diff --git a/cell2mol/test/test_one_by_one.ipynb b/cell2mol/test/test_one_by_one.ipynb
index f9e8db85..7ecb7601 100644
--- a/cell2mol/test/test_one_by_one.ipynb
+++ b/cell2mol/test/test_one_by_one.ipynb
@@ -33,7 +33,11 @@
     "from cell2mol.read_write import readinfo\n",
     "from cell2mol.classes import cell\n",
     "from cell2mol.cell_reconstruction import classify_fragments, fragments_reconstruct\n",
-    "from cell2mol.charge_assignment import get_protonation_states_specie, balance_charge, get_list_of_charges_to_try, get_charge"
+    "from cell2mol.charge_assignment import (get_protonation_states_specie, \n",
+    "                                        balance_charge, \n",
+    "                                        get_list_of_charges_to_try, \n",
+    "                                        get_charge,\n",
+    "                                        prepare_mols)"
    ]
   },
   {
@@ -1481,7 +1485,9 @@
    "cell_type": "code",
    "execution_count": 21,
    "id": "6e2772ef",
-   "metadata": {},
+   "metadata": {
+    "scrolled": false
+   },
    "outputs": [
     {
      "data": {
@@ -1524,8 +1530,31 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "id": "5f305770",
+   "id": "838b8eb9",
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[[-1], [2, 3], [0], [0], [2, 3], [1]]"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "selected_cs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "a90e3045",
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -1582,6 +1611,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -1672,6 +1703,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -1782,6 +1815,8 @@
       "ref_data=['Cl']\n",
       "target_data=['Cl']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -1892,6 +1927,8 @@
       "ref_data=['Cl']\n",
       "target_data=['Cl']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -1981,6 +2018,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2071,6 +2110,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2125,7 +2166,11 @@
       "PREPARE: reordering with data: \n",
       "ref_data=['C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'O20', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10']\n",
       "target_data=['C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'O20', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with ['C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'O20', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with [array([ 9.3494897, 12.1903552, 15.2429643]), array([ 9.2503785, 11.6566577, 14.4151283]), array([10.314404 , 12.2675314, 15.4508048]), array([ 8.6286451, 11.513658 , 16.3827914]), array([ 8.7108809, 12.0604495, 17.1918845]), array([ 7.6814864, 11.4090764, 16.1540636]), array([ 8.7846918, 13.4878907, 15.0579171]), array([ 9.471571 , 14.2364155, 14.0572327]), array([10.4126702, 14.3786323, 14.3292759]), array([ 9.4670343, 13.7384022, 13.2015364]), array([ 8.7835726, 15.5620242, 13.8813982]), array([ 8.7874632, 16.0474661, 14.7327264]), array([ 9.2565273, 16.0881119, 13.2032201]), array([ 7.8584453, 15.4143785, 13.5937888]), array([ 9.0254048, 10.6319347, 16.5426468])]\n",
       "PREPARE: reordering protonation with [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14]\n",
+      "PROTONATION.REORDER. labels: ['C', 'H', 'H', 'C', 'H', 'H', 'O', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2189,6 +2234,8 @@
       "ref_data=['O31', 'H10', 'H10']\n",
       "target_data=['O31', 'H10', 'H10']\n",
       "PREPARE: reordering protonation with [0 1 2]\n",
+      "PROTONATION.REORDER. labels: ['O', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [0 1 2]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2278,6 +2325,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2368,6 +2417,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2458,6 +2509,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2504,7 +2557,11 @@
       "PREPARE: reordering with data: \n",
       "ref_data=['C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'O20', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10']\n",
       "target_data=['C40', 'H10', 'H10', 'O20', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with ['C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'O20', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with [array([11.3862448,  0.9466867,  1.8266461]), array([12.0703526, -0.864364 ,  1.1511523]), array([12.9993706, -0.2312764,  2.29009  ]), array([12.0742433, -0.378922 ,  2.0024806]), array([11.3907815,  1.4446999,  2.6823424]), array([10.4451456,  0.8044698,  1.5546029]), array([12.073124 ,  1.6952115,  0.8259617]), array([11.5083262,  2.992747 ,  0.6409145]), array([13.1763294,  3.7740258, -0.2701848]), array([12.146935 ,  3.1226527, -1.3080057]), array([12.2291708,  3.6694442, -0.4989126]), array([11.6074373,  3.5264445,  1.4687505]), array([11.8324111,  4.5511675, -0.658768 ]), array([10.5434119,  2.9155708,  0.433074 ]), array([11.6012886, -0.9050097,  2.6806587])]\n",
       "PREPARE: reordering protonation with [ 7 11 13 10  9  8  3  0  6  5  4  1 14  2 12]\n",
+      "PROTONATION.REORDER. labels: ['C', 'H', 'H', 'C', 'H', 'H', 'O', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [ 7 11 13 10  9  8  3  0  6  5  4  1 14  2 12]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2601,6 +2658,8 @@
       "ref_data=['O31', 'H10', 'H10']\n",
       "target_data=['O31', 'H10', 'H10']\n",
       "PREPARE: reordering protonation with [0 2 1]\n",
+      "PROTONATION.REORDER. labels: ['O', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [0 2 1]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2698,6 +2757,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2796,6 +2857,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2894,6 +2957,8 @@
       "ref_data=['Cl11']\n",
       "target_data=['Cl11']\n",
       "PREPARE: reordering protonation with [0]\n",
+      "PROTONATION.REORDER. labels: ['Cl']\n",
+      "PROTONATION.REORDER. received map: [0]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2940,9 +3005,15 @@
       "PREPARE: reordering with data: \n",
       "ref_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
       "target_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with ['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with [array([4.9621174, 4.887537 , 5.5174241]), array([7.446192 , 5.1831638, 4.9629179]), array([7.7980526, 4.4848237, 5.5700315]), array([7.3825766, 6.0292661, 5.4728857]), array([5.3205863, 4.1031323, 6.7652617]), array([6.1425014, 4.4939143, 7.1551156]), array([4.5936461, 4.2189016, 7.4272541]), array([5.5471833, 2.6222711, 6.5581359]), array([6.2077828, 2.4852999, 5.8335769]), array([4.6983522, 2.190974 , 6.2868233]), array([6.057791 , 1.9826907, 7.8434593]), array([6.9391501, 2.3707361, 8.0733785]), array([5.431816 , 2.189434 , 8.5820279]), array([3.7022164, 4.3387205, 4.8561783]), array([3.4349677, 4.9618726, 4.1348754]), array([3.9279863, 3.47383  , 4.4306174]), array([4.7422056, 6.3247204, 5.9588371]), array([5.4589056, 6.5656443, 6.5977344]), array([4.7174606, 7.3703135, 4.8550664]), array([4.1561668, 7.0530765, 4.1037748]), array([5.6347919, 7.5218327, 4.5148655]), array([6.0618142, 4.7800359, 4.475124 ]), array([5.821105 , 5.3510029, 3.7030087]), array([6.1009802, 3.8444751, 4.1536978]), array([8.4029106, 5.3669283, 3.7930703]), array([8.0834706, 6.1239713, 3.2408513]), array([9.2930954, 5.6125316, 4.1497904]), array([8.5582499, 4.1598483, 2.9070675]), array([9.2762403, 4.3201036, 2.2596406]), array([7.7185373, 3.9948779, 2.4295346]), array([8.7811323, 3.3787333, 3.4553631]), array([6.1935533, 0.4757138, 7.7087641]), array([6.8234881, 0.2677101, 6.9874295]), array([5.3187317, 0.0862111, 7.5010665]), array([6.5263333, 0.1012263, 8.5510861]), array([4.1489323, 8.6746576, 5.4130671]), array([3.1850923, 8.5523697, 5.6035306]), array([4.6023802, 8.8863394, 6.2671909]), array([4.3209594, 9.8367515, 4.4597166]), array([3.8962041, 9.6226212, 3.6031785]), array([ 3.9031592, 10.6368824,  4.841025 ]), array([2.501525 , 4.121721 , 5.7660068]), array([2.2683222, 4.9687278, 6.2223666]), array([2.7208457, 3.447188 , 6.4566855]), array([1.3217582, 3.6424323, 4.9319444]), array([1.004624 , 4.3858764, 4.3603789]), array([1.6204577, 2.9086724, 4.3382209]), array([0.1732351, 3.1506209, 5.7917387]), array([-0.5540774,  2.834949 ,  5.2158846]), array([-0.1508494,  3.8844927,  6.3547269]), array([0.4825944, 2.4148768, 6.3604133]), array([3.8826125, 6.3703461, 6.4479176]), array([ 5.2765576, 10.003726 ,  4.3176354])]\n",
       "PREPARE: reordering protonation with [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23\n",
       " 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47\n",
       " 48 49 50 51 52]\n",
+      "PROTONATION.REORDER. labels: ['N', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23\n",
+      " 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47\n",
+      " 48 49 50 51 52]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2970,9 +3041,15 @@
       "PREPARE: reordering with data: \n",
       "ref_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
       "target_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with ['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with [array([10.0428971, 10.5229266,  3.4523611]), array([11.8733989, 12.2257773,  4.0834276]), array([12.3589362, 11.4822276,  4.5210125]), array([14.1921027, 13.2701784,  5.0182256]), array([ 9.2878696, 10.8380621,  4.7368903]), array([ 9.9484661, 10.9871945,  5.4590032]), array([ 8.7499872, 10.0449656,  4.9857113]), array([10.8496662,  9.2774969,  3.7581257]), array([10.2243057,  8.561043 ,  4.0332345]), array([8.7778871, 8.247786 , 2.3477802]), array([11.7099487,  8.7509024,  2.6200458]), array([11.4384746,  9.4697312,  4.5304793]), array([ 8.6083835, 12.4769568,  6.6898609]), array([ 9.0950741, 10.2957077,  2.28982  ]), array([ 8.5075189, 11.0887502,  2.2120207]), array([7.8023242, 9.1628057, 0.3292887]), array([ 8.3680694, 12.0388317,  4.6754197]), array([11.3500672, 12.7030406,  4.7750275]), array([ 7.8446269, 12.3841443,  6.0668475]), array([ 9.6323575, 10.2446887,  1.4598555]), array([10.3649155, 12.4140361,  2.7063906]), array([10.9407695, 11.6750669,  3.0261966]), array([11.4876705, 11.3732003,  2.2581316]), array([11.193046 ,  8.7700827,  1.7758335]), array([12.8714532, 13.1846309,  3.4390186]), array([13.4673836, 12.6741091,  2.8354312]), array([14.3603219, 14.4935384,  4.0003072]), array([13.0363529,  6.7607148,  1.8171157]), array([12.5610689,  6.8045682,  0.9612129]), array([12.5048515,  9.3303049,  2.5081121]), array([13.8620919,  7.2853566,  1.759489 ]), array([12.1535844,  7.3255982,  2.9158036]), array([13.2556564,  5.8277528,  2.0215889]), array([11.3539741,  6.7508332,  3.0181117]), array([12.6502934,  7.3107043,  3.7719447]), array([ 7.0420666, 13.6758184,  6.0600174]), array([ 6.2671024, 13.5758343,  5.46874  ]), array([ 6.7357016, 13.8748155,  6.9694171]), array([13.7137002, 13.9195235,  4.4616227]), array([12.3782166, 13.8451074,  2.8908977]), array([ 7.6064926, 14.409338 ,  5.7377176]), array([8.2163096, 9.0630001, 2.3590737]), array([ 7.6063365, 11.8420287,  4.0744849]), array([7.6932824, 9.0687737, 3.1995691]), array([7.2709234, 9.0599274, 1.1582524]), array([6.661789 , 9.8374274, 1.225473 ]), array([7.0394425, 7.0132897, 1.0105641]), array([6.4427657, 7.7890359, 1.0608843]), array([5.8839448, 7.8240643, 0.2565564]), array([ 7.2723315, 11.6453853,  6.3936265]), array([5.8707793, 7.7103788, 1.8527909]), array([ 8.8598535, 12.813978 ,  4.3048171]), array([13.1334677, 14.4702878,  5.0275971])]\n",
       "PREPARE: reordering protonation with [ 0 41 43 48  1  2  3 25 27 16 28 26  8 12 14 19  4 42  7 13 39 38 40 29\n",
       " 44 46 50 34 36 30 37 31 35 32 33 10 51 52 47 45 11 15  6 17 18 20 24 21\n",
       " 23  9 22  5 49]\n",
+      "PROTONATION.REORDER. labels: ['N', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [ 0 41 43 48  1  2  3 25 27 16 28 26  8 12 14 19  4 42  7 13 39 38 40 29\n",
+      " 44 46 50 34 36 30 37 31 35 32 33 10 51 52 47 45 11 15  6 17 18 20 24 21\n",
+      " 23  9 22  5 49]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -2999,10 +3076,22 @@
       "]\n",
       "PREPARE: reordering with data: \n",
       "ref_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
-      "target_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "target_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "PREPARE: reordering with ['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with [array([15.8956985, 10.2955651, 10.3664547]), array([18.3562909, 11.0613812, 10.1178719]), array([19.8531919, 10.7972258, 11.5234999]), array([19.2373581, 12.2744298, 11.5456579]), array([17.1555994, 10.8443817, 11.0277005]), array([17.4228482, 10.2212295, 11.7490033]), array([15.0367109,  9.8320992, 12.1808701]), array([16.1403552,  7.8127887, 11.0288124]), array([16.2554357,  6.2967627,  9.6166879]), array([15.2230239,  7.6612695, 11.3690133]), array([16.7088835,  6.5084445, 10.4708117]), array([17.6727235,  6.6307324, 10.2803481]), array([16.701649 ,  8.1300257, 11.780104 ]), array([15.5372296, 11.0799698,  9.1186171]), array([14.7153144, 10.6891879,  8.7287632]), array([15.3989102,  8.6174578,  9.2861444]), array([14.7960017, 10.4030663, 11.4087548]), array([16.9298296, 11.7092722, 11.4532614]), array([15.3106326, 12.5608311,  9.3257429]), array([15.4259999, 12.9936682,  7.3018508]), array([16.1594636, 12.9921282,  9.5970554]), array([16.1156103,  8.8583817,  9.9250417]), array([16.2641697, 10.9642006,  8.4566247]), array([16.9752033,  8.8127561,  9.4359611]), array([19.5360577, 11.5406699, 10.9519344]), array([20.3752215, 12.7682254,  9.5234654]), array([21.4118933, 12.3481531, 10.6679942]), array([20.6845807, 12.0324812, 10.0921401]), array([21.0086653, 11.2986095,  9.5291519]), array([18.1369702, 11.7359142,  9.4271932]), array([18.5894937, 10.2143743,  9.6615122]), array([16.5368564,  5.3463507, 11.4241621]), array([16.9546566,  4.5462197, 11.0428537]), array([15.5812583,  5.1793761, 11.5662434]), array([16.9616118,  5.560481 , 12.2807003]), array([14.8000248, 13.2004114,  8.0404194]), array([13.9186658, 12.8123661,  7.8105003]), array([14.650033 , 12.6978022, 10.0503019]), array([14.6642625, 14.7073883,  8.1751147]), array([14.3314826, 15.0818759,  7.3327926]), array([14.0343277, 14.915392 ,  8.8964493]), array([13.4116238,  9.9999384, 10.9209609]), array([12.0766836, 11.8043689, 12.4285157]), array([13.1392786, 11.1882242, 13.4543442]), array([12.4549053,  9.8161739, 12.0908085]), array([13.0597633, 10.6982785, 10.3138472]), array([13.4752392,  9.1538361, 10.410993 ]), array([12.299566 , 11.0232539, 12.9768113]), array([11.5647205,  9.5705705, 11.7340884]), array([11.5815756, 10.8629985, 13.6242382]), array([12.7743452,  9.0591309, 12.6430275]), array([14.7568356, 11.3386271, 11.7301809]), array([15.5390842, 15.096891 ,  8.3828123])]\n",
       "PREPARE: reordering protonation with [ 0 41 45 46 13 14 22 18 37 20 35 36 19  4  5 17 21 15  7 12  9 16  6 51\n",
       " 44 50 48 47 49 43 42 38 40 52 39 10 11  8 31 34 32  1 30 29 24  2  3 27\n",
       " 26 28 25 23 33]\n",
+      "PROTONATION.REORDER. labels: ['N', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'C', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'H', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [ 0 41 45 46 13 14 22 18 37 20 35 36 19  4  5 17 21 15  7 12  9 16  6 51\n",
+      " 44 50 48 47 49 43 42 38 40 52 39 10 11  8 31 34 32  1 30 29 24  2  3 27\n",
+      " 26 28 25 23 33]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -3015,13 +3104,7 @@
       "smiles='[H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])[N+](C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])(C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]'\n",
       "1 52 H 0 1 1 1 0 True\n",
       "PREPARE: Success doing molecule 7. Created Charge State with total_charge=1\n",
-      "******************idx=8 mol.formula='H36-C16-N'******************\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "******************idx=8 mol.formula='H36-C16-N'******************\n",
       "PREPARE: Doing molecule 8 with unique_index: 5\n",
       "PREPARE: Specie with poscharges: [------------- Cell2mol Charge State ---------------\n",
       " Status                          = True\n",
@@ -3036,9 +3119,15 @@
       "PREPARE: reordering with data: \n",
       "ref_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
       "target_data=['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with ['N40', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'C40', 'H10', 'H10', 'H10', 'H10', 'H10']\n",
+      "PREPARE: reordering with [array([10.8149188,  4.6601756, 12.4315177]), array([12.6415063,  6.1201021, 13.5248051]), array([13.2514794,  3.3410734, 11.8093939]), array([13.1645334,  6.1143285, 12.6843097]), array([11.7627418,  4.8873944, 13.5940588]), array([12.350297 ,  4.0943519, 13.6718581]), array([11.2254583,  4.9384134, 14.4240233]), array([12.4897464,  3.1442705, 11.2084591]), array([11.9979623,  2.3691241, 11.5790617]), array([10.4929004,  2.7690661, 13.1774882]), array([13.5868925,  6.1231747, 14.7256263]), array([14.1960268,  5.3456747, 14.6584058]), array([13.0554917,  6.0202965, 15.5545901]), array([ 9.9170464,  3.5080353, 12.8576822]), array([ 9.4193412,  5.713371 , 11.3533995]), array([ 9.5077487,  2.4800616, 11.1088513]), array([ 9.1478672,  6.4321998, 13.263833 ]), array([12.0799287,  6.9353161, 13.5360985]), array([10.0081497,  5.9056053, 12.1257531]), array([10.6335102,  6.6220592, 11.8506443]), array([13.8183734,  8.1698125, 14.8733146]), array([11.5699463,  4.3450401, 11.1469885]), array([12.1078287,  5.1381366, 10.8981675]), array([10.9093498,  4.1959076, 10.4248756]), array([14.4150501,  7.3940663, 14.8229945]), array([12.2494324,  2.7061454,  9.1940179]), array([14.9870366,  7.4727233, 14.0310879]), array([13.0131889,  2.7989579,  9.8170313]), array([14.1221143,  1.3082867,  8.9144616]), array([13.5854843,  3.5377169,  9.4902522]), array([14.5907134,  1.6072678, 10.4151387]), array([13.8157492,  1.5072838,  9.8238614]), array([13.2513233,  0.7737641, 10.1461611]), array([ 8.4795992,  1.3379948, 12.9929811]), array([14.973871 ,  7.3590379, 15.6273224]), array([ 8.7042314,  7.857504 , 12.9680752]), array([ 6.995724 ,  7.8977456, 14.1243898]), array([ 8.296747 ,  8.378534 , 14.9226659]), array([ 7.8214629,  8.4223874, 14.0667631]), array([ 8.2075225,  7.8723979, 12.1119341]), array([ 7.6021595,  9.3553493, 13.8622899]), array([ 8.9844169,  2.9573249, 11.8004512]), array([ 8.3529643,  5.8527973, 13.3757667]), array([ 9.3701454,  3.8099018, 13.6257472]), array([ 7.9863626,  1.9984712, 12.4448602]), array([ 8.4988797,  3.7008746, 11.3628663]), array([ 7.7243481,  0.7128143, 10.8562817]), array([ 7.1441157,  1.2635787, 11.4222561]), array([ 6.6657131,  1.9129237, 10.8656532]), array([ 7.3904322,  2.5089931, 13.0484476]), array([ 6.497494 ,  0.6895638, 11.8835716]), array([ 9.6647698,  6.4130195, 14.1080453]), array([ 9.5038417,  8.432269 , 12.8657671])]\n",
       "PREPARE: reordering protonation with [ 0 15  6 17 12 14 13  4  5 39 18 20 19 38 26 42 28 16 25 27 24  1  3  2\n",
       " 21  8 22  7 49  9 51 10 11 45 23 31 37 36 34 33 35 41 30 40 44 43 52 47\n",
       " 48 46 50 29 32]\n",
+      "PROTONATION.REORDER. labels: ['N', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'H', 'C', 'C', 'H', 'C', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']\n",
+      "PROTONATION.REORDER. received map: [ 0 15  6 17 12 14 13  4  5 39 18 20 19 38 26 42 28 16 25 27 24  1  3  2\n",
+      " 21  8 22  7 49  9 51 10 11 45 23 31 37 36 34 33 35 41 30 40 44 43 52 47\n",
+      " 48 46 50 29 32]\n",
       "PREPARE: reordered protonation: \n",
       "------------- Cell2mol Protonation ----------------\n",
       " Status                          = True\n",
@@ -3047,7 +3136,13 @@
       " Atoms blocked (no atoms added)  = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\n",
       "---------------------------------------------------\n",
       "\n",
-      "*****get_charge******\n",
+      "*****get_charge******\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "smiles='[H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])[N+](C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])(C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]'\n",
       "1 52 H 0 1 1 1 0 True\n",
       "PREPARE: Success doing molecule 8. Created Charge State with total_charge=1\n"
@@ -3055,13 +3150,62 @@
     }
    ],
    "source": [
-    "from cell2mol.charge_assignment import prepare_mols\n",
-    "newcell.moleclist, newcell.error_prepare_mols = prepare_mols(newcell.moleclist, newcell.unique_indices, newcell.unique_species, selected_cs, final_charge_distribution[0], debug=2)"
+    "newcell.moleclist, newcell.error_prepare_mols = prepare_mols(newcell.moleclist, \n",
+    "                                                             newcell.unique_indices, \n",
+    "                                                             newcell.unique_species, \n",
+    "                                                             selected_cs, \n",
+    "                                                             final_charge_distribution[0], \n",
+    "                                                             debug=debug)\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 24,
+   "id": "7aa72fc7",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['N', 'C', 'H', 'H', 'C', 'H', 'H', 'C', 'H', 'H']"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "newcell.unique_species[5].labels[:10]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "99aa01a8",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "image/png": "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\n",
+      "text/plain": [
+       "<rdkit.Chem.rdchem.Mol at 0x1ba7edea0>"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "newcell.moleclist[8].rdkit_obj"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
    "id": "c5bcf712",
    "metadata": {
     "scrolled": false
@@ -3177,7 +3321,7 @@
        " ---------------------------------------------------]"
       ]
      },
-     "execution_count": 23,
+     "execution_count": 26,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3188,7 +3332,103 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 29,
+   "id": "d59b4c39",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Cl6-Fe2\n",
+      "[------------- Cell2mol Protonation ----------------\n",
+      " Status                          = True\n",
+      " Labels                          = ['Cl']\n",
+      " Atoms added in positions        = [0]\n",
+      " Atoms blocked (no atoms added)  = [1]\n",
+      "---------------------------------------------------\n",
+      "]\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "H10-C4-O\n",
+      "[------------- Cell2mol Protonation ----------------\n",
+      " Status                          = True\n",
+      " Labels                          = ['C', 'H', 'H', 'C', 'H', 'H', 'C', 'C', 'O', 'H', 'H', 'H', 'H', 'H', 'H']\n",
+      " Atoms added in positions        = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\n",
+      " Atoms blocked (no atoms added)  = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\n",
+      "---------------------------------------------------\n",
+      "]\n",
+      "H2-O-Cl3-Fe\n",
+      "[------------- Cell2mol Protonation ----------------\n",
+      " Status                          = True\n",
+      " Labels                          = ['O', 'H', 'H']\n",
+      " Atoms added in positions        = [0, 0, 0]\n",
+      " Atoms blocked (no atoms added)  = [1, 0, 0]\n",
+      "---------------------------------------------------\n",
+      "]\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "H10-C4-O\n",
+      "No protonation_states assigned H10-C4-O\n",
+      "H2-O-Cl3-Fe\n",
+      "No protonation_states assigned H2-O\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "No protonation_states assigned Cl\n",
+      "H36-C16-N\n",
+      "[------------- Cell2mol Protonation ----------------\n",
+      " Status                          = True\n",
+      " Labels                          = ['N', 'H', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'H', 'H', 'C', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'C', 'C', 'H', 'C', 'H', 'C', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H', 'C', 'C', 'H', 'H', 'H', 'H', 'C', 'H', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']\n",
+      " Atoms added in positions        = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\n",
+      " Atoms blocked (no atoms added)  = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\n",
+      "---------------------------------------------------\n",
+      "]\n",
+      "H36-C16-N\n",
+      "No protonation_states assigned H36-C16-N\n",
+      "H36-C16-N\n",
+      "No protonation_states assigned H36-C16-N\n",
+      "H36-C16-N\n",
+      "No protonation_states assigned H36-C16-N\n"
+     ]
+    }
+   ],
+   "source": [
+    "for mol in newcell.moleclist:\n",
+    "    print(mol.formula)\n",
+    "    if not mol.iscomplex:\n",
+    "#         try :\n",
+    "#             print(mol.possible_cs)\n",
+    "#         except:\n",
+    "#             print(\"No possible_cs assigned\", mol.formula)\n",
+    "        try :\n",
+    "            print(mol.protonation_states)\n",
+    "        except:\n",
+    "            print(\"No protonation_states assigned\", mol.formula)\n",
+    "    else :\n",
+    "        for lig in mol.ligands:\n",
+    "#             try :\n",
+    "#                 print(lig.possible_cs)\n",
+    "#             except:\n",
+    "#                 print(\"No possible_cs assigned\", lig.formula)\n",
+    "                \n",
+    "            try :\n",
+    "                print(lig.protonation_states)\n",
+    "            except:\n",
+    "                print(\"No protonation_states assigned\", lig.formula)\n",
+    "#         for met in mol.metals:\n",
+    "#             try :\n",
+    "#                 print(met.possible_cs)\n",
+    "#             except:\n",
+    "#                 print(\"No possible_cs assigned\", met.label)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
    "id": "ff13834d",
    "metadata": {
     "scrolled": false
@@ -3198,6 +3438,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "CELL.CREATE_BONDS: Creating Bonds for molecule Cl6-Fe2\n",
       "BUILD BONDS: atom 0 Cl\n",
       "BUILD BONDS: atom 0 Cl\n",
       "BUILD BONDS: atom 0 Cl\n",
@@ -3231,48 +3472,730 @@
       " Coordination Sphere Formula  = Cl4-Fe\n",
       "----------------------------------------------------\n",
       "]\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H10-C4-O\n",
       "BUILD BONDS: atom 0 C\n",
+      "BUILD BONDS: bond 0 1 1.0 C H H\n",
+      "BUILD BONDS: bond 0 2 1.0 C H H\n",
+      "BUILD BONDS: bond 0 3 1.0 C C C\n",
+      "BUILD BONDS: bond 0 6 1.0 C O O\n",
       "BUILD BONDS: atom 1 H\n",
+      "BUILD BONDS: bond 0 1 1.0 C H H\n",
       "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 0 2 1.0 C H H\n",
       "BUILD BONDS: atom 3 C\n",
+      "BUILD BONDS: bond 0 3 1.0 C C C\n",
+      "BUILD BONDS: bond 3 4 1.0 C H H\n",
+      "BUILD BONDS: bond 3 5 1.0 C H H\n",
+      "BUILD BONDS: bond 3 14 1.0 C H H\n",
       "BUILD BONDS: atom 4 H\n",
+      "BUILD BONDS: bond 3 4 1.0 C H H\n",
       "BUILD BONDS: atom 5 H\n",
+      "BUILD BONDS: bond 3 5 1.0 C H H\n",
       "BUILD BONDS: atom 6 O\n",
+      "BUILD BONDS: bond 0 6 1.0 C O O\n",
+      "BUILD BONDS: bond 6 7 1.0 O C C\n",
       "BUILD BONDS: atom 7 C\n",
+      "BUILD BONDS: bond 6 7 1.0 O C C\n",
+      "BUILD BONDS: bond 7 8 1.0 C H H\n",
+      "BUILD BONDS: bond 7 9 1.0 C H H\n",
+      "BUILD BONDS: bond 7 10 1.0 C C C\n",
       "BUILD BONDS: atom 8 H\n",
+      "BUILD BONDS: bond 7 8 1.0 C H H\n",
       "BUILD BONDS: atom 9 H\n",
+      "BUILD BONDS: bond 7 9 1.0 C H H\n",
       "BUILD BONDS: atom 10 C\n",
+      "BUILD BONDS: bond 7 10 1.0 C C C\n",
+      "BUILD BONDS: bond 10 11 1.0 C H H\n",
+      "BUILD BONDS: bond 10 12 1.0 C H H\n",
+      "BUILD BONDS: bond 10 13 1.0 C H H\n",
       "BUILD BONDS: atom 11 H\n",
+      "BUILD BONDS: bond 10 11 1.0 C H H\n",
       "BUILD BONDS: atom 12 H\n",
+      "BUILD BONDS: bond 10 12 1.0 C H H\n",
       "BUILD BONDS: atom 13 H\n",
+      "BUILD BONDS: bond 10 13 1.0 C H H\n",
       "BUILD BONDS: atom 14 H\n",
+      "BUILD BONDS: bond 3 14 1.0 C H H\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H2-O-Cl3-Fe\n",
       "BUILD BONDS: atom 0 O\n",
+      "BUILD BONDS: bond 0 1 1.0 O H H\n",
+      "BUILD BONDS: bond 0 2 1.0 O H H\n",
       "BUILD BONDS: atom 1 H\n",
+      "BUILD BONDS: bond 0 1 1.0 O H H\n",
       "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 0 2 1.0 O H H\n",
       "BUILD BONDS: atom 0 Cl\n",
       "BUILD BONDS: atom 0 Cl\n",
       "BUILD BONDS: atom 0 Cl\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H10-C4-O\n",
       "BUILD BONDS: atom 0 C\n",
-      "Error with Bond EndAtom O C\n"
+      "BUILD BONDS: bond 0 3 1.0 C O C\n",
+      "Error with Bond EndAtom O C\n",
+      "BUILD BONDS: bond 0 4 1.0 C C H\n",
+      "Error with Bond EndAtom C H\n",
+      "BUILD BONDS: bond 0 5 1.0 C H H\n",
+      "BUILD BONDS: bond 0 8 1.0 C H O\n",
+      "Error with Bond EndAtom H O\n",
+      "BUILD BONDS: atom 1 H\n",
+      "BUILD BONDS: bond 1 3 1.0 H O C\n",
+      "Error with Bond EndAtom O C\n",
+      "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 2 3 1.0 H O C\n",
+      "Error with Bond EndAtom O C\n",
+      "BUILD BONDS: atom 3 O\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: O C\n",
+      "BUILD BONDS: atom 4 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 5 H\n",
+      "BUILD BONDS: bond 0 5 1.0 C H H\n",
+      "BUILD BONDS: atom 6 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 7 C\n",
+      "BUILD BONDS: bond 6 7 1.0 H C C\n",
+      "BUILD BONDS: bond 7 8 1.0 C H O\n",
+      "Error with Bond EndAtom H O\n",
+      "BUILD BONDS: bond 7 11 1.0 C H H\n",
+      "BUILD BONDS: bond 7 13 1.0 C H H\n",
+      "BUILD BONDS: atom 8 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H O\n",
+      "BUILD BONDS: atom 9 H\n",
+      "BUILD BONDS: bond 6 9 1.0 H H H\n",
+      "BUILD BONDS: atom 10 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 11 H\n",
+      "BUILD BONDS: bond 7 11 1.0 C H H\n",
+      "BUILD BONDS: atom 12 H\n",
+      "BUILD BONDS: bond 6 12 1.0 H H H\n",
+      "BUILD BONDS: atom 13 H\n",
+      "BUILD BONDS: bond 7 13 1.0 C H H\n",
+      "BUILD BONDS: atom 14 H\n",
+      "BUILD BONDS: bond 3 14 1.0 O H H\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H2-O-Cl3-Fe\n",
+      "BUILD BONDS: atom 0 O\n",
+      "BUILD BONDS: bond 0 1 1.0 O H H\n",
+      "BUILD BONDS: bond 0 2 1.0 O H H\n",
+      "BUILD BONDS: atom 1 H\n",
+      "BUILD BONDS: bond 0 1 1.0 O H H\n",
+      "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 0 2 1.0 O H H\n",
+      "BUILD BONDS: atom 0 Cl\n",
+      "BUILD BONDS: atom 0 Cl\n",
+      "BUILD BONDS: atom 0 Cl\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H36-C16-N\n",
+      "BUILD BONDS: atom 0 N\n",
+      "BUILD BONDS: bond 0 4 1.0 N C C\n",
+      "BUILD BONDS: bond 0 13 1.0 N C C\n",
+      "BUILD BONDS: bond 0 16 1.0 N C C\n",
+      "BUILD BONDS: bond 0 21 1.0 N C C\n",
+      "BUILD BONDS: atom 1 C\n",
+      "BUILD BONDS: bond 1 2 1.0 C H H\n",
+      "BUILD BONDS: bond 1 3 1.0 C H H\n",
+      "BUILD BONDS: bond 1 21 1.0 C C C\n",
+      "BUILD BONDS: bond 1 24 1.0 C C C\n",
+      "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 1 2 1.0 C H H\n",
+      "BUILD BONDS: atom 3 H\n",
+      "BUILD BONDS: bond 1 3 1.0 C H H\n",
+      "BUILD BONDS: atom 4 C\n",
+      "BUILD BONDS: bond 0 4 1.0 N C C\n",
+      "BUILD BONDS: bond 4 5 1.0 C H H\n",
+      "BUILD BONDS: bond 4 6 1.0 C H H\n",
+      "BUILD BONDS: bond 4 7 1.0 C C C\n",
+      "BUILD BONDS: atom 5 H\n",
+      "BUILD BONDS: bond 4 5 1.0 C H H\n",
+      "BUILD BONDS: atom 6 H\n",
+      "BUILD BONDS: bond 4 6 1.0 C H H\n",
+      "BUILD BONDS: atom 7 C\n",
+      "BUILD BONDS: bond 4 7 1.0 C C C\n",
+      "BUILD BONDS: bond 7 8 1.0 C H H\n",
+      "BUILD BONDS: bond 7 9 1.0 C H H\n",
+      "BUILD BONDS: bond 7 10 1.0 C C C\n",
+      "BUILD BONDS: atom 8 H\n",
+      "BUILD BONDS: bond 7 8 1.0 C H H\n",
+      "BUILD BONDS: atom 9 H\n",
+      "BUILD BONDS: bond 7 9 1.0 C H H\n",
+      "BUILD BONDS: atom 10 C\n",
+      "BUILD BONDS: bond 7 10 1.0 C C C\n",
+      "BUILD BONDS: bond 10 11 1.0 C H H\n",
+      "BUILD BONDS: bond 10 12 1.0 C H H\n",
+      "BUILD BONDS: bond 10 31 1.0 C C C\n",
+      "BUILD BONDS: atom 11 H\n",
+      "BUILD BONDS: bond 10 11 1.0 C H H\n",
+      "BUILD BONDS: atom 12 H\n",
+      "BUILD BONDS: bond 10 12 1.0 C H H\n",
+      "BUILD BONDS: atom 13 C\n",
+      "BUILD BONDS: bond 0 13 1.0 N C C\n",
+      "BUILD BONDS: bond 13 14 1.0 C H H\n",
+      "BUILD BONDS: bond 13 15 1.0 C H H\n",
+      "BUILD BONDS: bond 13 41 1.0 C C C\n",
+      "BUILD BONDS: atom 14 H\n",
+      "BUILD BONDS: bond 13 14 1.0 C H H\n",
+      "BUILD BONDS: atom 15 H\n",
+      "BUILD BONDS: bond 13 15 1.0 C H H\n",
+      "BUILD BONDS: atom 16 C\n",
+      "BUILD BONDS: bond 0 16 1.0 N C C\n",
+      "BUILD BONDS: bond 16 17 1.0 C H H\n",
+      "BUILD BONDS: bond 16 18 1.0 C C C\n",
+      "BUILD BONDS: bond 16 51 1.0 C H H\n",
+      "BUILD BONDS: atom 17 H\n",
+      "BUILD BONDS: bond 16 17 1.0 C H H\n",
+      "BUILD BONDS: atom 18 C\n",
+      "BUILD BONDS: bond 16 18 1.0 C C C\n",
+      "BUILD BONDS: bond 18 19 1.0 C H H\n",
+      "BUILD BONDS: bond 18 20 1.0 C H H\n",
+      "BUILD BONDS: bond 18 35 1.0 C C C\n",
+      "BUILD BONDS: atom 19 H\n",
+      "BUILD BONDS: bond 18 19 1.0 C H H\n",
+      "BUILD BONDS: atom 20 H\n",
+      "BUILD BONDS: bond 18 20 1.0 C H H\n",
+      "BUILD BONDS: atom 21 C\n",
+      "BUILD BONDS: bond 0 21 1.0 N C C\n",
+      "BUILD BONDS: bond 1 21 1.0 C C C\n",
+      "BUILD BONDS: bond 21 22 1.0 C H H\n",
+      "BUILD BONDS: bond 21 23 1.0 C H H\n",
+      "BUILD BONDS: atom 22 H\n",
+      "BUILD BONDS: bond 21 22 1.0 C H H\n",
+      "BUILD BONDS: atom 23 H\n",
+      "BUILD BONDS: bond 21 23 1.0 C H H\n",
+      "BUILD BONDS: atom 24 C\n",
+      "BUILD BONDS: bond 1 24 1.0 C C C\n",
+      "BUILD BONDS: bond 24 25 1.0 C H H\n",
+      "BUILD BONDS: bond 24 26 1.0 C H H\n",
+      "BUILD BONDS: bond 24 27 1.0 C C C\n",
+      "BUILD BONDS: atom 25 H\n",
+      "BUILD BONDS: bond 24 25 1.0 C H H\n",
+      "BUILD BONDS: atom 26 H\n",
+      "BUILD BONDS: bond 24 26 1.0 C H H\n",
+      "BUILD BONDS: atom 27 C\n",
+      "BUILD BONDS: bond 24 27 1.0 C C C\n",
+      "BUILD BONDS: bond 27 28 1.0 C H H\n",
+      "BUILD BONDS: bond 27 29 1.0 C H H\n",
+      "BUILD BONDS: bond 27 30 1.0 C H H\n",
+      "BUILD BONDS: atom 28 H\n",
+      "BUILD BONDS: bond 27 28 1.0 C H H\n",
+      "BUILD BONDS: atom 29 H\n",
+      "BUILD BONDS: bond 27 29 1.0 C H H\n",
+      "BUILD BONDS: atom 30 H\n",
+      "BUILD BONDS: bond 27 30 1.0 C H H\n",
+      "BUILD BONDS: atom 31 C\n",
+      "BUILD BONDS: bond 10 31 1.0 C C C\n",
+      "BUILD BONDS: bond 31 32 1.0 C H H\n",
+      "BUILD BONDS: bond 31 33 1.0 C H H\n",
+      "BUILD BONDS: bond 31 34 1.0 C H H\n",
+      "BUILD BONDS: atom 32 H\n",
+      "BUILD BONDS: bond 31 32 1.0 C H H\n",
+      "BUILD BONDS: atom 33 H\n",
+      "BUILD BONDS: bond 31 33 1.0 C H H\n",
+      "BUILD BONDS: atom 34 H\n",
+      "BUILD BONDS: bond 31 34 1.0 C H H\n",
+      "BUILD BONDS: atom 35 C\n",
+      "BUILD BONDS: bond 18 35 1.0 C C C\n",
+      "BUILD BONDS: bond 35 36 1.0 C H H\n",
+      "BUILD BONDS: bond 35 37 1.0 C H H\n",
+      "BUILD BONDS: bond 35 38 1.0 C C C\n",
+      "BUILD BONDS: atom 36 H\n",
+      "BUILD BONDS: bond 35 36 1.0 C H H\n",
+      "BUILD BONDS: atom 37 H\n",
+      "BUILD BONDS: bond 35 37 1.0 C H H\n",
+      "BUILD BONDS: atom 38 C\n",
+      "BUILD BONDS: bond 35 38 1.0 C C C\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "BUILD BONDS: bond 38 39 1.0 C H H\n",
+      "BUILD BONDS: bond 38 40 1.0 C H H\n",
+      "BUILD BONDS: bond 38 52 1.0 C H H\n",
+      "BUILD BONDS: atom 39 H\n",
+      "BUILD BONDS: bond 38 39 1.0 C H H\n",
+      "BUILD BONDS: atom 40 H\n",
+      "BUILD BONDS: bond 38 40 1.0 C H H\n",
+      "BUILD BONDS: atom 41 C\n",
+      "BUILD BONDS: bond 13 41 1.0 C C C\n",
+      "BUILD BONDS: bond 41 42 1.0 C H H\n",
+      "BUILD BONDS: bond 41 43 1.0 C H H\n",
+      "BUILD BONDS: bond 41 44 1.0 C C C\n",
+      "BUILD BONDS: atom 42 H\n",
+      "BUILD BONDS: bond 41 42 1.0 C H H\n",
+      "BUILD BONDS: atom 43 H\n",
+      "BUILD BONDS: bond 41 43 1.0 C H H\n",
+      "BUILD BONDS: atom 44 C\n",
+      "BUILD BONDS: bond 41 44 1.0 C C C\n",
+      "BUILD BONDS: bond 44 45 1.0 C H H\n",
+      "BUILD BONDS: bond 44 46 1.0 C H H\n",
+      "BUILD BONDS: bond 44 47 1.0 C C C\n",
+      "BUILD BONDS: atom 45 H\n",
+      "BUILD BONDS: bond 44 45 1.0 C H H\n",
+      "BUILD BONDS: atom 46 H\n",
+      "BUILD BONDS: bond 44 46 1.0 C H H\n",
+      "BUILD BONDS: atom 47 C\n",
+      "BUILD BONDS: bond 44 47 1.0 C C C\n",
+      "BUILD BONDS: bond 47 48 1.0 C H H\n",
+      "BUILD BONDS: bond 47 49 1.0 C H H\n",
+      "BUILD BONDS: bond 47 50 1.0 C H H\n",
+      "BUILD BONDS: atom 48 H\n",
+      "BUILD BONDS: bond 47 48 1.0 C H H\n",
+      "BUILD BONDS: atom 49 H\n",
+      "BUILD BONDS: bond 47 49 1.0 C H H\n",
+      "BUILD BONDS: atom 50 H\n",
+      "BUILD BONDS: bond 47 50 1.0 C H H\n",
+      "BUILD BONDS: atom 51 H\n",
+      "BUILD BONDS: bond 16 51 1.0 C H H\n",
+      "BUILD BONDS: atom 52 H\n",
+      "BUILD BONDS: bond 38 52 1.0 C H H\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H36-C16-N\n",
+      "BUILD BONDS: atom 0 N\n",
+      "BUILD BONDS: bond 0 9 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 16 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 19 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 47 1.0 N C C\n",
+      "BUILD BONDS: atom 1 C\n",
+      "BUILD BONDS: bond 1 2 1.0 C H H\n",
+      "BUILD BONDS: bond 1 17 1.0 C H H\n",
+      "BUILD BONDS: bond 1 19 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 1 24 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 1 2 1.0 C H H\n",
+      "BUILD BONDS: atom 3 H\n",
+      "BUILD BONDS: bond 3 38 1.0 H C C\n",
+      "BUILD BONDS: atom 4 C\n",
+      "BUILD BONDS: bond 4 5 1.0 C H H\n",
+      "BUILD BONDS: bond 4 6 1.0 C H H\n",
+      "BUILD BONDS: bond 4 46 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 4 47 1.0 C C C\n",
+      "BUILD BONDS: atom 5 H\n",
+      "BUILD BONDS: bond 4 5 1.0 C H H\n",
+      "BUILD BONDS: atom 6 H\n",
+      "BUILD BONDS: bond 4 6 1.0 C H H\n",
+      "BUILD BONDS: atom 7 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 8 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 9 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 10 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 11 H\n",
+      "BUILD BONDS: bond 11 46 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 12 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 13 H\n",
+      "BUILD BONDS: bond 13 35 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 14 H\n",
+      "BUILD BONDS: bond 14 19 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 15 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 16 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 17 H\n",
+      "BUILD BONDS: bond 1 17 1.0 C H H\n",
+      "BUILD BONDS: atom 18 C\n",
+      "BUILD BONDS: bond 12 18 1.0 C C C\n",
+      "BUILD BONDS: bond 16 18 1.0 H C C\n",
+      "BUILD BONDS: bond 18 35 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 18 49 1.0 C H H\n",
+      "BUILD BONDS: atom 19 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 20 H\n",
+      "BUILD BONDS: bond 20 21 1.0 H C C\n",
+      "BUILD BONDS: atom 21 C\n",
+      "BUILD BONDS: bond 20 21 1.0 H C C\n",
+      "BUILD BONDS: bond 21 22 1.0 C H H\n",
+      "BUILD BONDS: bond 21 32 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 21 37 1.0 C H H\n",
+      "BUILD BONDS: atom 22 H\n",
+      "BUILD BONDS: bond 21 22 1.0 C H H\n",
+      "BUILD BONDS: atom 23 H\n",
+      "BUILD BONDS: bond 8 23 1.0 H H H\n",
+      "BUILD BONDS: atom 24 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 25 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 26 H\n",
+      "BUILD BONDS: bond 26 38 1.0 H C C\n",
+      "BUILD BONDS: atom 27 H\n",
+      "BUILD BONDS: bond 27 31 1.0 H C C\n",
+      "BUILD BONDS: atom 28 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 29 H\n",
+      "BUILD BONDS: bond 8 29 1.0 H H H\n",
+      "BUILD BONDS: atom 30 H\n",
+      "BUILD BONDS: bond 30 32 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 31 C\n",
+      "BUILD BONDS: bond 27 31 1.0 H C C\n",
+      "BUILD BONDS: bond 31 33 1.0 C H H\n",
+      "BUILD BONDS: bond 31 34 1.0 C C H\n",
+      "Error with Bond EndAtom C H\n",
+      "BUILD BONDS: bond 31 35 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 32 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 33 H\n",
+      "BUILD BONDS: bond 31 33 1.0 C H H\n",
+      "BUILD BONDS: atom 34 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 35 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 36 H\n",
+      "BUILD BONDS: bond 9 36 1.0 H H H\n",
+      "BUILD BONDS: atom 37 H\n",
+      "BUILD BONDS: bond 21 37 1.0 C H H\n",
+      "BUILD BONDS: atom 38 C\n",
+      "BUILD BONDS: bond 3 38 1.0 H C C\n",
+      "BUILD BONDS: bond 24 38 1.0 H C C\n",
+      "BUILD BONDS: bond 26 38 1.0 H C C\n",
+      "BUILD BONDS: bond 38 52 1.0 C H H\n",
+      "BUILD BONDS: atom 39 H\n",
+      "BUILD BONDS: bond 24 39 1.0 H H H\n",
+      "BUILD BONDS: atom 40 H\n",
+      "BUILD BONDS: bond 35 40 1.0 H H H\n",
+      "BUILD BONDS: atom 41 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 42 H\n",
+      "BUILD BONDS: bond 16 42 1.0 H H H\n",
+      "BUILD BONDS: atom 43 H\n",
+      "BUILD BONDS: bond 9 43 1.0 H H H\n",
+      "BUILD BONDS: atom 44 C\n",
+      "BUILD BONDS: bond 9 44 1.0 H C C\n",
+      "BUILD BONDS: bond 15 44 1.0 C C C\n",
+      "BUILD BONDS: bond 32 44 1.0 H C C\n",
+      "BUILD BONDS: bond 44 45 1.0 C H H\n",
+      "BUILD BONDS: atom 45 H\n",
+      "BUILD BONDS: bond 44 45 1.0 C H H\n",
+      "BUILD BONDS: atom 46 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 47 C\n",
+      "BUILD BONDS: bond 0 47 1.0 N C C\n",
+      "BUILD BONDS: bond 4 47 1.0 C C C\n",
+      "BUILD BONDS: bond 47 48 1.0 C H H\n",
+      "BUILD BONDS: bond 47 50 1.0 C H H\n",
+      "BUILD BONDS: atom 48 H\n",
+      "BUILD BONDS: bond 47 48 1.0 C H H\n",
+      "BUILD BONDS: atom 49 H\n",
+      "BUILD BONDS: bond 18 49 1.0 C H H\n",
+      "BUILD BONDS: atom 50 H\n",
+      "BUILD BONDS: bond 47 50 1.0 C H H\n",
+      "BUILD BONDS: atom 51 H\n",
+      "BUILD BONDS: bond 16 51 1.0 H H H\n",
+      "BUILD BONDS: atom 52 H\n",
+      "BUILD BONDS: bond 38 52 1.0 C H H\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H36-C16-N\n",
+      "BUILD BONDS: atom 0 N\n",
+      "BUILD BONDS: bond 0 12 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 20 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 21 1.0 N C C\n",
+      "BUILD BONDS: bond 0 27 1.0 N C C\n",
+      "BUILD BONDS: atom 1 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 2 24 1.0 H C C\n",
+      "BUILD BONDS: atom 3 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 4 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 5 H\n",
+      "BUILD BONDS: bond 5 12 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 6 H\n",
+      "BUILD BONDS: bond 6 16 1.0 H C C\n",
+      "BUILD BONDS: atom 7 C\n",
+      "BUILD BONDS: bond 7 10 1.0 C C C\n",
+      "BUILD BONDS: bond 7 19 1.0 C H H\n",
+      "BUILD BONDS: bond 7 21 1.0 C C C\n",
+      "BUILD BONDS: bond 7 28 1.0 C H H\n",
+      "BUILD BONDS: atom 8 H\n",
+      "BUILD BONDS: bond 8 16 1.0 H C C\n",
+      "BUILD BONDS: atom 9 H\n",
+      "BUILD BONDS: bond 9 16 1.0 H C C\n",
+      "BUILD BONDS: atom 10 C\n",
+      "BUILD BONDS: bond 4 10 1.0 C C C\n",
+      "BUILD BONDS: bond 7 10 1.0 C C C\n",
+      "BUILD BONDS: bond 10 32 1.0 C H H\n",
+      "BUILD BONDS: bond 10 38 1.0 C C C\n",
+      "BUILD BONDS: atom 11 H\n",
+      "BUILD BONDS: bond 11 20 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 12 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 13 C\n",
+      "BUILD BONDS: bond 3 13 1.0 H C C\n",
+      "BUILD BONDS: bond 13 14 1.0 C H H\n",
+      "BUILD BONDS: bond 13 22 1.0 C H H\n",
+      "BUILD BONDS: bond 13 27 1.0 C C C\n",
+      "BUILD BONDS: atom 14 H\n",
+      "BUILD BONDS: bond 13 14 1.0 C H H\n",
+      "BUILD BONDS: atom 15 H\n",
+      "BUILD BONDS: bond 15 41 1.0 H C C\n",
+      "BUILD BONDS: atom 16 C\n",
+      "BUILD BONDS: bond 6 16 1.0 H C C\n",
+      "BUILD BONDS: bond 8 16 1.0 H C C\n",
+      "BUILD BONDS: bond 9 16 1.0 H C C\n",
+      "BUILD BONDS: bond 16 40 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 17 H\n",
+      "BUILD BONDS: bond 17 24 1.0 H C C\n",
+      "BUILD BONDS: atom 18 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 19 H\n",
+      "BUILD BONDS: bond 7 19 1.0 C H H\n",
+      "BUILD BONDS: atom 20 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 21 C\n",
+      "BUILD BONDS: bond 0 21 1.0 N C C\n",
+      "BUILD BONDS: bond 7 21 1.0 C C C\n",
+      "BUILD BONDS: bond 21 23 1.0 C H H\n",
+      "BUILD BONDS: bond 21 30 1.0 C H H\n",
+      "BUILD BONDS: atom 22 H\n",
+      "BUILD BONDS: bond 13 22 1.0 C H H\n",
+      "BUILD BONDS: atom 23 H\n",
+      "BUILD BONDS: bond 21 23 1.0 C H H\n",
+      "BUILD BONDS: atom 24 C\n",
+      "BUILD BONDS: bond 2 24 1.0 H C C\n",
+      "BUILD BONDS: bond 17 24 1.0 H C C\n",
+      "BUILD BONDS: bond 20 24 1.0 H C C\n",
+      "BUILD BONDS: bond 24 40 1.0 C H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 25 H\n",
+      "BUILD BONDS: bond 25 27 1.0 H C C\n",
+      "BUILD BONDS: atom 26 H\n",
+      "BUILD BONDS: bond 26 27 1.0 H C C\n",
+      "BUILD BONDS: atom 27 C\n",
+      "BUILD BONDS: bond 0 27 1.0 N C C\n",
+      "BUILD BONDS: bond 13 27 1.0 C C C\n",
+      "BUILD BONDS: bond 25 27 1.0 H C C\n",
+      "BUILD BONDS: bond 26 27 1.0 H C C\n",
+      "BUILD BONDS: atom 28 H\n",
+      "BUILD BONDS: bond 7 28 1.0 C H H\n",
+      "BUILD BONDS: atom 29 H\n",
+      "BUILD BONDS: bond 20 29 1.0 H H H\n",
+      "BUILD BONDS: atom 30 H\n",
+      "BUILD BONDS: bond 21 30 1.0 C H H\n",
+      "BUILD BONDS: atom 31 C\n",
+      "BUILD BONDS: bond 31 33 1.0 C H H\n",
+      "BUILD BONDS: bond 31 44 1.0 C C C\n",
+      "BUILD BONDS: bond 31 46 1.0 C H H\n",
+      "BUILD BONDS: bond 31 48 1.0 C H H\n",
+      "BUILD BONDS: atom 32 H\n",
+      "BUILD BONDS: bond 10 32 1.0 C H H\n",
+      "BUILD BONDS: atom 33 H\n",
+      "BUILD BONDS: bond 31 33 1.0 C H H\n",
+      "BUILD BONDS: atom 34 H\n",
+      "BUILD BONDS: bond 34 44 1.0 H C C\n",
+      "BUILD BONDS: atom 35 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 36 H\n",
+      "BUILD BONDS: bond 3 36 1.0 H H H\n",
+      "BUILD BONDS: atom 37 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 38 C\n",
+      "BUILD BONDS: bond 10 38 1.0 C C C\n",
+      "BUILD BONDS: bond 38 39 1.0 C H H\n",
+      "BUILD BONDS: bond 38 47 1.0 C C H\n"
      ]
     },
     {
-     "ename": "UnboundLocalError",
-     "evalue": "local variable 'new_bond' referenced before assignment",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mUnboundLocalError\u001b[0m                         Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [24]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mnewcell\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_bonds\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdebug\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdebug\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m/opt/anaconda3/envs/cell2mol/lib/python3.10/site-packages/cell2mol/classes.py:1427\u001b[0m, in \u001b[0;36mcell.create_bonds\u001b[0;34m(self, debug)\u001b[0m\n\u001b[1;32m   1424\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m mol \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmoleclist:\n\u001b[1;32m   1425\u001b[0m     \u001b[38;5;66;03m# First part\u001b[39;00m\n\u001b[1;32m   1426\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m mol\u001b[38;5;241m.\u001b[39miscomplex: \n\u001b[0;32m-> 1427\u001b[0m         \u001b[43mmol\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_bonds\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdebug\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdebug\u001b[49m\u001b[43m)\u001b[49m          \u001b[38;5;66;03m### Creates bonds between molecule.atoms using the molecule.rdkit_object\u001b[39;00m\n\u001b[1;32m   1429\u001b[0m     \u001b[38;5;66;03m# Second part\u001b[39;00m\n\u001b[1;32m   1430\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m mol\u001b[38;5;241m.\u001b[39miscomplex:\n",
-      "File \u001b[0;32m/opt/anaconda3/envs/cell2mol/lib/python3.10/site-packages/cell2mol/classes.py:329\u001b[0m, in \u001b[0;36mspecie.create_bonds\u001b[0;34m(self, debug)\u001b[0m\n\u001b[1;32m    327\u001b[0m     \u001b[38;5;66;03m## This has changed. Now there is a bond object, and we send the atom objects, not only the index\u001b[39;00m\n\u001b[1;32m    328\u001b[0m     new_bond \u001b[38;5;241m=\u001b[39m bond(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms[start], \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms[end], bond_order) \n\u001b[0;32m--> 329\u001b[0m atom\u001b[38;5;241m.\u001b[39madd_bond(\u001b[43mnew_bond\u001b[49m)\n",
-      "\u001b[0;31mUnboundLocalError\u001b[0m: local variable 'new_bond' referenced before assignment"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Error with Bond EndAtom C H\n",
+      "BUILD BONDS: bond 38 52 1.0 C H H\n",
+      "BUILD BONDS: atom 39 H\n",
+      "BUILD BONDS: bond 38 39 1.0 C H H\n",
+      "BUILD BONDS: atom 40 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 41 C\n",
+      "BUILD BONDS: bond 12 41 1.0 H C C\n",
+      "BUILD BONDS: bond 15 41 1.0 H C C\n",
+      "BUILD BONDS: bond 41 44 1.0 C C C\n",
+      "BUILD BONDS: bond 41 45 1.0 C H H\n",
+      "BUILD BONDS: atom 42 H\n",
+      "BUILD BONDS: bond 40 42 1.0 H H H\n",
+      "BUILD BONDS: atom 43 H\n",
+      "BUILD BONDS: bond 37 43 1.0 H H H\n",
+      "BUILD BONDS: atom 44 C\n",
+      "BUILD BONDS: bond 31 44 1.0 C C C\n",
+      "BUILD BONDS: bond 34 44 1.0 H C C\n",
+      "BUILD BONDS: bond 41 44 1.0 C C C\n",
+      "BUILD BONDS: bond 44 50 1.0 C H H\n",
+      "BUILD BONDS: atom 45 H\n",
+      "BUILD BONDS: bond 41 45 1.0 C H H\n",
+      "BUILD BONDS: atom 46 H\n",
+      "BUILD BONDS: bond 31 46 1.0 C H H\n",
+      "BUILD BONDS: atom 47 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 48 H\n",
+      "BUILD BONDS: bond 31 48 1.0 C H H\n",
+      "BUILD BONDS: atom 49 H\n",
+      "BUILD BONDS: bond 40 49 1.0 H H H\n",
+      "BUILD BONDS: atom 50 H\n",
+      "BUILD BONDS: bond 44 50 1.0 C H H\n",
+      "BUILD BONDS: atom 51 H\n",
+      "BUILD BONDS: bond 37 51 1.0 H H H\n",
+      "BUILD BONDS: atom 52 H\n",
+      "BUILD BONDS: bond 38 52 1.0 C H H\n",
+      "CELL.CREATE_BONDS: Creating Bonds for molecule H36-C16-N\n",
+      "BUILD BONDS: atom 0 N\n",
+      "BUILD BONDS: bond 0 4 1.0 N C C\n",
+      "BUILD BONDS: bond 0 11 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 19 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: bond 0 24 1.0 N H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 1 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 2 H\n",
+      "BUILD BONDS: bond 2 17 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 3 H\n",
+      "BUILD BONDS: bond 3 20 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 4 C\n",
+      "BUILD BONDS: bond 0 4 1.0 N C C\n",
+      "BUILD BONDS: bond 4 8 1.0 C H H\n",
+      "BUILD BONDS: bond 4 21 1.0 C C H\n",
+      "Error with Bond EndAtom C H\n",
+      "BUILD BONDS: bond 4 41 1.0 C C C\n",
+      "BUILD BONDS: atom 5 H\n",
+      "BUILD BONDS: bond 5 6 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 6 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 7 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 8 H\n",
+      "BUILD BONDS: bond 4 8 1.0 C H H\n",
+      "BUILD BONDS: atom 9 H\n",
+      "BUILD BONDS: bond 9 13 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 10 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 11 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 12 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 13 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 14 H\n",
+      "BUILD BONDS: bond 14 19 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 15 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 16 H\n",
+      "BUILD BONDS: bond 16 27 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 17 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 18 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 19 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 20 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 21 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 22 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 23 H\n",
+      "BUILD BONDS: bond 20 23 1.0 H H H\n",
+      "BUILD BONDS: atom 24 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 25 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 26 H\n",
+      "BUILD BONDS: bond 6 26 1.0 H H H\n",
+      "BUILD BONDS: atom 27 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 28 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 29 H\n",
+      "BUILD BONDS: bond 17 29 1.0 H H H\n",
+      "BUILD BONDS: atom 30 H\n",
+      "BUILD BONDS: bond 30 36 1.0 H H C\n",
+      "Error with Bond EndAtom H C\n",
+      "BUILD BONDS: atom 31 C\n",
+      "BUILD BONDS: bond 7 31 1.0 C C C\n",
+      "BUILD BONDS: bond 13 31 1.0 H C C\n",
+      "BUILD BONDS: bond 27 31 1.0 H C C\n",
+      "BUILD BONDS: bond 31 52 1.0 C H H\n",
+      "BUILD BONDS: atom 32 H\n",
+      "BUILD BONDS: bond 11 32 1.0 H H H\n",
+      "BUILD BONDS: atom 33 H\n",
+      "BUILD BONDS: bond 33 41 1.0 H C C\n",
+      "BUILD BONDS: atom 34 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 35 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 36 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 37 H\n",
+      "BUILD BONDS: bond 22 37 1.0 H H H\n",
+      "BUILD BONDS: atom 38 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 39 H\n",
+      "BUILD BONDS: bond 35 39 1.0 H H H\n",
+      "BUILD BONDS: atom 40 H\n",
+      "BUILD BONDS: bond 36 40 1.0 H H H\n",
+      "BUILD BONDS: atom 41 C\n",
+      "BUILD BONDS: bond 1 41 1.0 C C C\n",
+      "BUILD BONDS: bond 4 41 1.0 C C C\n",
+      "BUILD BONDS: bond 33 41 1.0 H C C\n",
+      "BUILD BONDS: bond 41 44 1.0 C C C\n",
+      "BUILD BONDS: atom 42 H\n",
+      "BUILD BONDS: bond 24 42 1.0 H H H\n",
+      "BUILD BONDS: atom 43 H\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: H C\n",
+      "BUILD BONDS: atom 44 C\n",
+      "BUILD BONDS: bond 35 44 1.0 H C C\n",
+      "BUILD BONDS: bond 38 44 1.0 C C C\n",
+      "BUILD BONDS: bond 41 44 1.0 C C C\n",
+      "BUILD BONDS: bond 44 50 1.0 C H H\n",
+      "BUILD BONDS: atom 45 H\n",
+      "BUILD BONDS: bond 36 45 1.0 H H H\n",
+      "BUILD BONDS: atom 46 H\n",
+      "BUILD BONDS: bond 13 46 1.0 H H H\n",
+      "BUILD BONDS: atom 47 C\n",
+      "Error in Create Bonds. Atom labels do not coincide. GMOL vs. MOL: C H\n",
+      "BUILD BONDS: atom 48 H\n",
+      "BUILD BONDS: bond 35 48 1.0 H H H\n",
+      "BUILD BONDS: atom 49 H\n",
+      "BUILD BONDS: bond 35 49 1.0 H H H\n",
+      "BUILD BONDS: atom 50 H\n",
+      "BUILD BONDS: bond 44 50 1.0 C H H\n",
+      "BUILD BONDS: atom 51 H\n",
+      "BUILD BONDS: bond 11 51 1.0 H H H\n",
+      "BUILD BONDS: atom 52 H\n",
+      "BUILD BONDS: bond 31 52 1.0 C H H\n"
      ]
     }
    ],
    "source": [
     "newcell.create_bonds(debug=debug)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4167f2dd",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {