greglandrum/ChiralFlag_and_StereoGroups.ipynb

## ChiralFlag_and_StereoGroups.ipynb
{
  "cells": [
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:25:19.813554Z",
          "end_time": "2024-01-31T14:25:19.815829Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "from rdkit import Chem\nfrom rdkit.Chem import Draw\nfrom rdkit.Chem.Draw import IPythonConsole\nIPythonConsole.drawOptions.addStereoAnnotation = True",
      "execution_count": 4,
      "outputs": []
    },
    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "Example from Nick T on the mailing list"
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:33:47.648922Z",
          "end_time": "2024-01-31T14:33:47.654470Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "mb1 = ''' \n  ACCLDraw01312413482D\n \n  8  8  0  0  1  0  0  0  0  0999 V2000\n    4.6334   -6.5969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.6563   -6.0064    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0\n    6.6791   -6.5969    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0\n    6.6791   -7.7781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.6563   -8.3686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6334   -7.7781    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n    5.6563   -4.8257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6109   -8.3684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  3  2  1  0  0  0  0\n  4  3  1  0  0  0  0\n  5  4  1  0  0  0  0\n  1  6  1  0  0  0  0\n  6  5  1  0  0  0  0\n  2  7  1  1  0  0  0\n  6  8  1  1  0  0  0\nM  END\n'''\nm1 = Chem.MolFromMolBlock(mb1)\nm1",
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 14,
          "data": {
            "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f8d241a65e0>",
            "image/png": "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"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:40:49.275208Z",
          "end_time": "2024-01-31T14:40:49.278974Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "def translate_V2000_chiral_flag_to_stereo_groups(mol):\n    if not mol.HasProp('_MolFileChiralFlag'):\n        return Chem.Mol(mol)\n    chiflag = mol.GetIntProp('_MolFileChiralFlag')\n    aids = [at.GetIdx() for at in mol.GetAtoms() if at.GetChiralTag() in (Chem.ChiralType.CHI_TETRAHEDRAL_CCW,Chem.ChiralType.CHI_TETRAHEDRAL_CW)]\n    if not aids:\n        return mol\n\n    if chiflag:\n        sgt = Chem.StereoGroupType.STEREO_ABSOLUTE\n    else:\n        sgt = Chem.StereoGroupType.STEREO_AND\n    mol = Chem.RWMol(mol)\n    sgs = list(mol.GetStereoGroups())\n    ng = Chem.CreateStereoGroup(sgt,mol,aids)\n    sgs.append(ng)\n    mol.SetStereoGroups(sgs)\n    return mol.GetMol()\n",
      "execution_count": 28,
      "outputs": []
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:40:50.595721Z",
          "end_time": "2024-01-31T14:40:50.601723Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "tm1 = translate_V2000_chiral_flag_to_stereo_groups(m1)\ntm1",
      "execution_count": 29,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 29,
          "data": {
            "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f8d23c6f1b0>",
            "image/png": 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"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:40:53.091611Z",
          "end_time": "2024-01-31T14:40:53.093811Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "print(Chem.MolToV3KMolBlock(tm1))",
      "execution_count": 30,
      "outputs": [
        {
          "output_type": "stream",
          "text": " \n     RDKit          2D\n\n  0  0  0  0  0  0  0  0  0  0999 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 8 8 0 0 1\nM  V30 BEGIN ATOM\nM  V30 1 C 4.633400 -6.596900 0.000000 0\nM  V30 2 C 5.656300 -6.006400 0.000000 0\nM  V30 3 N 6.679100 -6.596900 0.000000 0\nM  V30 4 C 6.679100 -7.778100 0.000000 0\nM  V30 5 C 5.656300 -8.368600 0.000000 0\nM  V30 6 C 4.633400 -7.778100 0.000000 0\nM  V30 7 C 5.656300 -4.825700 0.000000 0\nM  V30 8 C 3.610900 -8.368400 0.000000 0\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 1 1 1 2\nM  V30 2 1 3 2\nM  V30 3 1 4 3\nM  V30 4 1 5 4\nM  V30 5 1 1 6\nM  V30 6 1 6 5\nM  V30 7 1 2 7 CFG=1\nM  V30 8 1 6 8 CFG=1\nM  V30 END BOND\nM  V30 BEGIN COLLECTION\nM  V30 MDLV30/STEABS ATOMS=(2 2 6)\nM  V30 END COLLECTION\nM  V30 END CTAB\nM  END\n\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:40:54.155621Z",
          "end_time": "2024-01-31T14:40:54.161655Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "mb2 = ''' \n  ACCLDraw01312413482D\n \n  8  8  0  0  0  0  0  0  0  0999 V2000\n    4.6334   -6.5969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.6563   -6.0064    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0\n    6.6791   -6.5969    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0\n    6.6791   -7.7781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.6563   -8.3686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6334   -7.7781    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n    5.6563   -4.8257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.6109   -8.3684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  3  2  1  0  0  0  0\n  4  3  1  0  0  0  0\n  5  4  1  0  0  0  0\n  1  6  1  0  0  0  0\n  6  5  1  0  0  0  0\n  2  7  1  1  0  0  0\n  6  8  1  1  0  0  0\nM  END\n'''\nm2 = Chem.MolFromMolBlock(mb2)\nm2",
      "execution_count": 31,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 31,
          "data": {
            "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f8d23c6e570>",
            "image/png": 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"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:40:55.195526Z",
          "end_time": "2024-01-31T14:40:55.201240Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "tm2 = translate_V2000_chiral_flag_to_stereo_groups(m2)\ntm2",
      "execution_count": 32,
      "outputs": [
        {
          "output_type": "execute_result",
          "execution_count": 32,
          "data": {
            "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f8d23c6e810>",
            "image/png": 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"
          },
          "metadata": {}
        }
      ]
    },
    {
      "metadata": {
        "ExecuteTime": {
          "start_time": "2024-01-31T14:41:15.259852Z",
          "end_time": "2024-01-31T14:41:15.262351Z"
        },
        "trusted": true
      },
      "cell_type": "code",
      "source": "print(Chem.MolToV3KMolBlock(tm2))",
      "execution_count": 33,
      "outputs": [
        {
          "output_type": "stream",
          "text": " \n     RDKit          2D\n\n  0  0  0  0  0  0  0  0  0  0999 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 8 8 0 0 0\nM  V30 BEGIN ATOM\nM  V30 1 C 4.633400 -6.596900 0.000000 0\nM  V30 2 C 5.656300 -6.006400 0.000000 0\nM  V30 3 N 6.679100 -6.596900 0.000000 0\nM  V30 4 C 6.679100 -7.778100 0.000000 0\nM  V30 5 C 5.656300 -8.368600 0.000000 0\nM  V30 6 C 4.633400 -7.778100 0.000000 0\nM  V30 7 C 5.656300 -4.825700 0.000000 0\nM  V30 8 C 3.610900 -8.368400 0.000000 0\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 1 1 1 2\nM  V30 2 1 3 2\nM  V30 3 1 4 3\nM  V30 4 1 5 4\nM  V30 5 1 1 6\nM  V30 6 1 6 5\nM  V30 7 1 2 7 CFG=1\nM  V30 8 1 6 8 CFG=1\nM  V30 END BOND\nM  V30 BEGIN COLLECTION\nM  V30 MDLV30/STERAC1 ATOMS=(2 2 6)\nM  V30 END COLLECTION\nM  V30 END CTAB\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 (ipykernel)",
      "language": "python"
    },
    "toc": {
      "nav_menu": {},
      "number_sections": true,
      "sideBar": true,
      "skip_h1_title": false,
      "base_numbering": 1,
      "title_cell": "Table of Contents",
      "title_sidebar": "Contents",
      "toc_cell": false,
      "toc_position": {},
      "toc_section_display": true,
      "toc_window_display": false
    },
    "language_info": {
      "name": "python",
      "version": "3.12.1",
      "mimetype": "text/x-python",
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "pygments_lexer": "ipython3",
      "nbconvert_exporter": "python",
      "file_extension": ".py"
    },
    "gist": {
      "id": "",
      "data": {
        "description": "ChiralFlag_and_StereoGroups",
        "public": true
      }
    }
  },
  "nbformat": 4,
  "nbformat_minor": 5
}