Taka_ConstrainedEmbedding.ipynb

Taka_ConstrainedEmbedding.ipynb

{
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    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "Inspired by: https://iwatobipen.wordpress.com/2019/06/04/constrain-embedding-with-mcs-as-a-core-rdkit-chemoinformatics/"
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "from rdkit import Chem\nfrom rdkit.Chem import AllChem\nfrom rdkit.Chem import rdFMCS\nfrom rdkit.Chem.Draw import IPythonConsole\nIPythonConsole.ipython_3d = True",
      "execution_count": 1,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "mol1 = Chem.MolFromSmiles('CCc1ccccc1')\nmol2 = Chem.MolFromSmiles('CCc1nnccc1')\nmcs = rdFMCS.FindMCS([mol1, mol2])\nprint(mcs.smartsString)\nmcs_mol = Chem.MolFromSmarts(mcs.smartsString)",
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": "[#6]-[#6]-[#6]:[#6]:[#6]:[#6]\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "AllChem.EmbedMolecule(mol1)",
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 3,
          "data": {
            "text/plain": "0"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "core = Chem.RWMol(AllChem.ReplaceSidechains(mol1,mcs_mol))\n# remove the dummy atoms that creates. We know that they are the highest numbered atoms:\nfor aidx in range(core.GetNumAtoms(),mcs_mol.GetNumAtoms(),-1):\n       core.RemoveAtom(aidx-1)\ncore.GetNumConformers()",
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 4,
          "data": {
            "text/plain": "1"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "_=AllChem.ConstrainedEmbed(mol2,core)",
      "execution_count": 5,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "print(Chem.MolToMolBlock(mol1))\nprint(Chem.MolToMolBlock(mol2))",
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "text": "\n     RDKit          3D\n\n  8  8  0  0  0  0  0  0  0  0999 V2000\n    2.7975    0.0839    0.7058 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.9966    0.0409   -0.5636 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.5291    0.0093   -0.2802 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0984   -1.2078   -0.1315 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4446   -1.2253    0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1521   -0.0544    0.2377 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4891    1.1401    0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1390    1.2133   -0.1791 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  2  0\n  4  5  1  0\n  5  6  2  0\n  6  7  1  0\n  7  8  2  0\n  8  3  1  0\nM  END\n\n\n     RDKit          3D\n\n  8  8  0  0  0  0  0  0  0  0999 V2000\n    2.7972    0.0849    0.7132 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0013    0.0551   -0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.5443    0.0073   -0.2790 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1738    1.1566   -0.1708 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4845    1.1340    0.0822 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1546   -0.0385    0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4628   -1.2423    0.1318 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0973   -1.2199   -0.1320 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  2  0\n  4  5  1  0\n  5  6  2  0\n  6  7  1  0\n  7  8  2  0\n  8  3  1  0\nM  END\n\n",
          "name": "stdout"
        }
      ]
    }
  ],
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