protect_atoms_in_reaction.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 在化学反应中保护原子\n",
    "有时在使用rxn文件时，很难准确表达或全面考虑到每个细节，导致不需要的原子发生反应，并产生副产物。而rdkit也提供了保护原子的操作，避免不需要的原子参与到反应中。还是以形成酰胺键为例。"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1.rxn文件创建反应\n",
    " - 通过rxn文件创建一个反应模式：ReactionFromRxnFile()\n",
    " - 检查一下该反应：ReactionToImage()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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nPPGE0TX14MqVKxUVFa+99lpra+v48eMLCwtXrlzJohjhIxD25PhxWblS/vxnEfnf558/6XA888wzRtcU3N///vf8/HyfzyciX/nKV1wul81mM7ooAACiWFtb229/+9tvf/vbdDoxCCklb74phYXy3ntisWzJy/vqqlVTpkwxuqwgtHdicXHxxYsXY2Jili1b9uqrr95zzz1G1zVIEAh7p66ufc2aJz76yPf++ykpKU6ns2Ox3YHggw8+KCsr+81vftPe3j558uSSkpIXX3xRe8AXAAAAuKNPP5Wf//zitm0Tfb6RI0fm5eUVFxdrW2oPELt37165cuXRo0dF5KmnnnI6nQ8//LDRRQ0qBMLeam1t3bhx409+8pNPPvlk2LBh2rtl7NixRtclLS0t999//+XLl0eMGLFq1aq1a9eOHj3a6KIAAAAQNc6dO7dmzZrq6mql1NSpU1955ZWsrCxtS21jvfXWW0uXLhWR6dOnb9iwISMjw+iKBiECYWguX7788ssv//KXv7xx48aECRN+/OMfr1ixYsiQIcZW9cMf/rC+vt7lcj344IPGVgIAAIAodfDgwfz8fG3r7Hnz5rlcrqSkJGNLam1tTUpKWrJkSVFRkbZiInRHIOyLI0eOFBQU7NmzR0Tmzp3rdDqffPJJA+tpb29ngigAAADC1N7evmXLlsLCwvPnz1sslhdeeOGVV16ZNGmSsSXR0e1XBMK+q62tzc/PP3PmjIgsXrx448aN06ZNM7ooAAAAICwtLS3r168vLy+/du3a6NGjV69evXbt2uHDhxtdF/oFabvv0tPTjx07Vl5ePmbMmO3btyckJBQVFTU3N9/pfJfLZbmdy+UK9UW9Xm+YLQAAAADdGD16dGlpaUNDQ2ZmZktLS1lZWWJi4tatW+90Pr3cqEYgDMvIkSMLCwuPHz+enZ39+eefV1RUxMfHb9q0qeu4q8Vi0Z7T1Xg8HhFpbGwM6eUcDse6des6GnE6nQUFBQ6HQ7e/DwAAACAiIlartbq6uq6ubvbs2X6/PysrKyUlpb6+vtNp9HKjHVNGdbN37978/Px//OMfIrJkyZI//vGPHV9KTk7WTrj1fL/fn5ub2+lgN7xeb1paWlNTk9Vq7TjocDjcbnengwAAAIBerl+//vrrr5eVlV25ciU2NvZ3v/vdsmXLtC/Ryx0EGCHUTXJy8qFDh6qqqiZNmvTss892HPd6vT6fr7i4uNP5Vqs1MTHR7/f3sv1Tp06JSFNT060HtbV3Ox0EAAAA9DJ06ND8/Hy/35+Xlzdy5MiOxRTp5Q4OBEI9WSyWnJycU6dOLV++vONgTU2NzWZLTU3ten5lZWWnzzz8fr/FYtE+a+lkxowZWms6Fw0AAAD05O6773a5XGfPnp0yZYp2hF7u4BBrdAGD0JgxY279o9vtttvtvfzeHTt2iIjP5/P7/Z3eRampqV3n92ofqMTFxfW9XAAAAKB3xo8f3/F7ermDAyOE/UsbK581a1Yvz3/uuedExGaz9XK2dHV1td1uZ2o1AAAAIole7qDBCOHAYrVae7/Mj8vl8vl8vX9gFwAAADAEvdwBixHCaOX1erUVfo0uBAAAANANvdwIIxBGJb/fv27dOj41AQAAwGBCLzfyCISREOrWnN3zer0hbe0CAAAA9Ad6uYMAgbB/Wa1Wm83W0NAQ9Ksul6v3O7RovF5vTU1Np/eJy+Xqe4kAAABAiOjlDhoEwn6XlZWlLbDb9UuNjY0hLZ2kvU8qKys7HdQ2bwEAAAAihl7u4EAg7HfaGrvr16/vdNzlcmVkZHQ62M2WnX6/v+v7RETS0tJ0qxUAAADoHXq5gwOBsN9ZrVaPx+N2ux0OR8dBh8PR2NiYmpra6eRbt+zs9KXc3Fy3223pQtiyEwAAABFHL3dwIBBGQmpqqlKqoaGh4+c7IyOj66cgEvqWnRq27AQAAEDk0csdBCxs8QEAAAAA5sQIIQAAAACYFIEQAAAAAEyKQAgAAAAAJkUgBAAAAACTIhACAAAAgEkRCAEAAADApAiEAAAAAGBSBEIAAAAAMCkCIQAAAACYFIEQAAAAAEyKQAgAAAAAJkUgBAAAAACTIhACAAAAgEkRCAEAAADApAiEAAAAAGBSBEIAAAAAMCkCIQAAAACYFIEQAAAAAEyKQAgAAAAAJkUgBAAAAACTIhACAAAAgEkRCAEAAADApP4PNEzWpZv/4ZwAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=1200x100 at 0x648DCC8>"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem as Chem\n",
    "from rdkit import RDConfig\n",
    "rxn_file = os.path.join(RDConfig.RDDocsDir, 'Book\\data\\AmideBond.rxn')\n",
    "rxn = Chem.ReactionFromRxnFile(rxn_file)\n",
    "img = Chem.Draw.ReactionToImage(rxn, subImgSize=(300, 100))\n",
    "img"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "img.save('data/protect_atoms_reaction_1.png')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "在这个反应中，氮原子只要连有氢原子，就可以发生反应。当使用一个已经含有酰胺键的化合物作为反应物时，同样也可以发生反应。\n",
    " - 设置反应物acid和base\n",
    " - 按照模式进行反应：rxn.RunReactants()\n",
    " - 对反应物进行核对：SanitizeMol()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=500x250 at 0x6830A48>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "acid = Chem.MolFromSmiles('CC(=O)O')\n",
    "base = Chem.MolFromSmiles('CC(=O)NCCN')\n",
    "ps = rxn.RunReactants((acid,base))\n",
    "[Chem.SanitizeMol(x[0]) for x in ps]\n",
    "img = Chem.Draw.MolsToGridImage([x[0] for x in ps], molsPerRow=2, subImgSize=(250, 250))\n",
    "img"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "img.save('data/protect_atoms_reaction_2.png')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2.保护目标原子\n",
    "如果不想让酰胺氮原子发生反应，可以将它保护起来\n",
    " - 将要保护的基团转成SMARTS，记录在amidep中\n",
    " - 在反应物中查找所有符合amidep的子结构\n",
    " - 遍历每个符合的子结构，设置属性，键为\"_protected\"，值随意"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "amidep = Chem.MolFromSmarts('[N;$(NC=[O,S])]')\n",
    "for match in base.GetSubstructMatches(amidep):\n",
    "    base.GetAtomWithIdx(match[0]).SetProp('_protected', '1')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " - 再进行反应，被保护的基团就不会发生反应了"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'CC(=O)NCCNC(C)=O'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ps = rxn.RunReactants((acid,base))\n",
    "print(len(ps))\n",
    "Chem.MolToSmiles(ps[0][0])"
   ]
  }
 ],
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