diff --git a/docs/tutorial/analysis.ipynb b/docs/tutorial/analysis.ipynb
index 4bd4a5160..b77a283aa 100644
--- a/docs/tutorial/analysis.ipynb
+++ b/docs/tutorial/analysis.ipynb
@@ -1,227 +1,285 @@
 {
-  "cells": [
+  "cells" : [
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "TOqzF3QC_p6U"
-      },
-      "source": [
-        "# Tutorial: Analysis\n",
-        "\n",
-        "[![Open in Bohrium](https://cdn.dp.tech/bohrium/web/static/images/open-in-bohrium.svg)](https://bohrium.dp.tech/notebook/52a1b090ba2a4761836b5f19df1814e7)\n",
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "TOqzF3QC_p6U"},
+      "source" : [
+        "# Tutorial: Analysis\n", "\n",
+        "[![Open in "
+        "Bohrium](https://cdn.dp.tech/bohrium/web/static/images/"
+        "open-in-bohrium.svg)](https://bohrium.dp.tech/notebook/"
+        "52a1b090ba2a4761836b5f19df1814e7)\n",
         "\n",
-        "In this tutorial, we analyze a simple trajectroy as an example. The trajectory is taken from the real case [the thermal decomposition of CL-20](cl20.md).\n",
-        "\n",
-        "Download this trajectory using `wget`:"
+        "In this tutorial, we analyze a simple trajectroy as an example. The "
+        "trajectory is taken from the real case [the thermal decomposition of "
+        "CL-20](cl20.md).\n",
+        "\n", "Download this trajectory using `wget`:"
       ]
     },
     {
-      "cell_type": "code",
-      "execution_count": 7,
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "8tAra7vQ_JOL",
-        "outputId": "d44cc292-1e6c-4735-88e1-21c685b6d885"
+      "cell_type" : "code",
+      "execution_count" : 7,
+      "metadata" : {
+        "colab" : {"base_uri" : "https://localhost:8080/"},
+        "id" : "8tAra7vQ_JOL",
+        "outputId" : "d44cc292-1e6c-4735-88e1-21c685b6d885"
       },
-      "outputs": [
-        {
-          "name": "stderr",
-          "output_type": "stream",
-          "text": [
-            "--2022-11-05 08:51:40--  https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj\n",
-            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...\n",
-            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n",
-            "HTTP request sent, awaiting response... 200 OK\n",
-            "Length: 920127 (899K) [text/plain]\n",
-            "Saving to: ‘cl20.lammpstrj’\n",
-            "\n",
-            "     0K .......... .......... .......... .......... ..........  5% 4.24M 0s\n",
-            "    50K .......... .......... .......... .......... .......... 11% 5.15M 0s\n",
-            "   100K .......... .......... .......... .......... .......... 16% 24.7M 0s\n",
-            "   150K .......... .......... .......... .......... .......... 22% 20.2M 0s\n",
-            "   200K .......... .......... .......... .......... .......... 27% 7.99M 0s\n",
-            "   250K .......... .......... .......... .......... .......... 33% 42.7M 0s\n",
-            "   300K .......... .......... .......... .......... .......... 38% 38.7M 0s\n",
-            "   350K .......... .......... .......... .......... .......... 44% 40.9M 0s\n",
-            "   400K .......... .......... .......... .......... .......... 50% 54.6M 0s\n",
-            "   450K .......... .......... .......... .......... .......... 55% 58.8M 0s\n",
-            "   500K .......... .......... .......... .......... .......... 61% 9.66M 0s\n",
-            "   550K .......... .......... .......... .......... .......... 66% 45.7M 0s\n",
-            "   600K .......... .......... .......... .......... .......... 72% 38.5M 0s\n",
-            "   650K .......... .......... .......... .......... .......... 77% 80.2M 0s\n",
-            "   700K .......... .......... .......... .......... .......... 83% 70.4M 0s\n",
-            "   750K .......... .......... .......... .......... .......... 89% 68.7M 0s\n",
-            "   800K .......... .......... .......... .......... .......... 94% 67.0M 0s\n",
-            "   850K .......... .......... .......... .......... ........  100% 79.9M=0.05s\n",
-            "\n",
-            "2022-11-05 08:51:41 (18.5 MB/s) - ‘cl20.lammpstrj’ saved [920127/920127]\n",
-            "\n"
-          ]
-        }
-      ],
-      "source": [
-        "%%bash\n",
-        "wget https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj -O cl20.lammpstrj"
+      "outputs" : [ {
+        "name" : "stderr",
+        "output_type" : "stream",
+        "text" : [
+          "--2022-11-05 08:51:40--  "
+          "https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/"
+          "f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj\n",
+          "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... "
+          "185.199.109.133, 185.199.110.133, 185.199.111.133, ...\n",
+          "Connecting to raw.githubusercontent.com "
+          "(raw.githubusercontent.com)|185.199.109.133|:443... connected.\n",
+          "HTTP request sent, awaiting response... 200 OK\n",
+          "Length: 920127 (899K) [text/plain]\n",
+          "Saving to: ‘cl20.lammpstrj’\n",
+          "\n",
+          "     0K .......... .......... .......... .......... ..........  5% "
+          "4.24M 0s\n",
+          "    50K .......... .......... .......... .......... .......... 11% "
+          "5.15M 0s\n",
+          "   100K .......... .......... .......... .......... .......... 16% "
+          "24.7M 0s\n",
+          "   150K .......... .......... .......... .......... .......... 22% "
+          "20.2M 0s\n",
+          "   200K .......... .......... .......... .......... .......... 27% "
+          "7.99M 0s\n",
+          "   250K .......... .......... .......... .......... .......... 33% "
+          "42.7M 0s\n",
+          "   300K .......... .......... .......... .......... .......... 38% "
+          "38.7M 0s\n",
+          "   350K .......... .......... .......... .......... .......... 44% "
+          "40.9M 0s\n",
+          "   400K .......... .......... .......... .......... .......... 50% "
+          "54.6M 0s\n",
+          "   450K .......... .......... .......... .......... .......... 55% "
+          "58.8M 0s\n",
+          "   500K .......... .......... .......... .......... .......... 61% "
+          "9.66M 0s\n",
+          "   550K .......... .......... .......... .......... .......... 66% "
+          "45.7M 0s\n",
+          "   600K .......... .......... .......... .......... .......... 72% "
+          "38.5M 0s\n",
+          "   650K .......... .......... .......... .......... .......... 77% "
+          "80.2M 0s\n",
+          "   700K .......... .......... .......... .......... .......... 83% "
+          "70.4M 0s\n",
+          "   750K .......... .......... .......... .......... .......... 89% "
+          "68.7M 0s\n",
+          "   800K .......... .......... .......... .......... .......... 94% "
+          "67.0M 0s\n",
+          "   850K .......... .......... .......... .......... ........  100% "
+          "79.9M=0.05s\n",
+          "\n",
+          "2022-11-05 08:51:41 (18.5 MB/s) - ‘cl20.lammpstrj’ saved "
+          "[920127/920127]\n",
+          "\n"
+        ]
+      } ],
+      "source" : [
+        "%%bash\n", "wget "
+                    "https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/"
+                    "f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/"
+                    "cl20.lammpstrj -O cl20.lammpstrj"
       ]
     },
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "PmUV6VDyALqi"
-      },
-      "source": [
-        "Then use `reacnetgenerator` to analyze it. Note the order of elements (`H C N O`) MUST map to those in the trajectory."
-      ]
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "PmUV6VDyALqi"},
+      "source" :
+          ["Then use `reacnetgenerator` to analyze it. Note the order of "
+           "elements (`H C N O`) MUST map to those in the trajectory."]
     },
     {
-      "cell_type": "code",
-      "execution_count": 8,
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "AgVDORot8sfl",
-        "outputId": "bd357812-f3f7-4dee-e5cf-6a793b542ee6"
+      "cell_type" : "code",
+      "execution_count" : 8,
+      "metadata" : {
+        "colab" : {"base_uri" : "https://localhost:8080/"},
+        "id" : "AgVDORot8sfl",
+        "outputId" : "bd357812-f3f7-4dee-e5cf-6a793b542ee6"
       },
-      "outputs": [
-        {
-          "name": "stderr",
-          "output_type": "stream",
-          "text": [
-            "2022-11-05 08:51:46,154 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: ReacNetGenerator: an automatic reaction network generator for reactive\n",
-            "molecular dynamics simulation.\n",
-            "\n",
-            "Please cite: ReacNetGenerator: an automatic reaction network generator\n",
-            "for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys.,\n",
-            "2020, 22 (2): 683-691, doi: 10.1039/C9CP05091D\n",
-            "\n",
-            "Jinzhe Zeng (jinzhe.zeng@rutgers.edu), Tong Zhu (tzhu@lps.ecnu.edu.cn)\n",
-            "\n",
-            "==================\n",
-            "Features\n",
-            "==================\n",
-            "* Processing of MD trajectory containing atomic coordinates or bond orders\n",
-            "* Hidden Markov Model (HMM) based noise filtering\n",
-            "* Isomers identifying accoarding to SMILES\n",
-            "* Generation of reaction network for visualization using force-directed\n",
-            "  algorithm\n",
-            "* Parallel computing\n",
-            "\n",
-            "==================\n",
-            "Simple example\n",
-            "==================\n",
-            "ReacNetGenerator can process any kind of trajectory files containing \n",
-            "atomic coordinates, e.g. a LAMMPS dump file prepared by running “dump 1\n",
-            "all custom 100 dump.reaxc id type x y z” in LAMMPS:\n",
-            "$ reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm\n",
-            "where C, H, and O are atomic names in the input file. Analysis report\n",
-            "will be generated automatically.\n",
-            "\n",
-            "Also, ReacNetGenerator can process files containing bond information, \n",
-            "e.g. LAMMPS bond file:\n",
-            "$ reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm\n",
-            "\n",
-            "You can running the following script for help:\n",
-            "$ reacnetgenerator -h\n",
-            "\n",
-            "2022-11-05 08:51:46,154 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Version: 1.6.6.dev24+g068dac4  Creation date: 2018-03-11\n",
-            "\rRead bond information and Detect molecules: 0timestep [00:00, ?timestep/s]\rRead bond information and Detect molecules: 2timestep [00:01,  1.40timestep/s]\rRead bond information and Detect molecules: 101timestep [00:01, 70.84timestep/s]\n",
-            "\rSave molecules:   0%|          | 0/11 [00:00<?, ?molecule/s]\rSave molecules: 100%|██████████| 11/11 [00:00<00:00, 3376.31molecule/s]\n",
-            "2022-11-05 08:51:47,881 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 1: Done! Time consumed (s): 1.726 (Read bond information and detect molecules)\n",
-            "2022-11-05 08:51:47,941 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 2: Done! Time consumed (s): 0.060 (Merge isomers)\n",
-            "\rHMM filter: 0molecule [00:00, ?molecule/s]\rHMM filter: 11molecule [00:00, 2628.61molecule/s]\n",
-            "2022-11-05 08:51:48,139 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 3: Done! Time consumed (s): 0.198 (HMM filter)\n",
-            "\rIndentify isomers:   0%|          | 0/11 [00:00<?, ?molecule/s]\rIndentify isomers: 100%|██████████| 11/11 [00:00<00:00, 585.62molecule/s]\n",
-            "\rAnalyze atoms:   0%|          | 0/11 [00:00<?, ?molecule/s]\rAnalyze atoms: 100%|██████████| 11/11 [00:00<00:00, 7775.08molecule/s]\n",
-            "\rCollect reaction paths:   0%|          | 0/288 [00:00<?, ?atom/s]\rCollect reaction paths: 100%|██████████| 288/288 [00:00<00:00, 11114.42atom/s]\n",
-            "\rAnalyze reactions (A+B->C+D):   0%|          | 0/100 [00:00<?, ?timestep/s]\rAnalyze reactions (A+B->C+D): 100%|██████████| 100/100 [00:00<00:00, 12790.24timestep/s]\n",
-            "2022-11-05 08:51:48,583 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 4: Done! Time consumed (s): 0.444 (Indentify isomers and collect reaction paths)\n",
-            "2022-11-05 08:51:48,651 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 5: Done! Time consumed (s): 0.068 (Reaction matrix generation)\n",
-            "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Species are:\n",
-            "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: 1 [H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n",
-            "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: 2 [H]C12NC3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n",
-            "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: 3 O=NO\n",
-            "2022-11-05 08:51:48,672 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: The position of the species in the network is:\n",
-            "2022-11-05 08:51:48,672 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: {1: array([-5.95629110e-05, -1.00129074e-04]), 2: array([-0.59480018, -0.99989987]), 3: array([0.59485974, 1.        ])}\n",
-            "2022-11-05 08:51:48,855 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 6: Done! Time consumed (s): 0.204 (Draw reaction network)\n",
-            "2022-11-05 08:51:48,878 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Report is generated. Please see cl20.lammpstrj.html for more details.\n",
-            "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 7: Done! Time consumed (s): 0.087 (Generate analysis report)\n",
-            "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: ====== Summary ======\n",
-            "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Total time(s): 2.787 s\n"
-          ]
-        }
-      ],
-      "source": [
+      "outputs" : [ {
+        "name" : "stderr",
+        "output_type" : "stream",
+        "text" : [
+          "2022-11-05 08:51:46,154 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: ReacNetGenerator: an automatic reaction network generator for "
+          "reactive\n",
+          "molecular dynamics simulation.\n",
+          "\n",
+          "Please cite: ReacNetGenerator: an automatic reaction network "
+          "generator\n",
+          "for reactive molecular dynamic simulations, Phys. Chem. Chem. "
+          "Phys.,\n",
+          "2020, 22 (2): 683-691, doi: 10.1039/C9CP05091D\n",
+          "\n",
+          "Jinzhe Zeng (jinzhe.zeng@rutgers.edu), Tong Zhu "
+          "(tzhu@lps.ecnu.edu.cn)\n",
+          "\n",
+          "==================\n",
+          "Features\n",
+          "==================\n",
+          "* Processing of MD trajectory containing atomic coordinates or bond "
+          "orders\n",
+          "* Hidden Markov Model (HMM) based noise filtering\n",
+          "* Isomers identifying accoarding to SMILES\n",
+          "* Generation of reaction network for visualization using "
+          "force-directed\n",
+          "  algorithm\n",
+          "* Parallel computing\n",
+          "\n",
+          "==================\n",
+          "Simple example\n",
+          "==================\n",
+          "ReacNetGenerator can process any kind of trajectory files "
+          "containing \n",
+          "atomic coordinates, e.g. a LAMMPS dump file prepared by running "
+          "“dump 1\n",
+          "all custom 100 dump.reaxc id type x y z” in LAMMPS:\n",
+          "$ reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm\n",
+          "where C, H, and O are atomic names in the input file. Analysis "
+          "report\n",
+          "will be generated automatically.\n",
+          "\n",
+          "Also, ReacNetGenerator can process files containing bond "
+          "information, \n",
+          "e.g. LAMMPS bond file:\n",
+          "$ reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm\n",
+          "\n",
+          "You can running the following script for help:\n",
+          "$ reacnetgenerator -h\n",
+          "\n",
+          "2022-11-05 08:51:46,154 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Version: 1.6.6.dev24+g068dac4  Creation date: 2018-03-11\n",
+          "\rRead bond information and Detect molecules: 0timestep [00:00, "
+          "?timestep/s]\rRead bond information and Detect molecules: 2timestep "
+          "[00:01,  1.40timestep/s]\rRead bond information and Detect "
+          "molecules: 101timestep [00:01, 70.84timestep/s]\n",
+          "\rSave molecules:   0%|          | 0/11 [00:00<?, "
+          "?molecule/s]\rSave molecules: 100%|██████████| 11/11 [00:00<00:00, "
+          "3376.31molecule/s]\n",
+          "2022-11-05 08:51:47,881 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 1: Done! Time consumed (s): 1.726 (Read bond information "
+          "and detect molecules)\n",
+          "2022-11-05 08:51:47,941 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 2: Done! Time consumed (s): 0.060 (Merge isomers)\n",
+          "\rHMM filter: 0molecule [00:00, ?molecule/s]\rHMM filter: "
+          "11molecule [00:00, 2628.61molecule/s]\n",
+          "2022-11-05 08:51:48,139 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 3: Done! Time consumed (s): 0.198 (HMM filter)\n",
+          "\rIndentify isomers:   0%|          | 0/11 [00:00<?, "
+          "?molecule/s]\rIndentify isomers: 100%|██████████| 11/11 "
+          "[00:00<00:00, 585.62molecule/s]\n",
+          "\rAnalyze atoms:   0%|          | 0/11 [00:00<?, "
+          "?molecule/s]\rAnalyze atoms: 100%|██████████| 11/11 [00:00<00:00, "
+          "7775.08molecule/s]\n",
+          "\rCollect reaction paths:   0%|          | 0/288 [00:00<?, "
+          "?atom/s]\rCollect reaction paths: 100%|██████████| 288/288 "
+          "[00:00<00:00, 11114.42atom/s]\n",
+          "\rAnalyze reactions (A+B->C+D):   0%|          | 0/100 [00:00<?, "
+          "?timestep/s]\rAnalyze reactions (A+B->C+D): 100%|██████████| "
+          "100/100 [00:00<00:00, 12790.24timestep/s]\n",
+          "2022-11-05 08:51:48,583 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 4: Done! Time consumed (s): 0.444 (Indentify isomers and "
+          "collect reaction paths)\n",
+          "2022-11-05 08:51:48,651 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 5: Done! Time consumed (s): 0.068 (Reaction matrix "
+          "generation)\n",
+          "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Species are:\n",
+          "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: 1 "
+          "[H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)"
+          "C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n",
+          "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: 2 "
+          "[H]C12NC3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N("
+          "N(=O)=O)C1([H])N2N(=O)=O\n",
+          "2022-11-05 08:51:48,667 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: 3 O=NO\n",
+          "2022-11-05 08:51:48,672 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: The position of the species in the network is:\n",
+          "2022-11-05 08:51:48,672 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: {1: array([-5.95629110e-05, -1.00129074e-04]), 2: "
+          "array([-0.59480018, -0.99989987]), 3: array([0.59485974, 1.        "
+          "])}\n",
+          "2022-11-05 08:51:48,855 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 6: Done! Time consumed (s): 0.204 (Draw reaction "
+          "network)\n",
+          "2022-11-05 08:51:48,878 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Report is generated. Please see cl20.lammpstrj.html for more "
+          "details.\n",
+          "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Step 7: Done! Time consumed (s): 0.087 (Generate analysis "
+          "report)\n",
+          "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: ====== Summary ======\n",
+          "2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - "
+          "INFO: Total time(s): 2.787 s\n"
+        ]
+      } ],
+      "source" : [
         "%%bash\n",
         "reacnetgenerator -i cl20.lammpstrj -a H C N O --type dump --nohmm"
       ]
     },
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "PO14aadxA4Cy"
-      },
-      "source": [
-        "The results are shown in `cl20.lammpstrj.html`. In addition, we can view an overview of reactions in the trajectory in the command line:"
-      ]
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "PO14aadxA4Cy"},
+      "source" : ["The results are shown in `cl20.lammpstrj.html`. In "
+                  "addition, we can view an overview of reactions in the "
+                  "trajectory in the command line:"]
     },
     {
-      "cell_type": "code",
-      "execution_count": 9,
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "GQNtq6mLAoJK",
-        "outputId": "1fcc9399-5b5b-4fa6-b0aa-f753fcfb9fd2"
+      "cell_type" : "code",
+      "execution_count" : 9,
+      "metadata" : {
+        "colab" : {"base_uri" : "https://localhost:8080/"},
+        "id" : "GQNtq6mLAoJK",
+        "outputId" : "1fcc9399-5b5b-4fa6-b0aa-f753fcfb9fd2"
       },
-      "outputs": [
-        {
-          "name": "stdout",
-          "output_type": "stream",
-          "text": [
-            "1 [H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O->O=NO+[H]C12NC3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O\n"
-          ]
-        }
-      ],
-      "source": [
-        "%%bash\n",
-        "cat cl20.lammpstrj.reactionabcd"
-      ]
+      "outputs" : [ {
+        "name" : "stdout",
+        "output_type" : "stream",
+        "text" : ["1 "
+                  "[H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N("
+                  "N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O->O=NO+[H]C12NC3(["
+                  "H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(="
+                  "O)=O)C1([H])N2N(=O)=O\n"]
+      } ],
+      "source" : [ "%%bash\n", "cat cl20.lammpstrj.reactionabcd" ]
     },
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "4xL87CdoBPQz"
-      },
-      "source": [
-        "Here we can clearly see that the CL-20 molecule is decomposited into a nitrogen dioxide molecule.\n"
-      ]
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "4xL87CdoBPQz"},
+      "source" : ["Here we can clearly see that the CL-20 molecule is "
+                  "decomposited into a nitrogen dioxide molecule.\n"]
     }
   ],
-  "metadata": {
-    "colab": {
-      "authorship_tag": "ABX9TyN2IDYefbmLYArmNHl2104Q",
-      "include_colab_link": true,
-      "provenance": []
-    },
-    "kernelspec": {
-      "display_name": "Python 3.10.6 64-bit",
-      "language": "python",
-      "name": "python3"
+  "metadata" : {
+    "colab" : {
+      "authorship_tag" : "ABX9TyN2IDYefbmLYArmNHl2104Q",
+      "include_colab_link" : true,
+      "provenance" : []
     },
-    "language_info": {
-      "name": "python",
-      "version": "3.10.6"
+    "kernelspec" : {
+      "display_name" : "Python 3.10.6 64-bit",
+      "language" : "python",
+      "name" : "python3"
     },
-    "vscode": {
-      "interpreter": {
-        "hash": "916dbcbb3f70747c44a77c7bcd40155683ae19c65e1c03b4aa3499c5328201f1"
+    "language_info" : {"name" : "python", "version" : "3.10.6"},
+    "vscode" : {
+      "interpreter" : {
+        "hash" :
+            "916dbcbb3f70747c44a77c7bcd40155683ae19c65e1c03b4aa3499c5328201f1"
       }
     }
   },
-  "nbformat": 4,
-  "nbformat_minor": 0
+  "nbformat" : 4,
+  "nbformat_minor" : 0
 }
diff --git a/docs/tutorial/install.ipynb b/docs/tutorial/install.ipynb
index 4b9eef838..2b99ffd32 100644
--- a/docs/tutorial/install.ipynb
+++ b/docs/tutorial/install.ipynb
@@ -1,201 +1,279 @@
 {
-  "cells": [
+  "cells" : [
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "wRfG0B6jxcT0"
-      },
-      "source": [
-        "# Tutorial: Installation\n",
-        "\n",
-        "In this series of tutorials, we will try to install and run ReacNetGenerator.\n",
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "wRfG0B6jxcT0"},
+      "source" : [
+        "# Tutorial: Installation\n", "\n",
+        "In this series of tutorials, we will try to install and run "
+        "ReacNetGenerator.\n",
         "\n",
-        "In this tutorial, we will use `pip` to install ReacNetGenerator. This is the eastiest way without compiling the package."
+        "In this tutorial, we will use `pip` to install ReacNetGenerator. This "
+        "is the eastiest way without compiling the package."
       ]
     },
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "sfF2fuVHyu2M"
-      },
-      "source": [
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "sfF2fuVHyu2M"},
+      "source" : [
         "## Install ReacNetGenerator\n",
-        "We use `pip` to install the ReacNetGenerator. It's very simple as follows!"
+        "We use `pip` to install the ReacNetGenerator. It's very simple as "
+        "follows!"
       ]
     },
     {
-      "cell_type": "code",
-      "execution_count": 1,
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "c5oBZFSQtKFi",
-        "outputId": "8d63a695-7630-499a-b4ff-d598bf86248a"
+      "cell_type" : "code",
+      "execution_count" : 1,
+      "metadata" : {
+        "colab" : {"base_uri" : "https://localhost:8080/"},
+        "id" : "c5oBZFSQtKFi",
+        "outputId" : "8d63a695-7630-499a-b4ff-d598bf86248a"
       },
-      "outputs": [
-        {
-          "name": "stdout",
-          "output_type": "stream",
-          "text": [
-            "Collecting reacnetgenerator\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/1f/e9/56819faadf4d9c253b4110fb0e1304a2a80094e03c4e9e9a8a67fb6c1751/reacnetgenerator-1.4.164-cp37-cp37m-manylinux2010_x86_64.whl (4.3MB)\n",
-            "\u001b[K     |████████████████████████████████| 4.3MB 6.3MB/s \n",
-            "\u001b[?25hCollecting lz4\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/e3/52/151c815a486290608e4dc6699a0cfd74141dc5191f8fe928e7d1b28b569e/lz4-3.1.3-cp37-cp37m-manylinux2010_x86_64.whl (1.8MB)\n",
-            "\u001b[K     |████████████████████████████████| 1.8MB 37.9MB/s \n",
-            "\u001b[?25hCollecting coloredlogs\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/84/a6/837dbf6eac344cb74f0ba86b79e8180855570af3e26bcb1ea5f650cf944c/coloredlogs-15.0-py2.py3-none-any.whl (45kB)\n",
-            "\u001b[K     |████████████████████████████████| 51kB 4.6MB/s \n",
-            "\u001b[?25hCollecting scour\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/75/19/f519ef8aa2f379935a44212c5744e2b3a46173bf04e0110fb7f4af4028c9/scour-0.38.2.tar.gz (52kB)\n",
-            "\u001b[K     |████████████████████████████████| 61kB 5.7MB/s \n",
-            "\u001b[?25hRequirement already satisfied: networkx in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (2.5)\n",
-            "Collecting ase\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/a5/36/de17e79f29e06d9a92746d0dd9ec4636487ab03f6af10e78586aae533f7a/ase-3.21.1-py3-none-any.whl (2.2MB)\n",
-            "\u001b[K     |████████████████████████████████| 2.2MB 33.9MB/s \n",
-            "\u001b[?25hRequirement already satisfied: requests in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (2.23.0)\n",
-            "Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (3.2.2)\n",
-            "Collecting openbabel-wheel\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/f3/e8/74018a601ec40dd76b9ba6d0ddfa22a67bb5802fd6ffa46a344915d46ff4/openbabel_wheel-3.1.1.5-cp37-cp37m-manylinux2014_x86_64.whl (13.6MB)\n",
-            "\u001b[K     |████████████████████████████████| 13.6MB 258kB/s \n",
-            "\u001b[?25hRequirement already satisfied: numpy in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (1.19.5)\n",
-            "Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (1.1.5)\n",
-            "Collecting pybase64\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/71/9c/fc5a2734645f9cdc7c0a549a4ee063cf25c05e728d287508fd14c437ac4e/pybase64-1.1.4-cp37-cp37m-manylinux2014_x86_64.whl (170kB)\n",
-            "\u001b[K     |████████████████████████████████| 174kB 50.0MB/s \n",
-            "\u001b[?25hRequirement already satisfied: scipy>=0.20.1 in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (1.4.1)\n",
-            "Collecting rdkit-pypi\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/6f/1b/053bddf14b39000ff95c59d012934fcbe96fef681ece0f8315c126c0bb5b/rdkit_pypi-2021.3.1.2-cp37-cp37m-manylinux2014_x86_64.whl (31.4MB)\n",
-            "\u001b[K     |████████████████████████████████| 31.4MB 111kB/s \n",
-            "\u001b[?25hCollecting hmmlearn>=0.2.1\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/4b/98/a2829aeb942b7146034d497afb3fc738a78a4fbd4797a039c19a94bb31f7/hmmlearn-0.2.5-cp37-cp37m-manylinux1_x86_64.whl (369kB)\n",
-            "\u001b[K     |████████████████████████████████| 378kB 34.7MB/s \n",
-            "\u001b[?25hRequirement already satisfied: tqdm in /usr/local/lib/python3.7/dist-packages (from reacnetgenerator) (4.41.1)\n",
-            "Collecting humanfriendly>=9.1\n",
-            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/93/66/363d01a81da2108a5cf446daf619779f06d49a0c4426dd02b40734f10e2f/humanfriendly-9.1-py2.py3-none-any.whl (86kB)\n",
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-            "Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.7/dist-packages (from networkx->reacnetgenerator) (4.4.2)\n",
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-            "Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (1.24.3)\n",
-            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (2020.12.5)\n",
-            "Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests->reacnetgenerator) (2.10)\n",
-            "Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (2.8.1)\n",
-            "Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (2.4.7)\n",
-            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (1.3.1)\n",
-            "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib->reacnetgenerator) (0.10.0)\n",
-            "Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->reacnetgenerator) (2018.9)\n",
-            "Requirement already satisfied: scikit-learn>=0.16 in /usr/local/lib/python3.7/dist-packages (from hmmlearn>=0.2.1->reacnetgenerator) (0.22.2.post1)\n",
-            "Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.7/dist-packages (from scikit-learn>=0.16->hmmlearn>=0.2.1->reacnetgenerator) (1.0.1)\n",
-            "Building wheels for collected packages: scour\n",
-            "  Building wheel for scour (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
-            "  Created wheel for scour: filename=scour-0.38.2-cp37-none-any.whl size=54253 sha256=5c236125ed4b03b44f5f87c711b62d82acf7d183e110bee4250ae7cfbd78aa33\n",
-            "  Stored in directory: /root/.cache/pip/wheels/0e/85/c0/989d78aef861a7859c2ec1e56157abc1255498e49dcbfa23f4\n",
-            "Successfully built scour\n",
-            "Installing collected packages: lz4, humanfriendly, coloredlogs, scour, ase, openbabel-wheel, pybase64, rdkit-pypi, hmmlearn, reacnetgenerator\n",
-            "Successfully installed ase-3.21.1 coloredlogs-15.0 hmmlearn-0.2.5 humanfriendly-9.1 lz4-3.1.3 openbabel-wheel-3.1.1.5 pybase64-1.1.4 rdkit-pypi-2021.3.1.2 reacnetgenerator-1.4.164 scour-0.38.2\n"
-          ]
-        }
-      ],
-      "source": [
-        "%%bash\n",
-        "pip install reacnetgenerator"
-      ]
+      "outputs" : [ {
+        "name" : "stdout",
+        "output_type" : "stream",
+        "text" : [
+          "Collecting reacnetgenerator\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/1f/e9/"
+          "56819faadf4d9c253b4110fb0e1304a2a80094e03c4e9e9a8a67fb6c1751/"
+          "reacnetgenerator-1.4.164-cp37-cp37m-manylinux2010_x86_64.whl "
+          "(4.3MB)\n",
+          "\u001b[K     |████████████████████████████████| 4.3MB 6.3MB/s \n",
+          "\u001b[?25hCollecting lz4\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/e3/52/"
+          "151c815a486290608e4dc6699a0cfd74141dc5191f8fe928e7d1b28b569e/"
+          "lz4-3.1.3-cp37-cp37m-manylinux2010_x86_64.whl (1.8MB)\n",
+          "\u001b[K     |████████████████████████████████| 1.8MB 37.9MB/s \n",
+          "\u001b[?25hCollecting coloredlogs\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/84/a6/"
+          "837dbf6eac344cb74f0ba86b79e8180855570af3e26bcb1ea5f650cf944c/"
+          "coloredlogs-15.0-py2.py3-none-any.whl (45kB)\n",
+          "\u001b[K     |████████████████████████████████| 51kB 4.6MB/s \n",
+          "\u001b[?25hCollecting scour\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/75/19/"
+          "f519ef8aa2f379935a44212c5744e2b3a46173bf04e0110fb7f4af4028c9/"
+          "scour-0.38.2.tar.gz (52kB)\n",
+          "\u001b[K     |████████████████████████████████| 61kB 5.7MB/s \n",
+          "\u001b[?25hRequirement already satisfied: networkx in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(2.5)\n",
+          "Collecting ase\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/a5/36/"
+          "de17e79f29e06d9a92746d0dd9ec4636487ab03f6af10e78586aae533f7a/"
+          "ase-3.21.1-py3-none-any.whl (2.2MB)\n",
+          "\u001b[K     |████████████████████████████████| 2.2MB 33.9MB/s \n",
+          "\u001b[?25hRequirement already satisfied: requests in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(2.23.0)\n",
+          "Requirement already satisfied: matplotlib in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(3.2.2)\n",
+          "Collecting openbabel-wheel\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/f3/e8/"
+          "74018a601ec40dd76b9ba6d0ddfa22a67bb5802fd6ffa46a344915d46ff4/"
+          "openbabel_wheel-3.1.1.5-cp37-cp37m-manylinux2014_x86_64.whl "
+          "(13.6MB)\n",
+          "\u001b[K     |████████████████████████████████| 13.6MB 258kB/s \n",
+          "\u001b[?25hRequirement already satisfied: numpy in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(1.19.5)\n",
+          "Requirement already satisfied: pandas in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(1.1.5)\n",
+          "Collecting pybase64\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/71/9c/"
+          "fc5a2734645f9cdc7c0a549a4ee063cf25c05e728d287508fd14c437ac4e/"
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+          "\u001b[K     |████████████████████████████████| 174kB 50.0MB/s \n",
+          "\u001b[?25hRequirement already satisfied: scipy>=0.20.1 in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(1.4.1)\n",
+          "Collecting rdkit-pypi\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/6f/1b/"
+          "053bddf14b39000ff95c59d012934fcbe96fef681ece0f8315c126c0bb5b/"
+          "rdkit_pypi-2021.3.1.2-cp37-cp37m-manylinux2014_x86_64.whl "
+          "(31.4MB)\n",
+          "\u001b[K     |████████████████████████████████| 31.4MB 111kB/s \n",
+          "\u001b[?25hCollecting hmmlearn>=0.2.1\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/4b/98/"
+          "a2829aeb942b7146034d497afb3fc738a78a4fbd4797a039c19a94bb31f7/"
+          "hmmlearn-0.2.5-cp37-cp37m-manylinux1_x86_64.whl (369kB)\n",
+          "\u001b[K     |████████████████████████████████| 378kB 34.7MB/s \n",
+          "\u001b[?25hRequirement already satisfied: tqdm in "
+          "/usr/local/lib/python3.7/dist-packages (from reacnetgenerator) "
+          "(4.41.1)\n",
+          "Collecting humanfriendly>=9.1\n",
+          "\u001b[?25l  Downloading "
+          "https://files.pythonhosted.org/packages/93/66/"
+          "363d01a81da2108a5cf446daf619779f06d49a0c4426dd02b40734f10e2f/"
+          "humanfriendly-9.1-py2.py3-none-any.whl (86kB)\n",
+          "\u001b[K     |████████████████████████████████| 92kB 7.4MB/s \n",
+          "\u001b[?25hRequirement already satisfied: six>=1.9.0 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "scour->reacnetgenerator) (1.15.0)\n",
+          "Requirement already satisfied: decorator>=4.3.0 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "networkx->reacnetgenerator) (4.4.2)\n",
+          "Requirement already satisfied: chardet<4,>=3.0.2 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "requests->reacnetgenerator) (3.0.4)\n",
+          "Requirement already satisfied: "
+          "urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "requests->reacnetgenerator) (1.24.3)\n",
+          "Requirement already satisfied: certifi>=2017.4.17 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "requests->reacnetgenerator) (2020.12.5)\n",
+          "Requirement already satisfied: idna<3,>=2.5 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "requests->reacnetgenerator) (2.10)\n",
+          "Requirement already satisfied: python-dateutil>=2.1 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "matplotlib->reacnetgenerator) (2.8.1)\n",
+          "Requirement already satisfied: "
+          "pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "matplotlib->reacnetgenerator) (2.4.7)\n",
+          "Requirement already satisfied: kiwisolver>=1.0.1 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "matplotlib->reacnetgenerator) (1.3.1)\n",
+          "Requirement already satisfied: cycler>=0.10 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "matplotlib->reacnetgenerator) (0.10.0)\n",
+          "Requirement already satisfied: pytz>=2017.2 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "pandas->reacnetgenerator) (2018.9)\n",
+          "Requirement already satisfied: scikit-learn>=0.16 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "hmmlearn>=0.2.1->reacnetgenerator) (0.22.2.post1)\n",
+          "Requirement already satisfied: joblib>=0.11 in "
+          "/usr/local/lib/python3.7/dist-packages (from "
+          "scikit-learn>=0.16->hmmlearn>=0.2.1->reacnetgenerator) (1.0.1)\n",
+          "Building wheels for collected packages: scour\n",
+          "  Building wheel for scour (setup.py) ... "
+          "\u001b[?25l\u001b[?25hdone\n",
+          "  Created wheel for scour: filename=scour-0.38.2-cp37-none-any.whl "
+          "size=54253 "
+          "sha256="
+          "5c236125ed4b03b44f5f87c711b62d82acf7d183e110bee4250ae7cfbd78aa33\n",
+          "  Stored in directory: "
+          "/root/.cache/pip/wheels/0e/85/c0/"
+          "989d78aef861a7859c2ec1e56157abc1255498e49dcbfa23f4\n",
+          "Successfully built scour\n",
+          "Installing collected packages: lz4, humanfriendly, coloredlogs, "
+          "scour, ase, openbabel-wheel, pybase64, rdkit-pypi, hmmlearn, "
+          "reacnetgenerator\n",
+          "Successfully installed ase-3.21.1 coloredlogs-15.0 hmmlearn-0.2.5 "
+          "humanfriendly-9.1 lz4-3.1.3 openbabel-wheel-3.1.1.5 pybase64-1.1.4 "
+          "rdkit-pypi-2021.3.1.2 reacnetgenerator-1.4.164 scour-0.38.2\n"
+        ]
+      } ],
+      "source" : [ "%%bash\n", "pip install reacnetgenerator" ]
     },
     {
-      "cell_type": "markdown",
-      "metadata": {
-        "id": "Z-8L5vVKy9tc"
-      },
-      "source": [
-        "Now, ReacNetGenerator has been already installed in the environment. Try it now!"
-      ]
+      "cell_type" : "markdown",
+      "metadata" : {"id" : "Z-8L5vVKy9tc"},
+      "source" : ["Now, ReacNetGenerator has been already installed in the "
+                  "environment. Try it now!"]
     },
     {
-      "cell_type": "code",
-      "execution_count": 2,
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "ceO8qwJtxGxo",
-        "outputId": "35312703-c874-4f25-d685-8592b577a3d2"
+      "cell_type" : "code",
+      "execution_count" : 2,
+      "metadata" : {
+        "colab" : {"base_uri" : "https://localhost:8080/"},
+        "id" : "ceO8qwJtxGxo",
+        "outputId" : "35312703-c874-4f25-d685-8592b577a3d2"
       },
-      "outputs": [
-        {
-          "name": "stdout",
-          "output_type": "stream",
-          "text": [
-            "usage: reacnetgenerator [-h] -i [INPUTFILENAME [INPUTFILENAME ...]] -a\n",
-            "                        [ATOMNAME [ATOMNAME ...]] [--nohmm] [--dump]\n",
-            "                        [--type TYPE] [--nopbc] [--cell CELL CELL CELL]\n",
-            "                        [-n NPROC] [-s [SELECTATOMS [SELECTATOMS ...]]]\n",
-            "                        [--stepinterval STEPINTERVAL] [--split SPLIT]\n",
-            "                        [--maxspecies MAXSPECIES]\n",
-            "                        [--matrixa MATRIXA MATRIXA MATRIXA MATRIXA]\n",
-            "                        [--matrixb MATRIXB MATRIXB MATRIXB MATRIXB]\n",
-            "                        [--urls URLS URLS]\n",
-            "\n",
-            "ReacNetGenerator 1.4.164\n",
-            "\n",
-            "optional arguments:\n",
-            "  -h, --help            show this help message and exit\n",
-            "  -i [INPUTFILENAME [INPUTFILENAME ...]], --inputfilename [INPUTFILENAME [INPUTFILENAME ...]]\n",
-            "                        Input trajectory file, e.g. bonds.reaxc\n",
-            "  -a [ATOMNAME [ATOMNAME ...]], --atomname [ATOMNAME [ATOMNAME ...]]\n",
-            "                        Atomic names in the trajectory, e.g. C H O\n",
-            "  --nohmm               Process trajectory without Hidden Markov Model (HMM)\n",
-            "  --dump                Process the LAMMPS dump file\n",
-            "  --type TYPE, -t TYPE  Input file type\n",
-            "  --nopbc               Disable PBC.\n",
-            "  --cell CELL CELL CELL, -c CELL CELL CELL\n",
-            "                        Cell\n",
-            "  -n NPROC, -np NPROC, --nproc NPROC\n",
-            "                        Number of processes\n",
-            "  -s [SELECTATOMS [SELECTATOMS ...]], --selectatoms [SELECTATOMS [SELECTATOMS ...]]\n",
-            "                        Select atoms in the reaction network, e.g. C\n",
-            "  --stepinterval STEPINTERVAL\n",
-            "                        Step interval\n",
-            "  --split SPLIT         Split number for the time axis\n",
-            "  --maxspecies MAXSPECIES\n",
-            "                        Max number of nodes (species) in the network\n",
-            "  --matrixa MATRIXA MATRIXA MATRIXA MATRIXA\n",
-            "                        Matrix A of HMM parameters\n",
-            "  --matrixb MATRIXB MATRIXB MATRIXB MATRIXB\n",
-            "                        Matrix B of HMM parameters\n",
-            "  --urls URLS URLS      Download files\n"
-          ]
-        }
-      ],
-      "source": [
-        "%%bash\n",
-        "reacnetgenerator -h"
-      ]
+      "outputs" : [ {
+        "name" : "stdout",
+        "output_type" : "stream",
+        "text" : [
+          "usage: reacnetgenerator [-h] -i [INPUTFILENAME [INPUTFILENAME ...]] "
+          "-a\n",
+          "                        [ATOMNAME [ATOMNAME ...]] [--nohmm] "
+          "[--dump]\n",
+          "                        [--type TYPE] [--nopbc] [--cell CELL CELL "
+          "CELL]\n",
+          "                        [-n NPROC] [-s [SELECTATOMS [SELECTATOMS "
+          "...]]]\n",
+          "                        [--stepinterval STEPINTERVAL] [--split "
+          "SPLIT]\n",
+          "                        [--maxspecies MAXSPECIES]\n",
+          "                        [--matrixa MATRIXA MATRIXA MATRIXA "
+          "MATRIXA]\n",
+          "                        [--matrixb MATRIXB MATRIXB MATRIXB "
+          "MATRIXB]\n",
+          "                        [--urls URLS URLS]\n",
+          "\n",
+          "ReacNetGenerator 1.4.164\n",
+          "\n",
+          "optional arguments:\n",
+          "  -h, --help            show this help message and exit\n",
+          "  -i [INPUTFILENAME [INPUTFILENAME ...]], --inputfilename "
+          "[INPUTFILENAME [INPUTFILENAME ...]]\n",
+          "                        Input trajectory file, e.g. bonds.reaxc\n",
+          "  -a [ATOMNAME [ATOMNAME ...]], --atomname [ATOMNAME [ATOMNAME "
+          "...]]\n",
+          "                        Atomic names in the trajectory, e.g. C H "
+          "O\n",
+          "  --nohmm               Process trajectory without Hidden Markov "
+          "Model (HMM)\n",
+          "  --dump                Process the LAMMPS dump file\n",
+          "  --type TYPE, -t TYPE  Input file type\n",
+          "  --nopbc               Disable PBC.\n",
+          "  --cell CELL CELL CELL, -c CELL CELL CELL\n",
+          "                        Cell\n",
+          "  -n NPROC, -np NPROC, --nproc NPROC\n",
+          "                        Number of processes\n",
+          "  -s [SELECTATOMS [SELECTATOMS ...]], --selectatoms [SELECTATOMS "
+          "[SELECTATOMS ...]]\n",
+          "                        Select atoms in the reaction network, e.g. "
+          "C\n",
+          "  --stepinterval STEPINTERVAL\n",
+          "                        Step interval\n",
+          "  --split SPLIT         Split number for the time axis\n",
+          "  --maxspecies MAXSPECIES\n",
+          "                        Max number of nodes (species) in the "
+          "network\n",
+          "  --matrixa MATRIXA MATRIXA MATRIXA MATRIXA\n",
+          "                        Matrix A of HMM parameters\n",
+          "  --matrixb MATRIXB MATRIXB MATRIXB MATRIXB\n",
+          "                        Matrix B of HMM parameters\n",
+          "  --urls URLS URLS      Download files\n"
+        ]
+      } ],
+      "source" : [ "%%bash\n", "reacnetgenerator -h" ]
     }
   ],
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-    "colab": {
-      "authorship_tag": "ABX9TyO+cxekv9t83GNtp5C+grJf",
-      "include_colab_link": true,
-      "name": "install.ipynb",
-      "provenance": []
-    },
-    "kernelspec": {
-      "display_name": "Python 3.10.6 64-bit",
-      "language": "python",
-      "name": "python3"
+  "metadata" : {
+    "colab" : {
+      "authorship_tag" : "ABX9TyO+cxekv9t83GNtp5C+grJf",
+      "include_colab_link" : true,
+      "name" : "install.ipynb",
+      "provenance" : []
     },
-    "language_info": {
-      "name": "python",
-      "version": "3.10.6"
+    "kernelspec" : {
+      "display_name" : "Python 3.10.6 64-bit",
+      "language" : "python",
+      "name" : "python3"
     },
-    "vscode": {
-      "interpreter": {
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+    "vscode" : {
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       }
     }
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-  "nbformat_minor": 0
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+  "nbformat_minor" : 0
 }