Chembl-analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/pawan/anaconda3/envs/cadd-py36/lib/python3.6/site-packages/grequests.py:21: MonkeyPatchWarning: Monkey-patching ssl after ssl has already been imported may lead to errors, including RecursionError on Python 3.6. It may also silently lead to incorrect behaviour on Python 3.7. Please monkey-patch earlier. See https://github.com/gevent/gevent/issues/1016. Modules that had direct imports (NOT patched): ['urllib3.util (/home/pawan/anaconda3/envs/cadd-py36/lib/python3.6/site-packages/urllib3/util/__init__.py)', 'urllib3.contrib.pyopenssl (/home/pawan/anaconda3/envs/cadd-py36/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py)']. \n",
      "  curious_george.patch_all(thread=False, select=False)\n"
     ]
    }
   ],
   "source": [
    "from chembl_webresource_client.new_client import new_client\n",
    "import pandas as pd\n",
    "import math\n",
    "from rdkit.Chem import PandasTools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "targets = new_client.target\n",
    "molecule = new_client.molecule\n",
    "bioactivities = new_client.activity\n",
    "similarity = new_client.similarity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "p = molecule.filter(molecule_chembl_id__in = 'CHEMBL25') \\\n",
    "                         .only('molecule_chembl_id','molecule_type','max_phase','natural_product')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>max_phase</th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>molecule_type</th>\n",
       "      <th>natural_product</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>4</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>Small molecule</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>4</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>Small molecule</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   max_phase molecule_chembl_id   molecule_type natural_product\n",
       "0          4           CHEMBL25  Small molecule               0\n",
       "1          4           CHEMBL25  Small molecule               0"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.DataFrame.from_records(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "ID = [\"CHEMBL3740844\",\"CHEMBL3739689\",\"CHEMBL3740472\",\"CHEMBL3740669\",\"CHEMBL3741918\",\"CHEMBL3741377\",\"CHEMBL3739611\",\"CHEMBL3741608\",\"CHEMBL3742145\",\"CHEMBL3741062\",\"CHEMBL3741595\",\"CHEMBL3740732\",\"CHEMBL3741224\",\"CHEMBL3739931\",\"CHEMBL3740612\",\"CHEMBL3739647\",\"CHEMBL3741787\",\"CHEMBL3741821\",\"CHEMBL3739862\",\"CHEMBL3741733\",\"CHEMBL3740864\",\"CHEMBL3740278\",\"CHEMBL3740030\",\"CHEMBL3739459\",\"CHEMBL3740400\",\"CHEMBL3739470\",\"CHEMBL3739826\",\"CHEMBL3741548\",\"CHEMBL3741322\",\"CHEMBL3742080\",\"CHEMBL123632\",\"CHEMBL8602\",\"CHEMBL2158972\",\"CHEMBL1778269\"]\n",
    "\n",
    "for x in ID:\n",
    "    activities = bioactivities.filter(molecule_chembl_id__in=x)\\\n",
    "                      .only('activity_id','assay_chembl_id', 'assay_description', 'assay_type', \\\n",
    "                            'molecule_chembl_id', 'type', 'units', 'relation', 'value', \\\n",
    "                            'target_chembl_id', 'target_organism')\n",
    "    bioact_df = pd.DataFrame.from_records(activities)\n",
    "    bioact_df.to_csv(\"../Phase-CQS/cluster/Bioactivity/\"+x+\".csv\")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>activity_id</th>\n",
       "      <th>assay_chembl_id</th>\n",
       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>relation</th>\n",
       "      <th>target_chembl_id</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>91852</td>\n",
       "      <td>CHEMBL760085</td>\n",
       "      <td>Inhibitory concentration in DMSO with purified...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL230</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>62.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>91852</td>\n",
       "      <td>CHEMBL760085</td>\n",
       "      <td>Inhibitory concentration in DMSO with purified...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL230</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>62.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>91853</td>\n",
       "      <td>CHEMBL764258</td>\n",
       "      <td>Inhibitory concentration in DMSO with purified...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL2949</td>\n",
       "      <td>Ovis aries</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>12.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>278685</td>\n",
       "      <td>CHEMBL767951</td>\n",
       "      <td>Inhibition of PG synthetase activity obtained ...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL2096674</td>\n",
       "      <td>Bos taurus</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>1500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>579272</td>\n",
       "      <td>CHEMBL764147</td>\n",
       "      <td>Tested for inhibitory activity against Prostag...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL2949</td>\n",
       "      <td>Ovis aries</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>1280</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>579273</td>\n",
       "      <td>CHEMBL769654</td>\n",
       "      <td>Tested for inhibitory activity against Prostag...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL230</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>18000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>698812</td>\n",
       "      <td>CHEMBL767507</td>\n",
       "      <td>In vitro inhibitory activity against cyclooxyg...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL2094253</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>IC50</td>\n",
       "      <td>M</td>\n",
       "      <td>0.000015</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>792482</td>\n",
       "      <td>CHEMBL763975</td>\n",
       "      <td>Inhibitory activity against Prostaglandin G/H ...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL2949</td>\n",
       "      <td>Ovis aries</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>240</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>792484</td>\n",
       "      <td>CHEMBL766669</td>\n",
       "      <td>Inhibitory activity against Prostaglandin G/H ...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL4102</td>\n",
       "      <td>Ovis aries</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>660</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>1485808</td>\n",
       "      <td>CHEMBL831085</td>\n",
       "      <td>In vitro inhibition of ovine prostaglandin G/H...</td>\n",
       "      <td>B</td>\n",
       "      <td>CHEMBL25</td>\n",
       "      <td>=</td>\n",
       "      <td>CHEMBL2949</td>\n",
       "      <td>Ovis aries</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>0.35</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   activity_id assay_chembl_id  \\\n",
       "0        91852    CHEMBL760085   \n",
       "1        91852    CHEMBL760085   \n",
       "2        91853    CHEMBL764258   \n",
       "3       278685    CHEMBL767951   \n",
       "4       579272    CHEMBL764147   \n",
       "5       579273    CHEMBL769654   \n",
       "6       698812    CHEMBL767507   \n",
       "7       792482    CHEMBL763975   \n",
       "8       792484    CHEMBL766669   \n",
       "9      1485808    CHEMBL831085   \n",
       "\n",
       "                                   assay_description assay_type  \\\n",
       "0  Inhibitory concentration in DMSO with purified...          B   \n",
       "1  Inhibitory concentration in DMSO with purified...          B   \n",
       "2  Inhibitory concentration in DMSO with purified...          B   \n",
       "3  Inhibition of PG synthetase activity obtained ...          B   \n",
       "4  Tested for inhibitory activity against Prostag...          B   \n",
       "5  Tested for inhibitory activity against Prostag...          B   \n",
       "6  In vitro inhibitory activity against cyclooxyg...          B   \n",
       "7  Inhibitory activity against Prostaglandin G/H ...          B   \n",
       "8  Inhibitory activity against Prostaglandin G/H ...          B   \n",
       "9  In vitro inhibition of ovine prostaglandin G/H...          B   \n",
       "\n",
       "  molecule_chembl_id relation target_chembl_id target_organism  type units  \\\n",
       "0           CHEMBL25        =        CHEMBL230    Homo sapiens  IC50    uM   \n",
       "1           CHEMBL25        =        CHEMBL230    Homo sapiens  IC50    uM   \n",
       "2           CHEMBL25        =       CHEMBL2949      Ovis aries  IC50    uM   \n",
       "3           CHEMBL25        =    CHEMBL2096674      Bos taurus  IC50    uM   \n",
       "4           CHEMBL25        =       CHEMBL2949      Ovis aries  IC50    uM   \n",
       "5           CHEMBL25        =        CHEMBL230    Homo sapiens  IC50    uM   \n",
       "6           CHEMBL25        =    CHEMBL2094253    Homo sapiens  IC50     M   \n",
       "7           CHEMBL25        =       CHEMBL2949      Ovis aries  IC50    uM   \n",
       "8           CHEMBL25        =       CHEMBL4102      Ovis aries  IC50    uM   \n",
       "9           CHEMBL25        =       CHEMBL2949      Ovis aries  IC50    uM   \n",
       "\n",
       "      value  \n",
       "0      62.5  \n",
       "1      62.5  \n",
       "2      12.5  \n",
       "3      1500  \n",
       "4      1280  \n",
       "5     18000  \n",
       "6  0.000015  \n",
       "7       240  \n",
       "8       660  \n",
       "9      0.35  "
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "\n",
    "bioact_df = pd.DataFrame.from_records(activities)\n",
    "bioact_df.head(10)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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