04_calc_descr.ipynb

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     "text": [
      "RDKit WARNING: [16:34:28] Enabling RDKit 2019.09.3 jupyter extensions\n"
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   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import Descriptors\n",
    "from rdkit.ML.Descriptors import MoleculeDescriptors\n",
    "import pandas as pd\n",
    "import tqdm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
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   "source": [
    "df = pd.read_csv('herg_compound_from_chembl_processed_largestFrag_delDupl.csv')"
   ]
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   "cell_type": "code",
   "execution_count": 3,
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   "outputs": [],
   "source": [
    "df.Mol = [Chem.MolFromSmiles(x) for x in df.smiles]"
   ]
  },
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     "text": [
      "200\n"
     ]
    }
   ],
   "source": [
    "nms = [x[0] for x in Descriptors._descList if x[0] != 'MolecularFormula']\n",
    "print(len(nms))\n",
    "calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "for nam in nms:\n",
    "    df[nam] = 0\n",
    "    \n",
    "for i, s in enumerate(df.Mol[:]):\n",
    "    descrs = calc.CalcDescriptors(s)\n",
    "#     print(list(descrs))\n",
    "#     for j, x in enumerate(descrs):\n",
    "    df.loc[i, nms] = descrs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# list(df.columns)"
   ]
  },
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   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "s_list = ['smiles'] + nms + ['activity_comment']\n",
    "df[s_list].to_csv('herg_descr.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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