modifying_molecules.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 分子修改与编辑"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 一、初级篇"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1.氢原子显示与隐藏\n",
    "正常情况下，分子在rdkit中存储时，氢以隐式氢的形式存储，即不会在图片中显示出来。当需要加入氢原子时，例如要生成和优化立体结构，可以通过函数加上氢原子。\n",
    "- 加氢：AddHs()\n",
    "- 去氢：RemoveHs()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3\n",
      "9\n",
      "3\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "m = Chem.MolFromSmiles('CCO')\n",
    "print(m.GetNumAtoms())\n",
    "m2 = Chem.AddHs(m)\n",
    "print(m2.GetNumAtoms())\n",
    "m2 = Chem.RemoveHs(m2)\n",
    "print(m2.GetNumAtoms())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2.芳香键与kekule式转换\n",
    "- 芳香键在Rdkit中存储类型为\"AROMATIC\"，可以转化为kelule式：Kekulize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AROMATIC\n",
      "DOUBLE\n",
      "SINGLE\n"
     ]
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('c1ccccc1')\n",
    "print(m.GetBondWithIdx(0).GetBondType())\n",
    "Chem.Kekulize(m)\n",
    "print(m.GetBondWithIdx(0).GetBondType())\n",
    "print(m.GetBondWithIdx(1).GetBondType())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "转化后，类型中虽然变为单键和双键，但依然是芳香键\n",
    "- 查看是否为芳香键：GetIsAromatic()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "True\n"
     ]
    }
   ],
   "source": [
    "print(m.GetBondWithIdx(1).GetIsAromatic())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 之所以仍然为芳香键，是因为分子有一个跟芳香性相关的属性Flags，记录了芳香性的信息。可以在kelulize时将clearAromaticFlags参数设置为True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DOUBLE\n",
      "False\n"
     ]
    }
   ],
   "source": [
    "Chem.Kekulize(m, clearAromaticFlags=True)\n",
    "print(m.GetBondWithIdx(0).GetBondType())\n",
    "print(m.GetBondWithIdx(1).GetIsAromatic())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 如果想修改回芳香键，可以对分子进行检查：SanitizeMol()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AROMATIC\n"
     ]
    }
   ],
   "source": [
    "Chem.SanitizeMol(m)\n",
    "print(m.GetBondWithIdx(0).GetBondType())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 二、高级篇"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1.Atom和Bond对象的编辑功能\n",
    "在rdkit的Atom对象中也提供了一系列功能，可以对分子进行原位编辑。\n",
    "- 修改形式电荷：atom.SetFormalCharge(int)\n",
    "- 修改杂化方式为SP3：atom.HybridizationType(Chem.HybridizationType.SP3)\n",
    "- 修改为芳香原子：atom.SetIsAromatic(True)\n",
    "- 修改为同位素标记原子：atom.SetIsotope(int)\n",
    "- 不带隐式氢：atom.SetNoImplicit(True)\n",
    "- 固定显示氢：atom.SetNumExplicitHs(int)\n",
    "\n",
    "Bond对象类似\n",
    "\n",
    "- 修改键的显示方式：SetBondDir(Chem.BondDir.BEGINDASH)\n",
    "- 修改为芳香键：SetBondType(Chem.BondType.AROMATIC)\n",
    "- 修改键芳香性的Flags：SetIsAromatic(bool)\n",
    "- 是否共轭：SetIsConjugated(bool)\n",
    "\n",
    "不一一说明了，感兴趣可以试试各个函数及相关参数，举几个可能会遇到的例子\n",
    "- 修改手性碳：SetChiralTag()<br />\n",
    "参数设置为Chem.ChiralType.CHI_TETRAHEDRAL_CCW时，为S型（Counter Clockwise，逆时针）<br />\n",
    "参数设置为Chem.ChiralType.CHI_TETRAHEDRAL_CW时，为R型（Clockwise，顺时针）<br />\n",
    "还有CHI_OTHER、CHI_UNSPECIFIED不指定类型"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7899670>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('OC(N)C')\n",
    "m.GetAtomWithIdx(1).SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW)\n",
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "Chem.Draw.MolToFile(m, 'data/modifying_mols_0.png', size=(250, 250))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 修改原子：atom.SetAtomicNum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x78b0300>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('c1ccccc1')\n",
    "m.GetAtomWithIdx(0).SetAtomicNum(7)\n",
    "Chem.SanitizeMol(m)\n",
    "Chem.MolToSmiles(m)\n",
    "m"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 别忘了检查步骤，虽然有时候看起来没什么问题"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'c1ccocc1'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('c1ccccc1')\n",
    "m.GetAtomWithIdx(0).SetAtomicNum(8)\n",
    "Chem.MolToSmiles(m)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 但该分子本身其实是错误的：SanitizeMol()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "ename": "KekulizeException",
     "evalue": "Can't kekulize mol.  Unkekulized atoms: 1 2 3 4 5\n",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mKekulizeException\u001b[0m                         Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-10-8aabfab76642>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mChem\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSanitizeMol\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mm\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mKekulizeException\u001b[0m: Can't kekulize mol.  Unkekulized atoms: 1 2 3 4 5\n"
     ]
    }
   ],
   "source": [
    "Chem.SanitizeMol(m)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2.RWMol的编辑功能\n",
    "更复杂的操作可以使用rdkit.Chem.rdchem.RWMol类（用于分子读写的类）。这个类在修改分子方面，性能更好，它可以提供一个“活动的”分子，并且共享了mol对象的操作接口。修改完毕后，只需要用GetMol()就可以获得最终的分子"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAABmJLR0QA/wD/AP+gvaeTAAAT4UlEQVR4nO3de1BU5f8H8M8iKBdZxS7e74Ko3MwyxTQ1TUWyTLf/mJyx1hmbWa3Jtv4oHf/CydF15mfT4uhE//htUSNUkDTvQlmGIFrKRTQV8AaIgEDs+f3x1LazXNzLczjnPOf9Gv9odPfwaYW3z3me8zwfgyRJBAAA/gpSugAAAG1DjAIABAQxCgAQEMQoAEBAEKMAAAFBjAKA2h08eHDevHktLS1KF9I1xCgAqFdNTc2KFSuWLVt28uTJb775RulyuoYYBQCVysrKio+PP3DggNFotNlsa9asUbqirgUrXQAAgKfq6uq1a9dmZ2cT0aJFizIyMkaNGqV0Ud3CaBQAVESSpG+//TYuLi47O3vgwIF2uz0vL0/NGUoYjQKAelRVVb3//vvHjh0joqVLl3799dcjRoxQuqinw2gUAJQnSVJGRkZCQsKxY8eioqLsdvuhQ4c0kaGE0SgAKK6ysvK99947ceIEEZlMpp07dz733HNKF+UDjEZB19ggaO3atdOmTduyZYtqn0wUldPpZIPQEydODB48eN++fQ6HQ1sZSkQkAVfNzc07duzo6OhQuhB4usrKyvnz57v/OIwYMWLnzp1PnjxRujRdKC0tffnll9knbzKZ7t+/r3RFfkKM8nTu3LnY2Fgi2rZtm9K1QE+cTqfdbu/fvz8RPf/885mZmUePHp02bRr7kR45cqTNZmtpaVG6TGG1t7enp6f369ePiIYOHZqdna10RQFBjPLR1NRktVr79OlDRFOmTPnll1+Urgi6VV5ePnfuXNcg6O7du+z3nU5nTk7OCy+8gDCVVUlJyYsvvkhEBoMhLS3t4cOHSlcUKMQoB6dPn46Ojiai4OBgq9WKW0LV6ujosNvtERERRDRkyJD9+/d3fo1HmI4aNcpms+HvlIu2trb09PS+ffsS0ZgxY44ePap0RXwgRgPS0NBgsViCgoKIKCEh4bffflO6IuhWaWnp9OnTvZyJY2E6depUhCkvRUVF7PM0GAxms7mxsVHpirhBjPovLy9v5MiRRBQSEmK1WltbW5WuCLrmPhM3bNiwH374wcs3sjBNSkpiYTp69GiEqR9aWlpcU17jx48/ceKE0hVxhhj1R11dndlsZj9aM2bMuHz5stIVQbeKi4vZ2hEbBDU0NPh6hY6OjpycnMTERFeY2u329vZ2OaoVj2vdNTg42GKxPH78WOmK+EOM+uzgwYPDhw8norCwsPT09L///rvn19+4cWPBggXi/Qusfu4zcWPHjj127FggV+vo6HA4HCwR2NQewrRn+ll3RYz6oLa2Ni0tjf0UzZo1688///TmXevWrWNvmTt37qlTp+QuEpjCwsLJkydzn4ljYTpx4kSEac90te6KGPWWa3NFeHh4enq69w/YNzY2pqenDxo0yJW/P/30k6yl6lxzc7P7TNzJkye5fwmPMB07dizC1EWH666I0aerrq5+++232Q/MnDlzysrK/LgIC9OoqCiEqazOnj3L0o3NxDU1Ncn3tViYxsTEuIfpUyd5xKbPdVfE6FM4HI5nnnmGiAYMGGC3251OZyBXe/TokUeYHj9+nFepOsdm4tggKC4u7vz5873zdT3CdNy4cfoMUz2vuyJGu3X79u1ly5axb4slS5bcvHmT15VZmA4cONAVpliACtCpU6cmTJig4EwcC1M2G0hEkyZNyszM1E+Y+rruKhjEaBfYhmuj0UhE7PxtXld2//bqHKZyzOIJr76+3mw2GwwGIkpMTLxw4YKCxbS1tWVmZrJAJ6LJkycLH6b+rbsKBjHqqbKy8rXXXmPfFqmpqbdu3eJyWafTmZmZGRMT49rBzXiE6YIFCwR+LoS73NxcNhMXGhq6cePGtrY2pSuSJD2Fqd/rroJBjP6n86k/vK5cWVm5YMEC9kNls9k6v+DBgwcbN24cMGAAwtRLHjNxV65cUboiTyxMx48fz4qcMmVKZmamMEHDZd1VGIjRf5SXl7/66qvs28JkMt27d4/LZVk0R0ZGEhFrjdDDi+/fv+8Rpr22TqItOTk5WpmJY2E6btw49ncaFxfncDgCXKhUHN91VwEgRqX29nabzRYeHk5EQ4YMOXDgAK8rV1RUzJs3zxXNHrfz3WFhymZmWZj++uuvvErSOo3OxLW2tooRpvKtu2qa3mP00qVLL730kivpHjx4wOWy7geysdYIvl7h3r17HmGqh8eYe+ZwOJ599lntzsS1trba7XZXm7b4+HgNhal8664C0G+Mup/6M3r06Pz8fF5X5tgawT1MDQZDamqqPsO0urp6+fLl7CNdtGhRVVUVryvv3bu3sLCQ19W8wcKUTUoQUUJCgvrDVKZ1V2HoNEYvXrzIzuVlG64fPXrE5bIytUa4d++e1Wpl0w4sTJV9rKeXORwOtpWW70zcnTt33nrrLSKKjY3t/edMtRKm8q27ikR3MdrS0rJx48aQkBAiGjduHMcdmcXFxbK2Rrh7967Vag0LC3OF6e+//873S6hNVVXV66+/zoImJSXlr7/+4nVl1yKJ0WhUcJGEhemwYcPY/2NiYqKqwtSj2wqvdVfx6CtGCwsLJ02aRERBQUEcT/3xOJBN1tYIOglTn55w8MmdO3fefPNNVS2SPHnyxD1MZ8yYkZOTo2xJ8q27CkkvMep+6s+ECRM4HlhXVFTETkfvzdYItbW1rjANCgpKTU0tKirqha/bOyoqKlx9j1NTU2/fvs3lsipfJGFhOnToUMXDVKZ1V4HpIkbPnDnjOvXHarXy6vWoeGsEjzA1mUx//PFHL9fAF3vCgc3EDR48OCsri9eV3XdAqHmRpKmpyWazucJ05syZvRmm8q27ik3wGHU/9Sc+Pp7j0+zqaY1QU1NjtVpDQ0O1HqZlZWVz5szhPhOnxUWSx48f22y2IUOGsE8jOTm5F8K0uLhYjnVXPRA5Ro8cOTJ69GjiffShezSrpzXCzZs3LRaLe5hq5dF06d9BECt+6NCh33//Pa8rd9eSXhNYmA4ePFjuMPWY3MdJuL4SM0Y9Tv3huAij8tYIncP06tWrShf1FCUlJXLMxLFFkp5b0muCR5jOmjUrwKZSHmRad9UVAWP08OHDbKMI31N/GhoaXNGs8tYIN27csFgsbIZLzWHqPggaM2bMjz/+yOvKPrWk14TOrWgCD1OPdVec0+g3oWL04cOHrlN/Zs6cyXGK0HUgm4ZaI3QO02vXrild1H8uXrw4depUWXdA+NSSXhM49vVy77bCcd1Vn8SJ0ZycHPbkHd9Tf7TeGqGqqspsNgcHB7N/A9LS0hQ/08xjBwTHNioeLelFXSTp3NfLp89QqW4rAhMhRmtqalauXMm+pV555RWON7DCtEZQT5gWFBS4z8TxesKBb0t6Tejc18ubR+7y8/PlWHfVOc3HqOvUH6PRaLPZeJ36o9ED2Xp2/fp1jzAtLy/vta/uPhM3ZcqUn3/+mdeVZWpJrwnet6JRVbcVwWg4Rl1HSxDRokWLbty4wevKYrdGUCRMz5w5w3pn8n3CAYskTOdWNB7/Ssm07gqMVmNUplN/9NMaobKy0iNMKyoq5PhCDQ0NFovFtQOC4xHUWCTx0GUrGvfJ/ZkzZ6qw24oAtBej169fX7hwIfu2WLp0qRyn/uinNUJFRYXZbGajub59+5rNZo6fpyRJR44cGTVqlKw7ILBI4uH+/fufffYZ27VFROw/wsPDt2/f7rqvqq+vLysr09ZmBDXTUozKd+qPe2uElJQUNZz605uuXLmSlpbmHqaBbzl3n4lLSkriuAPC1ZKeRbPadkAooqKioqCgoK6uzvU7rr5eK1eu7Lzu+tFHHxHR1q1be71SMWkmRv3ra/RU7tGswlN/ehPHMD106JBrJo7jEw5YJOkOO5q+8wmN9fX1ra2tne+rNm3aRESff/55bxUoOA3EaOB9jbrj0RqB14Fsmnb58mWPMPXpY3HfAZGcnMxxB8Thw4dV2JJeJViHFe9/NLZv305EFotF1qr0Q+0xyrGvkTuPU38cDgeXywqjtLTUFab9+vXzMkw9nnCQYwcEFkm6tGrVKiLavXu3l6/fs2cPEa1atUrWqvRDvTEqU18jSZLKysrkaEkvHhambCWHhemdO3e6fGVNTc2KFSvYRzp79myOu05l2pwmmHXr1hHRtm3bvHz9vn37iGj58uWyVqUfKo3RkpISOfoauR/IhtYIXrp06ZLJZGIzkuHh4RaLxSNM3fsa8d0BYTKZWDTz3Zwmni+++IKINm3a5OXrjx49SkTz58+XtSr9UF2Mepz6w7GvEVojBKKkpMQVphERERaLpbq62r2v0eLFizk+4aD1lvS9bOvWrUT04Ycfevn68+fPE9G0adNkrUo/1BWjRUVF7qf+yNFyju+BbHpz4cKFN954wzUyZS3PBg0axPFIeY+W9Bw3pwls165dRLR69WovX3/16lUiio6OlrUq/VBLjHZ0dGzYsIGtaUycOPHMmTO8rixTS3o9Ky4uNplMYWFhiYmJfPsaybQ5TXjfffcdEa1cudLL11dXV7PFVVmr0g+1xKgkSe+8806fPn049jWSryU9SJJ0+/bt+vp6XlerqqpybU7j25JeD44cOUJECxcu9PL1zc3NbNlQ1qr0Q0UxWltby7GvkUwHsgF38m1O04/CwkIimj59uvdvYXNc2APGhYpilBf5WtIDdzK1pNebK1euEFFsbKz3b2EreLW1tfJVpR9BJJazZ88mJSVt2bLFYDBYrdbS0lJXz15QFafTmZGRkZCQcPz4cdaS/uDBg+wRUfCV0WgkooaGBu/fwg6CevTokVw16Umw0gVw09zcvHnz5i+//NLpdMbHx+/Zs4c9eQoqVF5evnr16tOnTxORyWT66quv2OAI/MMy0acY9SN5oTuCxGh+fr7ZbL5582ZISMiGDRs2b97Mpn5Aha5du5aQkNDa2jpixAi73Z6SkqJ0RZoXERERHBzc3Nzc3t7O1lSfyo/khe5oPkYbGho++eSTXbt2SZKUlJS0Z88e9uQpqFZMTMyyZctCQ0NtNpurySUEwmAwREZG1tXVNTY2evmRIkY50naM5ubmrlmz5tatW6GhoZs2bfr444/ZyhKo3N69e/E3xZfRaKyrq2toaPApRjE3yoVWY7Suru7TTz/NyMggouTk5N27d8fGxipdFHgLGcqdr6NLzI1ypMmV+qysrIkTJ2ZkZLBTf06fPo0MBZ3zNUZxU8+RxkajtbW1H3zwwf79+4lo9uzZu3fvjo6OVrooAOWx0aX3N+m4qedIS6PRrKysuLi4/fv3swPZTp48iQwFYHBTryBtjEarq6vXrl2bnZ1NRIsXL7bb7azfJAAwuKlXkAZitLm5OSkp6e7du1FRUdu3b3/33XeVrghAdXy9ScdNPUcaiNHw8PD169efO3fObrcPHz5c6XIA1MjXm3Tc1HOkgRglIqvVyjoCAUCX/BuNIka50EY2IUMBeubr6BIxyhHiCUAE/i0xYW6UC8QogAh8jdHIyMigoKDHjx93dHTIWZcuIEYBRODr6NJgMPTv31+SpMbGRjnr0gXEKIAI/D65GdOjgUOMAojAj0xEjPKCGAUQgdFoNBgMrH+4l2/BKhMviFEAEQQHB4eHhzudzqamJi/fgifweUGMAggCj44qBTEKIAhfY/GZqKixAweGNDfLWZQuaGMzKAA8VeLIkSOfPJG8nuv8v8hIqq+nBw9krUoPEKMAgvifwUBVVeT9TbrRSEQ+vB66gZt6AFH4GosDBhARYaU+YIhRAFGwWMRotNchRgFE4WuM+vp66AZiFEAUbHTp/U06YpQTxCiAKPwbjWJuNGCIUQBRYG5UIYhRAFH4OrrETT0niFEAUeCBJ4UgRgFE4evoMiSEwsLo778J+0EDgxgFEIUfo0tMj/KAGAUQhR+ZiOlRHhCjAKLwIxMRozwgRgFEERZGfftSayu1tnr7Fqwy8YAYBRCIr/f1mBvlATEKIBA8OqoExCiAQPDoqBIQowACwX5QJSBGAQSCs/KUgBgFEIh/c6O4qQ8MYhRAIFipVwJiFEAguKlXAmIUQCC4qVcCYhRAILipVwJiFEAguKlXAmIUQCCIUSUgRgEE4utcZ0QEBQdTSwu1tclXlPAQowAC8WOuk72lsVGWevQBMQogED9u0rHKFDDEKIBAcHKzEhCjAAKJjKSgIGpqoo4Ob9+CR0cDhhgFEIjBQJGRJEk+zHXipj5giFEAsfh35ChiNACIUQCx+BqLAwcSEVrVB8IgSZLSNQAAP3Pn0qVLlJ9PL77o1etbWigsTOaaBIcYBQAICG7qAQACghgFAAgIYhRAB8rLyWD471dentIFCQUxCiC6HTsoOppyc0mS/vmVkkJr1ihdljiClS4AAOSUl0fr11NuLi1Z8t9vShIZDDR5Mq1bp1xl4sBKPYDQZs0iIjp3zvP3d+yg9esJP/484KYeQFx5eVRQQO+808UfLV1KRLRjRy9XJCTEKIC4srOJ/k1MDxMmEBE5HL1aj6AQowDiKi0l+jcxO0tOpoKC3ixHVIhRAHF5k5Ll5fLXITjEKABAQBCjAAABQYwCiCs5WekKdAExCiC6nmc/u1uAAq8hRgHE1eUToy4FBRiucoEYBRBXTAwR0eHDXfwRG6L2nLPgHcQogLiWLKHk5K6fsWfZ2uWT+eAjxCiA0DIzqaDAc9NneTmtX082GyZGucAJTwBCmzCBcnMpJYWI/jnPqbycoqPJbMbxTrzghCcAfTAY/vtvj3PzIDAYjQLoAwZMssHcKABAQBCjAAABQYwCAAQEMQoAEBDEKABAQBCjAAAB+X9E94fA3V89TAAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x7ad15f0>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('CC(=O)C=CC=C')\n",
    "mw = Chem.RWMol(m)\n",
    "mw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "Chem.Draw.MolToFile(mw, 'data/modifying_mols_1.png', size=(250, 250))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 替换原子：ReplaceAtom(index, newAtom, updateLabel, preserveProps)<br />\n",
    "index：要替换的原子索引<br />\n",
    "newAtom：新的原子对象"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x7ad15f0>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mw.ReplaceAtom(4, Chem.Atom(7))\n",
    "mw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "Chem.Draw.MolToFile(mw, 'data/modifying_mols_2.png', size=(250, 250))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 添加原子：AddAtom(atom)<br />\n",
    "atom：要添加的原子对象<br />\n",
    "返回值是新添加原子的索引"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x7ad15f0>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mw.AddAtom(Chem.Atom(6))\n",
    "mw.AddAtom(Chem.Atom(6))\n",
    "mw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "Chem.Draw.MolToFile(mw, 'data/modifying_mols_3.png', size=(250, 250))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 添加键：AddBond(beginAtomIdx, endAtomIdx, order)<br />\n",
    "beginAtomIdx：键的起始原子<br />\n",
    "endAtomIdx：键的末尾原子<br />\n",
    "order：键的类型<br />"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x7ad15f0>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mw.AddBond(6, 7, Chem.BondType.SINGLE)\n",
    "mw.AddBond(7, 8, Chem.BondType.DOUBLE)\n",
    "mw.AddBond(8, 3, Chem.BondType.SINGLE)\n",
    "mw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "Chem.Draw.MolToFile(mw, 'data/modifying_mols_4.png', size=(250, 250))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 删除原子：RemoveAtom()<br />\n",
    "传入原子索引<br />\n",
    "每次删除后，索引都会更新"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x7ad15f0>"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mw.RemoveAtom(0)\n",
    "mw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "Chem.Draw.MolToFile(mw, 'data/modifying_mols_5.png', size=(250, 250))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 其他一些Mol的方法，对RWMol也同样适用"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "O=CC1=NC=CC=C1\n",
      "SANITIZE_NONE\n",
      "O=Cc1ccccn1\n"
     ]
    }
   ],
   "source": [
    "print(Chem.MolToSmiles(mw))\n",
    "print(Chem.SanitizeMol(mw))\n",
    "print(Chem.MolToSmiles(mw))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- 修改完后，可以获取该分子的Mol对象：mw.GetMol()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rdkit.Chem.rdchem.Mol"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m_edit = mw.GetMol()\n",
    "type(m_edit)"
   ]
  }
 ],
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