{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "63655531-ed94-40be-8dda-2c56a64390ca",
   "metadata": {},
   "source": [
    "# Pulling Template/Predictor "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "76825840-094c-4a84-b29b-a9178378e501",
   "metadata": {},
   "outputs": [],
   "source": [
    "import modelseedpy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c608799e-484b-48e7-8ba4-a9aa4e5dce7d",
   "metadata": {},
   "outputs": [],
   "source": [
    "from modelseedpy.helpers import get_classifier, get_template, get_file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "56a998d6-d2e6-4eec-bad4-7e3dd81796b6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/usr/local/lib/python3.8/site-packages/modelseedpy//data/ml/knn_filter_features.json'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_file('template_core.json', 'data', 'template_folder')\n",
    "get_file('template_gram_neg.json', 'data', 'template_folder')\n",
    "get_file('template_gram_pos.json', 'data', 'template_folder')\n",
    "get_file('knn_filter.pickle', 'data', 'classifier_folder')\n",
    "get_file('knn_filter_features.json', 'data', 'classifier_folder')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "91b47516-0120-47ef-9933-725a10410d50",
   "metadata": {},
   "source": [
    "### load classifier\n",
    "options\n",
    "* knn_filter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "7959ee2b-1520-43ac-b791-815861b0a63c",
   "metadata": {},
   "outputs": [],
   "source": [
    "genome_cls = get_classifier('knn_filter')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1db81e21-97c7-4373-8173-33218abd8caf",
   "metadata": {},
   "source": [
    "### load template\n",
    "options\n",
    "* template_core\n",
    "* template_gram_neg\n",
    "* template_gram_pos"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "90b7bb44-d639-44ea-8f9d-482e31a95f03",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CoreModelTemplateV2'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "core_template = get_template('template_core')\n",
    "core_template['id']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "9bd57712-b46d-49d3-9182-ae3016245fff",
   "metadata": {},
   "outputs": [],
   "source": [
    "from modelseedpy.core.mstemplate import MSTemplateBuilder\n",
    "template = MSTemplateBuilder.from_dict(core_template).build()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8dd8aa70-11cf-43a7-9b0f-bf865b7a8b3d",
   "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>0x07ff7918e46d0</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 0x7ff7918e46d0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "template"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "ea2265a0-342c-4f1b-b0d0-991c9cf74f6e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Reaction identifier</strong></td><td>rxn01975_c</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>beta-D-Glucose-6-phosphate:NADP+ 1-oxoreductase</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x07ff790433310</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Stoichiometry</strong></td>\n",
       "                <td>\n",
       "                    <p style='text-align:right'>cpd00006_c + cpd00863_c --> cpd00005_c + cpd00067_c + cpd00911_c</p>\n",
       "                    <p style='text-align:right'>NADP + beta-D-Glucose 6-phosphate --> NADPH + H+ + 6-phospho-D-glucono-1-5-lactone</p>\n",
       "                </td>\n",
       "            </tr><tr>\n",
       "                <td><strong>GPR</strong></td><td>cpx00354 or cpx30278</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Lower bound</strong></td><td>0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Upper bound</strong></td><td>1000</td>\n",
       "            </tr>\n",
       "        </table>\n",
       "        "
      ],
      "text/plain": [
       "<MSTemplateReaction rxn01975_c at 0x7ff790433310>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "template_reaction = template.reactions[0]\n",
    "template_reaction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "7616ea40-6e7a-4644-98c2-3c28266c6655",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Reaction identifier</strong></td><td>rxn01975_c0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>beta-D-Glucose-6-phosphate:NADP+ 1-oxoreductase [c0]</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x07ff7901ef220</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Stoichiometry</strong></td>\n",
       "                <td>\n",
       "                    <p style='text-align:right'>cpd00006_c0 + cpd00863_c0 --> cpd00005_c0 + cpd00067_c0 + cpd00911_c0</p>\n",
       "                    <p style='text-align:right'>NADP [c0] + beta-D-Glucose 6-phosphate [c0] --> NADPH [c0] + H+ [c0] + 6-phospho-D-glucono-1-5-lactone [c0]</p>\n",
       "                </td>\n",
       "            </tr><tr>\n",
       "                <td><strong>GPR</strong></td><td></td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Lower bound</strong></td><td>0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Upper bound</strong></td><td>1000</td>\n",
       "            </tr>\n",
       "        </table>\n",
       "        "
      ],
      "text/plain": [
       "<Reaction rxn01975_c0 at 0x7ff7901ef220>"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "template_reaction.to_reaction()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "38b051f9-b068-4c2e-945a-14d47c53d3e0",
   "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": 5
}