BiopythonSASA.ipynb

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   "source": [
    "Looks like it needs Biopython 1.79\n",
    "\n",
    "```\n",
    "conda install -c conda-forge biopython \n",
    "```\n",
    "\n",
    "Then, I don't know how to tell Biopython download structures from the web, so I downloaded 1lcd manually.\n",
    "\n",
    "Then, for SOME REASON, the biopython site doesn't use real quotes. So I couldn't just copy and paste without changing \"smart quotes\" into real quotes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "2ead59d6-bbe2-4ab2-97e3-1e59116f8cce",
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.PDB import PDBParser"
   ]
  },
  {
   "cell_type": "code",
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   "id": "4e1318a3-34ae-415f-8a7c-25e21a4ae5ef",
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   "source": [
    "p = PDBParser(QUIET=1)"
   ]
  },
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   "execution_count": 3,
   "id": "9df61cca-1a34-496c-9745-1974283a31ee",
   "metadata": {},
   "outputs": [],
   "source": [
    "#struct = p.get_structure(\"1LCD\", \"PDB/1LCD.pdb\")\n",
    "struct = p.get_structure(\"1LCD\", \"1lcd.pdb\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "d168091c-8ebc-432a-8f8d-90143ba70292",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Needed this line\n",
    "from Bio.PDB import SASA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "264c5dc8-da1f-4c8b-83f4-5b4a19222ab3",
   "metadata": {},
   "outputs": [],
   "source": [
    "#sr = ShrakeRupley()\n",
    "sr = SASA.ShrakeRupley()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "8b337c70-a615-407f-b59d-f21ca9c06125",
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   "outputs": [],
   "source": [
    "sr.compute(struct, level=\"S\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "8798c32f-a4ad-4b0b-a01d-66ff2a70e229",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "7053.43\n"
     ]
    }
   ],
   "source": [
    "print(round(struct.sasa, 2))\n",
    "# expect 7053.43"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "2f06eab6-83b9-4766-9e61-12d0ba61ee9c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "9.64\n"
     ]
    }
   ],
   "source": [
    "print(round(struct[0][\"A\"][11][\"OE1\"].sasa, 2))\n",
    "# expect 9.64"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8ba4b03f-3025-4aa9-935b-62144dd0eaed",
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   "outputs": [],
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  }
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