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pka.ipynb

@@ -0,0 +1,171 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import requests\n",
+    "import random\n",
+    "import os\n",
+    "import pandas as pd\n",
+    "from rdkit import Chem\n",
+    "\n",
+    "upload_url=r'http://xundrug.cn:5001/modules/upload0/'\n",
+    "\n",
+    "def predict_pka(smi):\n",
+    "    param={\"Smiles\" : (\"tmg\", smi)}\n",
+    "    headers={'token':'O05DriqqQLlry9kmpCwms2IJLC0MuLQ7'}\n",
+    "    response=requests.post(url=upload_url, files=param, headers=headers)\n",
+    "    jsonbool=int(response.headers['ifjson'])\n",
+    "    if jsonbool==1:\n",
+    "        res_json=response.json()\n",
+    "        if res_json['status'] == 200:\n",
+    "            pka_datas = res_json['gen_datas']\n",
+    "            return pka_datas\n",
+    "        else:\n",
+    "            raise RuntimeError(\"Error for pKa prediction\")\n",
+    "    else:\n",
+    "        raise RuntimeError(\"Error for pKa prediction\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "#BBB Score\n",
+    "#Gupta, M.; Lee, H. J.; Barden, C. J.; Weaver, D. F. The Blood–Brain Barrier (BBB) Score. J. Med. Chem. 2019, 62 (21), 9824–9836. https://doi.org/10.1021/acs.jmedchem.9b01220.\n",
+    "\n",
+    "def pka_bbb(base,acid):\n",
+    "    if len(base) == 0 and len(acid) == 0:\n",
+    "        # If molecule has neither (neutral molecule), \n",
+    "        # take the pKa that would give the maximal score for pKa descriptor (pKa=0 for MPO, pKa = 8.81 for BBB)\n",
+    "        pka = 8.81\n",
+    "        \n",
+    "    elif len(base) != 0 and max(base) >= 5:\n",
+    "        # If the molecule has basic pKa's ≥ 5, take the most basic pKa\n",
+    "        pka = max(base)\n",
+    "    \n",
+    "    elif len(base) == 0 and len(acid) != 0:\n",
+    "        if max(acid) >= 9.0:\n",
+    "            pka = 9.0\n",
+    "        else:\n",
+    "            pka = max(acid)\n",
+    "    elif len(base) != 0 and max(base) < 5 and len(acid) != 0:\n",
+    "        pka = max(acid)\n",
+    "    return pka"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "# run \n",
+    "smi = \"CC(=O)Nc1ccc(O)cc1\"\n",
+    "data_pka = predict_pka(smi)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "# get result\n",
+    "base = data_pka['Base'].values()\n",
+    "acid = data_pka['Acid'].values()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "# String to number\n",
+    "base = list(map(float,list(base)))\n",
+    "acid = list(map(float,list(acid)))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Base pka []\n",
+      "Acid pka: [13.84, 10.1]\n"
+     ]
+    }
+   ],
+   "source": [
+    "print('Base pka',base)\n",
+    "print('Acid pka:',acid)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "BBB pka: 9.0\n"
+     ]
+    }
+   ],
+   "source": [
+    "x = pka_bbb(base,acid)\n",
+    "print('BBB pka:', x)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}