1_Data_collection.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## DATA COLLECTION\n",
    "##### chEMBL is an open large-scale bioactivity database.\n",
    "##### chembl_webresource_client is the library developed and supported by chEMBL group. The library helps accessing chEMBL data.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd #for data processing \n",
    "from chembl_webresource_client.new_client import new_client"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "###### Lets download the biological activity data from chEMBL database. The dataset  is comprised of compounds that have been biologically tested for their activity towards target ###### "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\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>cross_references</th>\n",
       "      <th>organism</th>\n",
       "      <th>pref_name</th>\n",
       "      <th>score</th>\n",
       "      <th>species_group_flag</th>\n",
       "      <th>target_chembl_id</th>\n",
       "      <th>target_components</th>\n",
       "      <th>target_type</th>\n",
       "      <th>tax_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[]</td>\n",
       "      <td>Mus musculus</td>\n",
       "      <td>Receptor-type tyrosine-protein kinase FLT3</td>\n",
       "      <td>18.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL2034796</td>\n",
       "      <td>[{'accession': 'Q00342', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>10090</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[{'xref_id': 'P36888', 'xref_name': None, 'xre...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>16.0</td>\n",
       "      <td>False</td>\n",
       "      <td>CHEMBL1974</td>\n",
       "      <td>[{'accession': 'P36888', 'component_descriptio...</td>\n",
       "      <td>SINGLE PROTEIN</td>\n",
       "      <td>9606</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                    cross_references      organism  \\\n",
       "0                                                 []  Mus musculus   \n",
       "1  [{'xref_id': 'P36888', 'xref_name': None, 'xre...  Homo sapiens   \n",
       "\n",
       "                                    pref_name  score  species_group_flag  \\\n",
       "0  Receptor-type tyrosine-protein kinase FLT3   18.0               False   \n",
       "1       Tyrosine-protein kinase receptor FLT3   16.0               False   \n",
       "\n",
       "  target_chembl_id                                  target_components  \\\n",
       "0    CHEMBL2034796  [{'accession': 'Q00342', 'component_descriptio...   \n",
       "1       CHEMBL1974  [{'accession': 'P36888', 'component_descriptio...   \n",
       "\n",
       "      target_type  tax_id  \n",
       "0  SINGLE PROTEIN   10090  \n",
       "1  SINGLE PROTEIN    9606  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "target = new_client.target  \n",
    "target_query = target.search('FLT3')  #search the target,'FLT3' is genetic code for Tyrosine protein kinase receptor\n",
    "targets = pd.DataFrame.from_dict(target_query)\n",
    "targets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CHEMBL1974'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#selecting our target\n",
    "selected_target = targets.target_chembl_id[1]  \n",
    "selected_target"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Lets retrieve biological activity data for Tyrosine Protein kinase receptor that are reported as IC50 values in nM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "activity = new_client.activity  \n",
    "data = activity.filter(target_chembl_id=selected_target).filter(standard_type=\"IC50\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>activity_comment</th>\n",
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       "      <th>assay_description</th>\n",
       "      <th>assay_type</th>\n",
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       "      <th>bao_format</th>\n",
       "      <th>bao_label</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>...</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>target_pref_name</th>\n",
       "      <th>target_tax_id</th>\n",
       "      <th>text_value</th>\n",
       "      <th>toid</th>\n",
       "      <th>type</th>\n",
       "      <th>units</th>\n",
       "      <th>uo_units</th>\n",
       "      <th>upper_value</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>866063</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.128</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>872532</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>872564</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>8.79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>879718</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>1.91</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>884645</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>30.0</td>\n",
       "    </tr>\n",
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       "<p>5 rows × 43 columns</p>\n",
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      ],
      "text/plain": [
       "  activity_comment  activity_id activity_properties assay_chembl_id  \\\n",
       "0             None       866063                  []    CHEMBL766072   \n",
       "1             None       872532                  []    CHEMBL766072   \n",
       "2             None       872564                  []    CHEMBL766072   \n",
       "3             None       879718                  []    CHEMBL766072   \n",
       "4             None       884645                  []    CHEMBL766072   \n",
       "\n",
       "                                   assay_description assay_type bao_endpoint  \\\n",
       "0  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "1  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "2  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "3  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "4  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "\n",
       "    bao_format          bao_label  \\\n",
       "0  BAO_0000219  cell-based format   \n",
       "1  BAO_0000219  cell-based format   \n",
       "2  BAO_0000219  cell-based format   \n",
       "3  BAO_0000219  cell-based format   \n",
       "4  BAO_0000219  cell-based format   \n",
       "\n",
       "                                    canonical_smiles  ... target_organism  \\\n",
       "0  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...  ...    Homo sapiens   \n",
       "1  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...  ...    Homo sapiens   \n",
       "2  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...  ...    Homo sapiens   \n",
       "3  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...  ...    Homo sapiens   \n",
       "4  Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...  ...    Homo sapiens   \n",
       "\n",
       "                        target_pref_name target_tax_id text_value  toid  type  \\\n",
       "0  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "1  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "2  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "3  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "4  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "\n",
       "  units    uo_units upper_value  value  \n",
       "0    uM  UO_0000065        None  0.128  \n",
       "1    uM  UO_0000065        None   0.22  \n",
       "2    uM  UO_0000065        None   8.79  \n",
       "3    uM  UO_0000065        None   1.91  \n",
       "4    uM  UO_0000065        None   30.0  \n",
       "\n",
       "[5 rows x 43 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#convert data to dataframe using pandas \n",
    "df = pd.DataFrame.from_dict(data)\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(3464, 43)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#dimension of dataframe \n",
    "df.shape "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>0</th>\n",
       "      <td>None</td>\n",
       "      <td>866063</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.128</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>None</td>\n",
       "      <td>872532</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>0.22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>None</td>\n",
       "      <td>872564</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>8.79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>None</td>\n",
       "      <td>879718</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>1.91</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>None</td>\n",
       "      <td>884645</td>\n",
       "      <td>[]</td>\n",
       "      <td>CHEMBL766072</td>\n",
       "      <td>Inhibition of chimeric PDGF receptor with FLT-...</td>\n",
       "      <td>B</td>\n",
       "      <td>BAO_0000190</td>\n",
       "      <td>BAO_0000219</td>\n",
       "      <td>cell-based format</td>\n",
       "      <td>Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...</td>\n",
       "      <td>...</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>Tyrosine-protein kinase receptor FLT3</td>\n",
       "      <td>9606</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>IC50</td>\n",
       "      <td>uM</td>\n",
       "      <td>UO_0000065</td>\n",
       "      <td>None</td>\n",
       "      <td>30.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 43 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  activity_comment  activity_id activity_properties assay_chembl_id  \\\n",
       "0             None       866063                  []    CHEMBL766072   \n",
       "1             None       872532                  []    CHEMBL766072   \n",
       "2             None       872564                  []    CHEMBL766072   \n",
       "3             None       879718                  []    CHEMBL766072   \n",
       "4             None       884645                  []    CHEMBL766072   \n",
       "\n",
       "                                   assay_description assay_type bao_endpoint  \\\n",
       "0  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "1  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "2  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "3  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "4  Inhibition of chimeric PDGF receptor with FLT-...          B  BAO_0000190   \n",
       "\n",
       "    bao_format          bao_label  \\\n",
       "0  BAO_0000219  cell-based format   \n",
       "1  BAO_0000219  cell-based format   \n",
       "2  BAO_0000219  cell-based format   \n",
       "3  BAO_0000219  cell-based format   \n",
       "4  BAO_0000219  cell-based format   \n",
       "\n",
       "                                    canonical_smiles  ... target_organism  \\\n",
       "0  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...  ...    Homo sapiens   \n",
       "1  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...  ...    Homo sapiens   \n",
       "2  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...  ...    Homo sapiens   \n",
       "3  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...  ...    Homo sapiens   \n",
       "4  Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...  ...    Homo sapiens   \n",
       "\n",
       "                        target_pref_name target_tax_id text_value  toid  type  \\\n",
       "0  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "1  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "2  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "3  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "4  Tyrosine-protein kinase receptor FLT3          9606       None  None  IC50   \n",
       "\n",
       "  units    uo_units upper_value  value  \n",
       "0    uM  UO_0000065        None  0.128  \n",
       "1    uM  UO_0000065        None   0.22  \n",
       "2    uM  UO_0000065        None   8.79  \n",
       "3    uM  UO_0000065        None   1.91  \n",
       "4    uM  UO_0000065        None   30.0  \n",
       "\n",
       "[5 rows x 43 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#removing data which has 'Nan' standard value \n",
    "df2 = df[df.standard_value.notna()]\n",
    "df2.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(3383, 43)"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2.shape "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### 81 entries with NaN value are removed \n",
    "\n",
    "#### Lets Combine all those features/columns that are important for model training"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL330863</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>128.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL124660</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>220.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL126699</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>8790.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL445636</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>1910.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL941</td>\n",
       "      <td>Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...</td>\n",
       "      <td>30000.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  molecule_chembl_id                                   canonical_smiles  \\\n",
       "0       CHEMBL330863  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...   \n",
       "1       CHEMBL124660  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...   \n",
       "2       CHEMBL126699  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...   \n",
       "3       CHEMBL445636  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...   \n",
       "4          CHEMBL941  Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...   \n",
       "\n",
       "  standard_value  \n",
       "0          128.0  \n",
       "1          220.0  \n",
       "2         8790.0  \n",
       "3         1910.0  \n",
       "4        30000.0  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "columns= ['molecule_chembl_id','canonical_smiles','standard_value']\n",
    "df3 = df2[columns]\n",
    "df3.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Labeling the compounds as Active/Inactive/Intermediate\n",
    "\n",
    "Compunds are being labeled(Active\\Inactive\\Intermediate) based on their potency value(Standard_values)\n",
    "compounds having values < 1000 nM will be considered active , Those greater than 10000 nM will be considered to be inactive"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "bioactivity_threshold = []\n",
    "for i in df3.standard_value:\n",
    "    if float(i) >= 10000:\n",
    "        bioactivity_threshold.append(\"inactive\")\n",
    "    elif float(i) <= 1000:\n",
    "        bioactivity_threshold.append(\"active\")\n",
    "    else:\n",
    "        bioactivity_threshold.append(\"intermediate\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Let's Add Bioactivity data to our dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>molecule_chembl_id</th>\n",
       "      <th>canonical_smiles</th>\n",
       "      <th>standard_value</th>\n",
       "      <th>bioactivity</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CHEMBL330863</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>128.0</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMBL124660</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...</td>\n",
       "      <td>220.0</td>\n",
       "      <td>active</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CHEMBL126699</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>8790.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CHEMBL445636</td>\n",
       "      <td>COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...</td>\n",
       "      <td>1910.0</td>\n",
       "      <td>intermediate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CHEMBL941</td>\n",
       "      <td>Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...</td>\n",
       "      <td>30000.0</td>\n",
       "      <td>inactive</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  molecule_chembl_id                                   canonical_smiles  \\\n",
       "0       CHEMBL330863  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...   \n",
       "1       CHEMBL124660  COc1cc2c(N3CCN(C(=O)Nc4ccc(OC(C)C)cc4)CC3)ncnc...   \n",
       "2       CHEMBL126699  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...   \n",
       "3       CHEMBL445636  COc1cc2c(N3CCN(C(=O)Nc4ccc(C#N)cc4)CC3)ncnc2cc...   \n",
       "4          CHEMBL941  Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc...   \n",
       "\n",
       "  standard_value   bioactivity  \n",
       "0          128.0        active  \n",
       "1          220.0        active  \n",
       "2         8790.0  intermediate  \n",
       "3         1910.0  intermediate  \n",
       "4        30000.0      inactive  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bioactivity_class = pd.Series(bioactivity_threshold, name='bioactivity')\n",
    "df5 = pd.concat([df3, bioactivity_class], axis=1)\n",
    "df5.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "active          1645\n",
       "inactive        1283\n",
       "intermediate     455\n",
       "Name: bioactivity, dtype: int64"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df5.bioactivity.value_counts()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "###### There are 1645 Active and 1283 inactive compounds/molecules present in our dataset "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Lets save this dataset "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df5.to_csv('TPKR_data2.csv',index=False)"
   ]
  }
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