CaseStudy-SearchSpace.ipynb

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    {
     "data": {
      "text/markdown": [
       "This notebook has been executed using the docker image `colomoto/colomoto-docker:2021-02-01`"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
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     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import networkx as nx\n",
    "import bonesis\n",
    "import clingo\n",
    "from functools import reduce"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c9656bbf",
   "metadata": {
    "execution": {
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   "outputs": [],
   "source": [
    "model = 'CaseStudy'\n",
    "inputs = {'Carbon1', 'Carbon2', 'Oxygen'}\n",
    "regulators = {'RPO2', 'RPcl'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "16c9df11",
   "metadata": {
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     "text": [
      "# computing graph layout...\n"
     ]
    },
    {
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       "<!-- Oxygen -->\n",
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       "<title>Oxygen</title>\n",
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      ],
      "text/plain": [
       "<networkx.classes.digraph.DiGraph at 0x7f35b09a57c0>"
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     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pkn = nx.DiGraph()\n",
    "with open(f'./data/{model}/interactions.txt') as fp:\n",
    "    for line in fp:\n",
    "        line = line.strip()\n",
    "        if not line:\n",
    "            continue\n",
    "        a, b = line.split()\n",
    "        if b not in inputs:\n",
    "            pkn.add_edge(a, b, sign=0)\n",
    "        if a not in inputs:\n",
    "            pkn.add_edge(b, a, sign=0)\n",
    "pkn"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2b0caa3a",
   "metadata": {
    "execution": {
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   },
   "outputs": [],
   "source": [
    "bo = bonesis.BoNesis(bonesis.InfluenceGraph(pkn, allow_skipping_nodes=False))\n",
    "# inputs are constants 0\n",
    "for k in inputs:\n",
    "    bo.custom(f\"constant({clingo.String(k)}, -1)\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "c03f399f",
   "metadata": {
    "execution": {
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   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Grounding...done in 0.0s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'Carbon1': 1,\n",
       " 'RPcl': 2170,\n",
       " 'Carbon2': 1,\n",
       " 'Oxygen': 1,\n",
       " 'RPO2': 14,\n",
       " 'Rres': 4,\n",
       " 'Tc2': 4,\n",
       " 'Tc1': 4}"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "space = bo.local_functions().as_dict(\"count\")\n",
    "space"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "dfde39dc",
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    {
     "data": {
      "text/plain": [
       "1944320"
      ]
     },
     "execution_count": 1,
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   ],
   "source": [
    "reduce(int.__mul__, space.values())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ebc1bc59",
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   "source": []
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