FP3_Fingerprint.ipynb

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   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Fingerprints import FingerprintMols\n",
    "import pandas as pd\n",
    "from molvs import standardize_smiles\n",
    "from openbabel import pybel"
   ]
  },
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   "cell_type": "code",
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   "source": [
    "def CalculateFP3Fingerprint(mol):\n",
    "    res = {}\n",
    "    NumFinger = 210\n",
    "    temp = mol.calcfp(\"FP3\").bits\n",
    "    for i in temp:\n",
    "        res.update({i: 1})\n",
    "\n",
    "    return NumFinger, res"
   ]
  },
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    "filename = 'temp.csv'\n",
    "df = pd.read_csv(filename)               \n",
    "smiles = [standardize_smiles(i) for i in df['smiles'].values] \n",
    "all_ecfp2_data = []\n",
    "df = pd.DataFrame()\n",
    "for smile in smiles:\n",
    "    mol = pybel.readstring(\"smi\", smile)\n",
    "    result=CalculateFP3Fingerprint(mol)\n",
    "    df = pd.concat([df, pd.DataFrame([result])], ignore_index=True)\n",
    "\n",
    "df.insert(loc = 0,\n",
    "          column = \"smiles\",\n",
    "          value = smiles)\n",
    "   \n",
    "df.to_csv('output_FP3.csv', index=False)"
   ]
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