{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Edit Model"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add a single reaction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Forward reaction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Attempt 1:\n",
      "ERROR: The modelseed reaction rxn00002 is absent from the model.\n",
      "\n",
      "Attempt 2:\n",
      "rxn00002: cpd00001 + 3.0 cpd00067 + cpd00742 --> 2.0 cpd00011 + 2.0 cpd00013\n"
     ]
    }
   ],
   "source": [
    "import modelseedpy\n",
    "from modelseedpy.biochem import from_local\n",
    "import cobra\n",
    "import sys\n",
    "\n",
    "# locally importing the ModelSEEDpy editor API\n",
    "sys.path.insert(1, 'C:\\\\Users\\\\Andrew Freiburger\\\\Dropbox\\\\My PC (DESKTOP-M302P50)\\\\Documents\\\\UVic Civil Engineering\\\\Internships\\\\Agronne\\\\ModelSEEDpy\\\\modelseedpy\\\\core')\n",
    "import mseditorapi\n",
    "\n",
    "# locally import a BiGG model and the ModelSEEDpy\n",
    "bigg_model_path = '.\\e_coli_core metabolism from BiGG.json'\n",
    "model = cobra.io.load_json_model(bigg_model_path)\n",
    "modelseed_path = '..\\..\\..\\..\\..\\..\\Biofilm growth code\\GSWL code\\ModelSEEDDatabase'\n",
    "modelseed = modelseedpy.biochem.from_local(modelseed_path)\n",
    "\n",
    "# demonstrating the addition of the reaction to the model \n",
    "example_reaction = 'rxn00002'\n",
    "\n",
    "print('Attempt 1:')\n",
    "try:\n",
    "    print(model.reactions.get_by_id(example_reaction))\n",
    "except:\n",
    "    print('ERROR: The modelseed reaction {} is absent from the model.'.format(example_reaction))\n",
    "    \n",
    "mseditorapi.MSEditorAPI.add_ms_reaction(model, rxn_id = example_reaction, modelseed = modelseed, compartment_equivalents = {'0':'c0', '1':'e0'}, direction = '>')\n",
    "\n",
    "print('\\nAttempt 2:')\n",
    "try:\n",
    "    print(model.reactions.get_by_id(example_reaction))\n",
    "except:\n",
    "    print('ERROR: The modelseed reaction {} is absent from the model.'.format(example_reaction))\n",
    "\n",
    "# remove the reaction from the model\n",
    "model.reactions.get_by_id(example_reaction).remove_from_model()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Backward and reversible reactions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The directionality of the modelseed reaction may be either ``>``, ``<``, or ``=``. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Backward reaction:\n",
      "rxn00002: cpd00001 + 3.0 cpd00067 + cpd00742 <-- 2.0 cpd00011 + 2.0 cpd00013\n",
      "\n",
      "Reversible reaction:\n",
      "rxn00002: cpd00001 + 3.0 cpd00067 + cpd00742 <=> 2.0 cpd00011 + 2.0 cpd00013\n"
     ]
    }
   ],
   "source": [
    "# add a backward reaction \n",
    "print('Backward reaction:')\n",
    "mseditorapi.MSEditorAPI.add_ms_reaction(model, rxn_id = example_reaction, modelseed = modelseed, compartment_equivalents = {'0':'c0', '1':'e0'}, direction = '<')\n",
    "\n",
    "try:\n",
    "    print(model.reactions.get_by_id(example_reaction))\n",
    "except:\n",
    "    print('ERROR: The modelseed reaction {} is absent from the model.'.format(example_reaction))\n",
    "    \n",
    "model.reactions.get_by_id(example_reaction).remove_from_model()\n",
    "\n",
    "# add a reversible reaction \n",
    "print('\\nReversible reaction:')\n",
    "mseditorapi.MSEditorAPI.add_ms_reaction(model, rxn_id = example_reaction, modelseed = modelseed, compartment_equivalents = {'0':'c0', '1':'e0'}, direction = '=')\n",
    "\n",
    "try:\n",
    "    print(model.reactions.get_by_id(example_reaction))\n",
    "except:\n",
    "    print('ERROR: The modelseed reaction {} is absent from the model.'.format(example_reaction))\n",
    "    \n",
    "model.reactions.get_by_id(example_reaction).remove_from_model()"
   ]
  }
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