01_Constuct eciYW1475_DLKcat.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "37c78f2a",
   "metadata": {},
   "source": [
    "# Import related functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "4e59daa3",
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import cobra\n",
    "import pandas as pd\n",
    "import re\n",
    "sys.path.append(r'./script/')#问题1\n",
    "from ECMpy_function import *\n",
    "from AutoPACMEN_function import *"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "088cf94c",
   "metadata": {},
   "source": [
    "# Input and output files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "ad910775",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "path exists\n"
     ]
    }
   ],
   "source": [
    "# Initial parameter\n",
    "obj='Biomass\n",
    "fluxes_outfile = './analysis/ECMpy_solution_%s_pfba.csv'%obj #？\n",
    "use_substrate='R2399'# substrate ID\n",
    "concentration=10 \n",
    "# The total protein fraction in cell.\n",
    "\n",
    "ptot = 0.4653\n",
    "# The approximated average saturation of enzyme.\n",
    "\n",
    "sigma = 0.5\n",
    "# Lowerbound  of enzyme concentration constraint. \n",
    "\n",
    "lowerbound = 0   \n",
    "enz_ratio=0.1\n",
    "\n",
    "# Input files\n",
    "autopacmen_folder = \"./iDL1450_get_data/\"\n",
    "gap_fill= 'mean'#'mean'#'median'\n",
    "project_name = \"iDL1450%s\"%gap_fill\n",
    "organism = \"Thermothelomyces thermophilus\"\n",
    "create_file(autopacmen_folder)\n",
    "reaction_gene_path = \"./data/reaction_gene_subunit_num.json\"\n",
    "\n",
    "protein_kcat_database_path = \"none\"\n",
    "bigg_metabolites_file = \"./data/bigg_models_metabolites.txt\"#date:20221008 http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt\n",
    "brenda_textfile_path = \"./data/brenda_download.txt\"#date:20221008 https://www.brenda-enzymes.org/brenda_download/file_download.php\n",
    "\n",
    "sbml_path=\"./model/iYT1475.xml\"\n",
    "\n",
    "c13reaction_file='./reaction_kcat/C13data.csv'#C13 data\n",
    "\n",
    "\n",
    "EC_max_file='./data/EC_kcat_max.json'\n",
    "brenda_json_path = \"%skcat_database_brenda.json\"%autopacmen_folder\n",
    "brenda_output_json_path = \"%skcat_database_brenda_for_model.json\"%autopacmen_folder\n",
    "bigg_id_name_mapping_path = \"%sbigg_id_name_mapping.json\"%autopacmen_folder\n",
    "sabio_rk_output_path = \"%skcat_database_sabio_rk.json\"%autopacmen_folder\n",
    "combined_output_path = \"%skcat_database_combined.json\"%autopacmen_folder\n",
    "reaction_kcat_MW_file=\"%s/reaction_kcat_MW.csv\"%autopacmen_folder\n",
    "uniprot_data_file='%s/%s_protein_id_mass_mapping.json'%(autopacmen_folder,project_name)\n",
    "\n",
    "\n",
    "modelgene2uniprot_file='./analysis/modelgene2uniprot.txt'\n",
    "paxdbgene2uniprot_file='./analysis/paxdbgene2uniprot.txt'\n",
    "ecModel_output_file=\"./model/ecMTM_DLkcat.json\" # \n",
    "\n",
    "json_output_file = './model/ecMTM_DLKcat_adj_enz.json'\n",
    "reaction_kcat_MW_outfile=\"./get_reaction_kcat/kcat/reaction_change_by_enzuse_DLKcat.csv\"\n",
    "reaction_kcat_MW_round2_outfile='./get_reaction_kcat/kcat/reaction_change_by_C13_DLkcat.csv'\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "06b28562",
   "metadata": {},
   "source": [
    "### Calculate f-value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "14943d2b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[0.5563635421646973, 0.5540772163224917, 0.558660486869679, 0.5486668910172237]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model=cobra.io.read_sbml_model(sbml_path)\n",
    "gene_abundance_file1 = './data/danbaizu/wt1.csv'\n",
    "gene_abundance_file2 = './data/danbaizu/wt2.csv'\n",
    "gene_abundance_file3 = './data/danbaizu/wt3.csv'\n",
    "gene_abundance_file4 = './data/danbaizu/wt4.csv'\n",
    "file_list=[gene_abundance_file1,gene_abundance_file2,gene_abundance_file3,gene_abundance_file4]\n",
    "f_list=[]\n",
    "for g_a_file in file_list:\n",
    "    f=calculate_f_special_new(model,g_a_file)\n",
    "    f_list.append(f)\n",
    "f_list"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1d76b8e1",
   "metadata": {},
   "source": [
    "# Constructing Enzyme-Constrained Mode"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "53de06f2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "upperbound is:0.128\n",
      "0.128\n",
      "IN FLUXES           OUT FLUXES    OBJECTIVES\n",
      "------------------  ------------  ---------------\n",
      "o2_e      1.47      h2o_e  1.91   Biomass  0.0219\n",
      "h_e       1.21      co2_e  1.5\n",
      "glc__D_e  0.452     ac_e   0.161\n",
      "nh4_e     0.164\n",
      "pi_e      0.00397\n",
      "so4_e     0.000317\n",
      "Enzyme cost total is:0.128\n",
      "0.021879981734168438\n"
     ]
    }
   ],
   "source": [
    "#The enzyme mass fraction \n",
    "f = round(np.mean(f_list), 2)\n",
    "# print(\"f is:\" + str(f))\n",
    "ptot = 0.4653\n",
    "# upperbound =0.128\n",
    "upperbound = round(ptot * f * sigma, 3)\n",
    "# upperbound = 0.1\n",
    "print(\"upperbound is:\" + str(upperbound))\n",
    "reaction_kcat_MW_file=\"./get_reaction_kcat/kcat/DLKcat3.30.csv\"# kcat data predicted by DLKcat method\n",
    "\n",
    "trans_model2enz_json_model_split_isoenzyme(sbml_path, reaction_kcat_MW_file, f, ptot, sigma, lowerbound, upperbound, ecModel_output_file)\n",
    "\n",
    "enz_model=get_enzyme_constraint_model(ecModel_output_file)\n",
    "enz_model.objective=obj\n",
    "enz_model.summary()\n",
    "[ori_obj_id,ori_substrate_id_list,ori_sub_concentration,ori_ATPM]=get_model_substrate_obj(enz_model)\n",
    "for eachsubid in ori_substrate_id_list:\n",
    "    if re.search('_reverse',eachsubid):\n",
    "        r_id_new=eachsubid.split('_reverse')[0]\n",
    "        enz_model.reactions.get_by_id(eachsubid).bounds = (0, 0) \n",
    "        enz_model.reactions.get_by_id(r_id_new).bounds = (0, 0)  \n",
    "    else:\n",
    "        r_id_new=eachsubid+'_reverse'\n",
    "        enz_model.reactions.get_by_id(eachsubid).bounds = (0, 0) \n",
    "        enz_model.reactions.get_by_id(r_id_new).bounds = (0, 0) \n",
    "        \n",
    "enz_model.reactions.get_by_id(use_substrate).bounds = (-10, 0)\n",
    "enz_model.reactions.get_by_id(use_substrate+'_reverse').bounds = (0, 0)\n",
    "\n",
    "enz_model_pfba_solution = cobra.flux_analysis.pfba(enz_model)\n",
    "\n",
    "enz_model_pfba_solution = get_fluxes_detail_in_model(enz_model,enz_model_pfba_solution,fluxes_outfile,ecModel_output_file)\n",
    "print(enz_model_pfba_solution.fluxes[obj])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f7394ff2",
   "metadata": {},
   "source": [
    "# Calibration kcat according Enzyme usage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9a09efa7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Need changing reaction: \n",
      "R2160\n",
      "Changed reaction: \n",
      "['R2160']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:0.8418663312187247\n",
      "ecGEM max growth rates:0.060579546752058046\n",
      "Round 1: 0.06057954675205813\n",
      "\n",
      "Need changing reaction: \n",
      "R2158\n",
      "Changed reaction: \n",
      "['R2160']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:0.8418663312187247\n",
      "ecGEM max growth rates:0.060579546752058046\n",
      "Round 2: 0.06057954675205813\n",
      "\n",
      "Need changing reaction: \n",
      "R2165\n",
      "Changed reaction: \n",
      "['R2160']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:0.8418663312187247\n",
      "ecGEM max growth rates:0.060579546752058046\n",
      "Round 3: 0.06057954675205813\n",
      "\n",
      "Need changing reaction: \n",
      "R2306_reverse_num2\n",
      "Changed reaction: \n",
      "['R2160']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:0.8418663312187247\n",
      "ecGEM max growth rates:0.060579546752058046\n",
      "Round 4: 0.06057954675205813\n",
      "\n",
      "Need changing reaction: \n",
      "R25\n",
      "Changed reaction: \n",
      "['R2160', 'R25']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:0.8802722248933735\n",
      "ecGEM max growth rates:0.06366942517772614\n",
      "Round 5: 0.06366942517772624\n",
      "\n",
      "Need changing reaction: \n",
      "R61\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12799999999999978\n",
      "ecGEM max glucose uptake rates:0.9703311700890966\n",
      "ecGEM max growth rates:0.0663383185953937\n",
      "Round 6: 0.06633831859539371\n",
      "\n",
      "Need changing reaction: \n",
      "R16\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16']\n",
      "0.128\n",
      "Enzyme cost total is:0.1279999999999998\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.0021907991091246\n",
      "ecGEM max growth rates:0.06924102182336532\n",
      "Round 7: 0.06924102182336532\n",
      "\n",
      "Need changing reaction: \n",
      "R255_num2\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.1279999999999999\n",
      "ecGEM max glucose uptake rates:1.040970038098349\n",
      "ecGEM max growth rates:0.0722815693888634\n",
      "Round 8: 0.0722815693888637\n",
      "\n",
      "Need changing reaction: \n",
      "R351\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351']\n",
      "0.128\n",
      "Enzyme cost total is:0.1279999999999999\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.0644271148314972\n",
      "ecGEM max growth rates:0.07482711817208147\n",
      "Round 9: 0.07482711817208196\n",
      "\n",
      "Need changing reaction: \n",
      "R7_reverse\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.0644271148314972\n",
      "ecGEM max growth rates:0.07482711817208147\n",
      "Round 10: 0.07482711817208196\n",
      "\n",
      "Need changing reaction: \n",
      "R1974\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.0644271148314972\n",
      "ecGEM max growth rates:0.07482711817208147\n",
      "Round 11: 0.07482711817208196\n",
      "\n",
      "Need changing reaction: \n",
      "R145\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.1031200119213853\n",
      "ecGEM max growth rates:0.07688932474146824\n",
      "Round 12: 0.07688932474146812\n",
      "\n",
      "Need changing reaction: \n",
      "R56_num3\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.1276676035670303\n",
      "ecGEM max growth rates:0.07908171632274848\n",
      "Round 13: 0.07908171632274827\n",
      "\n",
      "Need changing reaction: \n",
      "R14\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.1868937074436956\n",
      "ecGEM max growth rates:0.08120764567304797\n",
      "Round 14: 0.0812076456730473\n",
      "\n",
      "Need changing reaction: \n",
      "R1442_num2\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.2072167127114808\n",
      "ecGEM max growth rates:0.08295467134758061\n",
      "Round 15: 0.0829546713475807\n",
      "\n",
      "Need changing reaction: \n",
      "R72\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.2552577024594782\n",
      "ecGEM max growth rates:0.08461286094576691\n",
      "Round 16: 0.08461286094576696\n",
      "\n",
      "Need changing reaction: \n",
      "R60\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.2552577024594782\n",
      "ecGEM max growth rates:0.08461286094576691\n",
      "Round 17: 0.08461286094576696\n",
      "\n",
      "Need changing reaction: \n",
      "R1378_num2\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "ecGEM max glucose uptake rates:1.2725393346441747\n",
      "ecGEM max growth rates:0.08605627871169128\n",
      "Round 18: 0.0860562787116915\n",
      "\n",
      "Need changing reaction: \n",
      "R50\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.286230976826376\n",
      "ecGEM max growth rates:0.08719984891124903\n",
      "Round 19: 0.08719984891124906\n",
      "\n",
      "Need changing reaction: \n",
      "R58_reverse\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.286230976826376\n",
      "ecGEM max growth rates:0.08719984891124903\n",
      "Round 20: 0.08719984891124906\n",
      "\n",
      "Need changing reaction: \n",
      "R70\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.3005164931953213\n",
      "ecGEM max growth rates:0.08839302140215304\n",
      "Round 21: 0.08839302140215337\n",
      "\n",
      "Need changing reaction: \n",
      "R66_num5\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.3132419369134434\n",
      "ecGEM max growth rates:0.08945589158384937\n",
      "Round 22: 0.08945589158384942\n",
      "\n",
      "Need changing reaction: \n",
      "R2251_num3\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.3132419369134434\n",
      "ecGEM max growth rates:0.08945589158384937\n",
      "Round 23: 0.08945589158384942\n",
      "\n",
      "Need changing reaction: \n",
      "R1122_num1\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.3240894184857837\n",
      "ecGEM max growth rates:0.09036190829846191\n",
      "Round 24: 0.09036190829846234\n",
      "\n",
      "Need changing reaction: \n",
      "R914\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.3216928587500918\n",
      "ecGEM max growth rates:0.09138802560718567\n",
      "Round 25: 0.09138802560718572\n",
      "\n",
      "Need changing reaction: \n",
      "R1377\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.3326354931700144\n",
      "ecGEM max growth rates:0.09231442058047024\n",
      "Round 26: 0.09231442058047105\n",
      "\n",
      "Need changing reaction: \n",
      "R1744\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "ecGEM max glucose uptake rates:1.34331290051594\n",
      "ecGEM max growth rates:0.09321836163464835\n",
      "Round 27: 0.09321836163464854\n",
      "\n",
      "Need changing reaction: \n",
      "R244\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.3546411738351722\n",
      "ecGEM max growth rates:0.094177404499129\n",
      "Round 28: 0.09417740449912823\n",
      "\n",
      "Need changing reaction: \n",
      "R1455_num1\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.363666930778408\n",
      "ecGEM max growth rates:0.09494151810664052\n",
      "Round 29: 0.09494151810664044\n",
      "\n",
      "Need changing reaction: \n",
      "R254_num1\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.3711760779278468\n",
      "ecGEM max growth rates:0.0955772367010804\n",
      "Round 30: 0.09557723670108025\n",
      "\n",
      "Need changing reaction: \n",
      "R185_num1\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "ecGEM max glucose uptake rates:1.3784597815684037\n",
      "ecGEM max growth rates:0.0961938694222889\n",
      "Round 31: 0.09619386942228811\n",
      "\n",
      "Need changing reaction: \n",
      "R936\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "ecGEM max glucose uptake rates:1.3857448054666075\n",
      "ecGEM max growth rates:0.09681061391549511\n",
      "Round 32: 0.09681061391549402\n",
      "\n",
      "Need changing reaction: \n",
      "R2249_num3\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "ecGEM max glucose uptake rates:1.3857448054666075\n",
      "ecGEM max growth rates:0.09681061391549511\n",
      "Round 33: 0.09681061391549402\n",
      "\n",
      "Need changing reaction: \n",
      "R1822\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "ecGEM max glucose uptake rates:1.3921547501285814\n",
      "ecGEM max growth rates:0.09735327487682559\n",
      "Round 34: 0.09735327487682559\n",
      "\n",
      "Need changing reaction: \n",
      "R1836\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.3987138110509982\n",
      "ecGEM max growth rates:0.09790855990552873\n",
      "Round 35: 0.0979085599055291\n",
      "\n",
      "Need changing reaction: \n",
      "R74\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.4051563765186643\n",
      "ecGEM max growth rates:0.09845398251907361\n",
      "Round 36: 0.09845398251907354\n",
      "\n",
      "Need changing reaction: \n",
      "R2325\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.4051563765186643\n",
      "ecGEM max growth rates:0.09845398251907361\n",
      "Round 37: 0.09845398251907354\n",
      "\n",
      "Need changing reaction: \n",
      "R54\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "ecGEM max glucose uptake rates:1.4113629946599582\n",
      "ecGEM max growth rates:0.09897943001430445\n",
      "Round 38: 0.09897943001430505\n",
      "\n",
      "Need changing reaction: \n",
      "R42_num1\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.4218712896587464\n",
      "ecGEM max growth rates:0.09949411790695363\n",
      "Round 39: 0.09949411790695366\n",
      "\n",
      "Need changing reaction: \n",
      "R41_num1\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "ecGEM max glucose uptake rates:1.4307410234163191\n",
      "ecGEM max growth rates:0.10023993725428378\n",
      "Round 40: 0.10023993725428351\n",
      "\n",
      "Need changing reaction: \n",
      "R51\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51']\n",
      "0.128\n",
      "Enzyme cost total is:0.12800000000000006\n",
      "Enzyme cost total is:0.1280000000000001\n",
      "ecGEM max glucose uptake rates:1.4377732955061477\n",
      "ecGEM max growth rates:0.10083303546792943\n",
      "Round 41: 0.10083303546792928\n",
      "\n",
      "Need changing reaction: \n",
      "R1458\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.128\n",
      "Enzyme cost total is:0.1280000000000001\n",
      "Enzyme cost total is:0.1280000000000001\n",
      "ecGEM max glucose uptake rates:1.4377732955061477\n",
      "ecGEM max growth rates:0.10083303546792943\n",
      "Round 42: 0.10083303546792928\n",
      "\n",
      "Need changing reaction: \n",
      "R9\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9']\n",
      "0.128\n",
      "Enzyme cost total is:0.1280000000000001\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.3581819366730201\n",
      "ecGEM max growth rates:0.10203552572417553\n",
      "Round 43: 0.10203552572417572\n",
      "\n",
      "Need changing reaction: \n",
      "R1583\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.3581819366730201\n",
      "ecGEM max growth rates:0.10203552572417553\n",
      "Round 44: 0.10203552572417572\n",
      "\n",
      "Need changing reaction: \n",
      "R906\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12800000000000003\n",
      "ecGEM max glucose uptake rates:1.3581819366730201\n",
      "ecGEM max growth rates:0.10203552572417553\n",
      "Round 45: 0.10203552572417572\n",
      "\n",
      "Need changing reaction: \n",
      "R802\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9', 'R802']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.3636112338439754\n",
      "ecGEM max growth rates:0.1024853314180636\n",
      "Round 46: 0.10248533141806512\n",
      "\n",
      "Need changing reaction: \n",
      "R1016\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9', 'R802', 'R1016']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.369001986378003\n",
      "ecGEM max growth rates:0.10289715377389172\n",
      "Round 47: 0.10289715377389108\n",
      "\n",
      "Need changing reaction: \n",
      "R36_num2\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9', 'R802', 'R1016', 'R36_num2']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "ecGEM max glucose uptake rates:1.3742448998446826\n",
      "ecGEM max growth rates:0.10329122250394644\n",
      "Round 48: 0.10329122250394675\n",
      "\n",
      "Need changing reaction: \n",
      "R178\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9', 'R802', 'R1016', 'R36_num2', 'R178']\n",
      "0.128\n",
      "Enzyme cost total is:0.12799999999999997\n",
      "Enzyme cost total is:0.12799999999999995\n",
      "ecGEM max glucose uptake rates:1.3794056846707745\n",
      "ecGEM max growth rates:0.10367911826795259\n",
      "Round 49: 0.10367911826795265\n",
      "\n",
      "Need changing reaction: \n",
      "R401\n",
      "Changed reaction: \n",
      "['R2160', 'R25', 'R61', 'R16', 'R255_num2', 'R351', 'R145', 'R56_num3', 'R14', 'R1442_num2', 'R72', 'R1378_num2', 'R50', 'R70', 'R66_num5', 'R1122_num1', 'R914', 'R1377', 'R1744', 'R244', 'R1455_num1', 'R254_num1', 'R185_num1', 'R936', 'R1822', 'R1836', 'R74', 'R54', 'R42_num1', 'R41_num1', 'R51', 'R9', 'R802', 'R1016', 'R36_num2', 'R178', 'R401']\n",
      "0.128\n",
      "Enzyme cost total is:0.128\n",
      "Enzyme cost total is:0.128\n",
      "ecGEM max glucose uptake rates:1.3845096238288048\n",
      "ecGEM max growth rates:0.10406274138801778\n",
      "Round 50: 0.10406274138801813\n"
     ]
    }
   ],
   "source": [
    "#Initial model and result\n",
    "fluxes_infile_ori = './analysis/ECMpy_solution_%s_pfba.csv'%obj\n",
    "fluxes_outfile = fluxes_infile_ori\n",
    "need_change_reaction_list=[]\n",
    "changed_reaction_list=[]\n",
    "round_num=1\n",
    "\n",
    "\n",
    "reaction_kcat_mw = pd.read_csv(reaction_kcat_MW_file, index_col=0)\n",
    "\n",
    "#Model adjustment\n",
    "enz_model_obj_max=0\n",
    "concentration = 3.0676\n",
    "# Reconstruction and analysis of genome-scale metabolic model for thermophilic fungus Myceliophthora thermophila [J]. Biotechnology and Bioengineering, 2022, 119(7): 1926-37.\n",
    "# Beyond growth rate 0.25: Elucidation of the metabolic mechanism for malate production in Myceliophthora thermophila via 13C metabolic flux analysis [Z]. Research Square. 2022.10.21203/rs.3.rs-2123109/v1\n",
    "while (enz_model_obj_max<0.2573):\n",
    "\n",
    " \n",
    "    \n",
    "    [enz_model,reaction_kcat_mw,need_change_reaction_list, changed_reaction_list]=change_enz_model_by_enz_usage(enz_ratio,\\\n",
    "                                                    ecModel_output_file,fluxes_outfile,EC_max_file,\\\n",
    "                                                    reaction_kcat_mw,need_change_reaction_list,changed_reaction_list,f, \\\n",
    "                                                    ptot, sigma, lowerbound, upperbound, json_output_file)\n",
    "    \n",
    "    #Using only the provided substrate\n",
    "   \n",
    "    [ori_obj_id,ori_substrate_id_list,ori_sub_concentration,ori_ATPM]=get_model_substrate_obj(enz_model)\n",
    "    for eachsubid in ori_substrate_id_list:\n",
    "        if re.search('_reverse',eachsubid):\n",
    "            r_id_new=eachsubid.split('_reverse')[0]\n",
    "            enz_model.reactions.get_by_id(eachsubid).bounds = (0, 0) \n",
    "            enz_model.reactions.get_by_id(r_id_new).bounds = (0, 0)  \n",
    "        else:\n",
    "            r_id_new=eachsubid+'_reverse'\n",
    "            enz_model.reactions.get_by_id(eachsubid).bounds = (0, 0) \n",
    "            enz_model.reactions.get_by_id(r_id_new).bounds = (0, 0) \n",
    "    enz_model.reactions.get_by_id(use_substrate).bounds = (-concentration, 0)\n",
    "    enz_model.reactions.get_by_id(use_substrate+'_reverse').bounds = (0, 0)\n",
    "  \n",
    "  \n",
    "    \n",
    "    enz_model_obj=enz_model.slim_optimize()\n",
    "\n",
    "    enz_model_pfba_solution = cobra.flux_analysis.pfba(enz_model)\n",
    "    fluxes_outfile = './analysis/ECMpy_solution_adjround%s.csv'%(round_num)\n",
    "    enz_model_pfba_solution = get_fluxes_detail_in_model(enz_model,enz_model_pfba_solution,fluxes_outfile,json_output_file)\n",
    "    \n",
    "    \n",
    "\n",
    "   # μmax condition substrate concentration\n",
    " \n",
    "    obj='Biomass'\n",
    "    substrate='R2399'\n",
    "    enz_model.reactions.get_by_id(substrate).bounds=(-1000,0)\n",
    "    enz_model.reactions.get_by_id('R2399_reverse').bounds=(0,0)\n",
    "    \n",
    "    enz_model.objective=obj\n",
    "    enz_model_solution = cobra.flux_analysis.pfba(enz_model)\n",
    "    print(\"ecGEM max glucose uptake rates:\"+str(-enz_model_solution.fluxes[substrate]))\n",
    "    print(\"ecGEM max growth rates:\"+str(enz_model_solution.fluxes[obj]))\n",
    "    enz_model_sub=-enz_model_solution.fluxes[substrate]\n",
    "    enz_model_obj_max=enz_model_solution.fluxes[obj]\n",
    "\n",
    "\n",
    "    print('Round %s: '%round_num+str(enz_model_obj))\n",
    "    round_num=round_num+1\n",
    "    if round_num>50:\n",
    "        break\n",
    "    print()\n",
    "reaction_kcat_mw.to_csv(reaction_kcat_MW_outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "1a166ec7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.128\n",
      "通量为： 0.0\n",
      "R6_num1 ECMpy_c13_reaction_flux: 0.00028451498566400005 flux: 3.0676\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R7 ECMpy_c13_reaction_flux: 0.00295410374016 flux: 1.4289\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R1036 ECMpy_c13_reaction_flux: 3.15923569216e-05 flux: 1.936\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R1044_num1 ECMpy_c13_reaction_flux: 0.002698297463040001 flux: 1.936\n",
      "0.128\n",
      "通量为： 0.39378958331877567\n",
      "R50 ECMpy_c13_reaction_flux: 0.158462757914232 flux: 4.1708\n",
      "0.128\n",
      "通量为： 0.39378958331877567\n",
      "R51 ECMpy_c13_reaction_flux: 1.3639262432400694 flux: 4.1708\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R42_num2 ECMpy_c13_reaction_flux: 0.006508857785600001 flux: 3.9965\n",
      "0.128\n",
      "通量为： 0.3793340141337602\n",
      "R40 ECMpy_c13_reaction_flux: 0.022370116505600002 flux: 3.9965\n",
      "0.128\n",
      "通量为： 0.19880746452182474\n",
      "R36_num2 ECMpy_c13_reaction_flux: 4.854059742128076 flux: 3.8319\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R55 ECMpy_c13_reaction_flux: 0.0031095719616000004 flux: 1.2271\n",
      "0.128\n",
      "通量为： 0.7483709222441511\n",
      "R60 ECMpy_c13_reaction_flux: 0.006412713715200001 flux: 1.2271\n",
      "0.128\n",
      "通量为： 1.195172944208321\n",
      "R56_num3 ECMpy_c13_reaction_flux: 0.235523188814883 flux: 1.2271\n",
      "0.128\n",
      "通量为： 0.7904673242264615\n",
      "R54 ECMpy_c13_reaction_flux: 6.0279066830490935 flux: 0.7284\n",
      "0.128\n",
      "通量为： 0.4047056199818593\n",
      "R58_reverse ECMpy_c13_reaction_flux: 0.00516718083392 flux: 0.4987\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R46 ECMpy_c13_reaction_flux: 4.2431135187200004e-05 flux: 2.3042\n",
      "0.128\n",
      "通量为： 0.04954181425256556\n",
      "R114_num2 ECMpy_c13_reaction_flux: 0.024578435104000002 flux: 2.0911\n",
      "0.128\n",
      "通量为： 0.049541814281534396\n",
      "R1033_num1 ECMpy_c13_reaction_flux: 0.094983404224 flux: 1.3615\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R117_num1 ECMpy_c13_reaction_flux: 0.00108822564096 flux: 1.3615\n",
      "0.128\n",
      "通量为： 0.0\n",
      "R118 ECMpy_c13_reaction_flux: 3.9183868748800004e-05 flux: 0.8886\n",
      "0.128\n",
      "通量为： 0.01209641354167834\n",
      "R111 ECMpy_c13_reaction_flux: 0.00469228338944 flux: 0.8886\n",
      "0.128\n",
      "通量为： 0.02170348467351364\n",
      "R104 ECMpy_c13_reaction_flux: 0.0025629118182400007 flux: 0.4597\n",
      "0.128\n",
      "通量为： 0.02404912811532377\n",
      "R108 ECMpy_c13_reaction_flux: 0.0019463942284799998 flux: 1.415\n",
      "0.128\n",
      "通量为： 0.1206197751073112\n",
      "R2308 ECMpy_c13_reaction_flux: 0.00552097754176 flux: 2.1536\n",
      "need changing reaction: \n",
      "['R6_num1', 'R7', 'R1036', 'R1044_num1', 'R50', 'R51', 'R42_num2', 'R40', 'R55', 'R60', 'R56_num3', 'R58_reverse', 'R46', 'R114_num2', 'R1033_num1', 'R117_num1', 'R118', 'R111', 'R104', 'R108', 'R2308']\n",
      "changed reaction: \n",
      "['R6_num1', 'R7', 'R1036', 'R1044_num1', 'R42_num2', 'R40', 'R55', 'R46', 'R114_num2', 'R1033_num1', 'R117_num1', 'R118', 'R111', 'R104', 'R108']\n",
      "0.128\n",
      "IN FLUXES          OUT FLUXES    OBJECTIVES\n",
      "-----------------  ------------  --------------\n",
      "h_e       5.52     h2o_e   6.53  Biomass  0.137\n",
      "o2_e      3.59     co2_e   4.97\n",
      "glc__D_e  3.06     ac_e    2.59\n",
      "nh4_e     1.11     etoh_e  1.22\n",
      "pi_e      0.0482\n",
      "so4_e     0.00199\n"
     ]
    }
   ],
   "source": [
    "\n",
    "c13_percentage=0.1\n",
    "# kcat_database_combined_file='./data/EC_kcat_max.json'##max kcat for EC number selected from BRENDA and SABIO-RK database(use autoPACMEN)\n",
    "model_name=sbml_path\n",
    "f=0.55 # Enzyme mass fraction\n",
    "ptot=0.4653 # total protein content in cells\n",
    "sigma=0.5 #approximate average saturation of the enzyme\n",
    "lowerbound= 0 \n",
    "upperbound=round(ptot * f * sigma, 3)\n",
    "\n",
    "json_round2_output_file='./model/eciYT1475_DL.json'\n",
    "\n",
    "\n",
    "enz_model=get_enz_model_use_c13(reaction_kcat_MW_outfile, ecModel_output_file, c13reaction_file, c13_percentage, \\\n",
    "                                EC_max_file,model_name, f, ptot, sigma, lowerbound, \\\n",
    "                                upperbound, json_round2_output_file,reaction_kcat_MW_round2_outfile)\n",
    "enz_model.reactions.get_by_id('R2399_reverse').bounds=(0,3.06)\n",
    "enz_model.summary()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "31413014",
   "metadata": {},
   "source": [
    "# Obtain the metabolic flux of this model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "7d7c9330",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.128\n"
     ]
    }
   ],
   "source": [
    "\n",
    "ecModel_output_file='./model/eciYT1475_DL.json'\n",
    "\n",
    "enz_model=get_enzyme_constraint_model(ecModel_output_file)\n",
    "\n",
    "enz_model.reactions.get_by_id('R2399_reverse').bounds=(0,3.06)\n",
    "enz_model.reactions.get_by_id(\"R1975_num2\").bounds=(0,0)\n",
    "enz_model.reactions.get_by_id(\"R1975_num3\").bounds=(0,0)\n",
    "enz_model.reactions.get_by_id(\"R1975_num4\").bounds=(0,0)\n",
    "enz_model.reactions.get_by_id(\"R1975_num5\").bounds=(0,0)\n",
    "\n",
    "\n",
    "solution = enz_model.optimize()\n",
    "reac=dict(solution.fluxes[solution.fluxes> 0.1])\n",
    "\n",
    "genelist=[]\n",
    "reactionlist=[]\n",
    "fluxlist=[]\n",
    "for i in reac:\n",
    "    #\n",
    "    reID=str(enz_model.reactions.get_by_id(i))\n",
    "    reID=str(enz_model.reactions.get_by_id(i)).split(':')[0]\n",
    "   \n",
    "    reID= reID.split('_')[0]\n",
    "    reactionlist.append(reID)\n",
    "    fluxlist.append(reac[i])\n",
    "df=pd.DataFrame({'reaction':reactionlist,'flux':fluxlist})\n",
    "\n",
    "df.to_csv(\"./flux/flux for DL.csv\",index=0)\n",
    "# enz_model.summary()"
   ]
  }
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