ptosco/substructureMatchWithExplicitHs.ipynb

## substructureMatchWithExplicitHs.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.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "smiles1 = \"ClCc1[nH]c(c2n1)cccc2\"\n",
    "smiles2 = \"c1(I)cc(I)c2c(c1)nc(CCl)[nH]2\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol1 = Chem.MolFromSmiles(smiles1)\n",
    "mol2 = Chem.MolFromSmiles(smiles2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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I9OnTXV1KtaWlpWG32yvcqf3NN9+koKCApxvDeokyBAUFVRiEZgkHq9VKQUEBv/56bTeE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\nMTUFoYiImJqCUERETO3/A3OgaPYst2m8AAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x283cfa0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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dkKhKxGntaay+sFrqOGYVFbUQ06cvRgt39Ol01Go16uvrUV5eLnUUs1MoFOjfv3+roz7e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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x28c4050>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "order_mol2 = mol2.GetSubstructMatch(mol1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(0, 11),\n",
       " (1, 10),\n",
       " (2, 9),\n",
       " (3, 8),\n",
       " (4, 6),\n",
       " (5, 5),\n",
       " (6, 12),\n",
       " (7, 7),\n",
       " (8, 0),\n",
       " (9, 2),\n",
       " (10, 3)]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[t for t in enumerate(order_mol2)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol1h = Chem.AddHs(mol1, explicitOnly = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol2h = Chem.AddHs(mol2, explicitOnly = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "order_mol2h = mol2h.GetSubstructMatch(mol1h)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(0, 11),\n",
       " (1, 10),\n",
       " (2, 9),\n",
       " (3, 12),\n",
       " (4, 5),\n",
       " (5, 6),\n",
       " (6, 8),\n",
       " (7, 3),\n",
       " (8, 2),\n",
       " (9, 0),\n",
       " (10, 7)]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[t for t in enumerate(order_mol2h) if mol1h.GetAtomWithIdx(t[0]).GetAtomicNum() > 1\n",
    "and mol2h.GetAtomWithIdx(t[1]).GetAtomicNum() > 1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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