2022_08_12-Vatheuer-GitHub_Copilot_RDKit.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem as Chem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x113a45480>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# SMILES of aspirin\n",
    "aspirin = 'CC(=O)Oc1ccccc1C(=O)O'\n",
    "# aspirin to mol\n",
    "mol = Chem.MolFromSmiles(aspirin)\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "180.042258736"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Calculate the molecular weight of aspirin\n",
    "Chem.CalcExactMolWt(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "C 0\n",
      "C 1\n",
      "O 2\n",
      "O 3\n",
      "C 4\n",
      "C 5\n",
      "C 6\n",
      "C 7\n",
      "C 8\n",
      "C 9\n",
      "C 10\n",
      "O 11\n",
      "O 12\n"
     ]
    }
   ],
   "source": [
    "# Print atomic symbol and indices of atoms in molecule mol\n",
    "for atom in mol.GetAtoms():\n",
    "    print(atom.GetSymbol(), atom.GetIdx())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.RWMol at 0x113a5a1b0>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Create a new molecule and replace the atom at index 0 with a new atom\n",
    "new_mol = Chem.RWMol(mol)\n",
    "new_mol.ReplaceAtom(3, Chem.Atom('S'))\n",
    "new_mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create3Dmol(mol):\n",
    "    \"\"\"Create a 3D molecule from a 2D molecule\"\"\"\n",
    "    # Add Explicit Hydrogens\n",
    "    mol = Chem.AddHs(mol)\n",
    "    # Create a 3D molecule from a 2D molecule\n",
    "    Chem.EmbedMolecule(mol)\n",
    "    # Optimize the geometry of the molecule\n",
    "    Chem.MMFFOptimizeMolecule(mol)\n",
    "    return mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[15:25:20] \n",
      "\n",
      "****\n",
      "Pre-condition Violation\n",
      "getNumImplicitHs() called without preceding call to calcImplicitValence()\n",
      "Violation occurred on line 299 in file /Users/runner/miniforge3/conda-bld/rdkit_1657061307449/work/Code/GraphMol/Atom.cpp\n",
      "Failed Expression: d_implicitValence > -1\n",
      "****\n",
      "\n"
     ]
    },
    {
     "ename": "RuntimeError",
     "evalue": "Pre-condition Violation\n\tgetNumImplicitHs() called without preceding call to calcImplicitValence()\n\tViolation occurred on line 299 in file Code/GraphMol/Atom.cpp\n\tFailed Expression: d_implicitValence > -1\n\tRDKIT: 2022.03.4\n\tBOOST: 1_74\n",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
      "\u001b[1;32m/Users/mhelvath/Desktop/5MinOfFame-2.ipynb Zelle 7\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/mhelvath/Desktop/5MinOfFame-2.ipynb#W6sZmlsZQ%3D%3D?line=0'>1</a>\u001b[0m create3Dmol(new_mol)\n",
      "\u001b[1;32m/Users/mhelvath/Desktop/5MinOfFame-2.ipynb Zelle 7\u001b[0m in \u001b[0;36mcreate3Dmol\u001b[0;34m(mol)\u001b[0m\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/mhelvath/Desktop/5MinOfFame-2.ipynb#W6sZmlsZQ%3D%3D?line=1'>2</a>\u001b[0m \u001b[39m\"\"\"Create a 3D molecule from a 2D molecule\"\"\"\u001b[39;00m\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/mhelvath/Desktop/5MinOfFame-2.ipynb#W6sZmlsZQ%3D%3D?line=2'>3</a>\u001b[0m \u001b[39m# Add Explicit Hydrogens\u001b[39;00m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/mhelvath/Desktop/5MinOfFame-2.ipynb#W6sZmlsZQ%3D%3D?line=3'>4</a>\u001b[0m mol \u001b[39m=\u001b[39m Chem\u001b[39m.\u001b[39;49mAddHs(mol)\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/mhelvath/Desktop/5MinOfFame-2.ipynb#W6sZmlsZQ%3D%3D?line=4'>5</a>\u001b[0m \u001b[39m# Create a 3D molecule from a 2D molecule\u001b[39;00m\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/mhelvath/Desktop/5MinOfFame-2.ipynb#W6sZmlsZQ%3D%3D?line=5'>6</a>\u001b[0m Chem\u001b[39m.\u001b[39mEmbedMolecule(mol)\n",
      "\u001b[0;31mRuntimeError\u001b[0m: Pre-condition Violation\n\tgetNumImplicitHs() called without preceding call to calcImplicitValence()\n\tViolation occurred on line 299 in file Code/GraphMol/Atom.cpp\n\tFailed Expression: d_implicitValence > -1\n\tRDKIT: 2022.03.4\n\tBOOST: 1_74\n"
     ]
    }
   ],
   "source": [
    "create3Dmol(new_mol)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Obviously, this is not an adequate way to create new_mols; quick fix and sanitize the mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x109db1a20>"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Sanitize new_mol\n",
    "Chem.SanitizeMol(new_mol)\n",
    "create3Dmol(new_mol)\n"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3.10.5 ('5MinOfFame')",
   "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": "3.10.5"
  },
  "orig_nbformat": 4,
  "vscode": {
   "interpreter": {
    "hash": "f491a773bd477dd0dc913c81b4e37809eaee29cf286d1e5a7620cc089a499512"
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}