analyze_rule.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_rule = pd.read_csv('./data/reaction_rule.csv',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1435, 7053)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_rule.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
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     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
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   "source": [
    "df_rule.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# read groups that exist in thermodynamic data\n",
    "df_groups = pd.read_csv('./data/group_names_TECRDB.txt',header=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "groups = df_groups[0].tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "263"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(groups)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# find reactions that do not decompose into groups that are not defined by TECRDB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_rule_2 = df_rule.drop(groups)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1172, 7053)"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_rule_2.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
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       "           R08505  R08852  R08851  R07882  R07885  R08856  R08503  R08854  \\\n",
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       "BO            0.0     0.0     0.0     0.0     0.0  \n",
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       "[5 rows x 7053 columns]"
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     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_rule_2.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- Find reactions that have groups outside of TECRDB (df_rule_3)\n",
    "- All - df_rule_3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_rule_3 = df_rule_2.loc[:, (df_rule_2 != 0).any(axis=0)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1172, 2166)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_rule_3.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "result = 7053 - 2166"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4887"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# An example of the reaction that cannot be describle by the 263 groups"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
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       "           R08859  R03359  R03358  R01267  R01269  R02006  R02007  R02004  \\\n",
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       "BO            0.0     0.0   ...       0.0     0.0     0.0     0.0     0.0   \n",
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       "\n",
       "           R08671  R08670  R08677  R08675  R08674  \n",
       "BO            0.0     0.0     0.0     0.0     0.0  \n",
       "Bc(c)c        0.0     0.0     0.0     0.0     0.0  \n",
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       "C#CBr         0.0     0.0     0.0     0.0     0.0  \n",
       "\n",
       "[5 rows x 2166 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_rule_3.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>R08250</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>CNN</th>\n",
       "      <td>1.0</td>\n",
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      ],
      "text/plain": [
       "     R08250\n",
       "CNN     1.0"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "example_df = df_rule_3['R08250'].to_frame()\n",
    "example_df[~(example_df == 0).any(axis=1)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  </thead>\n",
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       "    <tr>\n",
       "      <th>CC(=O)S</th>\n",
       "      <td>-1.0</td>\n",
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       "    <tr>\n",
       "      <th>CC(N)=O</th>\n",
       "      <td>1.0</td>\n",
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       "      <th>CNN</th>\n",
       "      <td>1.0</td>\n",
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       "    <tr>\n",
       "      <th>CS</th>\n",
       "      <td>1.0</td>\n",
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       "    <tr>\n",
       "      <th>CSC</th>\n",
       "      <td>-1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>NN</th>\n",
       "      <td>-1.0</td>\n",
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      ],
      "text/plain": [
       "         R08250\n",
       "CC(=O)S    -1.0\n",
       "CC(N)=O     1.0\n",
       "CNN         1.0\n",
       "CS          1.0\n",
       "CSC        -1.0\n",
       "NN         -1.0"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "example_df_1 = df_rule['R08250'].to_frame()\n",
    "example_df_1[~(example_df_1 == 0).any(axis=1)]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example of no group cahnge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>R00889</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>C[C@@H](C)O</th>\n",
       "      <td>-2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>C[C@H](C)O</th>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             R00889\n",
       "C[C@@H](C)O    -2.0\n",
       "C[C@H](C)O      2.0"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "example_df_2 = df_rule['R00889'].to_frame()\n",
    "example_df_2[~(example_df_2 == 0).any(axis=1)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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