f//e3t6dR0H5oZWVlYaGBr1ev7m5eW2fSCSC43goFLrNACcnJ1arVSgUEgQRiUQu4j6fr6+vr76+fmlpKTsTwzCz2ZydCQBTU1MTExPZEbfbbTKZ0un0DTIAkEqlHA6HWCw2Go0HBwc5Jm1tbUajMZPJ3GhCkqRcLi8w38vLyyqVqqura3t7m4kEg8HBwUGJRDIzM8MMMTk5KZPJAoFAdsdYLKbX64eGhrJ9rpdhODw8JAiiurraZrMxz0M0Gu3o6DAYDDlTks/GxoZOp9NoNC6Xq3BmMpm02WwikYggiHA4zAQ9Hk9ra2tLS8vY2JhMJtvd3c3vGIvFOjs7BwYGLp7VQjIMOzs7PT09SqVyYWHhNiY0TRMEgWGYzWY7Ozu7sf7vemUymZGREalUeq3JtT43yzCQJFlZWalQKBgTtRr4fPh/QQKnE5qbAQDW1taYOT46Orpl5Wy8Xm97ezuzsrlcritP15cv8OwZPHoEGAavXsHPnxc+er1+fHz8D2QAgKKo+fl55lqthqoqGB3NlXG73VtbW3fQyIZZ2Xp7ey+Wb/jwAQQCcDohHIbv36G7G5qaIJFgGk9PT4+Pj/9MJhu1Gt6+BT4fKOqKDFcwK1swGAQAiMfhyRP4+PGyORaDmhpwOHJ63X1vplSiFy/Qu3ccvLjzKS8vN5vNNTU1CCH07Rs6OkI4ftlcUYGeP0fLyzm9WG00LRb06RP68YNNjUKUlZUhhBBNo8ePEZ9/pU0sRjSdk89K5ulT9PIlevOGTY1bIBKhWAz9+nUlSFFIJMpJZHsEeP0aOZ0oEGBZpiDNzUggQHNzl5GTE0SSqLMzN/Nuf1C1Gubmzq9NJqiq4ngByOX9exAI4OtXCIdhZwe6u6GxEfI2xBzIUBRUVNyzDAB8/gyNjfDwIYhEYDBcvuOyeAClYzMDRVHr6+tc3Qp7WMl4vV6r1crVrbDnr33QuA9KMsVKSaZYKckUKyWZYqUkU6yUZIoVVjI8Ho/HK6LpYHU4SyQSwWBQoVBweENs+KdOmv8Brc8HwMxCO/cAAAAASUVORK5CYII=\n",
-      "text/plain": [
-       "Molecule(smiles=\"O=CN(C)C\")"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "from arc.species.converter import molecules_from_xyz, check_xyz_dict\n",
-    "from IPython.display import display\n",
-    "\n",
-    "\n",
-    "s_mol, b_mol = molecules_from_xyz(check_xyz_dict(coords))\n",
-    "\n",
-    "print(f'SMILES: {b_mol.to_smiles()}')\n",
-    "\n",
-    "display(b_mol)"
-   ]
+   "outputs": [],
+   "source": "from arc.species.converter import check_xyz_dict\nfrom arc.species.perceive import perceive_molecule_from_xyz\nfrom IPython.display import display\n\n\nmol = perceive_molecule_from_xyz(check_xyz_dict(coords))\n\nprint(f'SMILES: {mol.to_smiles()}')\n\ndisplay(mol)"
   },
   {
    "cell_type": "code",
@@ -104,4 +76,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
\ No newline at end of file
diff --git a/ipython/Tools/Plot xyz.ipynb b/ipython/Tools/Plot xyz.ipynb
index ec8ff3e30a..42ddbfa35f 100644
--- a/ipython/Tools/Plot xyz.ipynb	
+++ b/ipython/Tools/Plot xyz.ipynb	
@@ -32,20 +32,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from arc.plotter import show_sticks, plot_3d_mol_as_scatter\n",
-    "from arc.species.converter import check_xyz_dict, molecules_from_xyz\n",
-    "from arc.species.converter import xyz_to_pybel_mol, pybel_to_inchi\n",
-    "from IPython.display import display\n",
-    "%matplotlib inline\n",
-    "\n",
-    "xyz = '/home/alongd/Code/ARC/ipython/Tools/ts1016.log'\n",
-    "\n",
-    "xyz = check_xyz_dict(xyz)"
-   ]
+   "source": "from arc.plotter import show_sticks, plot_3d_mol_as_scatter\nfrom arc.species.converter import check_xyz_dict\nfrom arc.species.converter import xyz_to_pybel_mol, pybel_to_inchi\nfrom arc.species.perceive import perceive_molecule_from_xyz\nfrom IPython.display import display\n%matplotlib inline\n\nxyz = '/home/alongd/Code/ARC/ipython/Tools/ts1016.log'\n\nxyz = check_xyz_dict(xyz)"
   },
   {
    "cell_type": "code",
@@ -124,54 +114,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[O]N=C\n",
-      "\n",
-      "\n",
-      "InChI=1/CH2NO/c1-2-3/h1H2\n",
-      "\n",
-      "\n",
-      "multiplicity 2\n",
-      "1 O u1 p2 c0 {2,S}\n",
-      "2 N u0 p1 c0 {1,S} {3,D}\n",
-      "3 C u0 p0 c0 {2,D} {4,S} {5,S}\n",
-      "4 H u0 p0 c0 {3,S}\n",
-      "5 H u0 p0 c0 {3,S}\n",
-      "\n",
-      "\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "image/png": "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\n",
-      "text/plain": [
-       "Molecule(smiles=\"[O]N=C\")"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "# Analyze graph\n",
-    "\n",
-    "s_mol, b_mol = molecules_from_xyz(xyz)\n",
-    "mol = b_mol or s_mol\n",
-    "print(mol.to_smiles())\n",
-    "print('\\n')\n",
-    "print(pybel_to_inchi(xyz_to_pybel_mol(xyz)))\n",
-    "print('\\n')\n",
-    "print(mol.to_adjacency_list())\n",
-    "print('\\n')\n",
-    "display(mol)"
-   ]
+   "outputs": [],
+   "source": "# Analyze graph\n\nmol = perceive_molecule_from_xyz(xyz)\nprint(mol.to_smiles())\nprint('\\n')\nprint(pybel_to_inchi(xyz_to_pybel_mol(xyz)))\nprint('\\n')\nprint(mol.to_adjacency_list())\nprint('\\n')\ndisplay(mol)"
   },
   {
    "cell_type": "code",
@@ -312,4 +258,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
\ No newline at end of file
diff --git a/ipython/Tools/TS Guesses.ipynb b/ipython/Tools/TS Guesses.ipynb
index 17b9f88738..acf8b8c5d9 100644
--- a/ipython/Tools/TS Guesses.ipynb	
+++ b/ipython/Tools/TS Guesses.ipynb	
@@ -12,22 +12,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "5bae17f3",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from arc.imports import settings\n",
-    "from arc.job.adapters.common import all_families_ts_adapters, ts_adapters_by_rmg_family\n",
-    "from arc.plotter import draw_structure\n",
-    "from arc.reaction import ARCReaction\n",
-    "from arc.rmgdb import make_rmg_database_object, load_families_only\n",
-    "from arc.species import ARCSpecies\n",
-    "from arc.species.converter import xyz_to_str\n",
-    "from arc.scheduler import Scheduler\n",
-    "\n",
-    "%matplotlib inline"
-   ]
+   "source": "from arc.imports import settings\nfrom arc.job.adapters.common import all_families_ts_adapters, ts_adapters_by_rmg_family\nfrom arc.plotter import draw_structure\nfrom arc.reaction import ARCReaction\nfrom arc.species import ARCSpecies\nfrom arc.species.converter import xyz_to_str\nfrom arc.scheduler import Scheduler\n\n%matplotlib inline"
   },
   {
    "cell_type": "code",
@@ -54,17 +43,6 @@
     "dihedral_increment = 90"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "826ede9f",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "rmgdb = make_rmg_database_object()\n",
-    "load_families_only(rmgdb)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 5,
@@ -78,60 +56,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "348b3b0a",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Considering the following reaction:\n",
-      "\n",
-      "[OH] + CCC <=> O + [CH2]CC\n",
-      "\n",
-      "Reaction family: H_Abstraction\n"
-     ]
-    }
-   ],
-   "source": [
-    "r_species, p_species = list(), list()\n",
-    "for r_smiles in [r1_smiles, r2_smiles]:\n",
-    "    if r_smiles is not None:\n",
-    "        r_species.append(generate_species_from_smiles(r_smiles))\n",
-    "for p_smiles in [p1_smiles, p2_smiles]:\n",
-    "    if p_smiles is not None:\n",
-    "        p_species.append(generate_species_from_smiles(p_smiles))\n",
-    "\n",
-    "rxn = ARCReaction(r_species=r_species, p_species=p_species)\n",
-    "rxn.ts_species = ARCSpecies(label='TS', is_ts=True)\n",
-    "rxn.determine_family(rmg_database=rmgdb)\n",
-    "\n",
-    "print(f'Considering the following reaction:\\n\\n{rxn.label}\\n\\nReaction family: {rxn.family.label}')"
-   ]
+   "outputs": [],
+   "source": "r_species, p_species = list(), list()\nfor r_smiles in [r1_smiles, r2_smiles]:\n    if r_smiles is not None:\n        r_species.append(generate_species_from_smiles(r_smiles))\nfor p_smiles in [p1_smiles, p2_smiles]:\n    if p_smiles is not None:\n        p_species.append(generate_species_from_smiles(p_smiles))\n\nrxn = ARCReaction(r_species=r_species, p_species=p_species)\nrxn.ts_species = ARCSpecies(label='TS', is_ts=True)\nrxn.determine_family()\n\nprint(f'Considering the following reaction:\\n\\n{rxn.label}\\n\\nReaction family: {rxn.family.label}')"
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "2db720a0",
    "metadata": {
     "scrolled": false
    },
    "outputs": [],
-   "source": [
-    "sched = Scheduler(project='TS_search_1',\n",
-    "                  species_list=rxn.r_species + rxn.p_species,\n",
-    "                  rmg_database=rmgdb,\n",
-    "                  conformer_level='wb97xd/Def2TZVP',\n",
-    "                  opt_level='wb97xd/Def2TZVP',\n",
-    "                  sp_level='wb97xd/Def2TZVP',\n",
-    "                  freq_level='wb97xd/Def2TZVP',\n",
-    "                  ess_settings=None,\n",
-    "                  testing=True,\n",
-    "                  project_directory='/home/alon/Dropbox (MIT)/runs/TS_search_1',\n",
-    "                 )\n",
-    "sched.job_dict = {'TS': {'tsg': {}}}"
-   ]
+   "source": "sched = Scheduler(project='TS_search_1',\n                  species_list=rxn.r_species + rxn.p_species,\n                  conformer_level='wb97xd/Def2TZVP',\n                  opt_level='wb97xd/Def2TZVP',\n                  sp_level='wb97xd/Def2TZVP',\n                  freq_level='wb97xd/Def2TZVP',\n                  ess_settings=None,\n                  testing=True,\n                  project_directory='/home/alon/Dropbox (MIT)/runs/TS_search_1',\n                 )\nsched.job_dict = {'TS': {'tsg': {}}}"
   },
   {
    "cell_type": "code",
@@ -543,4 +482,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}
\ No newline at end of file
diff --git a/ipython/Tools/Visualize 1D Torsion scan.ipynb b/ipython/Tools/Visualize 1D Torsion scan.ipynb
index 71c7a94058..68b434b761 100644
--- a/ipython/Tools/Visualize 1D Torsion scan.ipynb	
+++ b/ipython/Tools/Visualize 1D Torsion scan.ipynb	
@@ -30,24 +30,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "WARNING:root:No kyotocabinet available\n"
-     ]
-    }
-   ],
-   "source": [
-    "from arc.species.species import determine_rotor_symmetry\n",
-    "from arc.parser import parse_1d_scan_energies\n",
-    "from arc.common import read_yaml_file\n",
-    "from arc.plotter import plot_1d_rotor_scan\n",
-    "%matplotlib notebook"
-   ]
+   "outputs": [],
+   "source": "from arc.species.species import determine_rotor_symmetry\nfrom arc.parser.parser import parse_1d_scan_energies\nfrom arc.common import read_yaml_file\nfrom arc.plotter import plot_1d_rotor_scan\n%matplotlib notebook"
   },
   {
    "cell_type": "code",
@@ -901,4 +887,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
\ No newline at end of file