RenumberAtoms2

RenumberAtoms2.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "m1 = Chem.AddHs(Chem.MolFromSmiles('NC(C)C(=O)O'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "for a in m1.GetAtoms():\n",
    "    a.SetAtomMapNum(a.GetIdx())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f7c031dc210>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "ps = Chem.SmilesParserParams()\n",
    "ps.removeHs = False\n",
    "m2 = Chem.MolFromSmiles(Chem.MolToSmiles(m1), ps)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f7c031eb0d0>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 0 N\n",
      "1 1 C\n",
      "2 2 C\n",
      "3 9 H\n",
      "4 10 H\n",
      "5 11 H\n",
      "6 3 C\n",
      "7 4 O\n",
      "8 5 O\n",
      "9 12 H\n",
      "10 8 H\n",
      "11 6 H\n",
      "12 7 H\n"
     ]
    }
   ],
   "source": [
    "for a in m2.GetAtoms():\n",
    "    print(a.GetIdx(), a.GetAtomMapNum(), a.GetSymbol())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Quoting from the RDKit docs:<br />\n",
    "http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=renumberatoms#rdkit.Chem.rdmolops.RenumberAtoms<br />\n",
    "Returns a copy of a molecule with renumbered atoms<br />\n",
    "ARGUMENTS:\n",
    "* `mol`: the molecule to be modified\n",
    "* `newOrder`: the new ordering the atoms (should be `numAtoms` long) for example: if newOrder is `[3,2,0,1]`, then atom `3` in the original molecule will be atom `0` in the new one\n",
    "\n",
    "So you need to resort `new_order` as follows:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "new_order = tuple(zip(*sorted([(j, i) for i, j in enumerate([a.GetAtomMapNum() for a in m2.GetAtoms()])])))[1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(0, 1, 2, 6, 7, 8, 11, 12, 10, 3, 4, 5, 9)"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_order"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]\n"
     ]
    }
   ],
   "source": [
    "m3 = Chem.RenumberAtoms(m2, new_order)\n",
    "print([a.GetAtomMapNum() for a in m3.GetAtoms()])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now the order is the expected one:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 0 N\n",
      "1 1 C\n",
      "2 2 C\n",
      "3 3 C\n",
      "4 4 O\n",
      "5 5 O\n",
      "6 6 H\n",
      "7 7 H\n",
      "8 8 H\n",
      "9 9 H\n",
      "10 10 H\n",
      "11 11 H\n",
      "12 12 H\n"
     ]
    }
   ],
   "source": [
    "for a in m3.GetAtoms():\n",
    "    print(a.GetIdx(), a.GetAtomMapNum(), a.GetSymbol())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.11"
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 },
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