peptoiddatabank.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "6491af52-4248-4c1d-b24b-ee5599e8987b",
   "metadata": {},
   "source": [
    "# Extracted the Sequences and SMILE string from Peptoid Data Bank\n",
    "\n",
    "#### Use the same conda environment as the one run the Peptoid Data Bank "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "8d02e0c7-3e51-4d81-ae55-ef8b144ffb44",
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "import json\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "42f5c377-22e5-4867-ade9-e89dbd5ea77d",
   "metadata": {},
   "source": [
    "## Extract data from url"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "023f6a8b-3362-4600-a0d6-587dd143c92a",
   "metadata": {},
   "outputs": [],
   "source": [
    "#The link from RESTful API\n",
    "#Change according to one's own server address\n",
    "\n",
    "pep_url = 'http://127.0.0.1:5000/api/peptoids'\n",
    "res_url = 'http://127.0.0.1:5000/api/residues'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "b33a68a3-bd88-4218-954a-1fe49b6233ab",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Sparce the json data\n",
    "\n",
    "peptoids = requests.get(pep_url).json()\n",
    "residues = requests.get(res_url).json()\n",
    "\n",
    "#Save them into .json file\n",
    "\n",
    "with open('data/peptoids.json', 'w') as pep_file:\n",
    "    json.dump(peptoids, pep_file, indent=4)\n",
    "\n",
    "with open('data/residues.json', 'w') as res_file:\n",
    "    json.dump(residues, res_file, indent=4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "2d2ed6bd-138c-4b93-8a50-1751d21a823f",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                                                        SMILES  \\\n",
      "(S)-N-(1-cyclohexylethyl)glycine  *N([C@@H](C)C1CCCCC1)CC(=O)*   \n",
      "(R)-N-(1-cyclohexylethyl)glycine   *N([C@H](C)C1CCCCC1)CC(=O)*   \n",
      "(S)-N-(2-butyl)glycine                  *N([C@@H](C)CC)CC(=O)*   \n",
      "(R)-N-(2-butyl)glycine                   *N([C@H](C)CC)CC(=O)*   \n",
      "(S)-N-(1-phenylethyl)glycine      *N([C@@H](C)c1ccccc1)CC(=O)*   \n",
      "...                                                        ...   \n",
      "N-(cyclohexyl)methylglycine               *N(CC1CCCCC1)CC(=O)*   \n",
      "N-pentylglycine                               *N(CCCCC)CC(=O)*   \n",
      "N-hexylglycine                               *N(CCCCCC)CC(=O)*   \n",
      "Glycine                                              *NCC(=O)*   \n",
      "beta-Alanine                                        *NCCC(=O)*   \n",
      "\n",
      "                                                 full_nomenclature  \\\n",
      "(S)-N-(1-cyclohexylethyl)glycine  (S)-N-(1-cyclohexylethyl)glycine   \n",
      "(R)-N-(1-cyclohexylethyl)glycine  (R)-N-(1-cyclohexylethyl)glycine   \n",
      "(S)-N-(2-butyl)glycine                      (S)-N-(2-butyl)glycine   \n",
      "(R)-N-(2-butyl)glycine                      (R)-N-(2-butyl)glycine   \n",
      "(S)-N-(1-phenylethyl)glycine          (S)-N-(1-phenylethyl)glycine   \n",
      "...                                                            ...   \n",
      "N-(cyclohexyl)methylglycine            N-(cyclohexyl)methylglycine   \n",
      "N-pentylglycine                                    N-pentylglycine   \n",
      "N-hexylglycine                                      N-hexylglycine   \n",
      "Glycine                                                    Glycine   \n",
      "beta-Alanine                                          beta-Alanine   \n",
      "\n",
      "                                 monomer_structure  \\\n",
      "(S)-N-(1-cyclohexylethyl)glycine                     \n",
      "(R)-N-(1-cyclohexylethyl)glycine                     \n",
      "(S)-N-(2-butyl)glycine                               \n",
      "(R)-N-(2-butyl)glycine                               \n",
      "(S)-N-(1-phenylethyl)glycine                         \n",
      "...                                            ...   \n",
      "N-(cyclohexyl)methylglycine                          \n",
      "N-pentylglycine                                      \n",
      "N-hexylglycine                                       \n",
      "Glycine                                              \n",
      "beta-Alanine                                         \n",
      "\n",
      "                                                                           peptoids  \\\n",
      "(S)-N-(1-cyclohexylethyl)glycine           {'03AA1-5-A': '/api/peptoids/03AA1-5-A'}   \n",
      "(R)-N-(1-cyclohexylethyl)glycine                                                 {}   \n",
      "(S)-N-(2-butyl)glycine                                                           {}   \n",
      "(R)-N-(2-butyl)glycine                                                           {}   \n",
      "(S)-N-(1-phenylethyl)glycine      {'06AA1-9-A': '/api/peptoids/06AA1-9-A', '08AC...   \n",
      "...                                                                             ...   \n",
      "N-(cyclohexyl)methylglycine                {'20AA3-3-A': '/api/peptoids/20AA3-3-A'}   \n",
      "N-pentylglycine                            {'20AC1-6-C': '/api/peptoids/20AC1-6-C'}   \n",
      "N-hexylglycine                             {'20AC2-6-C': '/api/peptoids/20AC2-6-C'}   \n",
      "Glycine                                                                          {}   \n",
      "beta-Alanine                                                                     {}   \n",
      "\n",
      "                                 short_name   type  \n",
      "(S)-N-(1-cyclohexylethyl)glycine       Nsch  alpha  \n",
      "(R)-N-(1-cyclohexylethyl)glycine       Nrch  alpha  \n",
      "(S)-N-(2-butyl)glycine                 Nssb  alpha  \n",
      "(R)-N-(2-butyl)glycine                 Nrsb  alpha  \n",
      "(S)-N-(1-phenylethyl)glycine           Nspe  alpha  \n",
      "...                                     ...    ...  \n",
      "N-(cyclohexyl)methylglycine             Ncy  alpha  \n",
      "N-pentylglycine                              alpha  \n",
      "N-hexylglycine                               alpha  \n",
      "Glycine                                 Gly  alpha  \n",
      "beta-Alanine                        betaAla   beta  \n",
      "\n",
      "[66 rows x 6 columns]\n"
     ]
    }
   ],
   "source": [
    "#Make residues dictionary \n",
    "flat_residues = {k: v for dictionary in residues for k, v in dictionary.items()} #flatten the residues dictionary \n",
    "df_res = pd.DataFrame(flat_residues.values(), index=flat_residues.keys()) #make a data frame\n",
    "df_res.to_csv('data/residues.csv', index=False)\n",
    "print(df_res)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "79f76e8a-72bb-4ac4-baef-d1977202c8a5",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "   c_term                                           citation cyc_points  \\\n",
      "0      *N  \\n\\n\\n@article{Wu_2003,\\n\\tdoi = {10.1021/ja03...              \n",
      "0      *N  \\n\\n\\n@article{Huang_2006,\\n\\tdoi = {10.1021/j...              \n",
      "0      *2  \\n\\n\\n@article{Shin_2007,\\n\\tdoi = {10.1021/ja...              \n",
      "0      *2  \\n\\n\\n@article{Shin_2007,\\n\\tdoi = {10.1021/ja...              \n",
      "0      *1  \\n\\n\\n@article{Roy_2008,\\n\\tdoi = {10.1021/ol7...              \n",
      "..    ...                                                ...        ...   \n",
      "0      *N  \\n\\n\\n@article{Ghosh_2020,\\n\\tdoi = {10.1002/c...       None   \n",
      "0      *N  \\n\\n\\n@article{Ghosh_2020,\\n\\tdoi = {10.1002/c...       None   \n",
      "0      *N  \\n\\n\\n@article{Ghosh_2020,\\n\\tdoi = {10.1002/c...       None   \n",
      "0      *N  \\n\\n\\n@article{Ghosh_2020,\\n\\tdoi = {10.1002/c...       None   \n",
      "0      *2  \\n\\n\\n@article{SHIMIZU_2009,\\n\\tdoi = {10.1111...       None   \n",
      "\n",
      "           experiment n_term                             pub_doi  \\\n",
      "0   X-Ray Diffraction      *                   10.1021/ja037540r   \n",
      "0        Solution NMR      *                   10.1021/ja0574318   \n",
      "0   X-Ray Diffraction     2*                   10.1021/ja066960o   \n",
      "0   X-Ray Diffraction     2*                   10.1021/ja066960o   \n",
      "0   X-Ray Diffraction     1*                   10.1021/ol7030763   \n",
      "..                ...    ...                                 ...   \n",
      "0   X-Ray Diffraction      *              10.1002/chem.202003612   \n",
      "0   X-Ray Diffraction      *              10.1002/chem.202003612   \n",
      "0   X-Ray Diffraction      *              10.1002/chem.202003612   \n",
      "0   X-Ray Diffraction      *              10.1002/chem.202003612   \n",
      "0   X-Ray Diffraction     2*  10.1111/j.1399-3011.1983.tb02090.x   \n",
      "\n",
      "                          release  \\\n",
      "0   Tue, 18 Nov 2003 00:00:00 GMT   \n",
      "0   Sat, 14 Jan 2006 00:00:00 GMT   \n",
      "0   Tue, 27 Feb 2007 00:00:00 GMT   \n",
      "0   Tue, 27 Feb 2007 00:00:00 GMT   \n",
      "0   Wed, 06 Feb 2008 00:00:00 GMT   \n",
      "..                            ...   \n",
      "0   Thu, 27 Aug 2020 00:00:00 GMT   \n",
      "0   Thu, 27 Aug 2020 00:00:00 GMT   \n",
      "0   Thu, 27 Aug 2020 00:00:00 GMT   \n",
      "0   Thu, 27 Aug 2020 00:00:00 GMT   \n",
      "0   Mon, 01 Aug 1983 00:00:00 GMT   \n",
      "\n",
      "                                             sequence  \\\n",
      "0   (S)-N-(1-cyclohexylethyl)glycine, (S)-N-(1-cyc...   \n",
      "0   (S)-N-(1-phenylethyl)glycine, (S)-N-(1-phenyle...   \n",
      "0   N-(methoxyethyl)glycine, N-(phenylmethyl)glyci...   \n",
      "0   N-(methoxyethyl)glycine, N-(phenylmethyl)glyci...   \n",
      "0   N-(propargyl)beta-alanine, N-(propargyl)beta-a...   \n",
      "..                                                ...   \n",
      "0   N-(2-picolyl)glycine, N-{2-[([2,2’-bipyridin]-...   \n",
      "0   N-(2-picolyl)glycine, N-{2-[([2,2’-bipyridin]-...   \n",
      "0   N-(2-picolyl)glycine, N-{2-[([2,2’-bipyridin]-...   \n",
      "0   N-(2-picolyl)glycine, N-{2-[([2,2’-bipyridin]-...   \n",
      "0   Proline, Sarcosine, Proline, Sarcosine, Prolin...   \n",
      "\n",
      "                   struct_doi struct_smiles  \\\n",
      "0             10.5517/cc7jql1                 \n",
      "0                                             \n",
      "0             10.5517/cc9xh6w                 \n",
      "0             10.5517/ccpn8q9                 \n",
      "0             10.5517/ccr0q1h                 \n",
      "..                        ...           ...   \n",
      "0   10.5517/ccdc.csd.cc22jr6l          None   \n",
      "0   10.5517/ccdc.csd.cc22jr5k          None   \n",
      "0   10.5517/ccdc.csd.cc22jr4j          None   \n",
      "0   10.5517/ccdc.csd.cc22jr3h          None   \n",
      "0                        None          None   \n",
      "\n",
      "                                                title topology peptoid_code  \\\n",
      "0   Polyproline Type I-Like Pentamer (a-chiral ali...        A    03AA1-5-A   \n",
      "0   Threaded Loop Nonamer (a-chiral aromatic side ...        A    06AA1-9-A   \n",
      "0                              N-Alkyl Cyclic Hexamer        C    07AA1-6-C   \n",
      "0                              N-Alkyl Cyclic Octamer        C    07AA2-8-C   \n",
      "0   Cyclic β-Peptoid Tetramer (propargyl side chains)        C    08AA1-4-C   \n",
      "..                                                ...      ...          ...   \n",
      "0        Metallopeptoid Dimeric Assembly (tert-butyl)        A    20AA4-3-A   \n",
      "0        Metallopeptoid Dimeric Assembly (cyclohexyl)        A    20AA3-3-A   \n",
      "0          Metallopeptoid Dimeric Assembly (naphthyl)        A    20AA2-3-A   \n",
      "0            Metallopeptoid Dimeric Assembly (phenyl)        A    20AA1-3-A   \n",
      "0              Cyclic Octamer (proline and sarcosine)        C    83AB1-8-C   \n",
      "\n",
      "                      _links.2d_image             _links.3d_image  \\\n",
      "0   /static/peptoids/03AA1-5-A_2d.png  /static/peptoids/03AA1.png   \n",
      "0   /static/peptoids/06AA1-9-A_2d.png  /static/peptoids/06AA1.png   \n",
      "0   /static/peptoids/07AA1-6-C_2d.png  /static/peptoids/07AA1.png   \n",
      "0   /static/peptoids/07AA2-8-C_2d.png  /static/peptoids/07AA2.png   \n",
      "0   /static/peptoids/08AA1-4-C_2d.png  /static/peptoids/08AA1.png   \n",
      "..                                ...                         ...   \n",
      "0   /static/peptoids/20AA4-3-A_2d.png  /static/peptoids/20AA4.png   \n",
      "0   /static/peptoids/20AA3-3-A_2d.png  /static/peptoids/20AA3.png   \n",
      "0   /static/peptoids/20AA2-3-A_2d.png  /static/peptoids/20AA2.png   \n",
      "0   /static/peptoids/20AA1-3-A_2d.png  /static/peptoids/20AA1.png   \n",
      "0   /static/peptoids/83AB1-8-C_2d.png  /static/peptoids/83AB1.png   \n",
      "\n",
      "                     _links.authors                   _links.residues  \\\n",
      "0   /api/peptoids/03AA1-5-A/authors  /api/peptoids/03AA1-5-A/residues   \n",
      "0   /api/peptoids/06AA1-9-A/authors  /api/peptoids/06AA1-9-A/residues   \n",
      "0   /api/peptoids/07AA1-6-C/authors  /api/peptoids/07AA1-6-C/residues   \n",
      "0   /api/peptoids/07AA2-8-C/authors  /api/peptoids/07AA2-8-C/residues   \n",
      "0   /api/peptoids/08AA1-4-C/authors  /api/peptoids/08AA1-4-C/residues   \n",
      "..                              ...                               ...   \n",
      "0   /api/peptoids/20AA4-3-A/authors  /api/peptoids/20AA4-3-A/residues   \n",
      "0   /api/peptoids/20AA3-3-A/authors  /api/peptoids/20AA3-3-A/residues   \n",
      "0   /api/peptoids/20AA2-3-A/authors  /api/peptoids/20AA2-3-A/residues   \n",
      "0   /api/peptoids/20AA1-3-A/authors  /api/peptoids/20AA1-3-A/residues   \n",
      "0   /api/peptoids/83AB1-8-C/authors  /api/peptoids/83AB1-8-C/residues   \n",
      "\n",
      "                _links.self  \n",
      "0   /api/peptoids/03AA1-5-A  \n",
      "0   /api/peptoids/06AA1-9-A  \n",
      "0   /api/peptoids/07AA1-6-C  \n",
      "0   /api/peptoids/07AA2-8-C  \n",
      "0   /api/peptoids/08AA1-4-C  \n",
      "..                      ...  \n",
      "0   /api/peptoids/20AA4-3-A  \n",
      "0   /api/peptoids/20AA3-3-A  \n",
      "0   /api/peptoids/20AA2-3-A  \n",
      "0   /api/peptoids/20AA1-3-A  \n",
      "0   /api/peptoids/83AB1-8-C  \n",
      "\n",
      "[88 rows x 18 columns]\n"
     ]
    }
   ],
   "source": [
    "#Make peptoids dictionary \n",
    "peptoids_list = []\n",
    "for peptoid in peptoids:\n",
    "    for peptoid_code, peptoid_info in peptoid.items():\n",
    "        peptoid_info['peptoid_code'] = peptoid_code #add a column for peptoid_code\n",
    "        df = pd.json_normalize(peptoid_info) #create a df for individual peptoid, Flatten the JSON data using pd.json_normalize\n",
    "        peptoids_list.append(df) \n",
    "\n",
    "df_pep = pd.concat(peptoids_list, axis=0) #stack all the df vertically \n",
    "df_pep.to_csv('data/peptoids.csv', index=False)   \n",
    "\n",
    "print(df_pep)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "42999527-57b7-415c-afe7-e09cff1013c9",
   "metadata": {},
   "source": [
    "## Make a sequence dictionary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "cdf03af1-e67d-4ab3-a591-dde06eb6fa00",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                      06AA1-9-A                       13AC1-6-A  \\\n",
      "0  (S)-N-(1-phenylethyl)glycine   N-(3,5-dimethylphenyl)glycine   \n",
      "1  (S)-N-(1-phenylethyl)glycine  (S)-N-(1-naphthylethyl)glycine   \n",
      "2  (S)-N-(1-phenylethyl)glycine   N-(2,6-dimethylphenyl)glycine   \n",
      "3  (S)-N-(1-phenylethyl)glycine  (S)-N-(1-naphthylethyl)glycine   \n",
      "4  (S)-N-(1-phenylethyl)glycine       N-(4-fluorophenyl)glycine   \n",
      "5  (S)-N-(1-phenylethyl)glycine  (S)-N-(1-naphthylethyl)glycine   \n",
      "6  (S)-N-(1-phenylethyl)glycine                            None   \n",
      "7  (S)-N-(1-phenylethyl)glycine                            None   \n",
      "8  (S)-N-(1-phenylethyl)glycine                            None   \n",
      "9                          None                            None   \n",
      "\n",
      "                        17AB1-5-A                       17AB2-8-A  \\\n",
      "0  (S)-N-(1-naphthylethyl)glycine   N-(2,6-dimethylphenyl)glycine   \n",
      "1   N-(3,5-dimethylphenyl)glycine  (R)-N-(1-naphthylethyl)glycine   \n",
      "2  (R)-N-(1-naphthylethyl)glycine       N-(4-fluorophenyl)glycine   \n",
      "3               N-(phenyl)glycine  (S)-N-(1-naphthylethyl)glycine   \n",
      "4                            None   N-(3,5-dimethylphenyl)glycine   \n",
      "5                            None  (R)-N-(1-naphthylethyl)glycine   \n",
      "6                            None               N-(phenyl)glycine   \n",
      "7                            None                            None   \n",
      "8                            None                            None   \n",
      "9                            None                            None   \n",
      "\n",
      "                      18AC2-7-A                18AC1-3-A  \\\n",
      "0     N-(2-carboxyethyl)glycine   N-carboxymethylglycine   \n",
      "1       N-(2-aminoethyl)glycine  N-(phenylmethyl)glycine   \n",
      "2     N-(2-hydroxyethyl)glycine                  Alanine   \n",
      "3  (S)-N-(1-phenylethyl)glycine                     None   \n",
      "4        N-carboxymethylglycine                     None   \n",
      "5       N-(phenylmethyl)glycine                     None   \n",
      "6                       Alanine                     None   \n",
      "7                          None                     None   \n",
      "8                          None                     None   \n",
      "9                          None                     None   \n",
      "\n",
      "                  19AE1-4-A                                        19AF1-10-A  \n",
      "0   N-(2-aminoethyl)glycine                     N-(3,5-dimethylphenyl)glycine  \n",
      "1  N-(2-phenylethyl)glycine        N-[2-(N,N-disopropyl)ammonium]ethylglycine  \n",
      "2   N-(2-aminoethyl)glycine                      N-(4-isopropyl)phenylglycine  \n",
      "3  N-(2-phenylethyl)glycine  N-[2-(N-benzyl-N,N-diethyl)ammonium]ethylglycine  \n",
      "4                      None                    N-(3,5-dimethoxyphenyl)glycine  \n",
      "5                      None            N-[2-(N-triethyl)ammonium]ethylglycine  \n",
      "6                      None                         N-(4-methyl)phenylglycine  \n",
      "7                      None           N-(2-(N-trimethylammonium)ethyl)glycine  \n",
      "8                      None                        N-(4-methoxy)phenylglycine  \n",
      "9                      None        N-[2-(N,N-disopropyl)ammonium]ethylglycine  \n"
     ]
    }
   ],
   "source": [
    "#create a csv with each indivual peptoid code as a column, and the sequence list in peptoid data bank and input\n",
    "sequences_dict = {}\n",
    "experimental_method = 'Solution NMR' #select the experimental method \n",
    "\n",
    "for peptoid in peptoids:\n",
    "    for peptoid_code, data in peptoid.items():\n",
    "        if data['experiment'] == experimental_method:\n",
    "            sequences = data['sequence'].split(\"ine,\")\n",
    "            sequences = [\n",
    "                seq.strip() + \"ine\" if i < len(sequences) - 1 else seq.strip() #making sure the sequence list are splited as desired \n",
    "                for i, seq in enumerate(sequences)\n",
    "            ]\n",
    "            sequences_dict[peptoid_code] = sequences\n",
    "\n",
    "# Convert sequences_dict to DataFrame\n",
    "df_seq = pd.DataFrame.from_dict(sequences_dict, orient='index').transpose()\n",
    "print(df_seq)\n",
    "df_seq.to_csv('data/sequences.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f7de4e77-77e8-4f18-b291-7cc441a057be",
   "metadata": {},
   "source": [
    "## Make a SMILE dictionary"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "5152767e-b772-40e2-9cb8-9df660468466",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                      06AA1-9-A                           13AC1-6-A  \\\n",
      "0  *N([C@@H](C)c1ccccc1)CC(=O)*           *N(c1cc(C)cc(C)c1)CC(=O)*   \n",
      "1  *N([C@@H](C)c1ccccc1)CC(=O)*  *N([C@@H](C)c1cccc2ccccc21)CC(=O)*   \n",
      "2  *N([C@@H](C)c1ccccc1)CC(=O)*           *N(c1c(C)cccc1(C))CC(=O)*   \n",
      "3  *N([C@@H](C)c1ccccc1)CC(=O)*  *N([C@@H](C)c1cccc2ccccc21)CC(=O)*   \n",
      "4  *N([C@@H](C)c1ccccc1)CC(=O)*              *N(c1ccc(F)cc1)CC(=O)*   \n",
      "5  *N([C@@H](C)c1ccccc1)CC(=O)*  *N([C@@H](C)c1cccc2ccccc21)CC(=O)*   \n",
      "6  *N([C@@H](C)c1ccccc1)CC(=O)*                                None   \n",
      "7  *N([C@@H](C)c1ccccc1)CC(=O)*                                None   \n",
      "8  *N([C@@H](C)c1ccccc1)CC(=O)*                                None   \n",
      "9                          None                                None   \n",
      "\n",
      "                            17AB1-5-A                           17AB2-8-A  \\\n",
      "0  *N([C@@H](C)c1cccc2ccccc21)CC(=O)*           *N(c1c(C)cccc1(C))CC(=O)*   \n",
      "1           *N(c1cc(C)cc(C)c1)CC(=O)*   *N([C@H](C)c1cccc2ccccc21)CC(=O)*   \n",
      "2   *N([C@H](C)c1cccc2ccccc21)CC(=O)*              *N(c1ccc(F)cc1)CC(=O)*   \n",
      "3                 *N(c1ccccc1)CC(=O)*  *N([C@@H](C)c1cccc2ccccc21)CC(=O)*   \n",
      "4                                None           *N(c1cc(C)cc(C)c1)CC(=O)*   \n",
      "5                                None   *N([C@H](C)c1cccc2ccccc21)CC(=O)*   \n",
      "6                                None                 *N(c1ccccc1)CC(=O)*   \n",
      "7                                None                                None   \n",
      "8                                None                                None   \n",
      "9                                None                                None   \n",
      "\n",
      "                      18AC2-7-A             18AC1-3-A              19AE1-4-A  \\\n",
      "0           *N(CCC(=O)O)CC(=O)*    *N(CC(=O)O)CC(=O)*         *N(CCN)CC(=O)*   \n",
      "1                *N(CCN)CC(=O)*  *N(Cc1ccccc1)CC(=O)*  *N(CCc1ccccc1)CC(=O)*   \n",
      "2                *N(CCO)CC(=O)*     *N[C@@H](C)C(=O)*         *N(CCN)CC(=O)*   \n",
      "3  *N([C@@H](C)c1ccccc1)CC(=O)*                  None  *N(CCc1ccccc1)CC(=O)*   \n",
      "4            *N(CC(=O)O)CC(=O)*                  None                   None   \n",
      "5          *N(Cc1ccccc1)CC(=O)*                  None                   None   \n",
      "6             *N[C@@H](C)C(=O)*                  None                   None   \n",
      "7                          None                  None                   None   \n",
      "8                          None                  None                   None   \n",
      "9                          None                  None                   None   \n",
      "\n",
      "                           19AF1-10-A  \n",
      "0           *N(c1cc(C)cc(C)c1)CC(=O)*  \n",
      "1       *N(CC[N+](C(C)C)C(C)C)CC(=O)*  \n",
      "2          *N(c1ccc(C(C)C)cc1)CC(=O)*  \n",
      "3  *N(CC[N+](Cc1ccccc1)(CC)CC)CC(=O)*  \n",
      "4         *N(c1cc(OC)cc(OC)c1)CC(=O)*  \n",
      "5         *N(CC[N+](CC)(CC)CC)CC(=O)*  \n",
      "6              *N(c1ccc(C)cc1)CC(=O)*  \n",
      "7            *N(CC[N+](C)(C)C)CC(=O)*  \n",
      "8             *N(c1ccc(OC)cc1)CC(=O)*  \n",
      "9       *N(CC[N+](C(C)C)C(C)C)CC(=O)*  \n"
     ]
    }
   ],
   "source": [
    "\n",
    "smiles_dict = {}\n",
    "\n",
    "# Iterate over the columns of the DataFrame\n",
    "for col in df_seq.columns:\n",
    "    smiles_dict[col] = []  # Initialize the list for storing SMILES\n",
    "    \n",
    "    # Iterate over each sequence in the column\n",
    "    for seq in df_seq[col]:\n",
    "        # Iterate over each row in res_df to find the corresponding SMILES\n",
    "        for index, row in df_res.iterrows():\n",
    "            if seq == row['full_nomenclature']:\n",
    "                smile = row['SMILES']\n",
    "                smiles_dict[col].append(smile)\n",
    "                break  # Exit the inner loop once a match is found\n",
    "\n",
    "df_smiles = pd.DataFrame.from_dict(smiles_dict, orient='index').transpose()\n",
    "print(df_smiles)\n",
    "\n",
    "df_smiles.to_csv('data/smiles.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "b209822e-9856-4701-bbc0-5202401add1d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                               06AA1-9-A  \\\n",
      "0  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "1  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "2  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "3  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "4  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "5  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "6  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "7  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "8  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C   \n",
      "9                                   None   \n",
      "\n",
      "                                     13AC1-6-A  \\\n",
      "0           CC(=O)N(c1cc(C)cc(C)c1)CC(=O)N(C)C   \n",
      "1  CC(=O)N([C@@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "2           CC(=O)N(c1c(C)cccc1(C))CC(=O)N(C)C   \n",
      "3  CC(=O)N([C@@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "4              CC(=O)N(c1ccc(F)cc1)CC(=O)N(C)C   \n",
      "5  CC(=O)N([C@@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "6                                         None   \n",
      "7                                         None   \n",
      "8                                         None   \n",
      "9                                         None   \n",
      "\n",
      "                                     17AB1-5-A  \\\n",
      "0  CC(=O)N([C@@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "1           CC(=O)N(c1cc(C)cc(C)c1)CC(=O)N(C)C   \n",
      "2   CC(=O)N([C@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "3                 CC(=O)N(c1ccccc1)CC(=O)N(C)C   \n",
      "4                                         None   \n",
      "5                                         None   \n",
      "6                                         None   \n",
      "7                                         None   \n",
      "8                                         None   \n",
      "9                                         None   \n",
      "\n",
      "                                     17AB2-8-A  \\\n",
      "0           CC(=O)N(c1c(C)cccc1(C))CC(=O)N(C)C   \n",
      "1   CC(=O)N([C@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "2              CC(=O)N(c1ccc(F)cc1)CC(=O)N(C)C   \n",
      "3  CC(=O)N([C@@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "4           CC(=O)N(c1cc(C)cc(C)c1)CC(=O)N(C)C   \n",
      "5   CC(=O)N([C@H](C)c1cccc2ccccc21)CC(=O)N(C)C   \n",
      "6                 CC(=O)N(c1ccccc1)CC(=O)N(C)C   \n",
      "7                                         None   \n",
      "8                                         None   \n",
      "9                                         None   \n",
      "\n",
      "                               18AC2-7-A                      18AC1-3-A  \\\n",
      "0           CC(=O)N(CCC(=O)O)CC(=O)N(C)C    CC(=O)N(CC(=O)O)CC(=O)N(C)C   \n",
      "1                CC(=O)N(CCN)CC(=O)N(C)C  CC(=O)N(Cc1ccccc1)CC(=O)N(C)C   \n",
      "2                CC(=O)N(CCO)CC(=O)N(C)C     CC(=O)N[C@@H](C)C(=O)N(C)C   \n",
      "3  CC(=O)N([C@@H](C)c1ccccc1)CC(=O)N(C)C                           None   \n",
      "4            CC(=O)N(CC(=O)O)CC(=O)N(C)C                           None   \n",
      "5          CC(=O)N(Cc1ccccc1)CC(=O)N(C)C                           None   \n",
      "6             CC(=O)N[C@@H](C)C(=O)N(C)C                           None   \n",
      "7                                   None                           None   \n",
      "8                                   None                           None   \n",
      "9                                   None                           None   \n",
      "\n",
      "                        19AE1-4-A                                   19AF1-10-A  \n",
      "0         CC(=O)N(CCN)CC(=O)N(C)C           CC(=O)N(c1cc(C)cc(C)c1)CC(=O)N(C)C  \n",
      "1  CC(=O)N(CCc1ccccc1)CC(=O)N(C)C       CC(=O)N(CC[N+](C(C)C)C(C)C)CC(=O)N(C)C  \n",
      "2         CC(=O)N(CCN)CC(=O)N(C)C          CC(=O)N(c1ccc(C(C)C)cc1)CC(=O)N(C)C  \n",
      "3  CC(=O)N(CCc1ccccc1)CC(=O)N(C)C  CC(=O)N(CC[N+](Cc1ccccc1)(CC)CC)CC(=O)N(C)C  \n",
      "4                            None         CC(=O)N(c1cc(OC)cc(OC)c1)CC(=O)N(C)C  \n",
      "5                            None         CC(=O)N(CC[N+](CC)(CC)CC)CC(=O)N(C)C  \n",
      "6                            None              CC(=O)N(c1ccc(C)cc1)CC(=O)N(C)C  \n",
      "7                            None            CC(=O)N(CC[N+](C)(C)C)CC(=O)N(C)C  \n",
      "8                            None             CC(=O)N(c1ccc(OC)cc1)CC(=O)N(C)C  \n",
      "9                            None       CC(=O)N(CC[N+](C(C)C)C(C)C)CC(=O)N(C)C  \n"
     ]
    }
   ],
   "source": [
    "#Capped all the smile for generating the mol2 file\n",
    "capped_smiles_dict = {}\n",
    "\n",
    "# Iterate over the columns of the DataFrame\n",
    "for col in df_seq.columns:\n",
    "    capped_smiles_dict[col] = []  # Initialize the list for storing SMILES\n",
    "    \n",
    "    # Iterate over each sequence in the column\n",
    "    for seq in df_seq[col]:\n",
    "        # Iterate over each row in res_df to find the corresponding SMILES\n",
    "        for index, row in df_res.iterrows():\n",
    "            if seq == row['full_nomenclature']:\n",
    "                smile = row['SMILES']\n",
    "                clean_smile = smile.replace('*','')\n",
    "                capped_smile = f\"CC(=O){clean_smile}N(C)C\"\n",
    "                capped_smiles_dict[col].append(capped_smile)\n",
    "                break  # Exit the inner loop once a match is found\n",
    "\n",
    "capped_smiles_df = pd.DataFrame.from_dict(capped_smiles_dict, orient='index').transpose()\n",
    "print(capped_smiles_df)\n",
    "\n",
    "capped_smiles_df.to_csv('data/capped_smiles.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1cce4e6e-a8a9-4d8c-933f-ab0e2389c56f",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9ffa9526-947f-4cd5-bbae-9f47c790efe3",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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