Mol Format Conversion.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "0a2a021c",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\dksik\\anaconda3\\lib\\site-packages\\pybel\\struct\\operations.py:8: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
      "  from tqdm.autonotebook import tqdm\n"
     ]
    }
   ],
   "source": [
    "from openbabel import openbabel as ob\n",
    "import pubchempy as pcp\n",
    "import pybel\n",
    "import os\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "79232d37",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of files: 243\n"
     ]
    }
   ],
   "source": [
    "directory_path = 'C://Users/dksik/Documents/Diptanshu/ASDRP/molecules/'\n",
    "number_of_files = len(os.listdir(directory_path))\n",
    "\n",
    "print(\"Number of files:\", str(number_of_files))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "dd927a20",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Should print 5 (atoms)\n",
      "5\n",
      "Should print 9 (atoms) after adding hydrogens\n",
      "9\n",
      "\n",
      " OpenBabel08082212122D\n",
      "\n",
      "  9  9  0  0  0  0  0  0  0  0999 V2000\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  5  1  0  0  0  0\n",
      "  1  2  2  0  0  0  0\n",
      "  1  6  1  0  0  0  0\n",
      "  2  3  1  0  0  0  0\n",
      "  2  7  1  0  0  0  0\n",
      "  3  4  2  0  0  0  0\n",
      "  3  8  1  0  0  0  0\n",
      "  4  5  1  0  0  0  0\n",
      "  4  9  1  0  0  0  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "obConversion1 = ob.OBConversion()\n",
    "obConversion1.SetInAndOutFormats(\"smi\", \"mdl\")\n",
    "\n",
    "mol1 = ob.OBMol()\n",
    "obConversion1.ReadString(mol1, \"C1=CC=CS1\")\n",
    "\n",
    "print('Should print 5 (atoms)')\n",
    "print(mol1.NumAtoms())\n",
    "\n",
    "mol1.AddHydrogens()\n",
    "print('Should print 9 (atoms) after adding hydrogens')\n",
    "print(mol1.NumAtoms())\n",
    "\n",
    "outMDL = obConversion1.WriteString(mol1)\n",
    "\n",
    "print(outMDL)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "fbc0923d",
   "metadata": {},
   "outputs": [],
   "source": [
    "def convertMolFormats(mol_str, input_format='smiles', output_format='sdf'):    \n",
    "    obConversionOut = ob.OBConversion()\n",
    "    obConversionOut.SetInAndOutFormats(input_format, output_format)\n",
    "\n",
    "    molecule = ob.OBMol()\n",
    "    obConversionOut.ReadString(molecule, mol_str)\n",
    "    \n",
    "    return obConversionOut.WriteString(molecule)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "3a352e1e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      " OpenBabel08082212122D\n",
      "\n",
      "  6  5  0  0  0  0  0  0  0  0999 V2000\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  2  0  0  0  0\n",
      "  1  3  1  0  0  0  0\n",
      "  1  6  1  0  0  0  0\n",
      "  3  4  2  0  0  0  0\n",
      "  3  5  1  0  0  0  0\n",
      "M  CHG  2   3   1   5  -1\n",
      "M  END\n",
      "$$$$\n",
      "\n"
     ]
    }
   ],
   "source": [
    "fm = convertMolFormats(\"C(=O)([N+](=O)[O-])O\")\n",
    "print(fm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "4ebc885d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "C(=O)([N+](=O)[O-])O\t\r\n",
      "\n"
     ]
    }
   ],
   "source": [
    "fm2 = convertMolFormats(fm, 'sdf', 'smiles')\n",
    "print(fm2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b086eec5",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[Compound(88689)]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pcp.get_compounds(fm2, 'smiles', record_type='3d')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "id": "89823c6f",
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "module 'pubchempy' has no attribute 'get_inchikey'",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "Input \u001b[1;32mIn [64]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[43mpcp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_inchikey\u001b[49m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mH2O\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m'\u001b[39m, record_type\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m2d\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
      "\u001b[1;31mAttributeError\u001b[0m: module 'pubchempy' has no attribute 'get_inchikey'"
     ]
    }
   ],
   "source": [
    "pcp.get_inchikey\\('H2O', 'name', record_type='2d')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "965e0370",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pybel\n",
    "\n",
    "def xyz_to_smiles(fname: str) -> str:\n",
    "    \n",
    "    mol = next(pybel.readfile(\"xyz\", fname))\n",
    "\n",
    "    smi = mol.write(format=\"smi\")\n",
    "\n",
    "    return smi.split()[0].strip()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "05e5a608",
   "metadata": {},
   "outputs": [],
   "source": [
    "df_mol = pd.DataFrame()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "a3e3fd4c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "No Molecule Found! \n",
      "\n",
      "0 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "10 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "20 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "30 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "40 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "50 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "60 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "70 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "80 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "90 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "100 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "110 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "120 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "130 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "140 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "150 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "160 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "170 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "180 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "190 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "200 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "210 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "220 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "230 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "240 done\n",
      "\n",
      "No Molecule Found! \n",
      "\n",
      "No Molecule Found! \n",
      "\n"
     ]
    }
   ],
   "source": [
    "for idx in range(number_of_files):\n",
    "    try:\n",
    "        smi = xyz_to_smiles(f\"/gen_mol{idx}.xyz\")\n",
    "        #smi = convertMolFormats(f\"/gen_mol{idx}.xyz\", 'xyz', 'smi')\n",
    "        #df_mol.loc[idx] = idx\n",
    "        print(smi)\n",
    "    except:\n",
    "        print(\"No Molecule Found! \\n\")\n",
    "    if idx % 10 == 0: print(str(idx), \"done\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "eb8e6e11",
   "metadata": {},
   "outputs": [],
   "source": [
    "#df_mol.describe()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "48bef17d",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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