PDB atom names

PDB_atom_names.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "m = Chem.MolFromSmiles('CCC')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "for i in range(m.GetNumAtoms()):\n",
    "    m.GetAtomWithIdx(i).SetProp('molFileAlias', 'C' + str(i + 1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
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   "outputs": [],
   "source": [
    "w = Chem.SDWriter(sys.stdout)"
   ]
  },
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   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "w.write(m)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          \n",
      "\n",
      "  3  2  0  0  0  0  0  0  0  0999 V2000\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  1  0\n",
      "A    1\n",
      "C1\n",
      "A    2\n",
      "C2\n",
      "A    3\n",
      "C3\n",
      "M  END\n",
      "$$$$\n"
     ]
    }
   ],
   "source": [
    "w.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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