others/Filtering.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from rdkit.Chem.rdmolops import GetFormalCharge\n",
    "from rdkit.Chem.rdMolDescriptors import CalcMolFormula, CalcExactMolWt\n",
    "from pandas import Series,DataFrame\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\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>Pubchem ID</th>\n",
       "      <th>Inchi</th>\n",
       "      <th>Exac Min</th>\n",
       "      <th>Exac Max</th>\n",
       "      <th>CCS Min</th>\n",
       "      <th>CCS Max</th>\n",
       "      <th>Exac</th>\n",
       "      <th>CCS</th>\n",
       "      <th>Adduct</th>\n",
       "      <th>ID</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>5280637</td>\n",
       "      <td>InChI=1S/C21H20O11/c22-7-16-18(27)19(28)20(29)...</td>\n",
       "      <td>448.088695</td>\n",
       "      <td>448.111100</td>\n",
       "      <td>201.21</td>\n",
       "      <td>216.81</td>\n",
       "      <td>448.099898</td>\n",
       "      <td>209.006823</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>Y1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>442439</td>\n",
       "      <td>InChI=1S/C28H34O15/c1-10-21(33)23(35)25(37)27(...</td>\n",
       "      <td>610.173852</td>\n",
       "      <td>610.204362</td>\n",
       "      <td>220.40</td>\n",
       "      <td>238.60</td>\n",
       "      <td>610.189107</td>\n",
       "      <td>229.497183</td>\n",
       "      <td>[M-H]-</td>\n",
       "      <td>Y2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>30231</td>\n",
       "      <td>InChI=1S/C28H36O15/c1-11-21(34)23(36)25(38)27(...</td>\n",
       "      <td>612.189452</td>\n",
       "      <td>612.220062</td>\n",
       "      <td>225.22</td>\n",
       "      <td>242.69</td>\n",
       "      <td>612.204757</td>\n",
       "      <td>233.956908</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>Y3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>73659</td>\n",
       "      <td>InChI=1S/C30H48O4/c1-25(2)12-14-30(24(33)34)15...</td>\n",
       "      <td>472.342788</td>\n",
       "      <td>472.366405</td>\n",
       "      <td>213.71</td>\n",
       "      <td>231.36</td>\n",
       "      <td>472.354597</td>\n",
       "      <td>222.535275</td>\n",
       "      <td>[M-H]-</td>\n",
       "      <td>Y4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>9809542</td>\n",
       "      <td>InChI=1S/C36H62O9/c1-19(2)10-9-13-36(8,45-31-2...</td>\n",
       "      <td>638.422759</td>\n",
       "      <td>638.454681</td>\n",
       "      <td>248.90</td>\n",
       "      <td>269.46</td>\n",
       "      <td>638.438720</td>\n",
       "      <td>259.180746</td>\n",
       "      <td>[M-H]-</td>\n",
       "      <td>Y5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Pubchem ID                                              Inchi    Exac Min  \\\n",
       "0     5280637  InChI=1S/C21H20O11/c22-7-16-18(27)19(28)20(29)...  448.088695   \n",
       "1      442439  InChI=1S/C28H34O15/c1-10-21(33)23(35)25(37)27(...  610.173852   \n",
       "2       30231  InChI=1S/C28H36O15/c1-11-21(34)23(36)25(38)27(...  612.189452   \n",
       "3       73659  InChI=1S/C30H48O4/c1-25(2)12-14-30(24(33)34)15...  472.342788   \n",
       "4     9809542  InChI=1S/C36H62O9/c1-19(2)10-9-13-36(8,45-31-2...  638.422759   \n",
       "\n",
       "     Exac Max  CCS Min  CCS Max        Exac         CCS  Adduct  ID  \n",
       "0  448.111100   201.21   216.81  448.099898  209.006823  [M+H]+  Y1  \n",
       "1  610.204362   220.40   238.60  610.189107  229.497183  [M-H]-  Y2  \n",
       "2  612.220062   225.22   242.69  612.204757  233.956908  [M+H]+  Y3  \n",
       "3  472.366405   213.71   231.36  472.354597  222.535275  [M-H]-  Y4  \n",
       "4  638.454681   248.90   269.46  638.438720  259.180746  [M-H]-  Y5  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "D = pd.read_csv('data.csv')\n",
    "adduct_type = list(D['Adduct'])\n",
    "pubchem_id  = list(D['Pubchem ID'])\n",
    "exact_min   = list(D['Exac Min'])\n",
    "exact_max   = list(D['Exac Max'])\n",
    "ccs_min     = list(D['CCS Min'])\n",
    "ccs_max     = list(D['CCS Max'])\n",
    "ccs_true    = list(D['CCS'])\n",
    "exact_true  = list(D['Exac'])\n",
    "ID          = list(D['ID'])\n",
    "D"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "fenshu = []\n",
    "excat_num = []\n",
    "ccs_num = []\n",
    "for index in range(len(adduct_type)):\n",
    "    \n",
    "    data_exm = []\n",
    "    data_ccs = []\n",
    "\n",
    "    for i in range(1,156000000,500000):\n",
    "        filename = str(i).zfill(9) + '_' + str(i+500000-1).zfill(9)\n",
    "        \n",
    "        data = pd.read_csv('Compound_'+filename+'.csv')\n",
    "        data = data[data['EXACT MASS'] >= exact_min[index]]\n",
    "        data = data[data['EXACT MASS'] <= exact_max[index]]\n",
    "        data_exm.append(data)\n",
    "        \n",
    "        data = data[data[adduct_type[index]] >= ccs_min[index]]\n",
    "        data = data[data[adduct_type[index]] <= ccs_max[index]]\n",
    "        data_ccs.append(data)\n",
    "        \n",
    "    data_exm_s = pd.concat(data_exm, axis=0, ignore_index=True)\n",
    "    data_ccs_s = pd.concat(data_ccs, axis=0, ignore_index=True)\n",
    "    \n",
    "    excat_num.append(len(list(data_exm_s['Pubchem ID'])))\n",
    "    ccs_num.append(len(list(data_ccs_s['Pubchem ID'])))\n",
    "    \n",
    "    inchis = []\n",
    "    data_ccs_s_smiles = list(data_ccs_s['ISO SMILES'])\n",
    "    for smi in data_ccs_s_smiles:\n",
    "        mol = Chem.MolFromSmiles(smi)\n",
    "        inchi = Chem.inchi.MolToInchi(mol)\n",
    "        inchis.append(inchi)\n",
    "    data_ccs_s['INCHI'] = inchis\n",
    "    \n",
    "    RE = []\n",
    "    ccs_pred = list(data_ccs_s[adduct_type[index]])\n",
    "    for ccs in ccs_pred:\n",
    "        RE.append((ccs_true[index]-ccs)/ccs_true[index]*100)\n",
    "        \n",
    "    try:\n",
    "        this_ccs_pred = list(data_ccs_s[data_ccs_s['Pubchem ID'].isin([pubchem_id[index]])][adduct_type[index]])[0]\n",
    "        this_ccs_re = (ccs_true[index]-this_ccs_pred)/ccs_true[index]*100\n",
    "        if this_ccs_re < 0:\n",
    "            fenshu.append((1-this_ccs_re/min(RE))*100)\n",
    "        else:\n",
    "            fenshu.append((1-this_ccs_re/max(RE))*100)\n",
    "    except:\n",
    "        fenshu.append('null')\n",
    "    \n",
    "    data_ccs_s.to_csv(str(ID[index])+'.csv',index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Pubchem ID</th>\n",
       "      <th>Inchi</th>\n",
       "      <th>Exac Min</th>\n",
       "      <th>Exac Max</th>\n",
       "      <th>CCS Min</th>\n",
       "      <th>CCS Max</th>\n",
       "      <th>Exac</th>\n",
       "      <th>CCS</th>\n",
       "      <th>Adduct</th>\n",
       "      <th>ID</th>\n",
       "      <th>excat_num</th>\n",
       "      <th>ccs_num</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>5280637</td>\n",
       "      <td>InChI=1S/C21H20O11/c22-7-16-18(27)19(28)20(29)...</td>\n",
       "      <td>448.088695</td>\n",
       "      <td>448.111100</td>\n",
       "      <td>201.21</td>\n",
       "      <td>216.81</td>\n",
       "      <td>448.099898</td>\n",
       "      <td>209.006823</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>Y1</td>\n",
       "      <td>14629</td>\n",
       "      <td>9472</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>442439</td>\n",
       "      <td>InChI=1S/C28H34O15/c1-10-21(33)23(35)25(37)27(...</td>\n",
       "      <td>610.173852</td>\n",
       "      <td>610.204362</td>\n",
       "      <td>220.40</td>\n",
       "      <td>238.60</td>\n",
       "      <td>610.189107</td>\n",
       "      <td>229.497183</td>\n",
       "      <td>[M-H]-</td>\n",
       "      <td>Y2</td>\n",
       "      <td>3827</td>\n",
       "      <td>1099</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>30231</td>\n",
       "      <td>InChI=1S/C28H36O15/c1-11-21(34)23(36)25(38)27(...</td>\n",
       "      <td>612.189452</td>\n",
       "      <td>612.220062</td>\n",
       "      <td>225.22</td>\n",
       "      <td>242.69</td>\n",
       "      <td>612.204757</td>\n",
       "      <td>233.956908</td>\n",
       "      <td>[M+H]+</td>\n",
       "      <td>Y3</td>\n",
       "      <td>3944</td>\n",
       "      <td>1542</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>73659</td>\n",
       "      <td>InChI=1S/C30H48O4/c1-25(2)12-14-30(24(33)34)15...</td>\n",
       "      <td>472.342788</td>\n",
       "      <td>472.366405</td>\n",
       "      <td>213.71</td>\n",
       "      <td>231.36</td>\n",
       "      <td>472.354597</td>\n",
       "      <td>222.535275</td>\n",
       "      <td>[M-H]-</td>\n",
       "      <td>Y4</td>\n",
       "      <td>2254</td>\n",
       "      <td>1807</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>9809542</td>\n",
       "      <td>InChI=1S/C36H62O9/c1-19(2)10-9-13-36(8,45-31-2...</td>\n",
       "      <td>638.422759</td>\n",
       "      <td>638.454681</td>\n",
       "      <td>248.90</td>\n",
       "      <td>269.46</td>\n",
       "      <td>638.438720</td>\n",
       "      <td>259.180746</td>\n",
       "      <td>[M-H]-</td>\n",
       "      <td>Y5</td>\n",
       "      <td>733</td>\n",
       "      <td>505</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Pubchem ID                                              Inchi    Exac Min  \\\n",
       "0     5280637  InChI=1S/C21H20O11/c22-7-16-18(27)19(28)20(29)...  448.088695   \n",
       "1      442439  InChI=1S/C28H34O15/c1-10-21(33)23(35)25(37)27(...  610.173852   \n",
       "2       30231  InChI=1S/C28H36O15/c1-11-21(34)23(36)25(38)27(...  612.189452   \n",
       "3       73659  InChI=1S/C30H48O4/c1-25(2)12-14-30(24(33)34)15...  472.342788   \n",
       "4     9809542  InChI=1S/C36H62O9/c1-19(2)10-9-13-36(8,45-31-2...  638.422759   \n",
       "\n",
       "     Exac Max  CCS Min  CCS Max        Exac         CCS  Adduct  ID  \\\n",
       "0  448.111100   201.21   216.81  448.099898  209.006823  [M+H]+  Y1   \n",
       "1  610.204362   220.40   238.60  610.189107  229.497183  [M-H]-  Y2   \n",
       "2  612.220062   225.22   242.69  612.204757  233.956908  [M+H]+  Y3   \n",
       "3  472.366405   213.71   231.36  472.354597  222.535275  [M-H]-  Y4   \n",
       "4  638.454681   248.90   269.46  638.438720  259.180746  [M-H]-  Y5   \n",
       "\n",
       "   excat_num  ccs_num  \n",
       "0      14629     9472  \n",
       "1       3827     1099  \n",
       "2       3944     1542  \n",
       "3       2254     1807  \n",
       "4        733      505  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "D['excat_num'] = excat_num\n",
    "D['ccs_num'] = ccs_num\n",
    "D"
   ]
  }
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