iwatobipen_reactions_and_coordinates

iwatobipen_reactions_and_coordinates.ipynb

{
  "cells": [
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "from rdkit import Chem\nfrom rdkit.Chem import AllChem\nfrom rdkit.Chem import rdChemReactions",
      "execution_count": 1,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "mol = Chem.AddHs(Chem.MolFromSmiles('c1ccncc1'))",
      "execution_count": 2,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "AllChem.EmbedMolecule(mol)",
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 3,
          "data": {
            "text/plain": "0"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "If we want to keep the coordinates of the H, we can include it in the reaction:"
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "rxn = rdChemReactions.ReactionFromSmarts('[c:1][#1:2]>>[c:1][F:2]')",
      "execution_count": 4,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "ps = rxn.RunReactants((mol,))",
      "execution_count": 5,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "om = ps[0][0]\nChem.SanitizeMol(om)",
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 7,
          "data": {
            "text/plain": "rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "print(Chem.MolToMolBlock(mol))",
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "stream",
          "text": "\n     RDKit          3D\n\n 11 11  0  0  0  0  0  0  0  0999 V2000\n   -0.1044    1.1576    0.0430 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.2030    0.3447    0.0302 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1017   -1.0368   -0.0208 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.1237   -1.5610   -0.0578 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2528   -0.8282   -0.0482 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1362    0.5521    0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1931    2.2308    0.0828 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1800    0.8222    0.0617 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.0157   -1.6087   -0.0278 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2472   -1.2554   -0.0783 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0380    1.1830    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0\n  2  3  1  0\n  3  4  2  0\n  4  5  1  0\n  5  6  2  0\n  6  1  1  0\n  1  7  1  0\n  2  8  1  0\n  3  9  1  0\n  5 10  1  0\n  6 11  1  0\nM  END\n\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "print(Chem.MolToMolBlock(om))",
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "stream",
          "text": "\n     RDKit          3D\n\n 11 11  0  0  0  0  0  0  0  0999 V2000\n   -0.1044    1.1576    0.0430 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1931    2.2308    0.0828 F   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.2030    0.3447    0.0302 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1362    0.5521    0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1017   -1.0368   -0.0208 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1800    0.8222    0.0617 H   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2528   -0.8282   -0.0482 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0380    1.1830    0.0122 H   0  0  0  0  0  0  0  0  0  0  0  0\n    0.1237   -1.5610   -0.0578 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.0157   -1.6087   -0.0278 H   0  0  0  0  0  0  0  0  0  0  0  0\n    2.2472   -1.2554   -0.0783 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  1  3  2  0\n  4  1  1  0\n  3  5  1  0\n  3  6  1  0\n  7  4  2  0\n  4  8  1  0\n  5  9  2  0\n  5 10  1  0\n  9  7  1  0\n  7 11  1  0\nM  END\n\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "",
      "execution_count": null,
      "outputs": []
    }
  ],
  "metadata": {
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3",
      "language": "python"
    },
    "language_info": {
      "name": "python",
      "version": "3.7.2",
      "mimetype": "text/x-python",
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "pygments_lexer": "ipython3",
      "nbconvert_exporter": "python",
      "file_extension": ".py"
    },
    "gist": {
      "id": "",
      "data": {
        "description": "iwatobipen_reactions_and_coordinates",
        "public": true
      }
    }
  },
  "nbformat": 4,
  "nbformat_minor": 2
}

Thank you for sharing your code! This is what I would like to do!!!!