{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Build Metabolic Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import modelseedpy\n",
    "from modelseedpy import MSBuilder, MSGenome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "genome = MSGenome.from_fasta('GCF_000005845.2_ASM584v2_protein.faa', split=' ')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of features: 4285\n"
     ]
    }
   ],
   "source": [
    "print('Number of features:', len(genome.features))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>ID</strong></td>\n",
       "                <td>CoreModelTemplateV2</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x07fcbc3ca95e0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of metabolites</strong></td>\n",
       "                <td>161</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of species</strong></td>\n",
       "                <td>187</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of reactions</strong></td>\n",
       "                <td>197</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of biomasses</strong></td>\n",
       "                <td>2</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of roles</strong></td>\n",
       "                <td>20552</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of complexes</strong></td>\n",
       "                <td>9423</td>\n",
       "            </tr>\n",
       "          </table>"
      ],
      "text/plain": [
       "<modelseedpy.core.mstemplate.MSTemplate at 0x7fcbc3ca95e0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from modelseedpy.helpers import get_template\n",
    "from modelseedpy.core.mstemplate import MSTemplateBuilder\n",
    "template = MSTemplateBuilder.from_dict(get_template('template_core')).build()\n",
    "template"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Name</strong></td>\n",
       "                <td>ecoli.core</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x07fcbc00f94c0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of metabolites</strong></td>\n",
       "                <td>148</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of reactions</strong></td>\n",
       "                <td>155</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of groups</strong></td>\n",
       "                <td>0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Objective expression</strong></td>\n",
       "                <td>1.0*bio1 - 1.0*bio1_reverse_b18f7</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Compartments</strong></td>\n",
       "                <td>c0, e0</td>\n",
       "            </tr>\n",
       "          </table>"
      ],
      "text/plain": [
       "<Model ecoli.core at 0x7fcbc00f94c0>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model = MSBuilder.build_metabolic_model('ecoli.core', genome, gapfill_media=None, template=template, allow_all_non_grp_reactions=True, annotate_with_rast=True)\n",
    "model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<h3>Objective</h3><p>1.0 bio1 = 0.05181669326590254</p><h4>Uptake</h4><table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>Metabolite</th>\n",
       "      <th>Reaction</th>\n",
       "      <th>Flux</th>\n",
       "      <th>C-Number</th>\n",
       "      <th>C-Flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>cpd00007_e0</td>\n",
       "      <td>EX_cpd00007_e0</td>\n",
       "      <td>4.049</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cpd00009_e0</td>\n",
       "      <td>EX_cpd00009_e0</td>\n",
       "      <td>0.2184</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cpd00027_e0</td>\n",
       "      <td>EX_cpd00027_e0</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>100.00%</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table><h4>Secretion</h4><table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>Metabolite</th>\n",
       "      <th>Reaction</th>\n",
       "      <th>Flux</th>\n",
       "      <th>C-Number</th>\n",
       "      <th>C-Flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>cpd00001_e0</td>\n",
       "      <td>EX_cpd00001_e0</td>\n",
       "      <td>-4.656</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cpd00011_e0</td>\n",
       "      <td>EX_cpd00011_e0</td>\n",
       "      <td>-3.684</td>\n",
       "      <td>1</td>\n",
       "      <td>100.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cpd00067_e0</td>\n",
       "      <td>EX_cpd00067_e0</td>\n",
       "      <td>-0.737</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>cpd11416_c0</td>\n",
       "      <td>SK_cpd11416_c0</td>\n",
       "      <td>-0.05182</td>\n",
       "      <td>0</td>\n",
       "      <td>0.00%</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>"
      ],
      "text/plain": [
       "<cobra.summary.model_summary.ModelSummary at 0x7fcb77503460>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.objective = 'bio1'\n",
    "model.medium = {\n",
    "    'EX_cpd00067_e0': 1000,\n",
    "    'EX_cpd00027_e0': 1,\n",
    "    'EX_cpd00007_e0': 1000,\n",
    "    'EX_cpd00001_e0': 1000,\n",
    "    'EX_cpd00009_e0': 1000,\n",
    "}\n",
    "model.summary()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}