adelenelai/DoubleBondStereo_MolBlockOutput.ipynb

## DoubleBondStereo_MolBlockOutput.ipynb
{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2020.03.1'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import rdkit\n",
    "rdkit.__version__"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import rdkit.Chem as Chem\n",
    "from rdkit.Chem import AllChem, Draw"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## First, let's inspect basic 'behaviour' of the Bond Block using simple 1,2-difluoroethene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x11935d670>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#cis\n",
    "a1 = Chem.MolFromSmiles('F\\C=C/F')\n",
    "a1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  4  3  0  0  0  0  0  0  0  0999 V2000\n",
      "   -0.7500   -1.2990    0.0000 F   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",
      "    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2500   -1.2990    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  2  0\n",
      "  3  4  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "a1_block = Chem.MolToMolBlock(a1)\n",
    "print(a1_block)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x11935c030>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#trans\n",
    "a2 = Chem.MolFromSmiles('F/C=C/F')\n",
    "a2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  4  3  0  0  0  0  0  0  0  0999 V2000\n",
      "   -0.7500   -1.2990    0.0000 F   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",
      "    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2500    1.2990    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  2  0\n",
      "  3  4  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "a2_block = Chem.MolToMolBlock(a2)\n",
    "print(a2_block)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "#undefined\n",
    "a3 = Chem.MolFromSmiles('FC=CF') "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  4  3  0  0  0  0  0  0  0  0999 V2000\n",
      "   -1.2990    0.7500    0.0000 F   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",
      "    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.5981   -0.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  2  3\n",
      "  3  4  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "a3_block = Chem.MolToMolBlock(a3)\n",
    "print(a3_block)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "When stereochemistry is explicitly defined (cis/trans), the double bond stereo has value 0 (`Use x-, y-, z-coords from atom block to determine cis or trans`).\n",
    "\n",
    "When stereochemistry is undefined, the double bond stereo has value 3 (`Cis or trans (either) double bond`).\n",
    "\n",
    "### What about 1,1-difluoroethene (symmetrical)?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1195108f0>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "b = Chem.MolFromSmiles('FC(F)=C')\n",
    "b"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  4  3  0  0  0  0  0  0  0  0999 V2000\n",
      "    2.5981   -0.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2990    2.2500    0.0000 F   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",
      "  2  4  2  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "b_block = Chem.MolToMolBlock(b)\n",
    "print(b_block)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Again, double bond stereo = 0.\n",
    "\n",
    "### 1,1-Difluoropropene"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x119512350>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c = Chem.MolFromSmiles('CC=C(F)F')\n",
    "c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  5  4  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",
      "    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.5981   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    3.8971    0.7500    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.5981   -1.5000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  2  3\n",
      "  3  4  1  0\n",
      "  3  5  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "c_block = Chem.MolToMolBlock(c)\n",
    "print(c_block)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Observation: When there is a non-H group, it triggers the double bond stereo = 3. (Not sure if this is a 'rule' though.)\n",
    "\n",
    "## Now, try the example from J. Davidson"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x119518670>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('FC(F)=CC1=CC=CC=C1')\n",
    "m"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      " 10 10  0  0  0  0  0  0  0  0999 V2000\n",
      "    5.2500   -1.2990    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    3.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    3.0000   -2.5981    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    3.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.7500    1.2990    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",
      "  2  4  2  3\n",
      "  4  5  1  0\n",
      "  5  6  2  0\n",
      "  6  7  1  0\n",
      "  7  8  2  0\n",
      "  8  9  1  0\n",
      "  9 10  2  0\n",
      " 10  5  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "m_block = Chem.MolToMolBlock(m)\n",
    "print(m_block)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> This behaviour is maybe what I would expect if the bond was explicitly set using bond.SetStereo(Chem.BondStereo.STEREOANY), but in the absence of this I would expect the bond to default to STEREONONE, and I guess I would expect this to be bond stereo “0” in the output molblock.\n",
    "\n",
    "Let's check the bond stereo."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "q = Chem.MolFromSmarts(\"C=CF\")\n",
    "bo = m.GetBondBetweenAtoms(*m.GetSubstructMatch(q)[:2])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rdkit.Chem.rdchem.BondType.DOUBLE"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bo.GetBondType()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rdkit.Chem.rdchem.BondStereo.STEREONONE"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bo.GetStereo()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Indeed there is no stereo assigned. \n",
    "\n",
    "### But does STEREONONE necessarily translate to bond stereo value = 0 in the Bond Block?\n",
    "\n",
    "I suspect that this assumption is not valid. Having bond stereo value = 0 simply means `Use x-, y-, z-coords from atom block to determine cis or trans` according to the CTAB documentation."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### About coordinates determining cis or trans:\n",
    "\n",
    "I was curious and did some further reading.\n",
    "\n",
    "\n",
    "From RDKit documentation https://www.rdkit.org/docs/GettingStartedInPython.html:\n",
    "\n",
    "> *In order for atom or bond stereochemistry to be recognised correctly by most software, it’s essential that the mol block have atomic coordinates*...Generating a mol block for a molecule that does not have coordinates will, by default, automatically cause coordinates to be generated. These are not, however, stored with the molecule.\n",
    "\n",
    "\n",
    "From an old thread \n",
    "https://rdkit-discuss.narkive.com/Hx3T9NGY/quick-one-stereochemistry-info-when-reading-mol-or-sdf-files:\n",
    "\n",
    "> The atomic flags are parsed out, but nothing is done with them. This is consistent with the CTAB documentation: atom parity flags are ignored when molecules are read.\n",
    "\n",
    "### What happens if we generate coordinates before generating the MolBlock? Would it change the double bond stereo value?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#2D\n",
    "AllChem.Compute2DCoords(m)  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      " 10 10  0  0  0  0  0  0  0  0999 V2000\n",
      "   -3.7985   -0.4910    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.3812    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.0977    1.4730    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.2473   -0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.1701   -0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.4536    0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.8709    1.4730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    3.0048    0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.7213   -0.9820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.3040   -1.4730    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",
      "  2  4  2  3\n",
      "  4  5  1  0\n",
      "  5  6  2  0\n",
      "  6  7  1  0\n",
      "  7  8  2  0\n",
      "  8  9  1  0\n",
      "  9 10  2  0\n",
      " 10  5  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(Chem.MolToMolBlock(m))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#3D\n",
    "m1 = Chem.AddHs(m) #to ensure good 3D conformations\n",
    "AllChem.EmbedMolecule(m1,randomSeed=0xf00d)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          3D\n",
      "\n",
      " 16 16  0  0  0  0  0  0  0  0999 V2000\n",
      "    4.0266    0.4598    0.2795 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.7128    0.6579    0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2660    1.8630   -0.3172 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.8619   -0.3152    0.3130 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.4083   -0.2120    0.1399 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.3450    0.8440    0.6754 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.7047    0.9202    0.4764 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.3338   -0.0685   -0.2675 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.6180   -1.1408   -0.8196 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.2531   -1.1747   -0.5930 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2626   -1.2936    0.6451 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.1865    1.5933    1.2586 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.2592    1.7298    0.9029 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -3.4100    0.0138   -0.4013 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.1358   -1.8958   -1.3934 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.3348   -1.9812   -0.9986 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  1  0\n",
      "  2  4  2  3\n",
      "  4  5  1  0\n",
      "  5  6  2  0\n",
      "  6  7  1  0\n",
      "  7  8  2  0\n",
      "  8  9  1  0\n",
      "  9 10  2  0\n",
      " 10  5  1  0\n",
      "  4 11  1  0\n",
      "  6 12  1  0\n",
      "  7 13  1  0\n",
      "  8 14  1  0\n",
      "  9 15  1  0\n",
      " 10 16  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(Chem.MolToMolBlock(m1)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          3D\n",
      "\n",
      " 16 16  0  0  0  0  0  0  0  0999 V2000\n",
      "    4.0266    0.4598    0.2795 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.7128    0.6579    0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2660    1.8630   -0.3172 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.8619   -0.3152    0.3130 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.4083   -0.2120    0.1399 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.3450    0.8440    0.6754 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.7047    0.9202    0.4764 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.3338   -0.0685   -0.2675 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.6180   -1.1408   -0.8196 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.2531   -1.1747   -0.5930 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2626   -1.2936    0.6451 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.1865    1.5933    1.2586 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.2592    1.7298    0.9029 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -3.4100    0.0138   -0.4013 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.1358   -1.8958   -1.3934 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.3348   -1.9812   -0.9986 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  1  0\n",
      "  2  4  2  3\n",
      "  4  5  1  0\n",
      "  5  6  2  0\n",
      "  6  7  1  0\n",
      "  7  8  2  0\n",
      "  8  9  1  0\n",
      "  9 10  2  0\n",
      " 10  5  1  0\n",
      "  4 11  1  0\n",
      "  6 12  1  0\n",
      "  7 13  1  0\n",
      "  8 14  1  0\n",
      "  9 15  1  0\n",
      " 10 16  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "#alternative 3D - supposedly cleans up invalid stereochem \n",
    "#https://github.com/rdkit/rdkit/issues/2540#issuecomment-510392691\n",
    "Chem.AssignStereochemistryFrom3D(m1)\n",
    "print(Chem.MolToMolBlock(m1)) "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Even after generating 2D and 3D coordinates, still getting bond stereo value = 3 for the double bond.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Bonus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x108ad08f0>"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#do explicit Hs make a difference?\n",
    "b_Hs = Chem.AddHs(b)\n",
    "b_Hs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  6  5  0  0  0  0  0  0  0  0999 V2000\n",
      "   -1.2990    0.7500    0.0000 F   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   -1.5000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.5981   -0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2990    2.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  1  0\n",
      "  2  3  1  0\n",
      "  2  4  2  3\n",
      "  4  5  1  0\n",
      "  4  6  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "b_Hs_block = Chem.MolToMolBlock(b_Hs)\n",
    "print(b_Hs_block)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      "  4  3  0  0  0  0  0  0  0  0999 V2000\n",
      "    2.5981   -0.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2990    2.2500    0.0000 F   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",
      "  2  4  2  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "#compare with implicit Hs\n",
    "print(b_block)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Interesting that adding H's changes the bond stereo, not sure why."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "rdkit-kernel",
   "language": "python",
   "name": "my-rdkit-env"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.7"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}