Morgan fingerprint fragment retrieval fails

Morgan_fingerprint_fragments.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Morgan Fingerprint Fragments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import PandasTools\n",
    "from rdkit.Chem import Draw\n",
    "# utilities\n",
    "from pprint import pprint"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol1 = Chem.MolFromSmiles('Oc1ccc(NC(=O)C)cc1')\n",
    "mol2 = Chem.MolFromSmiles('O=C(Nc1ccccc1)C')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Warning: unable to load font metrics from dir c:\\users\\shojiro_shibayama\\miniconda3\\envs\\cheminfo\\lib\\site-packages\\rdkit\\sping\\PIL\\pilfonts\n"
     ]
    },
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x24e7d3678f0>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x24e7f7d89e0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "[Visualize molecules](http://cheminformist.itmol.com/TEST/wp-content/uploads/2015/04/ipython01.html)\n",
    "\n",
    "```python\n",
    "from rdkit.Chem import Draw\n",
    "legends = [m.GetProp('_Name') for m in ms[:10]]\n",
    "Draw.MolsToGridImage(ms[:10],molsPerRow=5,subImgSize=(150,150),legends=legends)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "[FindAtomEnvironmentOfRadiusN](https://programtalk.com/python-examples/rdkit.Chem.FindAtomEnvironmentOfRadiusN/)\n",
    "\n",
    "```python\n",
    "env = Chem.FindAtomEnvironmentOfRadiusN(mol, radius, root)\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x24e7cd20850>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fragment_counts = {}\n",
    "n_radius = 2\n",
    "n_bits = 1024\n",
    "AllChem.GetHashedMorganFingerprint(mol1, n_radius, nBits=n_bits, bitInfo=fragment_counts)\n",
    "fragments = []\n",
    "for atom_pair in list(fragment_counts.values()):\n",
    "    atom_id = atom_pair[0][0]\n",
    "    radius = atom_pair[0][1]\n",
    "    env = Chem.FindAtomEnvironmentOfRadiusN(mol1, radius, atom_id)\n",
    "    sub_struct = Chem.PathToSubmol(mol1, env)\n",
    "    fragments.append(sub_struct)\n",
    "fragments[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<PIL.Image.Image image mode=RGBA size=900x600 at 0x24E7CD27588>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Draw.MolsToGridImage([Chem.MolFromSmiles(Chem.MolToSmiles(Chem.AddHs(mol))) for mol in fragments], \n",
    "                     molsPerRow=6, \n",
    "                     subImgSize=(150, 150))"
   ]
  }
 ],
 "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": "3.6.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}

Morgan_fingerprint_fragments_revision.ipynb