PDB_ligand_analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pypdb import *\n",
    "from pymol import *\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem import PandasTools\n",
    "IPythonConsole.ipython_useSVG=True\n",
    "\n",
    "import pprint\n",
    "import glob\n",
    "\n",
    "import pandas as pd\n",
    "from array import array\n",
    "import numpy as np\n",
    "import collections\n",
    "\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "PDBs = ['3FNU','3CKR','3CKP','3KYR','3UDJ','3UDK','3UDM','3UDN','3UDP','3UDQ','3UDR','3UDY','3VV7','3WB4','3WB5','5YGX','5YGY','3K5C','4GID','1FQ5','3VEU','3VF3','3VG1','4D85','4DI2','4DJU','4DJV','4DH6','4DJW','4DJX','4DJY','4DPF','4GJ5','4GJ6','4GJ7','4GJ8','4GJ9','4GJA','4GJB','4GJC','4DUS','4GJD','4DPI','1FQ6','1OD1','4FCO','4FM7','4FM8','4FRS','4FSE','4FSL','4GMI','4HZT','1PSA','4H1E','4H3F','4H3G','4H3I','4H3J','4HA5','3U6A','4B1C','4I0D','4I0E','4I0G','4I0Z','4I12','4I1C','4I0F','4I0H','4I10','4I11','4J0Z','4J0Y','4J0V','4J0P','4J1K','4J1I','4J1H','4J1F','4J1E','4J1C','4J17','2G1N','3IVH','4JOO','4JP9','4JPC','4JPE','3PRS','4K8S','4K9H','4KE1','4KE0','4KUP','4L6B','4LAP','4L7G','4L7H','4L7J','4LC7','4LXA','4LXK','4LXM','3KM4','2P4J','4N00','4B72','2G1O','3IVI','4OD9','4OC6','4OBZ','4PZW','4PZX','4PYV','1FQ4','1FQ7','1FQ8','4Q1N','3CIB','3CIC','3CID','4B05','3OHF','3OHH','2G1R','4R5N','4R8Y','4R91','4R92','4R95','4RCD','4RCE','4RCF','3OWN','3PI5','3RSV','3RU1','3KN0','4WTU','4RRN','4RRO','4RRS','4WY1','4WY6','4X2L','4X7I','4RYG','4RYC','4RZ1','3PMY','4XKX','4S1G','3IGB','4Y37','4Y39','4Y3D','4Y3A','4Y3N','4Y41','4Y43','4Y4U','4Y44','3IN3','4Y47','4Y51','4Y53','4Y4B','5J25','4Y58','4Y5B','4Y4X','4Y5E','4Y5G','4Y5C','4Y5M','4Y5P','4Y5N','4Y6M','4YCY','4YD3','4YD5','4YD4','4YBI','2G1S','4Z22','2G27','4ZL4','4ZPE','4ZPF','4ZPG','4ZSQ','4ZSR','4ZSP','3T7X','3UFL','5CLM','3S7M','4B77','3INH','3IXJ','3S7L','3IND','5DQC','1XE5','1XE6','5DR0','5DR1','5DR3','3TPP','5DR7','5DQ1','5DQ2','2G1Y','3EXO','5ENM','5ENK','5EZX','5EZZ','5F01','5F00','5HE5','5HE4','5HDX','5HDV','5HDU','5HE7','5HD0','5HCT','3L3A','5HU1','5HU0','5HTZ','5I3X','5I3Y','5I3W','5I3V','5IE1','2G22','2OHP','5IS4','4B1E','3ZLQ','4B1D','5KOQ','5KOS','5KOT','5KQF','5KR8','3ZMG','4XX3','4XX4','3GW5','3LNK','5T1W','5SXN','5SY2','5SZ9','5SY3','3DM6','4R93','5LWR','5TMK','5TMG','4AZY','5TOL','2G24','2OHQ','3T7P','3N4L','3L38','2OHR','5UYU','4BFD','5YIA','5YIB','5YIE','5YIC','5V0N','5V8V','4EXG','3IXK','5HDZ','3NSH','4EWO','5VPM','2OHS','2IGX','2IGY','3G70','3G72','3G6Z','2XFK','3DUY','3DV1','2F3F','2F3E','3K5F','3VV6','3VV8','3H0B','3ZKG','6EJ2','6EJ3','3DV5','3L59','3L5B','3L5C','3L5D','3L5E','3L5F','3K1W','3K5G','2VKM','6EQM','3IN4','4D89','4D88','2VA7','2VIJ','3QI1','6JSE','6JSG','6JSN','6JSF','6JT3','2VA5','2VNN','2VNM','2OF0','5YIA','2QK5','2QMD','2QMF','3KMY','6FGY','6BFD','6BFE','6BFW','6BFX','4FRI','4FRJ','4FRK','1LF3','6C2I','6C4G','3HW1','3MSJ','3MSK','3MSL','3S2O','3PBZ','3PLL','2ZJH','2ZJI','2ZJJ','2ZJK','2ZJL','2ZJM','2ZJN','2IQG','3PGI','3PM4','3PB5','3PMU','3PLD','3PI0','2FDP','3KMX','6DHC','4B0Q','2VA6','1QRP','3VUC','6E3Z','4B00','2BJU','5MXD','4ZEA','2OHT','2OHU','3WZ8','3WZ7','3WZ6','3QVI','4B78','1W51','2G20','2G21','6NV7','6NV9','6NW3','2HIZ','2HM1','2IL2','2IKU','3O9L','3OAD','3OAG','6OD6','2P83','3I25','1B5F','3T6I','3T6I','1FMU','4CKU','6PZ4','5T1U','3R2F','3SKF','3SKG','3WZ6','1BXO','1BXQ','2BKS','3QBH','4ACU','2WJO','3VSW','3VSX','1LEE','1LF2','3T7Q','3PSY','3D91','3PRS','3PWW','2BKT','3RSX','3RTH','3RTM','3RTN','3RVI','3Q3T','3Q4B','3Q5H','3Q6Y','3OQF','3OQK','3SFC','4ACX','2QMG','2QP8','4XXS','3FKT','3OOT','1W6H','2I4Q','2V00','2VIE','2VIY','2VIZ','2VJ6','2VJ7','2VJ9','4IVS','5OJE','4IVT','3VYD','3VYE','3VYF','4B70','3ZKI','3INE','3INF','2XFI','4BEK','3K5D','3LPI','3LPJ','3LPK','3LHG','3T6I','3OOZ','3UQU','3UQW','3UQX','2WF0','2WF1','2WF2','2WF3','2WF4','2WEZ']\n",
    "ligands_list = []\n",
    "for x in PDBs:\n",
    "    ligands = get_ligands(x)[\"ligandInfo\"][\"ligand\"]\n",
    "    if type(ligands) == dict:\n",
    "        ligands_list.append(ligands)\n",
    "    \n",
    "    \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "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>@chemicalID</th>\n",
       "      <th>@molecularWeight</th>\n",
       "      <th>@structureId</th>\n",
       "      <th>@type</th>\n",
       "      <th>InChI</th>\n",
       "      <th>InChIKey</th>\n",
       "      <th>chemicalName</th>\n",
       "      <th>formula</th>\n",
       "      <th>smiles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>006</td>\n",
       "      <td>631.782</td>\n",
       "      <td>3FNU</td>\n",
       "      <td>peptide-like</td>\n",
       "      <td>InChI=1S/C35H41N3O6S/c1-21-11-10-12-22(2)31(21...</td>\n",
       "      <td>KKTYZYHUPKXLPL-RIQJEONASA-N</td>\n",
       "      <td>(4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acety...</td>\n",
       "      <td>C35 H41 N3 O6 S</td>\n",
       "      <td>Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>009</td>\n",
       "      <td>605.769</td>\n",
       "      <td>3CKR</td>\n",
       "      <td>non-polymer</td>\n",
       "      <td>InChI=1S/C37H43N5O3/c1-41(2)32-20-12-19-31(21-...</td>\n",
       "      <td>DCJGHBWTJFHQCR-UEHMVRIRSA-N</td>\n",
       "      <td>(4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(d...</td>\n",
       "      <td>C37 H43 N5 O3</td>\n",
       "      <td>CN(C)c1cccc(c1)CNC[C@H]([C@H](Cc2ccccc2)NC(=O)...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>038</td>\n",
       "      <td>722.791</td>\n",
       "      <td>3KYR</td>\n",
       "      <td>peptide-like</td>\n",
       "      <td>InChI=1S/C34H46N10O8/c1-19(2)15-25(39-30(47)26...</td>\n",
       "      <td>FZZOBXKGDCMGAL-NAJARDBOSA-N</td>\n",
       "      <td>3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-azanyl-...</td>\n",
       "      <td>C34 H46 N10 O8</td>\n",
       "      <td>CC(C)C[C@@H](C(=O)NC[C@](CCc1ccccc1)(C(=O)Nc2c...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>09E</td>\n",
       "      <td>491.355</td>\n",
       "      <td>3UDQ</td>\n",
       "      <td>non-polymer</td>\n",
       "      <td>InChI=1S/C21H19BrN2O5S/c22-12-5-6-18-13(9-12)1...</td>\n",
       "      <td>AENVIUXFIDGFED-LLGFUMIMSA-N</td>\n",
       "      <td>(4S)-6-bromo-1,1-dioxido-3,4-dihydro-2H-thioch...</td>\n",
       "      <td>C21 H19 Br N2 O5 S</td>\n",
       "      <td>c1ccc2c(c1)[C@]3(C[C@@H](NC3)C(=O)O[C@H]4CCS(=...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0BI</td>\n",
       "      <td>571.749</td>\n",
       "      <td>3K5C</td>\n",
       "      <td>non-polymer</td>\n",
       "      <td>InChI=1S/C35H45N3O4/c1-24(2)27-9-7-10-29(20-27...</td>\n",
       "      <td>GCZHKZTYTMTFGU-JHOUSYSJSA-N</td>\n",
       "      <td>(4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl...</td>\n",
       "      <td>C35 H45 N3 O4</td>\n",
       "      <td>CC(C)c1cccc(c1)C2(CC2)NC[C@H]([C@@H]3Cc4cccc(c...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  @chemicalID @molecularWeight @structureId         @type  \\\n",
       "0         006          631.782         3FNU  peptide-like   \n",
       "1         009          605.769         3CKR   non-polymer   \n",
       "2         038          722.791         3KYR  peptide-like   \n",
       "3         09E          491.355         3UDQ   non-polymer   \n",
       "4         0BI          571.749         3K5C   non-polymer   \n",
       "\n",
       "                                               InChI  \\\n",
       "0  InChI=1S/C35H41N3O6S/c1-21-11-10-12-22(2)31(21...   \n",
       "1  InChI=1S/C37H43N5O3/c1-41(2)32-20-12-19-31(21-...   \n",
       "2  InChI=1S/C34H46N10O8/c1-19(2)15-25(39-30(47)26...   \n",
       "3  InChI=1S/C21H19BrN2O5S/c22-12-5-6-18-13(9-12)1...   \n",
       "4  InChI=1S/C35H45N3O4/c1-24(2)27-9-7-10-29(20-27...   \n",
       "\n",
       "                      InChIKey  \\\n",
       "0  KKTYZYHUPKXLPL-RIQJEONASA-N   \n",
       "1  DCJGHBWTJFHQCR-UEHMVRIRSA-N   \n",
       "2  FZZOBXKGDCMGAL-NAJARDBOSA-N   \n",
       "3  AENVIUXFIDGFED-LLGFUMIMSA-N   \n",
       "4  GCZHKZTYTMTFGU-JHOUSYSJSA-N   \n",
       "\n",
       "                                        chemicalName             formula  \\\n",
       "0  (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acety...     C35 H41 N3 O6 S   \n",
       "1  (4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(d...       C37 H43 N5 O3   \n",
       "2  3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-azanyl-...      C34 H46 N10 O8   \n",
       "3  (4S)-6-bromo-1,1-dioxido-3,4-dihydro-2H-thioch...  C21 H19 Br N2 O5 S   \n",
       "4  (4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl...       C35 H45 N3 O4   \n",
       "\n",
       "                                              smiles  \n",
       "0  Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O...  \n",
       "1  CN(C)c1cccc(c1)CNC[C@H]([C@H](Cc2ccccc2)NC(=O)...  \n",
       "2  CC(C)C[C@@H](C(=O)NC[C@](CCc1ccccc1)(C(=O)Nc2c...  \n",
       "3  c1ccc2c(c1)[C@]3(C[C@@H](NC3)C(=O)O[C@H]4CCS(=...  \n",
       "4  CC(C)c1cccc(c1)C2(CC2)NC[C@H]([C@@H]3Cc4cccc(c...  "
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pdbs = pd.DataFrame(ligands_list)\n",
    "pdbs.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdbs.to_csv('top_ligands.csv', header=True, index=False, sep='!')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "l = ['02U','166','167','1QO','2BR','2DP','31I','3O5','3W3','3W6','3XT','4AG','4H0','4PF','5HD','5VU','63U','63V','6LB','6LR','74C','7E9','A4G','AS2','BEO','BXC','C10','CD4','CN6','D01','DA9','DHJ','G6K','GR1','GR4','GVT','HG9','HGP','HSG','HSH','HSJ','HT3','IN','L44','LCO','LD2','LXB','LXZ','MAC','MDL','NSP','PA8','PC6','PD7','PLD','PX8','RHU','SCU','SMO','SPJ','SPW','SPZ','TCN','ULI','YB2','YI6','Z22','Z88','ZCM','1AG','28T','5WE','7E8','7HE','CE9','CMS','CMX','CN3','CNS','DDR','DPG','EAP','FJP','GHE','HB0','MH2','NER','NWA','OHO','P25','PC7','PC8','PSL','PTN','PX2','S85','TEA','THE','TRA','YF3','20S','2NV','4V4','6PE','6PH','9PE','B3H','CMJ','CON','DMI','DNO','HGX','L4P','M12','MGE','MVC','NGZ','P1O','PQ9','RG1','SB','TUE','UPL','ZWI','16P','6UL','BUD','C1O','CE','CUZ','DMN','DTL','KEN','LIO','PEH','PTL','PX6','RHD','SWE','TWT','XP4','8PE','AL','DGG','DTC','DVT','ENC','IPL','L1P','L2C','LPP','MG8','MYY','OES','PEV','PGF','SBT','SX','TBF','TE','TMA','UMC','03S','1DO','1EM','GGD','HTH','LPD','PBM','TCA','TTN','XEB','1KA','3NI','7PH','AE4','ALQ','ASO','BM3','BO4','CXE','DET','EP1','GA','GG5','LNK','PO2','POG','PT4','SE4','7PG','AUC','HAI','IWH','LCP','N2P','P22','SPK','AGA','ANL','AU3','AZR','CR','GBL','LOP','NDS','PCF','PXN','16D','CE1','GD3','IR3','NET','PHU','PYZ','EU3','HO','JZR','ME2','OPC','P3G','PGT','BGL','BU2','IR','NAA','OXD','P15','R16','TAU','TRT','U1','EU','LA','LGU','N8E','NEX','POV','6PL','BE7','CPQ','MXE','PCD','PHS','SO2','TEO','XAT','BHG','LU','LUT','M2M','MC3','MMC','PI','3PH','DUD','NBN','PIN','SQU','UQ','DDQ','L3P','MTL','PEU','XLS','XPE','BNZ','C15','FTT','MHA','OS','SOG','Y1','3PE','AE3','EDT','IBM','PD','C2O','FAR','KR','TCE','478','E64','HGB','PEF','W','HAE','NVP','TOE','BO3','DEP','FOR','PGR','PLR','DXE','ETE','MBN','MGF','PCW','PDO','2OP','B7G','BET','DHB','P4C','ACM','EMC','IRI','LMU','ETF','MPG','PAM','GLV','PMS','TG1','THJ','DKA','F09','MOS','TB','UMQ','XYL','CCN','ETX','GOA','LAC','MAE','144','DTV','HTG','P4G','PR','STE','TFA','CM5','HEX','PO3','AKR','HCS','PG5','SGM','SPH','DGA','ACN','AG','BAM','PTY','DTD','ASC','LI1','RU','CB3','HCA','PPI','ARS','DTU','PUT','Y01','CHT','OLB','PSC','YT3','DD9','PE3','PEK','C14','ICT','IUM','KAI','PC1','TGL','OXM','TRD','LFA','THM','7PE','PL9','SM','D12','DMF','UND','5AD','GUN','HP6','PX4','D1D','PE8','PEE','TBU','SAL','13P','MTE','PE5','PHB','CAD','LMR','PB','SQD','PLC','TL','CO2','HTO','L2P','PGV','KDO','RB','MYS','BU3','SPD','BU1','LMG','SRT','CPT','DGD','PG6','F','PGA','PEO','GD','12P','D10','DAO','URE','3PG','FOL','POL','MBO','CYC','MPO','PER','1PG','DPO','MYA','CPS','H2S','MOH','15P','CXS','LHG','PHQ','HC4','LI','AU','BCN','GAI','P33','BNG','CHD','BCR','OCT','OXL','GCP','VO4','SO3','YB','SAR','IPH','O','ORO','PPV','TAM','DMU','PG0','B3P','MLT','HEZ','XYS','TAR','SPM','CS','PT','2PE','NGA','PE4','XE','PGO','MLA','CDL','BEZ','OH','CLR','DOD','SR','A2G','OLA','CYN','DIO','BA','HED','LDA','UMP','PYR','NHE','BCT','GLA','CAS','BTB','SIN','AZI','FUL','NH4','MYR','DTT','BEN','LMT','EOH','NCO','SUC','OLC','XYP','TYS','POP','CAC','CO3','PLM','CMO','OGA','SCN','P6G','OXY','UNL','TLA','UDP','SIA','BOG','BR','MRD','SAM','FLC','NDG','HG','IPA','AMP','NO3','UNX','1PE','NDP','MLI','GLC','IMD','CO','UNK','ACY','BGC','IOD','BME','CIT','CD','EPE','PLP','GAL','PGE','FUC','FMT','PG4','NAP','NAD','TRS','CU','MES','FE','MPD','ACE','NI','DMS','FAD','BMA','MAN','K','PEG','MN','ACT','PO4','NAG','NA','MSE','EDO','CA','CL','MG','ZN','GOL','SO4','CYS','HOH','TRP','MET','HIS','TYR','PHE','GLN','PRO','ASN','ILE','ASP','ARG','THR','VAL','GLU','SER','LYS','ALA','LEU','GLY']\n",
    "chem_desc_New = []\n",
    "for y in l:\n",
    "    chem_desc = describe_chemical(y)['describeHet']['ligandInfo']['ligand']\n",
    "    if type(ligands) == dict:\n",
    "        chem_desc_New.append(chem_desc)\n",
    "    \n",
    "    \n",
    "Lig = pd.DataFrame(chem_desc_New)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdbs.to_csv('tobeskipped_ligands.csv', header=True, index=False, sep='!')"
   ]
  }
 ],
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