{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "5cbc8640",
   "metadata": {},
   "source": [
    "### Random Networks\n",
    "\n",
    "Early implementation"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5a3fe1d4-ffc9-4db9-ac0f-d51d2231d32b",
   "metadata": {},
   "source": [
    "### TAGS :   \"uniform compartment\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "97a57e9a-039b-479a-81dc-81399e22743a",
   "metadata": {},
   "outputs": [],
   "source": [
    "LAST_REVISED = \"Feb. 16, 2026\"\n",
    "LIFE123_VERSION = \"1.0.0rc7\"         # Library version this experiment is based on"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "b5b8a8b0-d417-4432-b6a8-c196af57b105",
   "metadata": {},
   "outputs": [],
   "source": [
    "#import set_path            # Using MyBinder?  Uncomment this before running the next cell!\n",
    "                            # Importing this module will add the project's home directory to sys.path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "a29db1c7",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "#import sys, os\n",
    "#os.getcwd()\n",
    "#sys.path.append(\"C:/some_path/my_env_or_install\")   # CHANGE to the folder containing your venv or libraries installation!\n",
    "# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path\n",
    "\n",
    "import ipynbname\n",
    "\n",
    "from life123 import check_version, RandomReactionNetwork, UniformCompartment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "ccd6701b-ae96-4d20-b537-40c2c40df9aa",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "OK\n"
     ]
    }
   ],
   "source": [
    "check_version(LIFE123_VERSION)    # To check compatibility"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "25281125-fcea-4cae-b5fd-790810e87200",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# Initialize the HTML logging (for the graphics)\n",
    "log_file = ipynbname.name() + \".log.htm\"    # Use the notebook base filename for the log file\n",
    "                                            # IN CASE OF PROBLEMS, set manually to any desired name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e4047c5b-3d34-43ca-95db-334435f7e8fe",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e104bbb5-f0a9-41d2-a2a2-9e2d8e0ef522",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "e0529a0c",
   "metadata": {},
   "source": [
    "## Set up Random Network (no thermodynamic nor kinetic data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c95bf9b8-e8bb-4c4d-ad92-8777768d03d1",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "net = RandomReactionNetwork(n_chems=4, n_rxns=6)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ac9eea69-174c-43e5-9eed-443cbc5e2ba7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['A', 'B', 'C', 'D']"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "net.chem_data.get_all_labels()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "33af1a01-644b-4acf-808e-ff8c4bd3d0aa",
   "metadata": {},
   "source": [
    "### The above chemical labels were auto-generated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "7f59733f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "net.registry.number_of_reactions()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "cf6e1c21-1627-4b97-8bcc-343911099cdd",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(0) D + B  <-> A  Elementary Synthesis reaction\n",
      "(1) A + D  <-> B  Elementary Synthesis reaction\n",
      "(2) C + A  <-> B  Elementary Synthesis reaction\n",
      "(3) 2 A  <-> B  Elementary Synthesis reaction\n",
      "(4) A + B  <-> C  Elementary Synthesis reaction\n",
      "(5) C <-> A + D  Elementary Decomposition reaction\n"
     ]
    }
   ],
   "source": [
    "for i in range(net.registry.number_of_reactions()):\n",
    "    rxn = net.registry.get_reaction(i)\n",
    "    print(f\"({i}) {rxn.describe(concise=False)}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eed8d982-d551-4790-ab4d-c20012f55466",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "2520814f-9cd4-401a-a81b-ef765d1f62f4",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# Instantiate the simulator with our chemicals and reactions\n",
    "uc = UniformCompartment(reactions=net.registry)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "52084745-7a4a-4c00-b51b-81d9c2f157e7",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "aab2d30b-ccdc-4fbf-a338-f47769406e4b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[GRAPHIC ELEMENT SENT TO FILE `random_networks_1.log.htm`]\n"
     ]
    }
   ],
   "source": [
    "# Send a plot of the network of reactions to the HTML log file\n",
    "uc.plot_reaction_network(log_file=log_file)"
   ]
  }
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