parse-halflife.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Parse the DrugBank XML and extract half-life of drugs to tsv files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Run using Python 3 to avoid a non-ascii character error when writing to file with the csv module."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import csv\n",
    "import gzip\n",
    "import collections\n",
    "import re\n",
    "import io\n",
    "import json\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "import requests\n",
    "import pandas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "xml_path = os.path.join('download', 'drugbank.xml.gz')\n",
    "with gzip.open(xml_path) as xml_file:\n",
    "    tree = ET.parse(xml_file)\n",
    "root = tree.getroot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "ns = '{http://www.drugbank.ca}'\n",
    "for i,drug in enumerate(root):\n",
    "    row = collections.OrderedDict()\n",
    "    assert drug.tag == ns + 'drug'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "ns = '{http://www.drugbank.ca}'\n",
    "# calculated properties \n",
    "cal_logp_template = \"{ns}calculated-properties/{ns}property[{ns}kind='logP']/{ns}value\"\n",
    "cal_logs_template = \"{ns}calculated-properties/{ns}property[{ns}kind='logS']/{ns}value\"\n",
    "cal_ws_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Water Solubility']/{ns}value\"\n",
    "cal_mw_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Molecular Weight']/{ns}value\"\n",
    "cal_psa_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Polar Surface Area (PSA)']/{ns}value\"\n",
    "cal_refr_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Refractivity']/{ns}value\"\n",
    "cal_pola_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Polarizability']/{ns}value\"\n",
    "cal_rbc_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Rotatable Bond Count']/{ns}value\"\n",
    "cal_hdac_template = \"{ns}calculated-properties/{ns}property[{ns}kind='H Bond Acceptor Count']/{ns}value\"\n",
    "cal_hbdc_template = \"{ns}calculated-properties/{ns}property[{ns}kind='H Bond Donor Count']/{ns}value\"\n",
    "cal_pkasa_template = \"{ns}calculated-properties/{ns}property[{ns}kind='pKa (strongest acidic)']/{ns}value\"\n",
    "cal_pkasb_template = \"{ns}calculated-properties/{ns}property[{ns}kind='pKa (strongest basic)']/{ns}value\"\n",
    "cal_pc_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Physiological Charge']/{ns}value\"\n",
    "cal_nr_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Number of Rings']/{ns}value\"\n",
    "cal_bioa_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Bioavailability']/{ns}value\"\n",
    "cal_rof_template = \"{ns}calculated-properties/{ns}property[{ns}kind='Rule of Five']/{ns}value\"\n",
    "# experimental properties\n",
    "exp_mw_template = \"{ns}experimental-properties/{ns}property[{ns}kind='Molecular Weight']/{ns}value\"\n",
    "exp_logp_template = \"{ns}experimental-properties/{ns}property[{ns}kind='logP']/{ns}value\"\n",
    "exp_pka_template = \"{ns}experimental-properties/{ns}property[{ns}kind='pKa']/{ns}value\"\n",
    "\n",
    "rows = list()\n",
    "for i, drug in enumerate(root):\n",
    "    row = collections.OrderedDict()\n",
    "    assert drug.tag == ns + 'drug'\n",
    "    row['type'] = drug.get('type')\n",
    "    row['drugbank_id'] = drug.findtext(ns + \"drugbank-id[@primary='true']\")\n",
    "    row['name'] = drug.findtext(ns + \"name\")\n",
    "    row['cal_logp'] = drug.findtext(cal_logp_template.format(ns = ns))\n",
    "    row['cal_logs'] = drug.findtext(cal_logs_template.format(ns = ns))\n",
    "    row['cal_water_solubility'] = drug.findtext(cal_ws_template.format(ns = ns))\n",
    "    row['cal_molecular_weight'] = drug.findtext(cal_mw_template.format(ns = ns))\n",
    "    row['cal_polar_surface_area'] = drug.findtext(cal_psa_template.format(ns = ns))\n",
    "    row['cal_refractivity'] = drug.findtext(cal_refr_template.format(ns = ns))\n",
    "    row['cal_polarizability'] = drug.findtext(cal_pola_template.format(ns = ns))\n",
    "    row['cal_rotatable_bond_count'] = drug.findtext(cal_rbc_template.format(ns = ns))\n",
    "    row['cal_h_bond_acceptor_count'] = drug.findtext(cal_hdac_template.format(ns = ns))\n",
    "    row['cal_h_bond_donor_count'] = drug.findtext(cal_hbdc_template.format(ns = ns))\n",
    "    row['cal_pka_acidic'] = drug.findtext(cal_pkasa_template.format(ns = ns))\n",
    "    row['cal_pka_basic'] = drug.findtext(cal_pkasb_template.format(ns = ns))\n",
    "    row['cal_physiological_charge'] = drug.findtext(cal_pc_template.format(ns = ns))\n",
    "    row['cal_number_of_rings'] = drug.findtext(cal_nr_template.format(ns = ns))\n",
    "    row['cal_bioavailability'] = drug.findtext(cal_bioa_template.format(ns = ns))\n",
    "    row['cal_rule_of_five'] = drug.findtext(cal_rof_template.format(ns = ns))\n",
    "    row['exp_molecular_weight'] = drug.findtext(exp_mw_template.format(ns = ns))\n",
    "    row['exp_logp'] = drug.findtext(exp_logp_template.format(ns = ns))\n",
    "    row['exp_pka'] = drug.findtext(exp_pka_template.format(ns = ns))\n",
    "    row['half_life'] = drug.findtext(ns + \"half-life\")\n",
    "    rows.append(row)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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>type</th>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>name</th>\n",
       "      <th>cal_logp</th>\n",
       "      <th>cal_logs</th>\n",
       "      <th>cal_water_solubility</th>\n",
       "      <th>cal_molecular_weight</th>\n",
       "      <th>cal_polar_surface_area</th>\n",
       "      <th>cal_refractivity</th>\n",
       "      <th>cal_polarizability</th>\n",
       "      <th>...</th>\n",
       "      <th>cal_pka_acidic</th>\n",
       "      <th>cal_pka_basic</th>\n",
       "      <th>cal_physiological_charge</th>\n",
       "      <th>cal_number_of_rings</th>\n",
       "      <th>cal_bioavailability</th>\n",
       "      <th>cal_rule_of_five</th>\n",
       "      <th>exp_molecular_weight</th>\n",
       "      <th>exp_logp</th>\n",
       "      <th>exp_pka</th>\n",
       "      <th>half_life</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>biotech</td>\n",
       "      <td>DB00001</td>\n",
       "      <td>Lepirudin</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>6963.4250</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Approximately 1.3 hours</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>biotech</td>\n",
       "      <td>DB00002</td>\n",
       "      <td>Cetuximab</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>145781.6000</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>114 hrs</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>biotech</td>\n",
       "      <td>DB00003</td>\n",
       "      <td>Dornase alfa</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>29253.9000</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>biotech</td>\n",
       "      <td>DB00004</td>\n",
       "      <td>Denileukin diftitox</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>57647.3000</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>70-80 min</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>biotech</td>\n",
       "      <td>DB00005</td>\n",
       "      <td>Etanercept</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>51234.9000</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>102 +/- 30 hrs in individuals with rheumatoid ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      type drugbank_id                 name cal_logp cal_logs  \\\n",
       "0  biotech     DB00001            Lepirudin     None     None   \n",
       "1  biotech     DB00002            Cetuximab     None     None   \n",
       "2  biotech     DB00003         Dornase alfa     None     None   \n",
       "3  biotech     DB00004  Denileukin diftitox     None     None   \n",
       "4  biotech     DB00005           Etanercept     None     None   \n",
       "\n",
       "  cal_water_solubility cal_molecular_weight cal_polar_surface_area  \\\n",
       "0                 None                 None                   None   \n",
       "1                 None                 None                   None   \n",
       "2                 None                 None                   None   \n",
       "3                 None                 None                   None   \n",
       "4                 None                 None                   None   \n",
       "\n",
       "  cal_refractivity cal_polarizability  \\\n",
       "0             None               None   \n",
       "1             None               None   \n",
       "2             None               None   \n",
       "3             None               None   \n",
       "4             None               None   \n",
       "\n",
       "                         ...                         cal_pka_acidic  \\\n",
       "0                        ...                                   None   \n",
       "1                        ...                                   None   \n",
       "2                        ...                                   None   \n",
       "3                        ...                                   None   \n",
       "4                        ...                                   None   \n",
       "\n",
       "  cal_pka_basic cal_physiological_charge cal_number_of_rings  \\\n",
       "0          None                     None                None   \n",
       "1          None                     None                None   \n",
       "2          None                     None                None   \n",
       "3          None                     None                None   \n",
       "4          None                     None                None   \n",
       "\n",
       "  cal_bioavailability cal_rule_of_five exp_molecular_weight exp_logp exp_pka  \\\n",
       "0                None             None            6963.4250     None    None   \n",
       "1                None             None          145781.6000     None    None   \n",
       "2                None             None           29253.9000     None    None   \n",
       "3                None             None           57647.3000     None    None   \n",
       "4                None             None           51234.9000     None    None   \n",
       "\n",
       "                                           half_life  \n",
       "0                            Approximately 1.3 hours  \n",
       "1                                            114 hrs  \n",
       "2                                                     \n",
       "3                                          70-80 min  \n",
       "4  102 +/- 30 hrs in individuals with rheumatoid ...  \n",
       "\n",
       "[5 rows x 23 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# combine multiple values of the same feature\n",
    "def collapse_list_values(row):\n",
    "    for key, value in row.items():\n",
    "        if isinstance(value, list):\n",
    "            row[key] = '|'.join(value)\n",
    "    return row\n",
    "\n",
    "rows = list(map(collapse_list_values, rows))\n",
    "drugbank_df = pandas.DataFrame.from_dict(rows)\n",
    "drugbank_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# output extracted features to tsv file\n",
    "drugbank_df.to_csv(path_or_buf='data/drugbank_halflife.tsv', sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Summary statistics of extracted structural information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "                                                                                                                                                                                           6439\n",
       "2 hours                                                                                                                                                                                      16\n",
       "1 hour                                                                                                                                                                                       12\n",
       "10 hours                                                                                                                                                                                     12\n",
       "3 hours                                                                                                                                                                                       8\n",
       "6-8 hours                                                                                                                                                                                     8\n",
       "2.5 hours                                                                                                                                                                                     8\n",
       "5 hours                                                                                                                                                                                       8\n",
       "20 hours                                                                                                                                                                                      8\n",
       "1-2 hours                                                                                                                                                                                     7\n",
       "2-3 hours                                                                                                                                                                                     7\n",
       "8 hours                                                                                                                                                                                       7\n",
       "4 hours                                                                                                                                                                                       7\n",
       "1.5 hours                                                                                                                                                                                     7\n",
       "2-4 hours                                                                                                                                                                                     6\n",
       "6 hours                                                                                                                                                                                       6\n",
       "3.5 hours                                                                                                                                                                                     5\n",
       "9 hours                                                                                                                                                                                       5\n",
       "12 hours                                                                                                                                                                                      5\n",
       "3-4 hours                                                                                                                                                                                     5\n",
       "4.5 hours                                                                                                                                                                                     5\n",
       "7 hours                                                                                                                                                                                       5\n",
       "0.8 hours (mammalian reticulocytes, in vitro)                                                                                                                                                 5\n",
       "10 minutes                                                                                                                                                                                    4\n",
       "3-8 hours                                                                                                                                                                                     4\n",
       "6-12 hours                                                                                                                                                                                    4\n",
       "36 hours                                                                                                                                                                                      4\n",
       "10-20 hours                                                                                                                                                                                   4\n",
       "24 hours                                                                                                                                                                                      4\n",
       "3-6 hours                                                                                                                                                                                     4\n",
       "                                                                                                                                                                                           ... \n",
       "Single-dose terminal half life: 14.2 hours\\r\\nEffective multiple-dose half life: 24 hours                                                                                                     1\n",
       "The half life of EPA is 89 hours.                                                                                                                                                             1\n",
       "2.1 to 3.4 hours.                                                                                                                                                                             1\n",
       "Initial half-life values range from 25-65 hours, decreasing to 12-17 hours on repeated doses.                                                                                                 1\n",
       "14-18 hours                                                                                                                                                                                   1\n",
       "70-100 hours                                                                                                                                                                                  1\n",
       "2 to 4 weeks                                                                                                                                                                                  1\n",
       "39 and 51 minutes                                                                                                                                                                             1\n",
       "Intravenous, healthy adults = 1.8 to 6.4 hours (mean of 3 hours)                                                                                                                              1\n",
       "Alpha phase: approximately 4 hours; Beta phase: 25-36 hours                                                                                                                                   1\n",
       "Fosphenytoin has a half-life of approximately 15 minutes.                                                                                                                                     1\n",
       "2 hours (range 1.5-3.5 hours).                                                                                                                                                                1\n",
       "21-24 hours                                                                                                                                                                                   1\n",
       "The terminal half life is 5-9 hours in adults and 11-13 hours in the elderly.                                                                                                                 1\n",
       "Golimumab has a long half-life of about 2 weeks.                                                                                                                                              1\n",
       "4.5 hours (Ophthalmic)                                                                                                                                                                        1\n",
       "7-14 hours                                                                                                                                                                                    1\n",
       "88 minutes                                                                                                                                                                                    1\n",
       "Rapid distribution half-life of about 2 minutes and an elimination half-life of about 9 minutes. The acid metabolite has an elimination half-life of about 3.7 hours.                         1\n",
       "The mean serum half-life is approximately 2.0 hours, independent of the route of administration.                                                                                              1\n",
       "11 ± 4 days                                                                                                                                                                                   1\n",
       "Elimination half-life of 22 minutes.                                                                                                                                                          1\n",
       "The mean half-life of OFP in blood 1.9 minutes                                                                                                                                                1\n",
       "T<sub>4</sub>, 6 to 7 days. T<sub>3</sub>, 1 to 2 days.                                                                                                                                       1\n",
       "Terminal plasma elimation half-life = 14 days (for all doses);                                                                                                                                1\n",
       "The observed half-lives in healthy subjects are approximately 45 minutes after oral dosing and 12 hours after topical dosing, indicating percutaneous absorption rate-limited kinetics.       1\n",
       "When a single oral dose is given, the terminal elimination half-life is approximately 17 hours.                                                                                               1\n",
       "4 to 6 hours.                                                                                                                                                                                 1\n",
       "Alpha: 1 hour. Beta: 24 hours, but lengthens to 72 to 115 hours with prolonged intravenous infusion.                                                                                          1\n",
       "21-25 hours                                                                                                                                                                                   1\n",
       "Name: half_life, Length: 1089, dtype: int64"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The half life information is in free text & various format\n",
    "drugbank_df['half_life'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7759"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# number of extracted drugs \n",
    "len(drugbank_df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1320"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# number of extracted drugs with half life information\n",
    "len(drugbank_df) - sum(drugbank_df['half_life'] == '')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "type                         7759\n",
       "drugbank_id                  7759\n",
       "name                         7759\n",
       "cal_logp                     6866\n",
       "cal_logs                     6746\n",
       "cal_water_solubility         6746\n",
       "cal_molecular_weight         6870\n",
       "cal_polar_surface_area       6868\n",
       "cal_refractivity             6868\n",
       "cal_polarizability           6863\n",
       "cal_rotatable_bond_count     6868\n",
       "cal_h_bond_acceptor_count    6868\n",
       "cal_h_bond_donor_count       6868\n",
       "cal_pka_acidic               5890\n",
       "cal_pka_basic                6438\n",
       "cal_physiological_charge     6868\n",
       "cal_number_of_rings          6868\n",
       "cal_bioavailability          6868\n",
       "cal_rule_of_five             5433\n",
       "exp_molecular_weight          153\n",
       "exp_logp                     1391\n",
       "exp_pka                       417\n",
       "half_life                    7759\n",
       "dtype: int64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# number of extracted drugs with other structural information\n",
    "len(drugbank_df) - drugbank_df.isin([None]).sum(axis=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "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>type</th>\n",
       "      <th>drugbank_id</th>\n",
       "      <th>name</th>\n",
       "      <th>cal_logp</th>\n",
       "      <th>cal_logs</th>\n",
       "      <th>cal_water_solubility</th>\n",
       "      <th>cal_molecular_weight</th>\n",
       "      <th>cal_polar_surface_area</th>\n",
       "      <th>cal_refractivity</th>\n",
       "      <th>cal_polarizability</th>\n",
       "      <th>...</th>\n",
       "      <th>cal_pka_acidic</th>\n",
       "      <th>cal_pka_basic</th>\n",
       "      <th>cal_physiological_charge</th>\n",
       "      <th>cal_number_of_rings</th>\n",
       "      <th>cal_bioavailability</th>\n",
       "      <th>cal_rule_of_five</th>\n",
       "      <th>exp_molecular_weight</th>\n",
       "      <th>exp_logp</th>\n",
       "      <th>exp_pka</th>\n",
       "      <th>half_life</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>small molecule</td>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>0.3</td>\n",
       "      <td>-4.7</td>\n",
       "      <td>2.83e-02 g/l</td>\n",
       "      <td>1269.4105</td>\n",
       "      <td>495.89</td>\n",
       "      <td>325.84</td>\n",
       "      <td>131.22</td>\n",
       "      <td>...</td>\n",
       "      <td>9.27</td>\n",
       "      <td>10.82</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>-2</td>\n",
       "      <td>None</td>\n",
       "      <td>4-5 hours</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>small molecule</td>\n",
       "      <td>DB00035</td>\n",
       "      <td>Desmopressin</td>\n",
       "      <td>-1</td>\n",
       "      <td>-4</td>\n",
       "      <td>1.10e-01 g/l</td>\n",
       "      <td>1069.217</td>\n",
       "      <td>435.41</td>\n",
       "      <td>279.78</td>\n",
       "      <td>106.19</td>\n",
       "      <td>...</td>\n",
       "      <td>9.5</td>\n",
       "      <td>11.77</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>-4.2</td>\n",
       "      <td>None</td>\n",
       "      <td>Oral t&lt;sub&gt;1/2&lt;/sub&gt;=1.5-2.5 hours. Intranasal...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>small molecule</td>\n",
       "      <td>DB00050</td>\n",
       "      <td>Cetrorelix</td>\n",
       "      <td>1.33</td>\n",
       "      <td>-5.3</td>\n",
       "      <td>6.94e-03 g/l</td>\n",
       "      <td>1431.038</td>\n",
       "      <td>495.67</td>\n",
       "      <td>384.16</td>\n",
       "      <td>148.09</td>\n",
       "      <td>...</td>\n",
       "      <td>9.49</td>\n",
       "      <td>11.11</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>~62.8 hours</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>86</th>\n",
       "      <td>small molecule</td>\n",
       "      <td>DB00091</td>\n",
       "      <td>Cyclosporine</td>\n",
       "      <td>4.12</td>\n",
       "      <td>-5.1</td>\n",
       "      <td>9.52e-03 g/l</td>\n",
       "      <td>1202.6112</td>\n",
       "      <td>278.8</td>\n",
       "      <td>327.14</td>\n",
       "      <td>133.24</td>\n",
       "      <td>...</td>\n",
       "      <td>11.83</td>\n",
       "      <td>-2.4</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Biphasic and variable, approximately 7 hours (...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>88</th>\n",
       "      <td>small molecule</td>\n",
       "      <td>DB00093</td>\n",
       "      <td>Felypressin</td>\n",
       "      <td>-1.1</td>\n",
       "      <td>-4.4</td>\n",
       "      <td>4.53e-02 g/l</td>\n",
       "      <td>1040.219</td>\n",
       "      <td>405.32</td>\n",
       "      <td>264.79</td>\n",
       "      <td>103.93</td>\n",
       "      <td>...</td>\n",
       "      <td>11.39</td>\n",
       "      <td>10.18</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              type drugbank_id          name cal_logp cal_logs  \\\n",
       "13  small molecule     DB00014     Goserelin      0.3     -4.7   \n",
       "34  small molecule     DB00035  Desmopressin       -1       -4   \n",
       "48  small molecule     DB00050    Cetrorelix     1.33     -5.3   \n",
       "86  small molecule     DB00091  Cyclosporine     4.12     -5.1   \n",
       "88  small molecule     DB00093   Felypressin     -1.1     -4.4   \n",
       "\n",
       "   cal_water_solubility cal_molecular_weight cal_polar_surface_area  \\\n",
       "13         2.83e-02 g/l            1269.4105                 495.89   \n",
       "34         1.10e-01 g/l             1069.217                 435.41   \n",
       "48         6.94e-03 g/l             1431.038                 495.67   \n",
       "86         9.52e-03 g/l            1202.6112                  278.8   \n",
       "88         4.53e-02 g/l             1040.219                 405.32   \n",
       "\n",
       "   cal_refractivity cal_polarizability  \\\n",
       "13           325.84             131.22   \n",
       "34           279.78             106.19   \n",
       "48           384.16             148.09   \n",
       "86           327.14             133.24   \n",
       "88           264.79             103.93   \n",
       "\n",
       "                          ...                         cal_pka_acidic  \\\n",
       "13                        ...                                   9.27   \n",
       "34                        ...                                    9.5   \n",
       "48                        ...                                   9.49   \n",
       "86                        ...                                  11.83   \n",
       "88                        ...                                  11.39   \n",
       "\n",
       "   cal_pka_basic cal_physiological_charge cal_number_of_rings  \\\n",
       "13         10.82                        2                   6   \n",
       "34         11.77                        1                   4   \n",
       "48         11.11                        1                   6   \n",
       "86          -2.4                        0                   1   \n",
       "88         10.18                        2                   4   \n",
       "\n",
       "   cal_bioavailability cal_rule_of_five exp_molecular_weight exp_logp exp_pka  \\\n",
       "13                   0             None                 None       -2    None   \n",
       "34                   0             None                 None     -4.2    None   \n",
       "48                   0             None                 None     None    None   \n",
       "86                   0             None                 None     None    None   \n",
       "88                   0             None                 None     None    None   \n",
       "\n",
       "                                            half_life  \n",
       "13                                          4-5 hours  \n",
       "34  Oral t<sub>1/2</sub>=1.5-2.5 hours. Intranasal...  \n",
       "48                                        ~62.8 hours  \n",
       "86  Biphasic and variable, approximately 7 hours (...  \n",
       "88                                                     \n",
       "\n",
       "[5 rows x 23 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# drugs with logP, MW, and solubility information. These features can be used to predict half-life of a drug\n",
    "other_info = drugbank_df.isin([None])['cal_logp'] & drugbank_df.isin([None])['cal_water_solubility'] & drugbank_df.isin([None])['cal_molecular_weight']\n",
    "drugbank_df1 = drugbank_df[~other_info]\n",
    "drugbank_df1.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1145"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# number of extracted drugs with logP, MW, solubility, and half life information\n",
    "len(drugbank_df1) - sum(drugbank_df1['half_life'] == '')"
   ]
  }
 ],
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