OpenFF_test.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "OpenFF_test.ipynb",
      "version": "0.3.2",
      "provenance": [],
      "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/iwatobipen/playground/blob/master/OpenFF_test.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "metadata": {
        "id": "JCuCFW6z8wKv",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 4117
        },
        "outputId": "b3cca613-7d35-4143-9766-97044753761c"
      },
      "cell_type": "code",
      "source": [
        "# install conda\n",
        "!wget https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh\n",
        "!chmod ./Miniconda3-4.4.10-Linux-x86_64.sh\n",
        "!time bash ./Miniconda3-4.4.10-Linux-x86_64.sh -b -f -p /usr/local\n",
        "# install rdkit via conda command\n",
        "!time conda install -c conda-forge rdkit -y"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2019-04-09 12:04:42--  https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh\n",
            "Resolving repo.continuum.io (repo.continuum.io)... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c94f, ...\n",
            "Connecting to repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 58304693 (56M) [application/x-sh]\n",
            "Saving to: ‘Miniconda3-4.4.10-Linux-x86_64.sh’\n",
            "\n",
            "Miniconda3-4.4.10-L 100%[===================>]  55.60M   143MB/s    in 0.4s    \n",
            "\n",
            "2019-04-09 12:04:43 (143 MB/s) - ‘Miniconda3-4.4.10-Linux-x86_64.sh’ saved [58304693/58304693]\n",
            "\n",
            "chmod: missing operand after ‘./Miniconda3-4.4.10-Linux-x86_64.sh’\n",
            "Try 'chmod --help' for more information.\n",
            "PREFIX=/usr/local\n",
            "installing: python-3.6.4-hc3d631a_1 ...\n",
            "Python 3.6.4 :: Anaconda, Inc.\n",
            "installing: ca-certificates-2017.08.26-h1d4fec5_0 ...\n",
            "installing: conda-env-2.6.0-h36134e3_1 ...\n",
            "installing: libgcc-ng-7.2.0-h7cc24e2_2 ...\n",
            "installing: libstdcxx-ng-7.2.0-h7a57d05_2 ...\n",
            "installing: libffi-3.2.1-hd88cf55_4 ...\n",
            "installing: ncurses-6.0-h9df7e31_2 ...\n",
            "installing: openssl-1.0.2n-hb7f436b_0 ...\n",
            "installing: tk-8.6.7-hc745277_3 ...\n",
            "installing: xz-5.2.3-h55aa19d_2 ...\n",
            "installing: yaml-0.1.7-had09818_2 ...\n",
            "installing: zlib-1.2.11-ha838bed_2 ...\n",
            "installing: libedit-3.1-heed3624_0 ...\n",
            "installing: readline-7.0-ha6073c6_4 ...\n",
            "installing: sqlite-3.22.0-h1bed415_0 ...\n",
            "installing: asn1crypto-0.24.0-py36_0 ...\n",
            "installing: certifi-2018.1.18-py36_0 ...\n",
            "installing: chardet-3.0.4-py36h0f667ec_1 ...\n",
            "installing: idna-2.6-py36h82fb2a8_1 ...\n",
            "installing: pycosat-0.6.3-py36h0a5515d_0 ...\n",
            "installing: pycparser-2.18-py36hf9f622e_1 ...\n",
            "installing: pysocks-1.6.7-py36hd97a5b1_1 ...\n",
            "installing: ruamel_yaml-0.15.35-py36h14c3975_1 ...\n",
            "installing: six-1.11.0-py36h372c433_1 ...\n",
            "installing: cffi-1.11.4-py36h9745a5d_0 ...\n",
            "installing: setuptools-38.4.0-py36_0 ...\n",
            "installing: cryptography-2.1.4-py36hd09be54_0 ...\n",
            "installing: wheel-0.30.0-py36hfd4bba0_1 ...\n",
            "installing: pip-9.0.1-py36h6c6f9ce_4 ...\n",
            "installing: pyopenssl-17.5.0-py36h20ba746_0 ...\n",
            "installing: urllib3-1.22-py36hbe7ace6_0 ...\n",
            "installing: requests-2.18.4-py36he2e5f8d_1 ...\n",
            "installing: conda-4.4.10-py36_0 ...\n",
            "installation finished.\n",
            "WARNING:\n",
            "    You currently have a PYTHONPATH environment variable set. This may cause\n",
            "    unexpected behavior when running the Python interpreter in Miniconda3.\n",
            "    For best results, please verify that your PYTHONPATH only points to\n",
            "    directories of packages that are compatible with the Python interpreter\n",
            "    in Miniconda3: /usr/local\n",
            "\n",
            "real\t0m13.053s\n",
            "user\t0m11.407s\n",
            "sys\t0m2.925s\n",
            "Solving environment: - \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\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\\ \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\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| \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\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/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| 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\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\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/ \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\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- \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\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\bdone\n",
            "\n",
            "\n",
            "==> WARNING: A newer version of conda exists. <==\n",
            "  current version: 4.4.10\n",
            "  latest version: 4.6.11\n",
            "\n",
            "Please update conda by running\n",
            "\n",
            "    $ conda update -n base conda\n",
            "\n",
            "\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs: \n",
            "    - rdkit\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
            "    freetype-2.9.1             |       h6debe1e_4         800 KB  conda-forge\n",
            "    cairo-1.16.0               |       h761e891_0         1.4 MB  conda-forge\n",
            "    libxml2-2.9.8              |       h422b904_5         1.8 MB  conda-forge\n",
            "    mkl_random-1.0.2           |           py36_0         1.3 MB  conda-forge\n",
            "    xorg-xextproto-7.3.0       |       h470a237_2          26 KB  conda-forge\n",
            "    ca-certificates-2019.3.9   |       hecc5488_0         146 KB  conda-forge\n",
            "    xz-5.2.4                   |       h470a237_1         328 KB  conda-forge\n",
            "    libgfortran-ng-7.3.0       |       hdf63c60_0         1.3 MB\n",
            "    xorg-libxext-1.3.3         |       h470a237_4          45 KB  conda-forge\n",
            "    pixman-0.34.0              |       h470a237_3         1.2 MB  conda-forge\n",
            "    libuuid-2.32.1             |       h470a237_2          24 KB  conda-forge\n",
            "    boost-cpp-1.68.0           |       h3a22d5f_0        20.1 MB  conda-forge\n",
            "    numpy-base-1.15.0          |   py36h3dfced4_0         4.2 MB\n",
            "    python-dateutil-2.8.0      |             py_0         219 KB  conda-forge\n",
            "    openssl-1.0.2p             |       h470a237_2         3.1 MB  conda-forge\n",
            "    libiconv-1.15              |       h470a237_4         2.0 MB  conda-forge\n",
            "    glib-2.58.2                |       h2dc5807_1         3.4 MB  conda-forge\n",
            "    libpng-1.6.36              |       ha92aebf_0         276 KB  conda-forge\n",
            "    xorg-kbproto-1.0.7         |       h470a237_2          25 KB  conda-forge\n",
            "    xorg-xproto-7.0.31         |       h470a237_7          72 KB  conda-forge\n",
            "    icu-58.2                   |       hfc679d8_0        22.8 MB  conda-forge\n",
            "    mkl-2018.0.3               |                1       198.7 MB\n",
            "    boost-1.68.0               |   py36h3e44d54_1         328 KB  conda-forge\n",
            "    libxcb-1.12                |                0         1.6 MB  conda-forge\n",
            "    jpeg-9c                    |       h470a237_1         229 KB  conda-forge\n",
            "    bzip2-1.0.6                |       h470a237_2         310 KB  conda-forge\n",
            "    xorg-libice-1.0.9          |       h470a237_4          55 KB  conda-forge\n",
            "    pandas-0.23.4              |   py36hf8a1672_0        27.8 MB  conda-forge\n",
            "    pytz-2018.9                |             py_0         229 KB  conda-forge\n",
            "    numpy-1.15.0               |   py36h1b885b7_0          35 KB\n",
            "    rdkit-2018.09.1            |   py36h548bfbe_1        19.6 MB  conda-forge\n",
            "    xorg-libxrender-0.9.10     |       h470a237_2          28 KB  conda-forge\n",
            "    fontconfig-2.13.1          |       h65d0f4c_0         320 KB  conda-forge\n",
            "    olefile-0.46               |             py_0          31 KB  conda-forge\n",
            "    mkl_fft-1.0.10             |           py36_0         650 KB  conda-forge\n",
            "    pycairo-1.15.4             |   py36h1b9232e_1          67 KB\n",
            "    intel-openmp-2019.3        |              199         886 KB\n",
            "    pcre-8.41                  |       hfc679d8_3         243 KB  conda-forge\n",
            "    certifi-2019.3.9           |           py36_0         149 KB  conda-forge\n",
            "    gettext-0.19.8.1           |       h5e8e0c9_1         3.5 MB  conda-forge\n",
            "    xorg-libsm-1.2.3           |       h8c8a85c_0          24 KB  conda-forge\n",
            "    xorg-libx11-1.6.6          |       h470a237_0         890 KB  conda-forge\n",
            "    libtiff-4.0.10             |       he6b73bb_1         517 KB  conda-forge\n",
            "    xorg-renderproto-0.11.1    |       h470a237_2           8 KB  conda-forge\n",
            "    blas-1.0                   |              mkl           6 KB\n",
            "    pillow-5.2.0               |   py36heded4f4_0         586 KB\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:       321.2 MB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "    blas:             1.0-mkl                             \n",
            "    boost:            1.68.0-py36h3e44d54_1    conda-forge\n",
            "    boost-cpp:        1.68.0-h3a22d5f_0        conda-forge\n",
            "    bzip2:            1.0.6-h470a237_2         conda-forge\n",
            "    cairo:            1.16.0-h761e891_0        conda-forge\n",
            "    fontconfig:       2.13.1-h65d0f4c_0        conda-forge\n",
            "    freetype:         2.9.1-h6debe1e_4         conda-forge\n",
            "    gettext:          0.19.8.1-h5e8e0c9_1      conda-forge\n",
            "    glib:             2.58.2-h2dc5807_1        conda-forge\n",
            "    icu:              58.2-hfc679d8_0          conda-forge\n",
            "    intel-openmp:     2019.3-199                          \n",
            "    jpeg:             9c-h470a237_1            conda-forge\n",
            "    libgfortran-ng:   7.3.0-hdf63c60_0                    \n",
            "    libiconv:         1.15-h470a237_4          conda-forge\n",
            "    libpng:           1.6.36-ha92aebf_0        conda-forge\n",
            "    libtiff:          4.0.10-he6b73bb_1        conda-forge\n",
            "    libuuid:          2.32.1-h470a237_2        conda-forge\n",
            "    libxcb:           1.12-0                   conda-forge\n",
            "    libxml2:          2.9.8-h422b904_5         conda-forge\n",
            "    mkl:              2018.0.3-1                          \n",
            "    mkl_fft:          1.0.10-py36_0            conda-forge\n",
            "    mkl_random:       1.0.2-py36_0             conda-forge\n",
            "    numpy:            1.15.0-py36h1b885b7_0               \n",
            "    numpy-base:       1.15.0-py36h3dfced4_0               \n",
            "    olefile:          0.46-py_0                conda-forge\n",
            "    pandas:           0.23.4-py36hf8a1672_0    conda-forge\n",
            "    pcre:             8.41-hfc679d8_3          conda-forge\n",
            "    pillow:           5.2.0-py36heded4f4_0                \n",
            "    pixman:           0.34.0-h470a237_3        conda-forge\n",
            "    pycairo:          1.15.4-py36h1b9232e_1               \n",
            "    python-dateutil:  2.8.0-py_0               conda-forge\n",
            "    pytz:             2018.9-py_0              conda-forge\n",
            "    rdkit:            2018.09.1-py36h548bfbe_1 conda-forge\n",
            "    xorg-kbproto:     1.0.7-h470a237_2         conda-forge\n",
            "    xorg-libice:      1.0.9-h470a237_4         conda-forge\n",
            "    xorg-libsm:       1.2.3-h8c8a85c_0         conda-forge\n",
            "    xorg-libx11:      1.6.6-h470a237_0         conda-forge\n",
            "    xorg-libxext:     1.3.3-h470a237_4         conda-forge\n",
            "    xorg-libxrender:  0.9.10-h470a237_2        conda-forge\n",
            "    xorg-renderproto: 0.11.1-h470a237_2        conda-forge\n",
            "    xorg-xextproto:   7.3.0-h470a237_2         conda-forge\n",
            "    xorg-xproto:      7.0.31-h470a237_7        conda-forge\n",
            "\n",
            "The following packages will be UPDATED:\n",
            "\n",
            "    ca-certificates:  2017.08.26-h1d4fec5_0                --> 2019.3.9-hecc5488_0 conda-forge\n",
            "    certifi:          2018.1.18-py36_0                     --> 2019.3.9-py36_0     conda-forge\n",
            "    openssl:          1.0.2n-hb7f436b_0                    --> 1.0.2p-h470a237_2   conda-forge\n",
            "    xz:               5.2.3-h55aa19d_2                     --> 5.2.4-h470a237_1    conda-forge\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "freetype 2.9.1: 100% 1.0/1 [00:00<00:00,  2.01it/s]               \n",
            "cairo 1.16.0: 100% 1.0/1 [00:00<00:00,  1.23it/s]               \n",
            "libxml2 2.9.8: 100% 1.0/1 [00:01<00:00,  1.15s/it]               \n",
            "mkl_random 1.0.2: 100% 1.0/1 [00:00<00:00,  1.80it/s]               \n",
            "xorg-xextproto 7.3.0: 100% 1.0/1 [00:00<00:00, 15.47it/s]\n",
            "ca-certificates 2019.3.9: 100% 1.0/1 [00:00<00:00, 10.87it/s]\n",
            "xz 5.2.4: 100% 1.0/1 [00:00<00:00,  4.40it/s] \n",
            "libgfortran-ng 7.3.0: 100% 1.0/1 [00:00<00:00,  1.37it/s]               \n",
            "xorg-libxext 1.3.3: 100% 1.0/1 [00:00<00:00, 16.49it/s]\n",
            "pixman 0.34.0: 100% 1.0/1 [00:00<00:00,  1.24it/s]              \n",
            "libuuid 2.32.1: 100% 1.0/1 [00:00<00:00, 12.86it/s]\n",
            "boost-cpp 1.68.0: 100% 1.0/1 [00:18<00:00, 18.61s/it]               \n",
            "numpy-base 1.15.0: 100% 1.0/1 [00:02<00:00,  2.27s/it]              \n",
            "python-dateutil 2.8.0: 100% 1.0/1 [00:00<00:00,  8.12it/s]               \n",
            "openssl 1.0.2p: 100% 1.0/1 [00:01<00:00,  1.46s/it]               \n",
            "libiconv 1.15: 100% 1.0/1 [00:00<00:00,  1.44it/s]               \n",
            "glib 2.58.2: 100% 1.0/1 [00:01<00:00,  1.88s/it]               \n",
            "libpng 1.6.36: 100% 1.0/1 [00:00<00:00,  5.57it/s] \n",
            "xorg-kbproto 1.0.7: 100% 1.0/1 [00:00<00:00, 20.67it/s]\n",
            "xorg-xproto 7.0.31: 100% 1.0/1 [00:00<00:00, 11.06it/s]\n",
            "icu 58.2: 100% 1.0/1 [00:09<00:00,  9.44s/it]               \n",
            "mkl 2018.0.3: 100% 1.0/1 [01:28<00:00, 764.29s/it]               \n",
            "boost 1.68.0: 100% 1.0/1 [00:00<00:00,  2.76it/s]              \n",
            "libxcb 1.12: 100% 1.0/1 [00:01<00:00,  1.52s/it]               \n",
            "jpeg 9c: 100% 1.0/1 [00:00<00:00,  5.40it/s] \n",
            "bzip2 1.0.6: 100% 1.0/1 [00:00<00:00,  5.19it/s] \n",
            "xorg-libice 1.0.9: 100% 1.0/1 [00:00<00:00, 17.69it/s]\n",
            "pandas 0.23.4: 100% 1.0/1 [00:11<00:00, 11.95s/it]               \n",
            "pytz 2018.9: 100% 1.0/1 [00:00<00:00,  2.67it/s]               \n",
            "numpy 1.15.0: 100% 1.0/1 [00:00<00:00, 18.53it/s]\n",
            "rdkit 2018.09.1: 100% 1.0/1 [00:08<00:00,  8.47s/it]               \n",
            "xorg-libxrender 0.9.10: 100% 1.0/1 [00:00<00:00, 16.08it/s]\n",
            "fontconfig 2.13.1: 100% 1.0/1 [00:00<00:00,  5.10it/s]               \n",
            "olefile 0.46: 100% 1.0/1 [00:00<00:00, 19.29it/s]\n",
            "mkl_fft 1.0.10: 100% 1.0/1 [00:00<00:00,  2.99it/s]               \n",
            "pycairo 1.15.4: 100% 1.0/1 [00:00<00:00, 14.07it/s]\n",
            "intel-openmp 2019.3: 100% 1.0/1 [00:00<00:00,  2.11it/s]               \n",
            "pcre 8.41: 100% 1.0/1 [00:00<00:00,  6.42it/s]               \n",
            "certifi 2019.3.9: 100% 1.0/1 [00:00<00:00,  8.99it/s]               \n",
            "gettext 0.19.8.1: 100% 1.0/1 [00:02<00:00,  2.42s/it]               \n",
            "xorg-libsm 1.2.3: 100% 1.0/1 [00:00<00:00, 16.46it/s]\n",
            "xorg-libx11 1.6.6: 100% 1.0/1 [00:00<00:00,  2.06it/s]               \n",
            "libtiff 4.0.10: 100% 1.0/1 [00:00<00:00,  3.16it/s]               \n",
            "xorg-renderproto 0.11.1: 100% 1.0/1 [00:00<00:00, 19.58it/s]\n",
            "blas 1.0: 100% 1.0/1 [00:00<00:00, 38.74it/s]\n",
            "pillow 5.2.0: 100% 1.0/1 [00:00<00:00,  2.98it/s]               \n",
            "Preparing transaction: / \b\b- \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\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| \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\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/ \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\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\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\\ \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\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| \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\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/ \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\b- \b\bdone\n",
            "\n",
            "real\t16m11.023s\n",
            "user\t15m41.363s\n",
            "sys\t0m13.059s\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "wF7o1dE58x7X",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        },
        "outputId": "8edf4ab3-1c74-4b62-a327-a39a50c7940e"
      },
      "cell_type": "code",
      "source": [
        "import sys\n",
        "import os\n",
        "sys.path.append('/usr/local/lib/python3.6/site-packages/')\n",
        "from rdkit import Chem\n",
        "from rdkit import rdBase\n",
        "print(rdBase.rdkitVersion)"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "2018.09.1\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "0DU8XtRnDEzy",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 85
        },
        "outputId": "737af562-7b27-441f-8e15-b7a8260c6174"
      },
      "cell_type": "code",
      "source": [
        "!nvcc --version"
      ],
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "nvcc: NVIDIA (R) Cuda compiler driver\n",
            "Copyright (c) 2005-2018 NVIDIA Corporation\n",
            "Built on Sat_Aug_25_21:08:01_CDT_2018\n",
            "Cuda compilation tools, release 10.0, V10.0.130\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "ggtQAzswDPHT",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 51
        },
        "outputId": "0e0e5934-f27d-4db2-c4d2-d8fe8d1c0de2"
      },
      "cell_type": "code",
      "source": [
        "! conda config --add channels omnia --add channels conda-forge"
      ],
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Warning: 'omnia' already in 'channels' list, moving to the top\n",
            "Warning: 'conda-forge' already in 'channels' list, moving to the top\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "udUafipaDcfR",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1394
        },
        "outputId": "58f45c96-fa7a-4fb8-8207-baf4f62f5a4f"
      },
      "cell_type": "code",
      "source": [
        "! conda install -y openforcefield"
      ],
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Solving environment: - \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\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\\ \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\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| \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\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/ \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\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- \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\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\\ \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\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| \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\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/ \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\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- \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\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",
            "\n",
            "\n",
            "==> WARNING: A newer version of conda exists. <==\n",
            "  current version: 4.4.10\n",
            "  latest version: 4.6.11\n",
            "\n",
            "Please update conda by running\n",
            "\n",
            "    $ conda update -n base conda\n",
            "\n",
            "\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs: \n",
            "    - openforcefield\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
            "    openmm-7.3.1               | py36_cuda92_rc_2        11.4 MB  omnia\n",
            "    networkx-2.2               |             py_1         1.1 MB  conda-forge\n",
            "    pyparsing-2.4.0            |             py_0          55 KB  conda-forge\n",
            "    decorator-4.4.0            |             py_0          11 KB  conda-forge\n",
            "    pyyaml-3.13                |   py36h470a237_1         460 KB  conda-forge\n",
            "    msgpack-python-0.6.0       |   py36h2d50403_0         257 KB  conda-forge\n",
            "    libgcc-7.2.0               |       h69d50b8_2         304 KB  conda-forge\n",
            "    parmed-3.1.0               |           py36_0         1.1 MB  omnia\n",
            "    openforcefield-0.2.0       |           py36_0        28.0 MB  omnia\n",
            "    bson-0.5.8                 |             py_0          13 KB  conda-forge\n",
            "    xmltodict-0.12.0           |             py_0          11 KB  conda-forge\n",
            "    fftw3f-3.3.4               |                2         1.2 MB  omnia\n",
            "    ambermini-16.16.0          |                7        21.7 MB  omnia\n",
            "    toml-0.10.0                |             py_0          16 KB  conda-forge\n",
            "    packaging-19.0             |             py_0          23 KB  conda-forge\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:        65.6 MB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "    ambermini:      16.16.0-7              omnia      \n",
            "    bson:           0.5.8-py_0             conda-forge\n",
            "    decorator:      4.4.0-py_0             conda-forge\n",
            "    fftw3f:         3.3.4-2                omnia      \n",
            "    libgcc:         7.2.0-h69d50b8_2       conda-forge\n",
            "    msgpack-python: 0.6.0-py36h2d50403_0   conda-forge\n",
            "    networkx:       2.2-py_1               conda-forge\n",
            "    openforcefield: 0.2.0-py36_0           omnia      \n",
            "    openmm:         7.3.1-py36_cuda92_rc_2 omnia      \n",
            "    packaging:      19.0-py_0              conda-forge\n",
            "    parmed:         3.1.0-py36_0           omnia      \n",
            "    pyparsing:      2.4.0-py_0             conda-forge\n",
            "    pyyaml:         3.13-py36h470a237_1    conda-forge\n",
            "    toml:           0.10.0-py_0            conda-forge\n",
            "    xmltodict:      0.12.0-py_0            conda-forge\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "openmm 7.3.1: 100% 1.0/1 [00:07<00:00,  7.02s/it]               \n",
            "networkx 2.2: 100% 1.0/1 [00:00<00:00,  1.06it/s]               \n",
            "pyparsing 2.4.0: 100% 1.0/1 [00:00<00:00, 13.30it/s]\n",
            "decorator 4.4.0: 100% 1.0/1 [00:00<00:00, 18.86it/s]\n",
            "pyyaml 3.13: 100% 1.0/1 [00:00<00:00,  3.98it/s] \n",
            "msgpack-python 0.6.0: 100% 1.0/1 [00:00<00:00,  4.00it/s]               \n",
            "libgcc 7.2.0: 100% 1.0/1 [00:00<00:00,  5.73it/s]               \n",
            "parmed 3.1.0: 100% 1.0/1 [00:01<00:00,  1.36s/it]               \n",
            "openforcefield 0.2.0: 100% 1.0/1 [00:13<00:00, 13.60s/it]                \n",
            "bson 0.5.8: 100% 1.0/1 [00:00<00:00, 12.94it/s]\n",
            "xmltodict 0.12.0: 100% 1.0/1 [00:00<00:00, 21.25it/s]\n",
            "fftw3f 3.3.4: 100% 1.0/1 [00:01<00:00,  1.16s/it]               \n",
            "ambermini 16.16.0: 100% 1.0/1 [00:12<00:00, 12.74s/it]               \n",
            "toml 0.10.0: 100% 1.0/1 [00:00<00:00, 19.26it/s]\n",
            "packaging 19.0: 100% 1.0/1 [00:00<00:00, 16.36it/s]\n",
            "Preparing transaction: \\ \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\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\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/ \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\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- \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\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\\ \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\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| \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\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/ \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\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- \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\b\\ \b\b| \b\b/ \b\b- \b\bdone\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "dQdSGt4rFMCB",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "from openforcefield.topology import Molecule\n",
        "from openforcefield.topology import Topology\n",
        "from openforcefield.utils import RDKitToolkitWrapper\n",
        "from openforcefield.typing.engines.smirnoff import ForceField\n",
        "from simtk import openmm\n",
        "from simtk import unit\n"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "gSk7MXzrGgC2",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "\n",
        "def get_energy(system, positions):\n",
        "    \"\"\"\n",
        "    Return the potential energy.\n",
        "\n",
        "    Parameters\n",
        "    ----------\n",
        "    system : simtk.openmm.System\n",
        "        The system to check\n",
        "    positions : simtk.unit.Quantity of dimension (natoms,3) with units of length\n",
        "        The positions to use\n",
        "    Returns\n",
        "    ---------\n",
        "    energy\n",
        "    \"\"\"\n",
        "\n",
        "    integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds)\n",
        "    context = openmm.Context(system, integrator)\n",
        "    context.setPositions(positions)\n",
        "    state = context.getState(getEnergy=True)\n",
        "    energy = state.getPotentialEnergy().in_units_of(unit.kilocalories_per_mole)\n",
        "    return energy\n"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "H2O5O4U0Gj7d",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "mol = Molecule.from_smiles('CCO')"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "kFOpuGP0G8Bq",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        },
        "outputId": "c102d473-3732-4d58-c977-5fb2e6533079"
      },
      "cell_type": "code",
      "source": [
        "mol"
      ],
      "execution_count": 17,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "Molecule with name '' and SMILES '[H][O][C]([H])([H])[C]([H])([H])[H]'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 17
        }
      ]
    },
    {
      "metadata": {
        "id": "vWLv2DK-G8tj",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "mol.generate_conformers()\n",
        "positions = mol.conformers[0]"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "DCGjiSmVHLBx",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "#load Force Field\n",
        "ff = ForceField('smirnoff99Frosst.offxml')"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "OMh8HShbHOcf",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "topology = mol.to_topology()"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "62Naw5rhHSUg",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 54
        },
        "outputId": "110c09e0-fe52-4a23-e369-758440c2bac1"
      },
      "cell_type": "code",
      "source": [
        "orginal_system = ff.create_openmm_system(topology)\n"
      ],
      "execution_count": 26,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "In AmberToolsToolkitwrapper.computer_partial_charges_am1bcc: Molecule '' has more than one conformer, but this function will only generate charges for the first one.\n"
          ],
          "name": "stderr"
        }
      ]
    },
    {
      "metadata": {
        "id": "Uiw4WZJVHuqC",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "orig_energy = get_energy(orginal_system, positions)"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "G4gxjj9GH0wz",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        },
        "outputId": "d2d77ac7-04cb-4dde-b2a7-a7f6e6be04f0"
      },
      "cell_type": "code",
      "source": [
        "print(orig_energy)"
      ],
      "execution_count": 29,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "2.3399880921635527 kcal/mol\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "WnHIdVsCIHoc",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "mol = Chem.MolFromSmiles('c1ccccc1')"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "KTTlD3GNILbg",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "rdw = RDKitToolkitWrapper()"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "xrkzvH_WIQ8H",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "ofmol = rdw.from_rdkit(mol)"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "ybqrHKtCIkQk",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        "ofmol.generate_conformers()"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "metadata": {
        "id": "7fBh7gG9IsZv",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 34
        },
        "outputId": "e97c15ac-525e-4c4e-fab6-82759a319a2b"
      },
      "cell_type": "code",
      "source": [
        "positions = ofmol.conformers[0]\n",
        "topology = ofmol.to_topology()\n",
        "orginal_system = ff.create_openmm_system(topology)\n",
        "orig_energy = get_energy(orginal_system, positions)\n",
        "print(orig_energy)"
      ],
      "execution_count": 38,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "7.987402593200566 kcal/mol\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "id": "3lWVxaA3Is41",
        "colab_type": "code",
        "colab": {}
      },
      "cell_type": "code",
      "source": [
        ""
      ],
      "execution_count": 0,
      "outputs": []
    }
  ]
}