comparison of rdChemReactions and editable mol

transform_mol.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from rdkit.Chem import rdChemReactions\n",
    "# from rdkit.Chem import EditableMol\n",
    "# Greg suggested to use RWMol instead of EditableMol\n",
    "from rdkit.Chem import RWMol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles('c1ccncc1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.AddHs(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "AllChem.EmbedMolecule(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "rxn = rdChemReactions.ReactionFromSmarts('[cH:1]>>[c:1](F)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "ps = rxn.RunReactants([mol,])\n",
    "mols = [p[0] for p in ps]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "m1 = mols[0]\n",
    "atoms = m1.GetAtoms()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "c1 = m1.GetConformer()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "C -0.10442110178100782 1.1575512339607825 0.04302466892403103\n",
      "F 0.0 0.0 0.0\n",
      "C -1.2030075044841062 0.34465105595859574 0.03016638855796142\n",
      "C 1.1361907036364194 0.5520704798363746 0.0029571500829689975\n",
      "H -0.1931426564236893 2.230796065998375 0.08277829197701424\n",
      "C -1.1017065279900353 -1.0368098339316463 -0.020831317255544882\n",
      "H -2.1800029609544134 0.8221660760383411 0.06174518137034971\n",
      "C 1.2528495602123897 -0.8282336133624136 -0.048225689649723444\n",
      "H 2.03804265885753 1.1830130796873037 0.012207819007894026\n",
      "N 0.12367737693039976 -1.5610454231756343 -0.057760303715081285\n",
      "H -2.01570281978104 -1.608727752662867 -0.027796083317350433\n",
      "H 2.247223271777564 -1.2554313683472025 -0.07826610598251835\n"
     ]
    }
   ],
   "source": [
    "for i in range(c1.GetNumAtoms()):\n",
    "    pos = c1.GetAtomPosition(i)\n",
    "    print(atoms[i].GetSymbol(), pos.x, pos.y, pos.z)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "q = Chem.MolFromSmarts('[H](c)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "maches = mol.GetSubstructMatches(q)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "atoms = mol.GetAtoms()\n",
    "mols2 = []\n",
    "for m in maches:\n",
    "    emol = RWMol(mol)\n",
    "    emol.ReplaceAtom(m[0], Chem.Atom(9))\n",
    "    res = emol.GetMol()\n",
    "    mols2.append(res)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol2 = mols2[0]\n",
    "c2 = mol2.GetConformer()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "C -0.10442110178100782 1.1575512339607825 0.04302466892403103\n",
      "C -1.2030075044841062 0.34465105595859574 0.03016638855796142\n",
      "C -1.1017065279900353 -1.0368098339316463 -0.020831317255544882\n",
      "N 0.12367737693039976 -1.5610454231756343 -0.057760303715081285\n",
      "C 1.2528495602123897 -0.8282336133624136 -0.048225689649723444\n",
      "C 1.1361907036364194 0.5520704798363746 0.0029571500829689975\n",
      "F -0.1931426564236893 2.230796065998375 0.08277829197701424\n",
      "H -2.1800029609544134 0.8221660760383411 0.06174518137034971\n",
      "H -2.01570281978104 -1.608727752662867 -0.027796083317350433\n",
      "H 2.247223271777564 -1.2554313683472025 -0.07826610598251835\n",
      "H 2.03804265885753 1.1830130796873037 0.012207819007894026\n"
     ]
    }
   ],
   "source": [
    "atoms2 = mol2.GetAtoms()\n",
    "for i in range(c2.GetNumAtoms()):\n",
    "    pos = c2.GetAtomPosition(i)\n",
    "    print(atoms2[i].GetSymbol(), pos.x, pos.y, pos.z)"
   ]
  },
  {
   "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": "3.6.8"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}