pre_reactive_docking_V02.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "gpuType": "T4",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "accelerator": "GPU"
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/c00jsw00/reactivedock/blob/main/pre_reactive_docking_V02.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "sMITd6s6hEGp"
      },
      "source": [
        "## Blind docking with qvina-w and database by Yeng-Tseng wang (c00jsw00@gmail.com)\n",
        "This Google Colab notebook"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "8eY4fchy-kh5"
      },
      "source": [
        "## Step 1. Install OpenBabel, RDKit and Py3Dmol tools --by wang YT"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "y2IaxgQ5hAZx",
        "outputId": "ca9bf999-6a63-41d0-8a74-7a6c46ca6bcd",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "!pip install -q condacolab\n",
        "import condacolab\n",
        "condacolab.install()\n",
        "!mamba install rdkit\n",
        "!mamba install openbabel\n",
        "!pip install meeko\n",
        "!pip install py3Dmol # 3D Molecular Visualizer"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "⏬ Downloading https://github.com/conda-forge/miniforge/releases/download/23.1.0-1/Mambaforge-23.1.0-1-Linux-x86_64.sh...\n",
            "📦 Installing...\n",
            "📌 Adjusting configuration...\n",
            "🩹 Patching environment...\n",
            "⏲ Done in 0:00:11\n",
            "🔁 Restarting kernel...\n",
            "\n",
            "                  __    __    __    __\n",
            "                 /  \\  /  \\  /  \\  /  \\\n",
            "                /    \\/    \\/    \\/    \\\n",
            "███████████████/  /██/  /██/  /██/  /████████████████████████\n",
            "              /  / \\   / \\   / \\   / \\  \\____\n",
            "             /  /   \\_/   \\_/   \\_/   \\    o \\__,\n",
            "            / _/                       \\_____/  `\n",
            "            |/\n",
            "        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗\n",
            "        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗\n",
            "        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║\n",
            "        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║\n",
            "        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║\n",
            "        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝\n",
            "\n",
            "        mamba (1.4.1) supported by @QuantStack\n",
            "\n",
            "        GitHub:  https://github.com/mamba-org/mamba\n",
            "        Twitter: https://twitter.com/QuantStack\n",
            "\n",
            "█████████████████████████████████████████████████████████████\n",
            "\n",
            "\n",
            "Looking for: ['rdkit']\n",
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            "conda-forge/linux-64 100%\u001b[2K\u001b[1A\u001b[2K\u001b[0Gconda-forge/linux-64                              \n",
            "\u001b[?25h\n",
            "Pinned packages:\n",
            "  - python 3.10.*\n",
            "  - python 3.10.*\n",
            "  - python_abi 3.10.* *cp310*\n",
            "  - cudatoolkit 11.8.*\n",
            "\n",
            "\n",
            "Transaction\n",
            "\n",
            "  Prefix: /usr/local\n",
            "\n",
            "  Updating specs:\n",
            "\n",
            "   - rdkit\n",
            "   - ca-certificates\n",
            "   - certifi\n",
            "   - openssl\n",
            "\n",
            "\n",
            "  Package                           Version  Build                Channel                   Size\n",
            "──────────────────────────────────────────────────────────────────────────────────────────────────\n",
            "  Install:\n",
            "──────────────────────────────────────────────────────────────────────────────────────────────────\n",
            "\n",
            "  \u001b[32m+ brotli                   \u001b[0m         1.1.0  hd590300_1           conda-forge/linux-64      19kB\n",
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            "  \u001b[32m+ munkres                  \u001b[0m         1.1.4  pyh9f0ad1d_0         conda-forge/noarch        12kB\n",
            "  \u001b[32m+ numpy                    \u001b[0m        1.26.2  py310hb13e2d6_0      conda-forge/linux-64       7MB\n",
            "  \u001b[32m+ openjpeg                 \u001b[0m         2.5.0  h488ebb8_3           conda-forge/linux-64     357kB\n",
            "  \u001b[32m+ packaging                \u001b[0m          23.2  pyhd8ed1ab_0         conda-forge/noarch        49kB\n",
            "  \u001b[32m+ pandas                   \u001b[0m         2.1.3  py310hcc13569_0      conda-forge/linux-64      12MB\n",
            "  \u001b[32m+ pcre2                    \u001b[0m         10.42  hcad00b1_0           conda-forge/linux-64       1MB\n",
            "  \u001b[32m+ pillow                   \u001b[0m        10.0.1  py310h29da1c1_1      conda-forge/linux-64      46MB\n",
            "  \u001b[32m+ pixman                   \u001b[0m        0.42.2  h59595ed_0           conda-forge/linux-64     385kB\n",
            "  \u001b[32m+ pthread-stubs            \u001b[0m           0.4  h36c2ea0_1001        conda-forge/linux-64       6kB\n",
            "  \u001b[32m+ pycairo                  \u001b[0m        1.25.1  py310hda9f760_0      conda-forge/linux-64     116kB\n",
            "  \u001b[32m+ pyparsing                \u001b[0m         3.1.1  pyhd8ed1ab_0         conda-forge/noarch        90kB\n",
            "  \u001b[32m+ python-dateutil          \u001b[0m         2.8.2  pyhd8ed1ab_0         conda-forge/noarch       246kB\n",
            "  \u001b[32m+ python-tzdata            \u001b[0m        2023.3  pyhd8ed1ab_0         conda-forge/noarch       143kB\n",
            "  \u001b[32m+ pytz                     \u001b[0m  2023.3.post1  pyhd8ed1ab_0         conda-forge/noarch       187kB\n",
            "  \u001b[32m+ rdkit                    \u001b[0m     2023.09.3  py310hb79e901_0      conda-forge/linux-64      37MB\n",
            "  \u001b[32m+ reportlab                \u001b[0m         4.0.7  py310h2372a71_0      conda-forge/linux-64       2MB\n",
            "  \u001b[32m+ rlpycairo                \u001b[0m         0.2.0  pyhd8ed1ab_0         conda-forge/noarch        15kB\n",
            "  \u001b[32m+ six                      \u001b[0m        1.16.0  pyh6c4a22f_0         conda-forge/noarch        14kB\n",
            "  \u001b[32m+ sqlalchemy               \u001b[0m        2.0.23  py310h2372a71_0      conda-forge/linux-64       3MB\n",
            "  \u001b[32m+ typing-extensions        \u001b[0m         4.8.0  hd8ed1ab_0           conda-forge/noarch        10kB\n",
            "  \u001b[32m+ typing_extensions        \u001b[0m         4.8.0  pyha770c72_0         conda-forge/noarch        35kB\n",
            "  \u001b[32m+ unicodedata2             \u001b[0m        15.1.0  py310h2372a71_0      conda-forge/linux-64     374kB\n",
            "  \u001b[32m+ xorg-kbproto             \u001b[0m         1.0.7  h7f98852_1002        conda-forge/linux-64      27kB\n",
            "  \u001b[32m+ xorg-libice              \u001b[0m         1.1.1  hd590300_0           conda-forge/linux-64      58kB\n",
            "  \u001b[32m+ xorg-libsm               \u001b[0m         1.2.4  h7391055_0           conda-forge/linux-64      27kB\n",
            "  \u001b[32m+ xorg-libx11              \u001b[0m         1.8.7  h8ee46fc_0           conda-forge/linux-64     829kB\n",
            "  \u001b[32m+ xorg-libxau              \u001b[0m        1.0.11  hd590300_0           conda-forge/linux-64      14kB\n",
            "  \u001b[32m+ xorg-libxdmcp            \u001b[0m         1.1.3  h7f98852_0           conda-forge/linux-64      19kB\n",
            "  \u001b[32m+ xorg-libxext             \u001b[0m         1.3.4  h0b41bf4_2           conda-forge/linux-64      50kB\n",
            "  \u001b[32m+ xorg-libxrender          \u001b[0m        0.9.11  hd590300_0           conda-forge/linux-64      38kB\n",
            "  \u001b[32m+ xorg-renderproto         \u001b[0m        0.11.1  h7f98852_1002        conda-forge/linux-64      10kB\n",
            "  \u001b[32m+ xorg-xextproto           \u001b[0m         7.3.0  h0b41bf4_1003        conda-forge/linux-64      30kB\n",
            "  \u001b[32m+ xorg-xproto              \u001b[0m        7.0.31  h7f98852_1007        conda-forge/linux-64      75kB\n",
            "  \u001b[32m+ zlib                     \u001b[0m        1.2.13  h166bdaf_4           conda-forge/linux-64      94kB\n",
            "\n",
            "  Change:\n",
            "──────────────────────────────────────────────────────────────────────────────────────────────────\n",
            "\n",
            "  \u001b[31m- libarchive               \u001b[0m         3.6.2  h3d51595_0           conda-forge                   \n",
            "  \u001b[32m+ libarchive               \u001b[0m         3.6.2  h039dbb9_1           conda-forge/linux-64     844kB\n",
            "\n",
            "  Upgrade:\n",
            "──────────────────────────────────────────────────────────────────────────────────────────────────\n",
            "\n",
            "  \u001b[31m- ca-certificates          \u001b[0m     2022.12.7  ha878542_0           conda-forge                   \n",
            "  \u001b[32m+ ca-certificates          \u001b[0m    2023.11.17  hbcca054_0           conda-forge/linux-64     154kB\n",
            "  \u001b[31m- certifi                  \u001b[0m     2022.12.7  pyhd8ed1ab_0         conda-forge                   \n",
            "  \u001b[32m+ certifi                  \u001b[0m    2023.11.17  pyhd8ed1ab_0         conda-forge/noarch       159kB\n",
            "  \u001b[31m- icu                      \u001b[0m          72.1  hcb278e6_0           conda-forge                   \n",
            "  \u001b[32m+ icu                      \u001b[0m          73.2  h59595ed_0           conda-forge/linux-64      12MB\n",
            "  \u001b[31m- libxml2                  \u001b[0m        2.10.3  hfdac1af_6           conda-forge                   \n",
            "  \u001b[32m+ libxml2                  \u001b[0m        2.11.6  h232c23b_0           conda-forge/linux-64     706kB\n",
            "  \u001b[31m- openssl                  \u001b[0m         3.1.0  h0b41bf4_0           conda-forge                   \n",
            "  \u001b[32m+ openssl                  \u001b[0m         3.2.0  hd590300_1           conda-forge/linux-64       3MB\n",
            "  \u001b[31m- zstd                     \u001b[0m         1.5.2  h3eb15da_6           conda-forge                   \n",
            "  \u001b[32m+ zstd                     \u001b[0m         1.5.5  hfc55251_0           conda-forge/linux-64     545kB\n",
            "\n",
            "  Summary:\n",
            "\n",
            "  Install: 75 packages\n",
            "  Change: 1 packages\n",
            "  Upgrade: 6 packages\n",
            "\n",
            "  Total download: 164MB\n",
            "\n",
            "──────────────────────────────────────────────────────────────────────────────────────────────────\n",
            "\n",
            "\n",
            "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n",
            "Downloading        0%\n",
            "Extracting         0%\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gxorg-libice                                         58.5kB @ 652.8kB/s  0.1s\n",
            "pixman                                             385.3kB @   3.9MB/s  0.1s\n",
            "[+] 0.1s\n",
            "Downloading  (5)   1%\n",
            "Extracting   (2)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Glibpng                                             282.6kB @   2.6MB/s  0.1s\n",
            "lerc                                               281.8kB @   2.2MB/s  0.0s\n",
            "xorg-libxau                                         14.5kB @ 109.8kB/s  0.0s\n",
            "unicodedata2                                       374.1kB @   2.5MB/s  0.0s\n",
            "zstd                                               545.2kB @   3.5MB/s  0.2s\n",
            "pcre2                                                1.0MB @   5.9MB/s  0.0s\n",
            "xorg-kbproto                                        27.3kB @ 155.4kB/s  0.0s\n",
            "xorg-libxdmcp                                       19.1kB @ 104.2kB/s  0.0s\n",
            "[+] 0.2s\n",
            "Downloading  (5)   3%\n",
            "Extracting  (10)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gxorg-libsm                                          27.4kB @ 141.0kB/s  0.0s\n",
            "libtiff                                            277.5kB @   1.3MB/s  0.0s\n",
            "libbrotlidec                                        32.8kB @ 139.0kB/s  0.1s\n",
            "libxcb                                             384.2kB @   1.5MB/s  0.1s\n",
            "openjpeg                                           356.7kB @   1.4MB/s  0.1s\n",
            "brotli-bin                                          19.0kB @  74.5kB/s  0.0s\n",
            "brotli                                              19.4kB @  67.2kB/s  0.0s\n",
            "[+] 0.3s\n",
            "Downloading  (5)   7%\n",
            "Extracting  (17)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Glibblas                                             14.4kB @  48.0kB/s  0.0s\n",
            "xorg-libxext                                        50.1kB @ 166.7kB/s  0.0s\n",
            "contourpy                                          238.9kB @ 675.4kB/s  0.1s\n",
            "python-tzdata                                      143.1kB @ 401.5kB/s  0.1s\n",
            "pytz                                               187.5kB @ 525.0kB/s  0.1s\n",
            "[+] 0.4s\n",
            "Downloading  (5)  11%\n",
            "Extracting  (22)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gsix                                                 14.3kB @  35.6kB/s  0.0s\n",
            "icu                                                 12.1MB @  29.2MB/s  0.4s\n",
            "typing_extensions                                   35.1kB @  83.4kB/s  0.1s\n",
            "fonttools                                            2.3MB @   4.9MB/s  0.1s\n",
            "rlpycairo                                           14.9kB @  31.7kB/s  0.1s\n",
            "[+] 0.5s\n",
            "Downloading  (5)  18%\n",
            "Extracting  (27)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gpycairo                                            116.2kB @ 228.7kB/s  0.1s\n",
            "libwebp-base                                       401.8kB @ 735.9kB/s  0.1s\n",
            "libjpeg-turbo                                      496.4kB @ 907.1kB/s  0.1s\n",
            "munkres                                             12.5kB @  22.1kB/s  0.2s\n",
            "libexpat                                            78.0kB @ 138.3kB/s  0.1s\n",
            "xorg-renderproto                                     9.6kB @  16.4kB/s  0.1s\n",
            "xorg-xproto                                         74.9kB @ 127.7kB/s  0.1s\n",
            "[+] 0.6s\n",
            "Downloading  (5)  24%\n",
            "Extracting  (32)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gfreetype                                           635.0kB @   1.0MB/s  0.1s\n",
            "lcms2                                              240.6kB @ 365.6kB/s  0.1s\n",
            "[+] 0.7s\n",
            "Downloading  (5)  30%\n",
            "Extracting  (35)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gliblapack                                           14.3kB @  19.7kB/s  0.1s\n",
            "libopenblas                                          5.5MB @   7.5MB/s  0.2s\n",
            "cycler                                              13.5kB @  17.2kB/s  0.0s\n",
            "[+] 0.8s\n",
            "Downloading  (5)  39%\n",
            "Extracting  (37)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gfont-ttf-source-code-pro                           700.8kB @ 873.9kB/s  0.1s\n",
            "fonts-conda-forge                                    4.1kB @   5.1kB/s  0.0s\n",
            "pillow                                              46.4MB @  55.8MB/s  0.6s\n",
            "cairo                                              982.4kB @   1.1MB/s  0.1s\n",
            "libboost                                             2.6MB @   3.0MB/s  0.3s\n",
            "[+] 0.9s\n",
            "Downloading  (5)  48%\n",
            "Extracting  (42)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gfonts-conda-ecosystem                                3.7kB @   4.0kB/s  0.1s\n",
            "xorg-xextproto                                      30.3kB @  33.0kB/s  0.0s\n",
            "libgfortran5                                         1.4MB @   1.6MB/s  0.0s\n",
            "greenlet                                           206.4kB @ 216.3kB/s  0.0s\n",
            "expat                                              136.8kB @ 142.7kB/s  0.0s\n",
            "[+] 1.0s\n",
            "Downloading  (5)  50%\n",
            "Extracting  (47)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gopenssl                                              2.9MB @   2.9MB/s  0.1s\n",
            "fontconfig                                         272.0kB @ 271.5kB/s  0.0s\n",
            "libcblas                                            14.4kB @  14.4kB/s  0.0s\n",
            "[+] 1.1s\n",
            "Downloading  (8)  53%\n",
            "Extracting  (49)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Glibboost-python                                    119.1kB @ 114.8kB/s  0.4s\n",
            "certifi                                            158.9kB @ 152.5kB/s  0.1s\n",
            "font-ttf-inconsolata                                96.5kB @  92.5kB/s  0.1s\n",
            "font-ttf-ubuntu                                      1.6MB @   1.5MB/s  0.1s\n",
            "[+] 1.2s\n",
            "Downloading  (6)  59%\n",
            "Extracting  (53)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gca-certificates                                    154.1kB @ 129.9kB/s  0.1s\n",
            "reportlab                                            2.4MB @   1.9MB/s  0.2s\n",
            "libbrotlienc                                       282.5kB @ 228.4kB/s  0.1s\n",
            "sqlalchemy                                           2.8MB @   2.2MB/s  0.2s\n",
            "[+] 1.3s\n",
            "Downloading  (4)  65%\n",
            "Extracting  (57)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Glibarchive                                         843.9kB @ 652.7kB/s  0.1s\n",
            "xorg-libx11                                        828.7kB @ 637.7kB/s  0.1s\n",
            "matplotlib-base                                      6.8MB @   5.1MB/s  0.3s\n",
            "pyparsing                                           89.5kB @  66.5kB/s  0.1s\n",
            "freetype-py                                         58.9kB @  43.8kB/s  0.1s\n",
            "python-dateutil                                    246.0kB @ 182.7kB/s  0.1s\n",
            "pthread-stubs                                        5.6kB @   4.1kB/s  0.0s\n",
            "[+] 1.4s\n",
            "Downloading  (5)  70%\n",
            "Extracting  (64)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gxorg-libxrender                                     37.8kB @  27.0kB/s  0.0s\n",
            "kiwisolver                                          73.1kB @  50.5kB/s  0.1s\n",
            "libxml2                                            705.6kB @ 486.4kB/s  0.1s\n",
            "libglib                                              2.7MB @   1.9MB/s  0.1s\n",
            "[+] 1.5s\n",
            "Downloading  (5)  76%\n",
            "Extracting  (67)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gpackaging                                           49.5kB @  32.7kB/s  0.1s\n",
            "typing-extensions                                   10.1kB @   6.7kB/s  0.1s\n",
            "numpy                                                6.9MB @   4.5MB/s  0.2s\n",
            "[+] 1.6s\n",
            "Downloading  (7)  85%\n",
            "Extracting  (70)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gzlib                                                94.1kB @  59.8kB/s  0.1s\n",
            "libdeflate                                          67.1kB @  42.6kB/s  0.1s\n",
            "libbrotlicommon                                     69.4kB @  42.5kB/s  0.1s\n",
            "[+] 1.7s\n",
            "Downloading  (5)  95%\n",
            "Extracting  (72)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Ggettext                                              4.3MB @   2.6MB/s  0.1s\n",
            "libgfortran-ng                                      23.3kB @  13.7kB/s  0.1s\n",
            "font-ttf-dejavu-sans-mono                          397.4kB @ 234.5kB/s  0.2s\n",
            "pandas                                              12.4MB @   7.2MB/s  0.3s\n",
            "rdkit                                               37.3MB @  21.2MB/s  0.9s\n",
            "[+] 1.8s\n",
            "Downloading      100%\n",
            "Extracting  (77)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 1.9s\n",
            "Downloading      100%\n",
            "Extracting  (77)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.0s\n",
            "Downloading      100%\n",
            "Extracting  (76)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.1s\n",
            "Downloading      100%\n",
            "Extracting  (75)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.2s\n",
            "Downloading      100%\n",
            "Extracting  (75)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.3s\n",
            "Downloading      100%\n",
            "Extracting  (75)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.4s\n",
            "Downloading      100%\n",
            "Extracting  (74)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.5s\n",
            "Downloading      100%\n",
            "Extracting  (73)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.6s\n",
            "Downloading      100%\n",
            "Extracting  (73)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.7s\n",
            "Downloading      100%\n",
            "Extracting  (71)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.8s\n",
            "Downloading      100%\n",
            "Extracting  (71)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 2.9s\n",
            "Downloading      100%\n",
            "Extracting  (70)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.0s\n",
            "Downloading      100%\n",
            "Extracting  (69)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.1s\n",
            "Downloading      100%\n",
            "Extracting  (69)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.2s\n",
            "Downloading      100%\n",
            "Extracting  (67)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.3s\n",
            "Downloading      100%\n",
            "Extracting  (67)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.4s\n",
            "Downloading      100%\n",
            "Extracting  (65)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.5s\n",
            "Downloading      100%\n",
            "Extracting  (65)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.6s\n",
            "Downloading      100%\n",
            "Extracting  (65)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.7s\n",
            "Downloading      100%\n",
            "Extracting  (64)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.8s\n",
            "Downloading      100%\n",
            "Extracting  (64)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 3.9s\n",
            "Downloading      100%\n",
            "Extracting  (64)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.0s\n",
            "Downloading      100%\n",
            "Extracting  (63)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.1s\n",
            "Downloading      100%\n",
            "Extracting  (63)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.2s\n",
            "Downloading      100%\n",
            "Extracting  (61)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.3s\n",
            "Downloading      100%\n",
            "Extracting  (61)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.4s\n",
            "Downloading      100%\n",
            "Extracting  (61)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.5s\n",
            "Downloading      100%\n",
            "Extracting  (59)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.6s\n",
            "Downloading      100%\n",
            "Extracting  (59)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.7s\n",
            "Downloading      100%\n",
            "Extracting  (57)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.8s\n",
            "Downloading      100%\n",
            "Extracting  (57)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 4.9s\n",
            "Downloading      100%\n",
            "Extracting  (56)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.0s\n",
            "Downloading      100%\n",
            "Extracting  (55)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.1s\n",
            "Downloading      100%\n",
            "Extracting  (55)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.2s\n",
            "Downloading      100%\n",
            "Extracting  (54)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.3s\n",
            "Downloading      100%\n",
            "Extracting  (54)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.4s\n",
            "Downloading      100%\n",
            "Extracting  (54)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.5s\n",
            "Downloading      100%\n",
            "Extracting  (54)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.6s\n",
            "Downloading      100%\n",
            "Extracting  (52)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.7s\n",
            "Downloading      100%\n",
            "Extracting  (52)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.8s\n",
            "Downloading      100%\n",
            "Extracting  (51)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 5.9s\n",
            "Downloading      100%\n",
            "Extracting  (50)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.0s\n",
            "Downloading      100%\n",
            "Extracting  (50)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.1s\n",
            "Downloading      100%\n",
            "Extracting  (49)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.2s\n",
            "Downloading      100%\n",
            "Extracting  (49)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.3s\n",
            "Downloading      100%\n",
            "Extracting  (47)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.4s\n",
            "Downloading      100%\n",
            "Extracting  (47)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.5s\n",
            "Downloading      100%\n",
            "Extracting  (46)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.6s\n",
            "Downloading      100%\n",
            "Extracting  (45)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.7s\n",
            "Downloading      100%\n",
            "Extracting  (45)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.8s\n",
            "Downloading      100%\n",
            "Extracting  (43)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 6.9s\n",
            "Downloading      100%\n",
            "Extracting  (43)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.0s\n",
            "Downloading      100%\n",
            "Extracting  (42)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.1s\n",
            "Downloading      100%\n",
            "Extracting  (41)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.2s\n",
            "Downloading      100%\n",
            "Extracting  (41)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.3s\n",
            "Downloading      100%\n",
            "Extracting  (39)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.4s\n",
            "Downloading      100%\n",
            "Extracting  (39)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.5s\n",
            "Downloading      100%\n",
            "Extracting  (38)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.6s\n",
            "Downloading      100%\n",
            "Extracting  (38)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.7s\n",
            "Downloading      100%\n",
            "Extracting  (38)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.8s\n",
            "Downloading      100%\n",
            "Extracting  (37)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 7.9s\n",
            "Downloading      100%\n",
            "Extracting  (37)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.0s\n",
            "Downloading      100%\n",
            "Extracting  (37)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.1s\n",
            "Downloading      100%\n",
            "Extracting  (37)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.2s\n",
            "Downloading      100%\n",
            "Extracting  (36)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.3s\n",
            "Downloading      100%\n",
            "Extracting  (35)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.4s\n",
            "Downloading      100%\n",
            "Extracting  (35)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.5s\n",
            "Downloading      100%\n",
            "Extracting  (34)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.6s\n",
            "Downloading      100%\n",
            "Extracting  (33)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.7s\n",
            "Downloading      100%\n",
            "Extracting  (33)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.8s\n",
            "Downloading      100%\n",
            "Extracting  (31)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 8.9s\n",
            "Downloading      100%\n",
            "Extracting  (31)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.0s\n",
            "Downloading      100%\n",
            "Extracting  (31)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.1s\n",
            "Downloading      100%\n",
            "Extracting  (29)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.2s\n",
            "Downloading      100%\n",
            "Extracting  (29)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.3s\n",
            "Downloading      100%\n",
            "Extracting  (28)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.4s\n",
            "Downloading      100%\n",
            "Extracting  (27)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.5s\n",
            "Downloading      100%\n",
            "Extracting  (27)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.6s\n",
            "Downloading      100%\n",
            "Extracting  (26)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.7s\n",
            "Downloading      100%\n",
            "Extracting  (26)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.8s\n",
            "Downloading      100%\n",
            "Extracting  (24)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 9.9s\n",
            "Downloading      100%\n",
            "Extracting  (24)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.0s\n",
            "Downloading      100%\n",
            "Extracting  (24)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.1s\n",
            "Downloading      100%\n",
            "Extracting  (23)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.2s\n",
            "Downloading      100%\n",
            "Extracting  (23)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.3s\n",
            "Downloading      100%\n",
            "Extracting  (22)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.4s\n",
            "Downloading      100%\n",
            "Extracting  (21)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.5s\n",
            "Downloading      100%\n",
            "Extracting  (21)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.6s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.7s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.8s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 10.9s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.0s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.1s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.2s\n",
            "Downloading      100%\n",
            "Extracting  (20)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.3s\n",
            "Downloading      100%\n",
            "Extracting  (19)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.4s\n",
            "Downloading      100%\n",
            "Extracting  (19)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.5s\n",
            "Downloading      100%\n",
            "Extracting  (19)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.6s\n",
            "Downloading      100%\n",
            "Extracting  (19)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.7s\n",
            "Downloading      100%\n",
            "Extracting  (19)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.8s\n",
            "Downloading      100%\n",
            "Extracting  (19)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 11.9s\n",
            "Downloading      100%\n",
            "Extracting  (18)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.0s\n",
            "Downloading      100%\n",
            "Extracting  (18)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.1s\n",
            "Downloading      100%\n",
            "Extracting  (18)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.2s\n",
            "Downloading      100%\n",
            "Extracting  (18)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.3s\n",
            "Downloading      100%\n",
            "Extracting  (18)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.4s\n",
            "Downloading      100%\n",
            "Extracting  (17)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.5s\n",
            "Downloading      100%\n",
            "Extracting  (17)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.6s\n",
            "Downloading      100%\n",
            "Extracting  (16)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.7s\n",
            "Downloading      100%\n",
            "Extracting  (16)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.8s\n",
            "Downloading      100%\n",
            "Extracting  (16)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 12.9s\n",
            "Downloading      100%\n",
            "Extracting  (15)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.0s\n",
            "Downloading      100%\n",
            "Extracting  (15)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.1s\n",
            "Downloading      100%\n",
            "Extracting  (14)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.2s\n",
            "Downloading      100%\n",
            "Extracting  (14)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.3s\n",
            "Downloading      100%\n",
            "Extracting  (14)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.4s\n",
            "Downloading      100%\n",
            "Extracting  (13)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.5s\n",
            "Downloading      100%\n",
            "Extracting  (12)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.6s\n",
            "Downloading      100%\n",
            "Extracting  (12)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.7s\n",
            "Downloading      100%\n",
            "Extracting  (12)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.8s\n",
            "Downloading      100%\n",
            "Extracting  (11)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 13.9s\n",
            "Downloading      100%\n",
            "Extracting  (10)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.0s\n",
            "Downloading      100%\n",
            "Extracting  (10)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 14.1s\n",
            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
            "Extracting   (3)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 15.9s\n",
            "Downloading      100%\n",
            "Extracting   (3)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.0s\n",
            "Downloading      100%\n",
            "Extracting   (3)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.1s\n",
            "Downloading      100%\n",
            "Extracting   (3)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.2s\n",
            "Downloading      100%\n",
            "Extracting   (2)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.3s\n",
            "Downloading      100%\n",
            "Extracting   (1)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.4s\n",
            "Downloading      100%\n",
            "Extracting   (1)  ⣾  \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 16.5s\n",
            "Downloading      100%\n",
            "Extracting       100%\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G\u001b[?25h\n",
            "Downloading and Extracting Packages\n",
            "\n",
            "Preparing transaction: - \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n",
            "Verifying transaction: | \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\bdone\n",
            "Executing transaction: / \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n",
            "/usr/local/lib/python3.10/site-packages/conda_package_streaming/package_streaming.py:19: UserWarning: zstandard could not be imported. Running without .conda support.\n",
            "  warnings.warn(\"zstandard could not be imported. Running without .conda support.\")\n",
            "/usr/local/lib/python3.10/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support\n",
            "  _warnings.warn(\"Install zstandard Python bindings for .conda support\")\n",
            "\n",
            "                  __    __    __    __\n",
            "                 /  \\  /  \\  /  \\  /  \\\n",
            "                /    \\/    \\/    \\/    \\\n",
            "███████████████/  /██/  /██/  /██/  /████████████████████████\n",
            "              /  / \\   / \\   / \\   / \\  \\____\n",
            "             /  /   \\_/   \\_/   \\_/   \\    o \\__,\n",
            "            / _/                       \\_____/  `\n",
            "            |/\n",
            "        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗\n",
            "        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗\n",
            "        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║\n",
            "        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║\n",
            "        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║\n",
            "        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝\n",
            "\n",
            "        mamba (1.4.1) supported by @QuantStack\n",
            "\n",
            "        GitHub:  https://github.com/mamba-org/mamba\n",
            "        Twitter: https://twitter.com/QuantStack\n",
            "\n",
            "█████████████████████████████████████████████████████████████\n",
            "\n",
            "/usr/local/lib/python3.10/site-packages/conda_package_streaming/package_streaming.py:19: UserWarning: zstandard could not be imported. Running without .conda support.\n",
            "  warnings.warn(\"zstandard could not be imported. Running without .conda support.\")\n",
            "/usr/local/lib/python3.10/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support\n",
            "  _warnings.warn(\"Install zstandard Python bindings for .conda support\")\n",
            "\n",
            "Looking for: ['openbabel']\n",
            "\n",
            "conda-forge/linux-64                                        Using cache\n",
            "conda-forge/noarch                                          Using cache\n",
            "\n",
            "Pinned packages:\n",
            "  - python 3.10.*\n",
            "  - python 3.10.*\n",
            "  - python_abi 3.10.* *cp310*\n",
            "  - cudatoolkit 11.8.*\n",
            "\n",
            "\n",
            "Transaction\n",
            "\n",
            "  Prefix: /usr/local\n",
            "\n",
            "  Updating specs:\n",
            "\n",
            "   - openbabel\n",
            "   - ca-certificates\n",
            "   - certifi\n",
            "   - openssl\n",
            "\n",
            "\n",
            "  Package      Version  Build            Channel                  Size\n",
            "────────────────────────────────────────────────────────────────────────\n",
            "  Install:\n",
            "────────────────────────────────────────────────────────────────────────\n",
            "\n",
            "  \u001b[32m+ openbabel\u001b[0m    3.1.1  py310h956b46e_8  conda-forge/linux-64      5MB\n",
            "\n",
            "  Summary:\n",
            "\n",
            "  Install: 1 packages\n",
            "\n",
            "  Total download: 5MB\n",
            "\n",
            "────────────────────────────────────────────────────────────────────────\n",
            "\n",
            "\n",
            "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n",
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            "Extracting         0%\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gopenbabel                                            5.2MB @  19.7MB/s  0.3s\n",
            "[+] 0.3s\n",
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            "Downloading      100%\n",
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            "Downloading      100%\n",
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            "Downloading and Extracting Packages\n",
            "\n",
            "Preparing transaction: - \b\bdone\n",
            "Verifying transaction: | \b\bdone\n",
            "Executing transaction: - \b\bdone\n",
            "Collecting meeko\n",
            "  Downloading meeko-0.5.0-py3-none-any.whl (144 kB)\n",
            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m144.4/144.4 kB\u001b[0m \u001b[31m5.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hRequirement already satisfied: numpy>=1.18 in /usr/local/lib/python3.10/site-packages (from meeko) (1.26.2)\n",
            "Installing collected packages: meeko\n",
            "Successfully installed meeko-0.5.0\n",
            "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
            "\u001b[0mCollecting py3Dmol\n",
            "  Downloading py3Dmol-2.0.4-py2.py3-none-any.whl (12 kB)\n",
            "Installing collected packages: py3Dmol\n",
            "Successfully installed py3Dmol-2.0.4\n",
            "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
            "\u001b[0m"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Installing the rdkit patkage"
      ],
      "metadata": {
        "id": "LOqfCOtYHcXy"
      }
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "YDBNN6Ygh8JF",
        "outputId": "8be92399-df6d-44c1-a5b7-f7a4ef695a94",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "import os\n",
        "import numpy as np\n",
        "from sklearn.ensemble import RandomForestClassifier\n",
        "from sklearn.model_selection import StratifiedKFold\n",
        "from sklearn.metrics import accuracy_score\n",
        "from rdkit import Chem\n",
        "from rdkit.Chem import AllChem\n",
        "from rdkit.Chem import Draw\n",
        "from rdkit.Chem.Draw import IPythonConsole\n",
        "from rdkit.Chem import DataStructs\n",
        "from rdkit.Chem import RDConfig\n",
        "from rdkit.Chem import rdBase\n",
        "import pickle\n",
        "from sklearn.metrics import classification_report, confusion_matrix, accuracy_score\n",
        "print(rdBase.rdkitVersion)"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "2023.09.3\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "yaLvbWwQkPRf",
        "outputId": "9bc5c5d6-7db8-43ac-ab8e-a1e7c6ebd929",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "!wget https://github.com/gnina/gnina/releases/download/v1.0.1/gnina\n",
        "!chmod +x gnina\n",
        "!./gnina --help"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2023-12-07 07:56:31--  https://github.com/gnina/gnina/releases/download/v1.0.1/gnina\n",
            "Resolving github.com (github.com)... 20.205.243.166\n",
            "Connecting to github.com (github.com)|20.205.243.166|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/45548146/47de2300-8bd4-11eb-8355-430c51e07fae?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20231207%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20231207T075631Z&X-Amz-Expires=300&X-Amz-Signature=e04edde8fe9e838684ae2ab9f9d446c3cb58a9b62e60b147b0bfe38fb1dec09e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=45548146&response-content-disposition=attachment%3B%20filename%3Dgnina&response-content-type=application%2Foctet-stream [following]\n",
            "--2023-12-07 07:56:31--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/45548146/47de2300-8bd4-11eb-8355-430c51e07fae?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20231207%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20231207T075631Z&X-Amz-Expires=300&X-Amz-Signature=e04edde8fe9e838684ae2ab9f9d446c3cb58a9b62e60b147b0bfe38fb1dec09e&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=45548146&response-content-disposition=attachment%3B%20filename%3Dgnina&response-content-type=application%2Foctet-stream\n",
            "Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...\n",
            "Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.108.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 562802104 (537M) [application/octet-stream]\n",
            "Saving to: ‘gnina’\n",
            "\n",
            "gnina               100%[===================>] 536.73M  17.3MB/s    in 32s     \n",
            "\n",
            "2023-12-07 07:57:04 (16.7 MB/s) - ‘gnina’ saved [562802104/562802104]\n",
            "\n",
            "\n",
            "Input:\n",
            "  -r [ --receptor ] arg            rigid part of the receptor\n",
            "  --flex arg                       flexible side chains, if any (PDBQT)\n",
            "  -l [ --ligand ] arg              ligand(s)\n",
            "  --flexres arg                    flexible side chains specified by comma \n",
            "                                   separated list of chain:resid\n",
            "  --flexdist_ligand arg            Ligand to use for flexdist\n",
            "  --flexdist arg                   set all side chains within specified \n",
            "                                   distance to flexdist_ligand to flexible\n",
            "  --flex_limit arg                 Hard limit for the number of flexible \n",
            "                                   residues\n",
            "  --flex_max arg                   Retain at at most the closest flex_max \n",
            "                                   flexible residues\n",
            "\n",
            "Search space (required):\n",
            "  --center_x arg                   X coordinate of the center\n",
            "  --center_y arg                   Y coordinate of the center\n",
            "  --center_z arg                   Z coordinate of the center\n",
            "  --size_x arg                     size in the X dimension (Angstroms)\n",
            "  --size_y arg                     size in the Y dimension (Angstroms)\n",
            "  --size_z arg                     size in the Z dimension (Angstroms)\n",
            "  --autobox_ligand arg             Ligand to use for autobox\n",
            "  --autobox_add arg                Amount of buffer space to add to \n",
            "                                   auto-generated box (default +4 on all six \n",
            "                                   sides)\n",
            "  --autobox_extend arg (=1)        Expand the autobox if needed to ensure the \n",
            "                                   input conformation of the ligand being \n",
            "                                   docked can freely rotate within the box.\n",
            "  --no_lig                         no ligand; for sampling/minimizing flexible \n",
            "                                   residues\n",
            "\n",
            "Scoring and minimization options:\n",
            "  --scoring arg                    specify alternative built-in scoring \n",
            "                                   function: ad4_scoring default dkoes_fast \n",
            "                                   dkoes_scoring dkoes_scoring_old vina vinardo\n",
            "  --custom_scoring arg             custom scoring function file\n",
            "  --custom_atoms arg               custom atom type parameters file\n",
            "  --score_only                     score provided ligand pose\n",
            "  --local_only                     local search only using autobox (you \n",
            "                                   probably want to use --minimize)\n",
            "  --minimize                       energy minimization\n",
            "  --randomize_only                 generate random poses, attempting to avoid \n",
            "                                   clashes\n",
            "  --num_mc_steps arg               number of monte carlo steps to take in each \n",
            "                                   chain\n",
            "  --num_mc_saved arg               number of top poses saved in each monte \n",
            "                                   carlo chain\n",
            "  --minimize_iters arg (=0)        number iterations of steepest descent; \n",
            "                                   default scales with rotors and usually isn't\n",
            "                                   sufficient for convergence\n",
            "  --accurate_line                  use accurate line search\n",
            "  --simple_ascent                  use simple gradient ascent\n",
            "  --minimize_early_term            Stop minimization before convergence \n",
            "                                   conditions are fully met.\n",
            "  --minimize_single_full           During docking perform a single full \n",
            "                                   minimization instead of a truncated \n",
            "                                   pre-evaluate followed by a full.\n",
            "  --approximation arg              approximation (linear, spline, or exact) to \n",
            "                                   use\n",
            "  --factor arg                     approximation factor: higher results in a \n",
            "                                   finer-grained approximation\n",
            "  --force_cap arg                  max allowed force; lower values more gently \n",
            "                                   minimize clashing structures\n",
            "  --user_grid arg                  Autodock map file for user grid data based \n",
            "                                   calculations\n",
            "  --user_grid_lambda arg (=-1)     Scales user_grid and functional scoring\n",
            "  --print_terms                    Print all available terms with default \n",
            "                                   parameterizations\n",
            "  --print_atom_types               Print all available atom types\n",
            "\n",
            "Convolutional neural net (CNN) scoring:\n",
            "  --cnn_scoring arg (=1)           Amount of CNN scoring: none, rescore \n",
            "                                   (default), refinement, all\n",
            "  --cnn arg                        built-in model to use, specify \n",
            "                                   PREFIX_ensemble to evaluate an ensemble of \n",
            "                                   models starting with PREFIX: \n",
            "                                   crossdock_default2018 crossdock_default2018_\n",
            "                                   1 crossdock_default2018_2 \n",
            "                                   crossdock_default2018_3 \n",
            "                                   crossdock_default2018_4 default2017 dense \n",
            "                                   dense_1 dense_2 dense_3 dense_4 \n",
            "                                   general_default2018 general_default2018_1 \n",
            "                                   general_default2018_2 general_default2018_3 \n",
            "                                   general_default2018_4 redock_default2018 \n",
            "                                   redock_default2018_1 redock_default2018_2 \n",
            "                                   redock_default2018_3 redock_default2018_4\n",
            "  --cnn_model arg                  caffe cnn model file; if not specified a \n",
            "                                   default model will be used\n",
            "  --cnn_weights arg                caffe cnn weights file (*.caffemodel); if \n",
            "                                   not specified default weights (trained on \n",
            "                                   the default model) will be used\n",
            "  --cnn_resolution arg (=0.5)      resolution of grids, don't change unless you\n",
            "                                   really know what you are doing\n",
            "  --cnn_rotation arg (=0)          evaluate multiple rotations of pose (max 24)\n",
            "  --cnn_update_min_frame           During minimization, recenter coordinate \n",
            "                                   frame as ligand moves\n",
            "  --cnn_freeze_receptor            Don't move the receptor with respect to a \n",
            "                                   fixed coordinate system\n",
            "  --cnn_mix_emp_force              Merge CNN and empirical minus forces\n",
            "  --cnn_mix_emp_energy             Merge CNN and empirical energy\n",
            "  --cnn_empirical_weight arg (=1)  Weight for scaling and merging empirical \n",
            "                                   force and energy \n",
            "  --cnn_outputdx                   Dump .dx files of atom grid gradient.\n",
            "  --cnn_outputxyz                  Dump .xyz files of atom gradient.\n",
            "  --cnn_xyzprefix arg (=gradient)  Prefix for atom gradient .xyz files\n",
            "  --cnn_center_x arg               X coordinate of the CNN center\n",
            "  --cnn_center_y arg               Y coordinate of the CNN center\n",
            "  --cnn_center_z arg               Z coordinate of the CNN center\n",
            "  --cnn_verbose                    Enable verbose output for CNN debugging\n",
            "\n",
            "Output:\n",
            "  -o [ --out ] arg                 output file name, format taken from file \n",
            "                                   extension\n",
            "  --out_flex arg                   output file for flexible receptor residues\n",
            "  --log arg                        optionally, write log file\n",
            "  --atom_terms arg                 optionally write per-atom interaction term \n",
            "                                   values\n",
            "  --atom_term_data                 embedded per-atom interaction terms in \n",
            "                                   output sd data\n",
            "  --pose_sort_order arg (=0)       How to sort docking results: CNNscore \n",
            "                                   (default), CNNaffinity, Energy\n",
            "\n",
            "Misc (optional):\n",
            "  --cpu arg                        the number of CPUs to use (the default is to\n",
            "                                   try to detect the number of CPUs or, failing\n",
            "                                   that, use 1)\n",
            "  --seed arg                       explicit random seed\n",
            "  --exhaustiveness arg (=8)        exhaustiveness of the global search (roughly\n",
            "                                   proportional to time)\n",
            "  --num_modes arg (=9)             maximum number of binding modes to generate\n",
            "  --min_rmsd_filter arg (=1)       rmsd value used to filter final poses to \n",
            "                                   remove redundancy\n",
            "  -q [ --quiet ]                   Suppress output messages\n",
            "  --addH arg                       automatically add hydrogens in ligands (on \n",
            "                                   by default)\n",
            "  --stripH arg                     remove hydrogens from molecule _after_ \n",
            "                                   performing atom typing for efficiency (on by\n",
            "                                   default)\n",
            "  --device arg (=0)                GPU device to use\n",
            "  --no_gpu                         Disable GPU acceleration, even if available.\n",
            "\n",
            "Configuration file (optional):\n",
            "  --config arg                     the above options can be put here\n",
            "\n",
            "Information (optional):\n",
            "  --help                           display usage summary\n",
            "  --help_hidden                    display usage summary with hidden options\n",
            "  --version                        display program version\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "iZGFOyXM_Chl"
      },
      "source": [
        "### update the zikans2bns3 protease and compounds (cvs file database and receptor pdb)"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "gCuJOcPRlMSv",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 240
        },
        "outputId": "795237b4-5c1d-4430-c7ef-049502d58c57"
      },
      "source": [
        "from google.colab import files\n",
        "uploaded = files.upload()\n",
        "uploaded = files.upload()\n",
        "!ls -l"
      ],
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ],
            "text/html": [
              "\n",
              "     <input type=\"file\" id=\"files-b49028b4-8e2b-48ef-802f-705239a2022d\" name=\"files[]\" multiple disabled\n",
              "        style=\"border:none\" />\n",
              "     <output id=\"result-b49028b4-8e2b-48ef-802f-705239a2022d\">\n",
              "      Upload widget is only available when the cell has been executed in the\n",
              "      current browser session. Please rerun this cell to enable.\n",
              "      </output>\n",
              "      <script>// Copyright 2017 Google LLC\n",
              "//\n",
              "// Licensed under the Apache License, Version 2.0 (the \"License\");\n",
              "// you may not use this file except in compliance with the License.\n",
              "// You may obtain a copy of the License at\n",
              "//\n",
              "//      http://www.apache.org/licenses/LICENSE-2.0\n",
              "//\n",
              "// Unless required by applicable law or agreed to in writing, software\n",
              "// distributed under the License is distributed on an \"AS IS\" BASIS,\n",
              "// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
              "// See the License for the specific language governing permissions and\n",
              "// limitations under the License.\n",
              "\n",
              "/**\n",
              " * @fileoverview Helpers for google.colab Python module.\n",
              " */\n",
              "(function(scope) {\n",
              "function span(text, styleAttributes = {}) {\n",
              "  const element = document.createElement('span');\n",
              "  element.textContent = text;\n",
              "  for (const key of Object.keys(styleAttributes)) {\n",
              "    element.style[key] = styleAttributes[key];\n",
              "  }\n",
              "  return element;\n",
              "}\n",
              "\n",
              "// Max number of bytes which will be uploaded at a time.\n",
              "const MAX_PAYLOAD_SIZE = 100 * 1024;\n",
              "\n",
              "function _uploadFiles(inputId, outputId) {\n",
              "  const steps = uploadFilesStep(inputId, outputId);\n",
              "  const outputElement = document.getElementById(outputId);\n",
              "  // Cache steps on the outputElement to make it available for the next call\n",
              "  // to uploadFilesContinue from Python.\n",
              "  outputElement.steps = steps;\n",
              "\n",
              "  return _uploadFilesContinue(outputId);\n",
              "}\n",
              "\n",
              "// This is roughly an async generator (not supported in the browser yet),\n",
              "// where there are multiple asynchronous steps and the Python side is going\n",
              "// to poll for completion of each step.\n",
              "// This uses a Promise to block the python side on completion of each step,\n",
              "// then passes the result of the previous step as the input to the next step.\n",
              "function _uploadFilesContinue(outputId) {\n",
              "  const outputElement = document.getElementById(outputId);\n",
              "  const steps = outputElement.steps;\n",
              "\n",
              "  const next = steps.next(outputElement.lastPromiseValue);\n",
              "  return Promise.resolve(next.value.promise).then((value) => {\n",
              "    // Cache the last promise value to make it available to the next\n",
              "    // step of the generator.\n",
              "    outputElement.lastPromiseValue = value;\n",
              "    return next.value.response;\n",
              "  });\n",
              "}\n",
              "\n",
              "/**\n",
              " * Generator function which is called between each async step of the upload\n",
              " * process.\n",
              " * @param {string} inputId Element ID of the input file picker element.\n",
              " * @param {string} outputId Element ID of the output display.\n",
              " * @return {!Iterable<!Object>} Iterable of next steps.\n",
              " */\n",
              "function* uploadFilesStep(inputId, outputId) {\n",
              "  const inputElement = document.getElementById(inputId);\n",
              "  inputElement.disabled = false;\n",
              "\n",
              "  const outputElement = document.getElementById(outputId);\n",
              "  outputElement.innerHTML = '';\n",
              "\n",
              "  const pickedPromise = new Promise((resolve) => {\n",
              "    inputElement.addEventListener('change', (e) => {\n",
              "      resolve(e.target.files);\n",
              "    });\n",
              "  });\n",
              "\n",
              "  const cancel = document.createElement('button');\n",
              "  inputElement.parentElement.appendChild(cancel);\n",
              "  cancel.textContent = 'Cancel upload';\n",
              "  const cancelPromise = new Promise((resolve) => {\n",
              "    cancel.onclick = () => {\n",
              "      resolve(null);\n",
              "    };\n",
              "  });\n",
              "\n",
              "  // Wait for the user to pick the files.\n",
              "  const files = yield {\n",
              "    promise: Promise.race([pickedPromise, cancelPromise]),\n",
              "    response: {\n",
              "      action: 'starting',\n",
              "    }\n",
              "  };\n",
              "\n",
              "  cancel.remove();\n",
              "\n",
              "  // Disable the input element since further picks are not allowed.\n",
              "  inputElement.disabled = true;\n",
              "\n",
              "  if (!files) {\n",
              "    return {\n",
              "      response: {\n",
              "        action: 'complete',\n",
              "      }\n",
              "    };\n",
              "  }\n",
              "\n",
              "  for (const file of files) {\n",
              "    const li = document.createElement('li');\n",
              "    li.append(span(file.name, {fontWeight: 'bold'}));\n",
              "    li.append(span(\n",
              "        `(${file.type || 'n/a'}) - ${file.size} bytes, ` +\n",
              "        `last modified: ${\n",
              "            file.lastModifiedDate ? file.lastModifiedDate.toLocaleDateString() :\n",
              "                                    'n/a'} - `));\n",
              "    const percent = span('0% done');\n",
              "    li.appendChild(percent);\n",
              "\n",
              "    outputElement.appendChild(li);\n",
              "\n",
              "    const fileDataPromise = new Promise((resolve) => {\n",
              "      const reader = new FileReader();\n",
              "      reader.onload = (e) => {\n",
              "        resolve(e.target.result);\n",
              "      };\n",
              "      reader.readAsArrayBuffer(file);\n",
              "    });\n",
              "    // Wait for the data to be ready.\n",
              "    let fileData = yield {\n",
              "      promise: fileDataPromise,\n",
              "      response: {\n",
              "        action: 'continue',\n",
              "      }\n",
              "    };\n",
              "\n",
              "    // Use a chunked sending to avoid message size limits. See b/62115660.\n",
              "    let position = 0;\n",
              "    do {\n",
              "      const length = Math.min(fileData.byteLength - position, MAX_PAYLOAD_SIZE);\n",
              "      const chunk = new Uint8Array(fileData, position, length);\n",
              "      position += length;\n",
              "\n",
              "      const base64 = btoa(String.fromCharCode.apply(null, chunk));\n",
              "      yield {\n",
              "        response: {\n",
              "          action: 'append',\n",
              "          file: file.name,\n",
              "          data: base64,\n",
              "        },\n",
              "      };\n",
              "\n",
              "      let percentDone = fileData.byteLength === 0 ?\n",
              "          100 :\n",
              "          Math.round((position / fileData.byteLength) * 100);\n",
              "      percent.textContent = `${percentDone}% done`;\n",
              "\n",
              "    } while (position < fileData.byteLength);\n",
              "  }\n",
              "\n",
              "  // All done.\n",
              "  yield {\n",
              "    response: {\n",
              "      action: 'complete',\n",
              "    }\n",
              "  };\n",
              "}\n",
              "\n",
              "scope.google = scope.google || {};\n",
              "scope.google.colab = scope.google.colab || {};\n",
              "scope.google.colab._files = {\n",
              "  _uploadFiles,\n",
              "  _uploadFilesContinue,\n",
              "};\n",
              "})(self);\n",
              "</script> "
            ]
          },
          "metadata": {}
        },
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Saving database.csv to database.csv\n"
          ]
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ],
            "text/html": [
              "\n",
              "     <input type=\"file\" id=\"files-3bba08e6-cbad-480c-965d-e67a18d045e9\" name=\"files[]\" multiple disabled\n",
              "        style=\"border:none\" />\n",
              "     <output id=\"result-3bba08e6-cbad-480c-965d-e67a18d045e9\">\n",
              "      Upload widget is only available when the cell has been executed in the\n",
              "      current browser session. Please rerun this cell to enable.\n",
              "      </output>\n",
              "      <script>// Copyright 2017 Google LLC\n",
              "//\n",
              "// Licensed under the Apache License, Version 2.0 (the \"License\");\n",
              "// you may not use this file except in compliance with the License.\n",
              "// You may obtain a copy of the License at\n",
              "//\n",
              "//      http://www.apache.org/licenses/LICENSE-2.0\n",
              "//\n",
              "// Unless required by applicable law or agreed to in writing, software\n",
              "// distributed under the License is distributed on an \"AS IS\" BASIS,\n",
              "// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
              "// See the License for the specific language governing permissions and\n",
              "// limitations under the License.\n",
              "\n",
              "/**\n",
              " * @fileoverview Helpers for google.colab Python module.\n",
              " */\n",
              "(function(scope) {\n",
              "function span(text, styleAttributes = {}) {\n",
              "  const element = document.createElement('span');\n",
              "  element.textContent = text;\n",
              "  for (const key of Object.keys(styleAttributes)) {\n",
              "    element.style[key] = styleAttributes[key];\n",
              "  }\n",
              "  return element;\n",
              "}\n",
              "\n",
              "// Max number of bytes which will be uploaded at a time.\n",
              "const MAX_PAYLOAD_SIZE = 100 * 1024;\n",
              "\n",
              "function _uploadFiles(inputId, outputId) {\n",
              "  const steps = uploadFilesStep(inputId, outputId);\n",
              "  const outputElement = document.getElementById(outputId);\n",
              "  // Cache steps on the outputElement to make it available for the next call\n",
              "  // to uploadFilesContinue from Python.\n",
              "  outputElement.steps = steps;\n",
              "\n",
              "  return _uploadFilesContinue(outputId);\n",
              "}\n",
              "\n",
              "// This is roughly an async generator (not supported in the browser yet),\n",
              "// where there are multiple asynchronous steps and the Python side is going\n",
              "// to poll for completion of each step.\n",
              "// This uses a Promise to block the python side on completion of each step,\n",
              "// then passes the result of the previous step as the input to the next step.\n",
              "function _uploadFilesContinue(outputId) {\n",
              "  const outputElement = document.getElementById(outputId);\n",
              "  const steps = outputElement.steps;\n",
              "\n",
              "  const next = steps.next(outputElement.lastPromiseValue);\n",
              "  return Promise.resolve(next.value.promise).then((value) => {\n",
              "    // Cache the last promise value to make it available to the next\n",
              "    // step of the generator.\n",
              "    outputElement.lastPromiseValue = value;\n",
              "    return next.value.response;\n",
              "  });\n",
              "}\n",
              "\n",
              "/**\n",
              " * Generator function which is called between each async step of the upload\n",
              " * process.\n",
              " * @param {string} inputId Element ID of the input file picker element.\n",
              " * @param {string} outputId Element ID of the output display.\n",
              " * @return {!Iterable<!Object>} Iterable of next steps.\n",
              " */\n",
              "function* uploadFilesStep(inputId, outputId) {\n",
              "  const inputElement = document.getElementById(inputId);\n",
              "  inputElement.disabled = false;\n",
              "\n",
              "  const outputElement = document.getElementById(outputId);\n",
              "  outputElement.innerHTML = '';\n",
              "\n",
              "  const pickedPromise = new Promise((resolve) => {\n",
              "    inputElement.addEventListener('change', (e) => {\n",
              "      resolve(e.target.files);\n",
              "    });\n",
              "  });\n",
              "\n",
              "  const cancel = document.createElement('button');\n",
              "  inputElement.parentElement.appendChild(cancel);\n",
              "  cancel.textContent = 'Cancel upload';\n",
              "  const cancelPromise = new Promise((resolve) => {\n",
              "    cancel.onclick = () => {\n",
              "      resolve(null);\n",
              "    };\n",
              "  });\n",
              "\n",
              "  // Wait for the user to pick the files.\n",
              "  const files = yield {\n",
              "    promise: Promise.race([pickedPromise, cancelPromise]),\n",
              "    response: {\n",
              "      action: 'starting',\n",
              "    }\n",
              "  };\n",
              "\n",
              "  cancel.remove();\n",
              "\n",
              "  // Disable the input element since further picks are not allowed.\n",
              "  inputElement.disabled = true;\n",
              "\n",
              "  if (!files) {\n",
              "    return {\n",
              "      response: {\n",
              "        action: 'complete',\n",
              "      }\n",
              "    };\n",
              "  }\n",
              "\n",
              "  for (const file of files) {\n",
              "    const li = document.createElement('li');\n",
              "    li.append(span(file.name, {fontWeight: 'bold'}));\n",
              "    li.append(span(\n",
              "        `(${file.type || 'n/a'}) - ${file.size} bytes, ` +\n",
              "        `last modified: ${\n",
              "            file.lastModifiedDate ? file.lastModifiedDate.toLocaleDateString() :\n",
              "                                    'n/a'} - `));\n",
              "    const percent = span('0% done');\n",
              "    li.appendChild(percent);\n",
              "\n",
              "    outputElement.appendChild(li);\n",
              "\n",
              "    const fileDataPromise = new Promise((resolve) => {\n",
              "      const reader = new FileReader();\n",
              "      reader.onload = (e) => {\n",
              "        resolve(e.target.result);\n",
              "      };\n",
              "      reader.readAsArrayBuffer(file);\n",
              "    });\n",
              "    // Wait for the data to be ready.\n",
              "    let fileData = yield {\n",
              "      promise: fileDataPromise,\n",
              "      response: {\n",
              "        action: 'continue',\n",
              "      }\n",
              "    };\n",
              "\n",
              "    // Use a chunked sending to avoid message size limits. See b/62115660.\n",
              "    let position = 0;\n",
              "    do {\n",
              "      const length = Math.min(fileData.byteLength - position, MAX_PAYLOAD_SIZE);\n",
              "      const chunk = new Uint8Array(fileData, position, length);\n",
              "      position += length;\n",
              "\n",
              "      const base64 = btoa(String.fromCharCode.apply(null, chunk));\n",
              "      yield {\n",
              "        response: {\n",
              "          action: 'append',\n",
              "          file: file.name,\n",
              "          data: base64,\n",
              "        },\n",
              "      };\n",
              "\n",
              "      let percentDone = fileData.byteLength === 0 ?\n",
              "          100 :\n",
              "          Math.round((position / fileData.byteLength) * 100);\n",
              "      percent.textContent = `${percentDone}% done`;\n",
              "\n",
              "    } while (position < fileData.byteLength);\n",
              "  }\n",
              "\n",
              "  // All done.\n",
              "  yield {\n",
              "    response: {\n",
              "      action: 'complete',\n",
              "    }\n",
              "  };\n",
              "}\n",
              "\n",
              "scope.google = scope.google || {};\n",
              "scope.google.colab = scope.google.colab || {};\n",
              "scope.google.colab._files = {\n",
              "  _uploadFiles,\n",
              "  _uploadFilesContinue,\n",
              "};\n",
              "})(self);\n",
              "</script> "
            ]
          },
          "metadata": {}
        },
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Saving rec.pdb to rec.pdb\n",
            "total 550032\n",
            "-rw-r--r-- 1 root root     20651 Dec  7 07:55 condacolab_install.log\n",
            "-rw-r--r-- 1 root root      4345 Dec  7 07:57 database.csv\n",
            "-rwxr-xr-x 1 root root 562802104 Dec  8  2021 gnina\n",
            "-rw-r--r-- 1 root root    386857 Dec  7 07:57 rec.pdb\n",
            "drwxr-xr-x 1 root root      4096 Dec  4 14:27 sample_data\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "rename"
      ],
      "metadata": {
        "id": "_m7aflvLQRnT"
      }
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "gETxEH6Dl7HN",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "87e183ff-6df1-47e6-ae5f-e29a1e474091"
      },
      "source": [
        "!mv *.pdb rec.pdb"
      ],
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "mv: 'rec.pdb' and 'rec.pdb' are the same file\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import csv\n",
        "import py3Dmol\n",
        "import os\n",
        "from openbabel import pybel\n",
        "from rdkit import Chem\n",
        "from rdkit.Chem import AllChem\n",
        "from rdkit.Chem.Draw import MolToImage\n",
        "#\n",
        "with open('database.csv', 'r', newline='') as csvfile:\n",
        "    csv_reader = csv.reader(csvfile)\n",
        "    for row in csv_reader:\n",
        "        parameter1, parameter2, parameter3, parameter4, parameter5, parameter6  = row[0], row[1], row[2], row[3], row[4], row[5]\n",
        "        namesdf  = parameter1+'.sdf'\n",
        "        namepdbqt = parameter1+'.pdbqt'\n",
        "        smiles = parameter2\n",
        "        mol = Chem.MolFromSmiles(smiles)\n",
        "        smi = Chem.MolToSmiles(mol)\n",
        "        out=pybel.Outputfile(filename=namepdbqt,format='pdbqt',overwrite=True)\n",
        "        pdbqt = pybel.readstring(\"smi\", smi)\n",
        "        pdbqt.make3D(forcefield='mmff94', steps=100)\n",
        "        out.write(pdbqt)\n",
        "        out.close()"
      ],
      "metadata": {
        "id": "mLSHiDHPz4Qh"
      },
      "execution_count": 5,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!ls -l"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "lL1FQlZj3BSV",
        "outputId": "c214a562-a0de-4f63-a5df-244636ef5bc8"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "total 550244\n",
            "-rw-r--r-- 1 root root      4843 Dec  7 07:57 Boceprevir.pdbqt\n",
            "-rw-r--r-- 1 root root      4057 Dec  7 07:57 calpain_inhibitors_I.pdbqt\n",
            "-rw-r--r-- 1 root root      4603 Dec  7 07:57 Calpain_Inhibitor_XII.pdbqt\n",
            "-rw-r--r-- 1 root root      5511 Dec  7 07:57 CI006628.pdbqt\n",
            "-rw-r--r-- 1 root root      5333 Dec  7 07:57 CI006629.pdbqt\n",
            "-rw-r--r-- 1 root root      5540 Dec  7 07:57 CI006630.pdbqt\n",
            "-rw-r--r-- 1 root root      5495 Dec  7 07:57 CI006632.pdbqt\n",
            "-rw-r--r-- 1 root root      5495 Dec  7 07:57 CI006634.pdbqt\n",
            "-rw-r--r-- 1 root root      4230 Dec  7 07:57 CI006651.pdbqt\n",
            "-rw-r--r-- 1 root root      4358 Dec  7 07:57 CI006653.pdbqt\n",
            "-rw-r--r-- 1 root root      4554 Dec  7 07:57 CI006655.pdbqt\n",
            "-rw-r--r-- 1 root root      4691 Dec  7 07:57 CI006656.pdbqt\n",
            "-rw-r--r-- 1 root root      4570 Dec  7 07:57 CI006657.pdbqt\n",
            "-rw-r--r-- 1 root root      4699 Dec  7 07:57 CI006659.pdbqt\n",
            "-rw-r--r-- 1 root root      4658 Dec  7 07:57 CI006660.pdbqt\n",
            "-rw-r--r-- 1 root root      4529 Dec  7 07:57 CI006661.pdbqt\n",
            "-rw-r--r-- 1 root root      5025 Dec  7 07:57 compound11.pdbqt\n",
            "-rw-r--r-- 1 root root      4765 Dec  7 07:57 compound12.pdbqt\n",
            "-rw-r--r-- 1 root root      4286 Dec  7 07:57 compound42.pdbqt\n",
            "-rw-r--r-- 1 root root      5720 Dec  7 07:57 compound7.pdbqt\n",
            "-rw-r--r-- 1 root root     20651 Dec  7 07:55 condacolab_install.log\n",
            "-rw-r--r-- 1 root root      4345 Dec  7 07:57 database.csv\n",
            "-rwxr-xr-x 1 root root 562802104 Dec  8  2021 gnina\n",
            "-rw-r--r-- 1 root root      3733 Dec  7 07:57 MI23.pdbqt\n",
            "-rw-r--r-- 1 root root      3733 Dec  7 07:57 MI30.pdbqt\n",
            "-rw-r--r-- 1 root root      4834 Dec  7 07:57 MPI3.pdbqt\n",
            "-rw-r--r-- 1 root root      4971 Dec  7 07:57 MPI8.pdbqt\n",
            "-rw-r--r-- 1 root root      4292 Dec  7 07:57 Nirmatrelvir.pdbqt\n",
            "-rw-r--r-- 1 root root      5507 Dec  7 07:57 P0C6X7.pdbqt\n",
            "-rw-r--r-- 1 root root      4529 Dec  7 07:57 PF-00835231.pdbqt\n",
            "-rw-r--r-- 1 root root    386857 Dec  7 07:57 rec.pdb\n",
            "drwxr-xr-x 1 root root      4096 Dec  4 14:27 sample_data\n",
            "-rw-r--r-- 1 root root      4553 Dec  7 07:57 UWAJ246.pdbqt\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "cvV6wjFqmAuu",
        "outputId": "d9656f66-8729-43c0-a47a-d598fac16273",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "!obabel rec.pdb -xr -O rec.pdbqt\n",
        "!ls -l"
      ],
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "==============================\n",
            "*** Open Babel Warning  in PerceiveBondOrders\n",
            "  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is rec.pdb)\n",
            "\n",
            "1 molecule converted\n",
            "total 550444\n",
            "-rw-r--r-- 1 root root      4843 Dec  7 07:57 Boceprevir.pdbqt\n",
            "-rw-r--r-- 1 root root      4057 Dec  7 07:57 calpain_inhibitors_I.pdbqt\n",
            "-rw-r--r-- 1 root root      4603 Dec  7 07:57 Calpain_Inhibitor_XII.pdbqt\n",
            "-rw-r--r-- 1 root root      5511 Dec  7 07:57 CI006628.pdbqt\n",
            "-rw-r--r-- 1 root root      5333 Dec  7 07:57 CI006629.pdbqt\n",
            "-rw-r--r-- 1 root root      5540 Dec  7 07:57 CI006630.pdbqt\n",
            "-rw-r--r-- 1 root root      5495 Dec  7 07:57 CI006632.pdbqt\n",
            "-rw-r--r-- 1 root root      5495 Dec  7 07:57 CI006634.pdbqt\n",
            "-rw-r--r-- 1 root root      4230 Dec  7 07:57 CI006651.pdbqt\n",
            "-rw-r--r-- 1 root root      4358 Dec  7 07:57 CI006653.pdbqt\n",
            "-rw-r--r-- 1 root root      4554 Dec  7 07:57 CI006655.pdbqt\n",
            "-rw-r--r-- 1 root root      4691 Dec  7 07:57 CI006656.pdbqt\n",
            "-rw-r--r-- 1 root root      4570 Dec  7 07:57 CI006657.pdbqt\n",
            "-rw-r--r-- 1 root root      4699 Dec  7 07:57 CI006659.pdbqt\n",
            "-rw-r--r-- 1 root root      4658 Dec  7 07:57 CI006660.pdbqt\n",
            "-rw-r--r-- 1 root root      4529 Dec  7 07:57 CI006661.pdbqt\n",
            "-rw-r--r-- 1 root root      5025 Dec  7 07:57 compound11.pdbqt\n",
            "-rw-r--r-- 1 root root      4765 Dec  7 07:57 compound12.pdbqt\n",
            "-rw-r--r-- 1 root root      4286 Dec  7 07:57 compound42.pdbqt\n",
            "-rw-r--r-- 1 root root      5720 Dec  7 07:57 compound7.pdbqt\n",
            "-rw-r--r-- 1 root root     20651 Dec  7 07:55 condacolab_install.log\n",
            "-rw-r--r-- 1 root root      4345 Dec  7 07:57 database.csv\n",
            "-rwxr-xr-x 1 root root 562802104 Dec  8  2021 gnina\n",
            "-rw-r--r-- 1 root root      3733 Dec  7 07:57 MI23.pdbqt\n",
            "-rw-r--r-- 1 root root      3733 Dec  7 07:57 MI30.pdbqt\n",
            "-rw-r--r-- 1 root root      4834 Dec  7 07:57 MPI3.pdbqt\n",
            "-rw-r--r-- 1 root root      4971 Dec  7 07:57 MPI8.pdbqt\n",
            "-rw-r--r-- 1 root root      4292 Dec  7 07:57 Nirmatrelvir.pdbqt\n",
            "-rw-r--r-- 1 root root      5507 Dec  7 07:57 P0C6X7.pdbqt\n",
            "-rw-r--r-- 1 root root      4529 Dec  7 07:57 PF-00835231.pdbqt\n",
            "-rw-r--r-- 1 root root    386857 Dec  7 07:57 rec.pdb\n",
            "-rw-r--r-- 1 root root    201840 Dec  7 07:57 rec.pdbqt\n",
            "drwxr-xr-x 1 root root      4096 Dec  4 14:27 sample_data\n",
            "-rw-r--r-- 1 root root      4553 Dec  7 07:57 UWAJ246.pdbqt\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "9nQzUMcl_VZy"
      },
      "source": [
        "## Step 4: Dock the ligand with qvina-w (bash shell only in the block)"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "6qDaEnIjmE9S",
        "outputId": "0ab5715b-fdc7-4cef-c681-e9898290986c",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "source": [
        "%%shell\n",
        "for f in *.pdbqt;\n",
        "    do  b=`basename $f .pdbqt`;\n",
        "    echo Processing ligand $b;\n",
        "    #./qvina-w --config conf.txt --ligand $f --out $f-out.pdbqt --log $f-out.txt;\n",
        "    ./gnina -r rec.pdbqt -l $f --center_x 12.06 --center_y 0.60 --center_z 4.9 --size_x 40 --size_y 60 --size_z 60 --num_modes 100 -o $f-out.sdf --log $f-out.txt;\n",
        "done"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Processing ligand Boceprevir\n",
            "              _             \n",
            "             (_)            \n",
            "   __ _ _ __  _ _ __   __ _ \n",
            "  / _` | '_ \\| | '_ \\ / _` |\n",
            " | (_| | | | | | | | | (_| |\n",
            "  \\__, |_| |_|_|_| |_|\\__,_|\n",
            "   __/ |                    \n",
            "  |___/                     \n",
            "\n",
            "gnina v1.0.1 HEAD:aa41230   Built Mar 23 2021.\n",
            "gnina is based on smina and AutoDock Vina.\n",
            "Please cite appropriately.\n",
            "\n",
            "Commandline: ./gnina -r rec.pdbqt -l Boceprevir.pdbqt --center_x 12.06 --center_y 0.60 --center_z 4.9 --size_x 40 --size_y 60 --size_z 60 --num_modes 100 -o Boceprevir.pdbqt-out.sdf --log Boceprevir.pdbqt-out.txt\n",
            "Using random seed: 1729026673\n",
            "\n",
            "0%   10   20   30   40   50   60   70   80   90   100%\n",
            "|----|----|----|----|----|----|----|----|----|----|\n",
            "****************************************"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Analyzing the docking results"
      ],
      "metadata": {
        "id": "k16ly7i4aCvc"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!rm -rf result*\n",
        "!grep \"   1 \" *.txt | awk '{print $1,$3}' >>result\n",
        "!sort -n -k 2  result >result2\n",
        "!cat result2"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "OqRz05BjaJVZ",
        "outputId": "fd6697cc-db7b-40cd-8040-ce160d575546"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "compound7.pdbqt-out.txt: -8.8\n",
            "MI23.pdbqt-out.txt: -8.6\n",
            "CI006632.pdbqt-out.txt: -8.2\n",
            "compound11.pdbqt-out.txt: -8.0\n",
            "MPI8.pdbqt-out.txt: -8.0\n",
            "CI006630.pdbqt-out.txt: -7.9\n",
            "CI006659.pdbqt-out.txt: -7.9\n",
            "MI30.pdbqt-out.txt: -7.9\n",
            "CI006634.pdbqt-out.txt: -7.8\n",
            "CI006653.pdbqt-out.txt: -7.8\n",
            "compound42.pdbqt-out.txt: -7.8\n",
            "CI006661.pdbqt-out.txt: -7.7\n",
            "PF-00835231.pdbqt-out.txt: -7.7\n",
            "CI006651.pdbqt-out.txt: -7.6\n",
            "CI006656.pdbqt-out.txt: -7.6\n",
            "CI006657.pdbqt-out.txt: -7.6\n",
            "CI006660.pdbqt-out.txt: -7.6\n",
            "Calpain_Inhibitor_XII.pdbqt-out.txt: -7.5\n",
            "compound12.pdbqt-out.txt: -7.5\n",
            "Nirmatrelvir.pdbqt-out.txt: -7.4\n",
            "UWAJ246.pdbqt-out.txt: -7.4\n",
            "Boceprevir.pdbqt-out.txt: -7.1\n",
            "CI006629.pdbqt-out.txt: -7.1\n",
            "CI006628.pdbqt-out.txt: -6.9\n",
            "CI006655.pdbqt-out.txt: -6.7\n",
            "MPI3.pdbqt-out.txt: -6.7\n",
            "P0C6X7.pdbqt-out.txt: -5.8\n",
            "calpain_inhibitors_I.pdbqt-out.txt: -5.7\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "download files"
      ],
      "metadata": {
        "id": "JqU-0o9n14mS"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!ls -l\n",
        "!mkdir dockresults\n",
        "!cp result* dockresults/\n",
        "!cp *.pdbqt dockresults/\n",
        "!cp *.txt dockresults/\n",
        "!cp *.pdb dockresults/\n",
        "!tar cvf dockresults.tar dockresults/\n",
        "files.download('dockresults.tar')"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "id": "ep8pp_2v18IB",
        "outputId": "8cb6d62d-c0fe-4bd3-b23b-d7dff2336208"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "total 6516\n",
            "-rw-r--r-- 1 root root    4843 Dec  4 12:44 Boceprevir.pdbqt\n",
            "-rw-r--r-- 1 root root   49101 Dec  4 12:47 Boceprevir.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 12:47 Boceprevir.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4057 Dec  4 12:44 calpain_inhibitors_I.pdbqt\n",
            "-rw-r--r-- 1 root root   41241 Dec  4 12:48 calpain_inhibitors_I.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3069 Dec  4 12:48 calpain_inhibitors_I.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4603 Dec  4 12:44 Calpain_Inhibitor_XII.pdbqt\n",
            "-rw-r--r-- 1 root root   46701 Dec  4 12:49 Calpain_Inhibitor_XII.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 12:49 Calpain_Inhibitor_XII.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5511 Dec  4 12:44 CI006628.pdbqt\n",
            "-rw-r--r-- 1 root root   55781 Dec  4 12:51 CI006628.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3069 Dec  4 12:51 CI006628.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5333 Dec  4 12:44 CI006629.pdbqt\n",
            "-rw-r--r-- 1 root root   54001 Dec  4 12:52 CI006629.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 12:52 CI006629.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5540 Dec  4 12:44 CI006630.pdbqt\n",
            "-rw-r--r-- 1 root root   56071 Dec  4 12:54 CI006630.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 12:54 CI006630.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5495 Dec  4 12:44 CI006632.pdbqt\n",
            "-rw-r--r-- 1 root root   55621 Dec  4 12:55 CI006632.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 12:55 CI006632.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5495 Dec  4 12:44 CI006634.pdbqt\n",
            "-rw-r--r-- 1 root root   55621 Dec  4 12:56 CI006634.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3068 Dec  4 12:56 CI006634.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4230 Dec  4 12:44 CI006651.pdbqt\n",
            "-rw-r--r-- 1 root root   42971 Dec  4 12:58 CI006651.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 12:58 CI006651.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4358 Dec  4 12:44 CI006653.pdbqt\n",
            "-rw-r--r-- 1 root root   44251 Dec  4 12:59 CI006653.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 12:59 CI006653.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4554 Dec  4 12:44 CI006655.pdbqt\n",
            "-rw-r--r-- 1 root root   46211 Dec  4 13:00 CI006655.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3069 Dec  4 13:00 CI006655.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4691 Dec  4 12:44 CI006656.pdbqt\n",
            "-rw-r--r-- 1 root root   47581 Dec  4 13:01 CI006656.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:01 CI006656.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4570 Dec  4 12:44 CI006657.pdbqt\n",
            "-rw-r--r-- 1 root root   46371 Dec  4 13:02 CI006657.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3069 Dec  4 13:02 CI006657.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4699 Dec  4 12:44 CI006659.pdbqt\n",
            "-rw-r--r-- 1 root root   47661 Dec  4 13:03 CI006659.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 13:03 CI006659.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4658 Dec  4 12:44 CI006660.pdbqt\n",
            "-rw-r--r-- 1 root root   47251 Dec  4 13:04 CI006660.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 13:04 CI006660.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4529 Dec  4 12:44 CI006661.pdbqt\n",
            "-rw-r--r-- 1 root root   45961 Dec  4 13:06 CI006661.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:06 CI006661.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5025 Dec  4 12:44 compound11.pdbqt\n",
            "-rw-r--r-- 1 root root   50921 Dec  4 13:07 compound11.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:07 compound11.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4765 Dec  4 12:44 compound12.pdbqt\n",
            "-rw-r--r-- 1 root root   48321 Dec  4 13:08 compound12.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 13:08 compound12.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4286 Dec  4 12:44 compound42.pdbqt\n",
            "-rw-r--r-- 1 root root   43531 Dec  4 13:10 compound42.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:10 compound42.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5720 Dec  4 12:44 compound7.pdbqt\n",
            "-rw-r--r-- 1 root root   57871 Dec  4 13:11 compound7.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:11 compound7.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root   20651 Dec  4 12:13 condacolab_install.log\n",
            "-rw-r--r-- 1 root root     148 Dec  4 12:45 conf.txt\n",
            "-rw-r--r-- 1 root root    4347 Dec  4 12:29 database.csv\n",
            "-rw-r--r-- 1 root root    3733 Dec  4 12:44 MI23.pdbqt\n",
            "-rw-r--r-- 1 root root   38001 Dec  4 13:12 MI23.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3069 Dec  4 13:12 MI23.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    3733 Dec  4 12:44 MI30.pdbqt\n",
            "-rw-r--r-- 1 root root   38001 Dec  4 13:14 MI30.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:14 MI30.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4834 Dec  4 12:44 MPI3.pdbqt\n",
            "-rw-r--r-- 1 root root   49011 Dec  4 13:15 MPI3.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:15 MPI3.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4971 Dec  4 12:44 MPI8.pdbqt\n",
            "-rw-r--r-- 1 root root   50381 Dec  4 13:16 MPI8.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 13:16 MPI8.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4292 Dec  4 12:44 Nirmatrelvir.pdbqt\n",
            "-rw-r--r-- 1 root root   43591 Dec  4 13:17 Nirmatrelvir.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 13:17 Nirmatrelvir.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    5507 Dec  4 12:44 P0C6X7.pdbqt\n",
            "-rw-r--r-- 1 root root   55741 Dec  4 13:18 P0C6X7.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3071 Dec  4 13:18 P0C6X7.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root    4529 Dec  4 12:44 PF-00835231.pdbqt\n",
            "-rw-r--r-- 1 root root   45961 Dec  4 13:20 PF-00835231.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3069 Dec  4 13:20 PF-00835231.pdbqt-out.txt\n",
            "drwxr-xr-x 8 root root    4096 Dec  4 12:28 qvina\n",
            "-rwxr--r-- 1 root root 4279488 Dec  4 12:28 qvina-w\n",
            "-rw-r--r-- 1 root root  386857 Dec  4 12:29 rec.pdb\n",
            "-rw-r--r-- 1 root root  201840 Dec  4 12:45 rec.pdbqt\n",
            "-rw-r--r-- 1 root root    2314 Dec  4 13:20 rec.pdbqt-out.txt\n",
            "-rw-r--r-- 1 root root     834 Dec  4 13:25 result\n",
            "-rw-r--r-- 1 root root     834 Dec  4 13:25 result2\n",
            "drwxr-xr-x 1 root root    4096 Nov 30 14:27 sample_data\n",
            "-rw-r--r-- 1 root root    4553 Dec  4 12:44 UWAJ246.pdbqt\n",
            "-rw-r--r-- 1 root root   46201 Dec  4 13:21 UWAJ246.pdbqt-out.pdbqt\n",
            "-rw-r--r-- 1 root root    3070 Dec  4 13:21 UWAJ246.pdbqt-out.txt\n",
            "dockresults/\n",
            "dockresults/Boceprevir.pdbqt-out.pdbqt\n",
            "dockresults/compound42.pdbqt-out.pdbqt\n",
            "dockresults/CI006653.pdbqt-out.pdbqt\n",
            "dockresults/CI006653.pdbqt-out.txt\n",
            "dockresults/CI006630.pdbqt\n",
            "dockresults/CI006659.pdbqt-out.txt\n",
            "dockresults/compound11.pdbqt-out.pdbqt\n",
            "dockresults/compound12.pdbqt\n",
            "dockresults/CI006628.pdbqt\n",
            "dockresults/CI006657.pdbqt-out.txt\n",
            "dockresults/Nirmatrelvir.pdbqt\n",
            "dockresults/MI23.pdbqt-out.pdbqt\n",
            "dockresults/P0C6X7.pdbqt-out.txt\n",
            "dockresults/compound42.pdbqt-out.txt\n",
            "dockresults/MI30.pdbqt\n",
            "dockresults/CI006656.pdbqt\n",
            "dockresults/CI006632.pdbqt\n",
            "dockresults/Calpain_Inhibitor_XII.pdbqt-out.pdbqt\n",
            "dockresults/MPI8.pdbqt-out.txt\n",
            "dockresults/CI006655.pdbqt\n",
            "dockresults/compound12.pdbqt-out.pdbqt\n",
            "dockresults/rec.pdbqt\n",
            "dockresults/CI006630.pdbqt-out.pdbqt\n",
            "dockresults/CI006661.pdbqt-out.pdbqt\n",
            "dockresults/CI006653.pdbqt\n",
            "dockresults/PF-00835231.pdbqt\n",
            "dockresults/calpain_inhibitors_I.pdbqt\n",
            "dockresults/Boceprevir.pdbqt-out.txt\n",
            "dockresults/CI006657.pdbqt-out.pdbqt\n",
            "dockresults/compound12.pdbqt-out.txt\n",
            "dockresults/CI006656.pdbqt-out.pdbqt\n",
            "dockresults/conf.txt\n",
            "dockresults/CI006660.pdbqt-out.pdbqt\n",
            "dockresults/CI006657.pdbqt\n",
            "dockresults/CI006651.pdbqt-out.pdbqt\n",
            "dockresults/CI006660.pdbqt-out.txt\n",
            "dockresults/MPI8.pdbqt\n",
            "dockresults/CI006634.pdbqt-out.txt\n",
            "dockresults/compound7.pdbqt\n",
            "dockresults/compound7.pdbqt-out.txt\n",
            "dockresults/CI006629.pdbqt-out.pdbqt\n",
            "dockresults/rec.pdb\n",
            "dockresults/Calpain_Inhibitor_XII.pdbqt-out.txt\n",
            "dockresults/CI006660.pdbqt\n",
            "dockresults/P0C6X7.pdbqt\n",
            "dockresults/CI006628.pdbqt-out.pdbqt\n",
            "dockresults/CI006656.pdbqt-out.txt\n",
            "dockresults/CI006628.pdbqt-out.txt\n",
            "dockresults/MI23.pdbqt\n",
            "dockresults/UWAJ246.pdbqt\n",
            "dockresults/MPI8.pdbqt-out.pdbqt\n",
            "dockresults/Calpain_Inhibitor_XII.pdbqt\n",
            "dockresults/MI30.pdbqt-out.pdbqt\n",
            "dockresults/CI006661.pdbqt-out.txt\n",
            "dockresults/CI006655.pdbqt-out.pdbqt\n",
            "dockresults/compound11.pdbqt\n",
            "dockresults/compound11.pdbqt-out.txt\n",
            "dockresults/CI006651.pdbqt\n",
            "dockresults/CI006651.pdbqt-out.txt\n",
            "dockresults/UWAJ246.pdbqt-out.pdbqt\n",
            "dockresults/CI006661.pdbqt\n",
            "dockresults/CI006634.pdbqt-out.pdbqt\n",
            "dockresults/calpain_inhibitors_I.pdbqt-out.txt\n",
            "dockresults/result\n",
            "dockresults/CI006659.pdbqt-out.pdbqt\n",
            "dockresults/Nirmatrelvir.pdbqt-out.txt\n",
            "dockresults/rec.pdbqt-out.txt\n",
            "dockresults/P0C6X7.pdbqt-out.pdbqt\n",
            "dockresults/compound7.pdbqt-out.pdbqt\n",
            "dockresults/MPI3.pdbqt\n",
            "dockresults/MI23.pdbqt-out.txt\n",
            "dockresults/CI006629.pdbqt\n",
            "dockresults/result2\n",
            "dockresults/PF-00835231.pdbqt-out.txt\n",
            "dockresults/CI006655.pdbqt-out.txt\n",
            "dockresults/CI006632.pdbqt-out.txt\n",
            "dockresults/CI006629.pdbqt-out.txt\n",
            "dockresults/CI006634.pdbqt\n",
            "dockresults/calpain_inhibitors_I.pdbqt-out.pdbqt\n",
            "dockresults/MPI3.pdbqt-out.pdbqt\n",
            "dockresults/compound42.pdbqt\n",
            "dockresults/Nirmatrelvir.pdbqt-out.pdbqt\n",
            "dockresults/UWAJ246.pdbqt-out.txt\n",
            "dockresults/CI006632.pdbqt-out.pdbqt\n",
            "dockresults/CI006630.pdbqt-out.txt\n",
            "dockresults/PF-00835231.pdbqt-out.pdbqt\n",
            "dockresults/MI30.pdbqt-out.txt\n",
            "dockresults/Boceprevir.pdbqt\n",
            "dockresults/CI006659.pdbqt\n",
            "dockresults/MPI3.pdbqt-out.txt\n"
          ]
        },
        {
          "output_type": "display_data",
          "data": {
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              "<IPython.core.display.Javascript object>"
            ],
            "application/javascript": [
              "\n",
              "    async function download(id, filename, size) {\n",
              "      if (!google.colab.kernel.accessAllowed) {\n",
              "        return;\n",
              "      }\n",
              "      const div = document.createElement('div');\n",
              "      const label = document.createElement('label');\n",
              "      label.textContent = `Downloading \"${filename}\": `;\n",
              "      div.appendChild(label);\n",
              "      const progress = document.createElement('progress');\n",
              "      progress.max = size;\n",
              "      div.appendChild(progress);\n",
              "      document.body.appendChild(div);\n",
              "\n",
              "      const buffers = [];\n",
              "      let downloaded = 0;\n",
              "\n",
              "      const channel = await google.colab.kernel.comms.open(id);\n",
              "      // Send a message to notify the kernel that we're ready.\n",
              "      channel.send({})\n",
              "\n",
              "      for await (const message of channel.messages) {\n",
              "        // Send a message to notify the kernel that we're ready.\n",
              "        channel.send({})\n",
              "        if (message.buffers) {\n",
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              "            progress.value = downloaded;\n",
              "          }\n",
              "        }\n",
              "      }\n",
              "      const blob = new Blob(buffers, {type: 'application/binary'});\n",
              "      const a = document.createElement('a');\n",
              "      a.href = window.URL.createObjectURL(blob);\n",
              "      a.download = filename;\n",
              "      div.appendChild(a);\n",
              "      a.click();\n",
              "      div.remove();\n",
              "    }\n",
              "  "
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            ]
          },
          "metadata": {}
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install biopython"
      ],
      "metadata": {
        "id": "DqvXvMhJEDzF"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "from Bio.PDB import PDBParser\n",
        "import math\n",
        "import glob\n",
        "\n",
        "def read_vina_result(file_path):\n",
        "    \"\"\"\n",
        "    读取 Vina 结果文件（PDBQT 格式）并提取每个模型的能量、原子坐标和质心\n",
        "\n",
        "    参数：\n",
        "    file_path: Vina 结果文件路径\n",
        "\n",
        "    返回值：\n",
        "    一个列表，每个元素是一个字典，包含模型的能量、原子坐标、质心信息\n",
        "    \"\"\"\n",
        "    #center_x = 14.09\n",
        "    #center_y = -5.69\n",
        "    #center_z = 20.70\n",
        "    #sphere_radius = 8.0\n",
        "\n",
        "    models_info = []\n",
        "    energy    = 0.00\n",
        "    partition_function_sum  = 0.00\n",
        "    partition_function_inside = 0.00\n",
        "    partition         = 0.00\n",
        "\n",
        "    with open(file_path, 'r') as file:\n",
        "        lines = file.readlines()\n",
        "\n",
        "        for line in lines:\n",
        "            if line.startswith(\"MODEL\"):\n",
        "                model_info = {\"AtomCoordinates\": [], \"Centroid\": None}\n",
        "            elif line.startswith(\"REMARK VINA RESULT\"):\n",
        "                # 提取能量信息\n",
        "                energy_line = line.strip().split()\n",
        "                model_info[\"Energy\"] = float(energy_line[3])\n",
        "                energy        = float(energy_line[3])\n",
        "            elif line.startswith(\"ATOM\") or line.startswith(\"HETATM\"):\n",
        "                # 提取原子坐标信息\n",
        "                x = float(line[30:38].strip())\n",
        "                y = float(line[38:46].strip())\n",
        "                z = float(line[46:54].strip())\n",
        "\n",
        "                atom_info = {\"x\": x, \"y\": y, \"z\": z}\n",
        "                model_info[\"AtomCoordinates\"].append(atom_info)\n",
        "            elif line.startswith(\"ENDMDL\"):\n",
        "                # 计算质心坐标\n",
        "                x_sum = sum(atom[\"x\"] for atom in model_info[\"AtomCoordinates\"])\n",
        "                y_sum = sum(atom[\"y\"] for atom in model_info[\"AtomCoordinates\"])\n",
        "                z_sum = sum(atom[\"z\"] for atom in model_info[\"AtomCoordinates\"])\n",
        "                num_atoms = len(model_info[\"AtomCoordinates\"])\n",
        "\n",
        "                centroid = {\"x\": x_sum / num_atoms, \"y\": y_sum / num_atoms, \"z\": z_sum / num_atoms}\n",
        "                model_info[\"Centroid\"] = centroid\n",
        "\n",
        "                models_info.append(model_info)\n",
        "\n",
        "                center_x = 14.09\n",
        "                center_y = -5.69\n",
        "                center_z = 20.70\n",
        "                sphere_radius = 12.0\n",
        "                x = x_sum / num_atoms\n",
        "                y = y_sum / num_atoms\n",
        "                z = z_sum / num_atoms\n",
        "                distance = math.sqrt((x - center_x)**2 + (y - center_y)**2 + (z - center_z)**2)\n",
        "                withinbox = sphere_radius - distance\n",
        "                KbT = 0.615593 # T = 310 (kcal/mol)\n",
        "                pa = -energy/KbT\n",
        "                partition_function =  math.exp(pa)\n",
        "\n",
        "                if withinbox>0:\n",
        "                    partition_function_sum = partition_function_sum + partition_function\n",
        "                    partition_function_inside = partition_function_inside + partition_function\n",
        "                else:\n",
        "                    partition_function_sum = partition_function_sum + partition_function\n",
        "\n",
        "    partition = partition_function_inside / partition_function_sum\n",
        "    return models_info, partition\n",
        "\n",
        "\n",
        "def main():\n",
        "    vina_result_file_path = \"PF-00835231.pdbqt-out.pdbqt\"\n",
        "#    sphere_center = (0, 0, 0)\n",
        "#    sphere_radius = 3.0\n",
        "\n",
        "    try:\n",
        "        models_info, partition = read_vina_result(vina_result_file_path)\n",
        "        print(partition)\n",
        "        print(\"\\n\")\n",
        "        #for i, model_info in enumerate(models_info):\n",
        "            #print(f\"Model {i + 1}\")\n",
        "            #print(f\"Energy: {model_info['Energy']}\")\n",
        "            #print(\"Atom Coordinates:\")\n",
        "            #for coord in model_info['AtomCoordinates']:\n",
        "            #    print(f\"  {coord}\")\n",
        "            #print(f\"Centroid: {model_info['Centroid']}\")\n",
        "\n",
        "            # 检查质心是否在球体内\n",
        "            #if is_centroid_inside_sphere(model_info['Centroid'], sphere_center, sphere_radius):\n",
        "            #    print(\"Centroid is inside the sphere.\")\n",
        "            #else:\n",
        "            #    print(\"Centroid is outside the sphere.\")\n",
        "\n",
        "            #print(\"\\n\")\n",
        "\n",
        "    except Exception as e:\n",
        "        print(f\"Error: {e}\")\n",
        "\n",
        "if __name__ == \"__main__\":\n",
        "    main()\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "jcvsrYywYKY_",
        "outputId": "c15ece8c-97c6-43b6-dbc3-e7a3cb96e591"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "0.4701170564480517\n",
            "\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "from Bio.PDB import PDBParser\n",
        "import math\n",
        "import glob\n",
        "\n",
        "def read_vina_result(file_path):\n",
        "    \"\"\"\n",
        "    读取 Vina 结果文件（PDBQT 格式）并提取每个模型的能量、原子坐标和质心\n",
        "\n",
        "    参数：\n",
        "    file_path: Vina 结果文件路径\n",
        "\n",
        "    返回值：\n",
        "    一个列表，每个元素是一个字典，包含模型的能量、原子坐标、质心信息\n",
        "    \"\"\"\n",
        "    #center_x = 14.09\n",
        "    #center_y = -5.69\n",
        "    #center_z = 20.70\n",
        "    #sphere_radius = 8.0\n",
        "\n",
        "    models_info = []\n",
        "    energy    = 0.00\n",
        "    partition_function_sum  = 0.00\n",
        "    partition_function_inside = 0.00\n",
        "    partition         = 0.00\n",
        "\n",
        "    with open(file_path, 'r') as file:\n",
        "        lines = file.readlines()\n",
        "\n",
        "        for line in lines:\n",
        "            if line.startswith(\"MODEL\"):\n",
        "                model_info = {\"AtomCoordinates\": [], \"Centroid\": None}\n",
        "            elif line.startswith(\"REMARK VINA RESULT\"):\n",
        "                # 提取能量信息\n",
        "                energy_line = line.strip().split()\n",
        "                model_info[\"Energy\"] = float(energy_line[3])\n",
        "                energy        = float(energy_line[3])\n",
        "            elif line.startswith(\"ATOM\") or line.startswith(\"HETATM\"):\n",
        "                # 提取原子坐标信息\n",
        "                x = float(line[30:38].strip())\n",
        "                y = float(line[38:46].strip())\n",
        "                z = float(line[46:54].strip())\n",
        "\n",
        "                atom_info = {\"x\": x, \"y\": y, \"z\": z}\n",
        "                model_info[\"AtomCoordinates\"].append(atom_info)\n",
        "            elif line.startswith(\"ENDMDL\"):\n",
        "                # 计算质心坐标\n",
        "                x_sum = sum(atom[\"x\"] for atom in model_info[\"AtomCoordinates\"])\n",
        "                y_sum = sum(atom[\"y\"] for atom in model_info[\"AtomCoordinates\"])\n",
        "                z_sum = sum(atom[\"z\"] for atom in model_info[\"AtomCoordinates\"])\n",
        "                num_atoms = len(model_info[\"AtomCoordinates\"])\n",
        "\n",
        "                centroid = {\"x\": x_sum / num_atoms, \"y\": y_sum / num_atoms, \"z\": z_sum / num_atoms}\n",
        "                model_info[\"Centroid\"] = centroid\n",
        "\n",
        "                models_info.append(model_info)\n",
        "\n",
        "                center_x = 14.09\n",
        "                center_y = -5.69\n",
        "                center_z = 20.70\n",
        "                sphere_radius = 12.0\n",
        "                x = x_sum / num_atoms\n",
        "                y = y_sum / num_atoms\n",
        "                z = z_sum / num_atoms\n",
        "                distance = math.sqrt((x - center_x)**2 + (y - center_y)**2 + (z - center_z)**2)\n",
        "                withinbox = sphere_radius - distance\n",
        "                KbT = 0.615593 # T = 310 (kcal/mol)\n",
        "                pa = -energy/KbT\n",
        "                partition_function =  math.exp(pa)\n",
        "\n",
        "                if withinbox>0:\n",
        "                    partition_function_sum = partition_function_sum + partition_function\n",
        "                    partition_function_inside = partition_function_inside + partition_function\n",
        "                else:\n",
        "                    partition_function_sum = partition_function_sum + partition_function\n",
        "\n",
        "    partition = partition_function_inside / partition_function_sum\n",
        "    return models_info, partition\n",
        "\n",
        "def main():\n",
        "    folder_path = \"/content\"\n",
        "    pdbqt_files = glob.glob(f\"{folder_path}/*-out.pdbqt\")\n",
        "    for pdbqt_file in pdbqt_files:\n",
        "        vina_result_file_path = pdbqt_file\n",
        "\n",
        "        try:\n",
        "            models_info, partition = read_vina_result(vina_result_file_path)\n",
        "            print(pdbqt_file,';',partition)\n",
        "        except Exception as e:\n",
        "            print(f\"Error: {e}\")\n",
        "\n",
        "if __name__ == \"__main__\":\n",
        "    main()\n",
        "\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "qFmO9EQJiUDe",
        "outputId": "774afc12-727d-41de-d63d-72044df69db7"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/Boceprevir.pdbqt-out.pdbqt ; 0.0\n",
            "/content/compound42.pdbqt-out.pdbqt ; 0.3666367563947776\n",
            "/content/CI006653.pdbqt-out.pdbqt ; 0.28487502057965025\n",
            "/content/compound11.pdbqt-out.pdbqt ; 0.0\n",
            "/content/MI23.pdbqt-out.pdbqt ; 0.1724345473099285\n",
            "/content/Calpain_Inhibitor_XII.pdbqt-out.pdbqt ; 0.2006476343777507\n",
            "/content/compound12.pdbqt-out.pdbqt ; 0.3090939965558559\n",
            "/content/CI006630.pdbqt-out.pdbqt ; 0.0\n",
            "/content/CI006661.pdbqt-out.pdbqt ; 0.5460648474170752\n",
            "/content/CI006657.pdbqt-out.pdbqt ; 0.3006072102450122\n",
            "/content/CI006656.pdbqt-out.pdbqt ; 0.4303248045977941\n",
            "/content/CI006660.pdbqt-out.pdbqt ; 0.3183213565154824\n",
            "/content/CI006651.pdbqt-out.pdbqt ; 0.2569210506080182\n",
            "/content/CI006629.pdbqt-out.pdbqt ; 0.32968877912987454\n",
            "/content/CI006628.pdbqt-out.pdbqt ; 0.11050742960042631\n",
            "/content/MPI8.pdbqt-out.pdbqt ; 0.0\n",
            "/content/MI30.pdbqt-out.pdbqt ; 0.21844323662659346\n",
            "/content/CI006655.pdbqt-out.pdbqt ; 0.45344458935335674\n",
            "/content/UWAJ246.pdbqt-out.pdbqt ; 0.6424914653999411\n",
            "/content/CI006634.pdbqt-out.pdbqt ; 0.0\n",
            "/content/CI006659.pdbqt-out.pdbqt ; 0.3338062046414855\n",
            "/content/P0C6X7.pdbqt-out.pdbqt ; 0.09228261186680484\n",
            "/content/compound7.pdbqt-out.pdbqt ; 0.05271085891433819\n",
            "/content/calpain_inhibitors_I.pdbqt-out.pdbqt ; 0.3598548378672745\n",
            "/content/MPI3.pdbqt-out.pdbqt ; 0.253689818949715\n",
            "/content/Nirmatrelvir.pdbqt-out.pdbqt ; 0.3474400271322638\n",
            "/content/CI006632.pdbqt-out.pdbqt ; 0.04611715580218888\n",
            "/content/PF-00835231.pdbqt-out.pdbqt ; 0.4701170564480517\n"
          ]
        }
      ]
    }
  ]
}