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   "source": [
    "# Read List Of Entries From Local Hadoop Sequence File\n",
    "\n",
    "Simple example reading a list of PDB entries from local Hadoop Sequence Files\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext\n",
    "from mmtfPyspark.io import mmtfReader\n",
    "from mmtfPyspark.structureViewer import view_structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"ReadListFromLocal\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read in local Hadoop Sequence Files and count number of entries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "number of pdb entries read : 3\n"
     ]
    }
   ],
   "source": [
    "path = \"../../resources/mmtf_full_sample/\"\n",
    "pdbIds = [\"1M4L\", \"1LXJ\", \"4XPX\"]\n",
    "\n",
    "pdb = mmtfReader.read_sequence_file(path, sc, pdbId = pdbIds,)\n",
    "\n",
    "count = pdb.count()\n",
    "\n",
    "print(f'number of pdb entries read : {count}')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize Structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "55343eb0124b446b849084eb7408e9d1",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(IntSlider(value=0, continuous_update=False, description='Structure', max=2), Output()), …"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<function mmtfPyspark.structureViewer.view_structure.<locals>.view3d(i=0)>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structures = pdb.keys().collect()\n",
    "view_structure(structures)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Terminate Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
 ],
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