ptosco/fragment_on_given_atom.ipynb

## fragment_on_given_atom.ipynb
{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import rdmolops\n",
    "from rdkit.Chem import rdFMCS\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles('CCC1CCCCC1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAPf0lEQVR4nO3de0zV9ePH8Rferygk\npqU4rbygCYaicA6KxSlFUNTWYllt6krsD5e51qY2arb1h0xrreumuVlueYkTghfwFhxMAUlnXjIp\nrZiAhnhryO33z8+zr+b36yXg/YH38/F3wos/7On7HD7vE9DY2NgoAAAs1c70AAAATCKEAACrEUIA\ngNUIIQDAaoQQAGA1QggAsBohBABYjRACAKxGCAEAViOEAACrEUIAgNUIIQDAaoQQAGA1QggAsBoh\nBABYjRACAKxGCAEAViOEAACrEUIAgNUIIQDAaoQQAGA1QggAsBohBABYjRACAKxGCAEAViOEAACr\nEUIAgNUIIQDAaoQQAGA1QggAsBohBABYjRACAKxGCAEAViOEAACrEUIAgNUIIQDAaoQQwF25fv26\n6QlAsyCEAG6rrKxMmZmZeuutt+R2uxUcHKzZs2frypUrpqcBTSqgsbGx0fQIAGZdv35dhw4d0v79\n+1VQUKCCggKVlZVp4MCBiomJUXR0tMLDw7V48WIFBQUpOztbnTt3Nj0baBKEELBQeXm5Dh48qOLi\nYvl8Pvl8PtXW1mro0KFyu91yuVyKjY3V4MGDb/pzlZWVio2N1YgRI7Rp0ya1b9/e0E8ANB1CCLRx\n9fX1OnHihD96+fn5On78uAIDAzVu3Di5XC5//Lp27XrHr1daWqrY2Fh5PB6tXbtWAQEBLfBTAM2H\nEAJtzOXLl3XgwAHl5+f743fp0iUNGzZMkZGR/uiFhYXdd8SOHj2qSZMmacGCBXrvvfea+CcAWlYH\n0wMA/DulpaU3Ra+kpETdu3fX6NGj5Xa79corr8jtdisoKKjJvueoUaOUnZ2t+Ph4BQUFacmSJU32\ntYGWxokQaEWuXr2qkpISf/T27Nmj8+fPa8iQIXK5XP4T35gxY9SuXfP/Unhubq6SkpL00Ucfad68\nec3+/YDmQAgBBysrK/O/r1dcXKzCwkJ17NhRERER/ujFxcUpJCTE2MYtW7YoJSVFX3/9tWbPnm1s\nB3C/CCHgQGvWrNHSpUt17tw5DRo0SC6XS9HR0f7HGDp0cNa7Gp988olef/11ZWZmyuPxmJ4D3BNC\nCDjM6dOn9dhjj+mTTz5RUlKSHnroIdOT7sq7776r9PR07d69W5GRkabnAHfNWf+sBKCMjAyFh4fr\n1VdfNT3lnrz99tuqrq7WlClTlJeXp+HDh5ueBNwVQgg4jNfr1YwZM0zPuC8rV65UVVWVPB6PfD6f\nQkNDTU8C7oiXRgEHuXDhgh588EEVFRUpIiLC9Jz7Ul9fr+eee05Hjx5VXl6e+vbta3oS8D9x6Tbg\nIF6vVwMGDFB4eLjpKfetffv2Wr9+vfr166fExEQu6YbjEULAQbxer5KTk1v9tWVdu3ZVZmam6urq\nNGPGDNXU1JieBPxXhBBwiGvXrik3N7fVvj94q8DAQO3YsUN//vmnnn/+edXV1ZmeBNwWIQQcYseO\nHerSpYtiY2NNT2kyISEhysnJUXFxsebPny9+JQFORAgBh/B6vUpMTHTcw/L/1sCBA5Wdna3MzEwt\nW7bM9BzgH9rW3ziglaqvr1dWVpY+++wz01OaBZd0w8kIIeAAeXl5unLlSpu+nmz8+PH69ttvlZSU\npKCgIC7phmMQQsABvF6vPB6PevbsaXpKs4qPj9dXX32llJQU9e7dm0u64Qi8Rwg4QGu+TeZezZo1\nS6tXr9YLL7ygnJwc03MAToSAaYcPH9aZM2c0bdo001NaTGpqqiorK/Xss89ySTeMI4SAYRkZGYqJ\niVG/fv1MT2lRXNINp+ClUcAwm14WvdXKlSuVlJQkj8ejM2fOmJ4DSxFCtJiamhp98MEHamhoMD3F\nMc6ePasff/xR06dPNz3FiICAAH3xxReKioqSx+NRRUWF6UmwECFEiykvL9f777+v1157zfQUx8jI\nyFBYWJiGDh1qeooxNy7p7t+/P5d0wwhCiBYTGhqqnJwcffPNN1q+fLnpOY5w45Jt2924pLu+vp5L\nutHiCCFa1KhRo5SVlaVVq1YpPT3d9ByjLl68qLy8PGvfH7xVYGCgsrKydO7cOfl8PtNzYBF+axQt\nbsKECcrIyFBiYqKCgoI0d+5c05OMyMzMVEhIiMaOHWt6imMEBQXpjz/+0PXr101PgUU4EcKI+Ph4\nrV27VgsWLNCWLVtMzzGirXz2YFPatWuXGhoaFBcXZ3oKLMKJEMakpKSoqqpKc+bM0fbt2zVx4kTT\nk1pMTU2Ndu7cqU2bNpme4iher1fTpk1Tly5dTE+BRTgRwqiFCxfqzTffVFJSkg4dOmR6TovJyclR\nu3btOPn8h4aGBmVmZvKeKVocJ0IYl5aWpkuXLvlvGBk2bJjpSc3O6/UqISFBnTp1Mj3FMQ4cOKDz\n589r6tSppqfAMpwI4Qjp6emaNm2aPB6Pzp49a3pOs2poaNDWrVs5+dzC6/Vq8uTJ6t27t+kpsAwh\nhCMEBATo888/1+jRo5WQkKALFy6YntRs9u/fr6qqKk4+t8jIyOAfBzCCEMIxOnbsqI0bNyo4OFgJ\nCQlt9oaRGyefwMBA01Mc49SpU/r555+tvWoOZhFCOMqNG0Zqa2uVnJzcJm8YsfmS7f9m8+bNGjt2\nrAYMGGB6CixECOE4vXr10vbt2/X7778rJSVF9fX1pic1mWPHjunUqVNKTEw0PcVR+McBTCKEcKS+\nfftq27Zt+uGHH9rUJd0ZGRmKiori5PMfysvLdfDgQe5chTGEEI41ZMgQ7dy5Uxs3bmwzl3Rz8vmn\njIwMDR48WCNHjjQ9BZbiOUI42o1LuuPj49W7d2+98cYbpifdt7KyMhUWFurLL780PcVRvF6vZs6c\naXoGLMaJEI5345LupUuXas2aNabn3Dev16tHHnlEI0aMMD3FMa5cuaI9e/ZwSoZRhBCtQlu4pNvr\n9WrWrFmmZzhKdna2AgMDFR0dbXoKLEYI0WqkpKRo9erVmjNnjvbt22d6zj0pLy/n5HMbXq9XSUlJ\nat++vekpsBjvEaJVWbhwoSoqKjR9+nTt2bNHTzzxhOlJt1VWVqbi4mL5fD7l5+erqKhIffv2bZPP\nRd6v2tpabdu2TevWrTM9BZYLaGxsbDQ9ArhXixcv1vr16x1xSXddXZ1Onjzpj15+fr5+/fVX9e/f\nX5GRkXK73XK5XNqxY4c+/PBD7d69W5GRkUY3O0FOTo6Sk5NVWVmpbt26mZ4Di3EiRKuUnp6uqqoq\neTwe5efnKzQ0tMW+d3V1tQoLC5Wfny+fzyefz6fa2loNHTpUbrdbaWlpioyM/MfjAG63W1evXtXU\nqVP1/fffa/jw4S222Ym8Xq+mTJlCBGEcJ0K0WrW1tZo5c6Z+++037du3Tw888ECTf4/6+nqdOHHi\nppc5jx8/rsDAQI0bN04ul0tut1sxMTF39T/0xsZGzZ07V7t27WrxgDtJY2OjBg0apBUrVuill14y\nPQeWI4Ro1f7++28988wzqqmp0a5du9SjR49/9fUuX76sw4cP+6Pn8/lUVVWlIUOG+KPncrkUFham\ngICA+/oeLRFwpysqKtKECRN07tw59enTx/QcWI4QotWrrq7W5MmTFRwcrKysLHXu3Pmu/2xpaany\n8/P9J76SkhJ169ZN4eHh/ui5XC4FBwc36eamDnhrs3z5cvl8Pu3evdv0FIAQom2oqKhQbGyswsLC\ntGnTptv+Ov7Vq1dVUlLij97evXtVWVmp/v37+6Pndrs1ZswYtWvX/E8W3Qh4UFCQsrOz7yngrd3j\njz+u+fPna9GiRaanAIQQbUdpaancbremT5+uTz/99B+PMBQWFqpDhw4aM2aM/7c54+LiFBISYmzz\n3QS8rTl9+rQeffRRlZaWavDgwabnAIQQbcuRI0f05JNPqn379qqoqFBoaKhiYmIUHR2tmJgYRURE\nqEMHZ/2y9K0Bb+vS09O1fv16lZSUmJ4CSOLxCbQxo0ePVmlpqfLy8hQREaGHH37Y9KQ7uvEpG5Mm\nTVKfPn20YsUK05OaFZ/AAafhRAg4xIEDB/TUU0/pnXfeadWfsvG/nD9/Xv369VNRUZEiIiJMzwEk\ncSIEHGP8+PHKyMhQYmKievfurXnz5pme1OS+++47DRgwQOHh4aanAH5cug04yI1P2UhNTdXmzZtN\nz2lyXq9XycnJ9/0MJtAcOBECDpOSkqKLFy/qxRdfVJ8+fTRp0iTTk5rEtWvXlJubq61bt5qeAtyE\nEAIOlJqaqvLycsd/ysa92LFjh7p06aLY2FjTU4CbEELAodLS0nTp0iVNmTKlTVzS7fV6lZiY6LjH\nVwDeIwQcLD09XdOmTdPTTz+ts2fPmp5z3+rr65WVlcVjE3AkHp8AHK4tXNK9d+9eJSQkqLKyUt27\ndzc9B7gJJ0LA4Tp27KiNGzcqODhYCQkJunLliulJ98zr9crj8RBBOBIhBFqBrl27KjMzU7W1tZox\nY4ZqampMT7orly5dUk5OjjZu3Kjp06ebngPcFi+NAq2I0y/p/uWXX1RQUKD9+/eroKBAP/30k7p1\n66bU1FQtW7ZMPXv2ND0R+AdCCLQyTrmku7a2VkeOHPF/gPG+fftUUVFx08daRUZGKioqSp06dTK2\nE7gTQgi0QkePHtWkSZOUmpraYpd03/qxVkVFRWpoaNDo0aP90YuLi1NoaGiL7AGaCiEEWqnmvKS7\nrq5OJ0+e9EevuLhYx44dU//+/f2f5ehyuTR27Fh16dKlSb830NIIIdCK5ebmKjExUR9//LHmzp17\n31+nurpahYWF/pc5CwoKVFNTo2HDht30MufIkSObcD3gDIQQaOU2bNigl19+WRs2bNDs2bPv+N/X\n19frxIkTN73Mefz4cfXs2VNRUVH+6E2cOFG9evVqgZ8AMIu7joBW7k6XdF++fFmHDx/2R6+goEB/\n/fWXhgwZIpfLpUWLFsnlciksLIxPhYCVOBECbURaWppWrVqldevW6eLFi/7HGI4dO6YePXpowoQJ\nio6OVnR0tCZMmMBpD/h/hBBoQ5YsWaKcnBxVVlb639tzu90aM2aM2rXj/gzgdggh0MZcv36d5/aA\ne0AIAQBW47USAIDVCCEAwGqEEABgNUIIALAaIQQAWI0QAgCsRggBAFYjhAAAqxFCAIDVCCEAwGqE\nEABgNUIIALAaIQQAWI0QAgCsRggBAFYjhAAAqxFCAIDVCCEAwGqEEABgNUIIALAaIQQAWI0QAgCs\nRggBAFYjhAAAqxFCAIDVCCEAwGqEEABgNUIIALAaIQQAWI0QAgCsRggBAFYjhAAAqxFCAIDVCCEA\nwGqEEABgNUIIALDa/wGasZh6JfKNAAAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x2eb8440>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "molCopy = Chem.Mol(mol)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Be 2 the given atom index:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "givenIdx = 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "givenAtom = mol.GetAtomWithIdx(givenIdx)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "givenAtom.SetBoolProp('__givenAtom', True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "rwMol = Chem.RWMol(mol)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Cleave bonds to neighbours:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "for nbr in givenAtom.GetNeighbors():\n",
    "    rwMol.RemoveBond(givenIdx, nbr.GetIdx())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Fragment, then remove the fragment with the given atom:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "frags = list(rdmolops.GetMolFrags(rwMol.GetMol(), asMols = True))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(frags)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(len(frags)):\n",
    "    if (frags[i].GetNumAtoms() == 1 and frags[i].GetAtomWithIdx(0).HasProp('__givenAtom')):\n",
    "        del frags[i]\n",
    "        break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(frags)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAACcklEQVR4nO3XQQ3DQBAEQTsKA6M1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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x2764c80>"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAJuElEQVR4nO3dTWwUBRjG8afYEj4K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\njRACAFwjhAAA1wghAMC13wH/KvDwxmenYgAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x303cd70>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags[1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Alternatively, if you are interested in the dummy labels, you can use the same approach with rdmolops.FragmentOnBonds():"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "givenAtom = molCopy.GetAtomWithIdx(givenIdx)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "givenAtom.SetBoolProp('__givenAtom', True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "bonds = []\n",
    "for nbr in givenAtom.GetNeighbors():\n",
    "    bonds.append(molCopy.GetBondBetweenAtoms(givenIdx, nbr.GetIdx()).GetIdx())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "fragmentedMol = rdmolops.FragmentOnBonds(molCopy, bonds)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAT1UlEQVR4nO3de1RVdd4G8IergCJK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\nrkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x2eb8520>"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fragmentedMol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Fragment, then remove the fragment with the given atom:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "frags = list(rdmolops.GetMolFrags(fragmentedMol, asMols = True))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(frags)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "found = False\n",
    "for i in range(len(frags)):\n",
    "    for a in frags[i].GetAtoms():\n",
    "        if (a.HasProp('__givenAtom')):\n",
    "            found = True\n",
    "            del frags[i]\n",
    "            break\n",
    "    if (found):\n",
    "        break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(frags)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAHdUlEQVR4nO3df4jXhR3H8dfVtZu2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\nAEoTQgBK+xcnyeNRPQzfPQAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x303cc80>"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
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      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x303cf50>"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags[1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}