Feed a string to a MolSupplier

FeedStringToMolSupplier.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from io import BytesIO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "sdf_block = \"\"\"\\\n",
    "CCO\n",
    "  Some API Name     3D\n",
    "\n",
    "  9  8  0  0  0  0  0  0  0  0999 V2000\n",
    "    0.9111   -0.0580    0.0833 C   0  -0.539850  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.5645   -0.3943   -0.0668 C   0   0.052144  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.3951    0.7270    0.2733 O   0  -0.556284  0  0  0  0  0  0  0  0  0  0\n",
    "    1.1128    0.3865    1.0677 H   0   0.172888  0  0  0  0  0  0  0  0  0  0\n",
    "    1.2517    0.6586   -0.6717 H   0   0.157527  0  0  0  0  0  0  0  0  0  0\n",
    "    1.5381   -0.9524   -0.0063 H   0   0.163812  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.8972   -1.1630    0.6576 H   0   0.138112  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.8158   -0.7181   -1.0929 H   0   0.106288  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.1410    1.5140   -0.2440 H   0   0.305363  0  0  0  0  0  0  0  0  0  0\n",
    "  1  2  1  0  0  0  0\n",
    "  1  4  1  0  0  0  0\n",
    "  1  5  1  0  0  0  0\n",
    "  1  6  1  0  0  0  0\n",
    "  2  3  1  0  0  0  0\n",
    "  2  7  1  0  0  0  0\n",
    "  2  8  1  0  0  0  0\n",
    "  3  9  1  0  0  0  0\n",
    "M  END\n",
    "\n",
    "> <Id>\n",
    "939090603255\n",
    "\n",
    "> <SMILES>\n",
    "CCO\n",
    "\n",
    "> <Atoms>\n",
    "9\n",
    "\n",
    "> <Bonds>\n",
    "8\n",
    "\n",
    "> <Chiral>\n",
    "false\n",
    "\n",
    "> <Energy>\n",
    "-14261.901904236434\n",
    "\n",
    "> <Enthalpy (kcal/mol @ 298 K)>\n",
    "47.3436630758052\n",
    "\n",
    "> <Gibbs energy (kcal/mol @ 298 K)>\n",
    "29.8354953675966\n",
    "\n",
    "> <Zero point energy (kcal/mol @ 0 K)>\n",
    "44.196874495459795\n",
    "\n",
    "> <Molecular dipole (X, Y, Z)>\n",
    "-1.761841, 0.283414, 1.207075\n",
    "\n",
    "> <Source energy>\n",
    "-14259.552636725288\n",
    "\n",
    "$$$$\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With `Chem.ForwardSDMolSupplier` and a file-like object:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-14259.552636725288\n"
     ]
    }
   ],
   "source": [
    "mol = None\n",
    "with BytesIO(sdf_block.encode(\"UTF-8\")) as hnd:\n",
    "    for mol in Chem.ForwardSDMolSupplier(hnd):\n",
    "        print(mol.GetProp(\"Source energy\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With `Chem.SDMolSupplier.SetData()`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-14259.552636725288\n"
     ]
    }
   ],
   "source": [
    "suppl = Chem.SDMolSupplier()\n",
    "suppl.SetData(sdf_block)\n",
    "for mol in suppl:\n",
    "    print(mol.GetProp(\"Source energy\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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