rdkit_from_pip.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "rdkit_from_pip.ipynb",
      "provenance": [],
      "authorship_tag": "ABX9TyOkIGqB2szLqktrQSWpm2SO",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/iwatobipen/playground/blob/master/rdkit_from_pip.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "id": "XKMbmVO6NOfL",
        "outputId": "55cb099f-06e4-492b-d947-612194a723a7"
      },
      "source": [
        "import sys\n",
        "sys.version"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'3.7.10 (default, May  3 2021, 02:48:31) \\n[GCC 7.5.0]'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 1
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Bmb6EZuLNW_q",
        "outputId": "bab5f44a-7aa1-4a6a-ac85-bdf7843f4363"
      },
      "source": [
        "!time pip install rdkit-pypi"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Requirement already satisfied: rdkit-pypi in /usr/local/lib/python3.7/dist-packages (2021.3.2.1)\n",
            "Requirement already satisfied: numpy>=1.19 in /usr/local/lib/python3.7/dist-packages (from rdkit-pypi) (1.19.5)\n",
            "\n",
            "real\t0m2.674s\n",
            "user\t0m2.497s\n",
            "sys\t0m0.146s\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "tNrKgoU-NiQp"
      },
      "source": [
        "from rdkit import Chem\n",
        "from rdkit.Chem import rdBase\n",
        "from rdkit.Chem import Draw\n",
        "from rdkit.Chem.Draw import IPythonConsole"
      ],
      "execution_count": 3,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "yTBDI6CkN8Q1",
        "outputId": "b9ded70b-205c-4af0-df97-6a89a8773b8f"
      },
      "source": [
        "print(rdBase.rdkitVersion)"
      ],
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "2021.03.2\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 167
        },
        "id": "ZV_Sp3jsN-ti",
        "outputId": "7952381a-898e-417b-eaa8-faf7cd56e9a2"
      },
      "source": [
        "mol = Chem.MolFromSmiles('C1COCC1')\n",
        "mol"
      ],
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "image/png": "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\n",
            "text/plain": [
              "<rdkit.Chem.rdchem.Mol at 0x7f384b8ca990>"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 5
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "oVPEmu2yOHQD"
      },
      "source": [
        ""
      ],
      "execution_count": 5,
      "outputs": []
    }
  ]
}