{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 168,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole, MolsToGridImage"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test cases for fragmentation with FragmentOnBonds"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Test case one"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In the following example, the fragments are not sanitized appropriately."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 205,
   "metadata": {},
   "outputs": [],
   "source": [
    "smiles1 = 'C[C@H]1C[C@H]1C'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 206,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f882d0d5350>"
      ]
     },
     "execution_count": 206,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1 = Chem.MolFromSmiles(smiles1)\n",
    "mol1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 207,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5"
      ]
     },
     "execution_count": 207,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bonds1 = mol1.GetBonds()\n",
    "len(bonds1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 208,
   "metadata": {},
   "outputs": [],
   "source": [
    "b = 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 209,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f882d521120>"
      ]
     },
     "execution_count": 209,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "f_mol1 = Chem.FragmentOnBonds(mol1, (b,))\n",
    "f_mol1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There is a carbon at to position 1 which is not saturated with hydrogen explicitly"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 210,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f882d521120>"
      ]
     },
     "execution_count": 210,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "for atom in f_mol1.GetAtoms():\n",
    "    if (atom.GetAtomicNum()==0):\n",
    "        atom.SetAtomicNum(1)\n",
    "        atom.SetIsotope(0)\n",
    "f_mol1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 211,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7F882D076D90>"
      ]
     },
     "execution_count": 211,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frags1 = Chem.GetMolFrags(f_mol1,asMols=True, sanitizeFrags=True)\n",
    "MolsToGridImage(frags1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This persists even after sanitizing the fragment (now the carbon atom is on the left of the molecule and has only one hydrogen atom attached)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Test case two"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 212,
   "metadata": {},
   "outputs": [],
   "source": [
    "smiles2 = 'N#CC1(C#N)[C@H]2C[C@@H]1N2'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 213,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f882d0789e0>"
      ]
     },
     "execution_count": 213,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol2 = Chem.MolFromSmiles(smiles2)\n",
    "mol2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 214,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "10"
      ]
     },
     "execution_count": 214,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bonds2 = mol2.GetBonds()\n",
    "len(bonds2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 215,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f882d07e0d0>"
      ]
     },
     "execution_count": 215,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "b = 1\n",
    "f_mol2 = Chem.FragmentOnBonds(mol2, (b,))\n",
    "f_mol2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The carbon in the smaller fragment is not saturated"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 216,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f882d07e0d0>"
      ]
     },
     "execution_count": 216,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "for atom in f_mol2.GetAtoms():\n",
    "    if (atom.GetAtomicNum()==0):\n",
    "        atom.SetAtomicNum(1)\n",
    "        atom.SetIsotope(0)\n",
    "f_mol2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 217,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7F882D07C6D0>"
      ]
     },
     "execution_count": 217,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "MolsToGridImage(Chem.GetMolFrags(f_mol2,asMols=True,sanitizeFrags=True))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now they are sanitized correctly "
   ]
  },
  {
   "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": "3.7.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}