pl2.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "source": [
        "# Protein Ligand Interaction Diagram Generator\n",
        "\n",
        "## Essentially, this is a free protein preparation process, and at last, you will get the prepared structure named as \n",
        "```complex_prepared.pdb``` \n",
        "## while the 2D interaction is just inside this online notebook, you can copy and paste it anywhere you want.\n",
        "\n",
        "- This workflow allows you to input a PDB bank protein-ligand co-crystal structure.\n",
        "- The structure will be split and prepared separately\n",
        "- The prepared structures then combined again\n",
        "- The 2D interaction is a draw based on the merged structure\n",
        "- The user is expected to provide the PDB ID and the ligand name as per in the PDB database, which is listed on the small molecule section of the PDB main page of the corresponding structure"
      ],
      "metadata": {
        "id": "onNJ9LWWznMC"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Install Conda"
      ],
      "metadata": {
        "id": "a4WNaxHtzsrg"
      }
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "execution": {
          "iopub.execute_input": "2021-10-17T09:46:47.190602Z",
          "iopub.status.busy": "2021-10-17T09:46:47.190226Z"
        },
        "id": "n-T9DTZWhQyh"
      },
      "outputs": [],
      "source": [
        "!pip install -q condacolab\n",
        "import condacolab\n",
        "condacolab.install()"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Install dependencies"
      ],
      "metadata": {
        "id": "DzAOumhnzfV_"
      }
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "execution": {
          "iopub.execute_input": "2021-10-17T09:30:42.950431Z",
          "iopub.status.busy": "2021-10-17T09:30:42.950122Z",
          "iopub.status.idle": "2021-10-17T09:31:36.742917Z",
          "shell.execute_reply": "2021-10-17T09:31:36.742146Z",
          "shell.execute_reply.started": "2021-10-17T09:30:42.950386Z"
        },
        "scrolled": true,
        "id": "MdLTT9VbhQyi",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "b52a359f-673b-4c4d-e269-e36dd6a7168b"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\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",
            "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\bdone\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - openmm\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
            "    ca-certificates-2022.12.7  |       ha878542_0         143 KB  conda-forge\n",
            "    certifi-2022.12.7          |     pyhd8ed1ab_0         147 KB  conda-forge\n",
            "    colorama-0.4.6             |     pyhd8ed1ab_0          25 KB  conda-forge\n",
            "    conda-23.1.0               |   py38h578d9bd_0         907 KB  conda-forge\n",
            "    cudatoolkit-11.8.0         |      h37601d7_11       635.9 MB  conda-forge\n",
            "    libblas-3.9.0              |16_linux64_openblas          13 KB  conda-forge\n",
            "    libcblas-3.9.0             |16_linux64_openblas          13 KB  conda-forge\n",
            "    libgfortran-ng-12.2.0      |      h69a702a_19          22 KB  conda-forge\n",
            "    libgfortran5-12.2.0        |      h337968e_19         1.8 MB  conda-forge\n",
            "    liblapack-3.9.0            |16_linux64_openblas          13 KB  conda-forge\n",
            "    libopenblas-0.3.21         |pthreads_h78a6416_3        10.1 MB  conda-forge\n",
            "    numpy-1.24.2               |   py38h10c12cc_0         6.3 MB  conda-forge\n",
            "    ocl-icd-2.3.1              |       h7f98852_0         119 KB  conda-forge\n",
            "    ocl-icd-system-1.0.0       |                1           4 KB  conda-forge\n",
            "    openmm-8.0.0               |   py38he9472fe_0        10.7 MB  conda-forge\n",
            "    openssl-3.0.8              |       h0b41bf4_0         2.5 MB  conda-forge\n",
            "    pluggy-1.0.0               |     pyhd8ed1ab_5          16 KB  conda-forge\n",
            "    ruamel.yaml-0.17.21        |   py38h0a891b7_2         172 KB  conda-forge\n",
            "    ruamel.yaml.clib-0.2.7     |   py38h1de0b5d_1         143 KB  conda-forge\n",
            "    tqdm-4.65.0                |     pyhd8ed1ab_1          86 KB  conda-forge\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:       669.1 MB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "  colorama           conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 None\n",
            "  cudatoolkit        conda-forge/linux-64::cudatoolkit-11.8.0-h37601d7_11 None\n",
            "  libblas            conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas None\n",
            "  libcblas           conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas None\n",
            "  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19 None\n",
            "  libgfortran5       conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19 None\n",
            "  liblapack          conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas None\n",
            "  libopenblas        conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3 None\n",
            "  numpy              conda-forge/linux-64::numpy-1.24.2-py38h10c12cc_0 None\n",
            "  ocl-icd            conda-forge/linux-64::ocl-icd-2.3.1-h7f98852_0 None\n",
            "  ocl-icd-system     conda-forge/linux-64::ocl-icd-system-1.0.0-1 None\n",
            "  openmm             conda-forge/linux-64::openmm-8.0.0-py38he9472fe_0 None\n",
            "  pluggy             conda-forge/noarch::pluggy-1.0.0-pyhd8ed1ab_5 None\n",
            "  ruamel.yaml        conda-forge/linux-64::ruamel.yaml-0.17.21-py38h0a891b7_2 None\n",
            "  ruamel.yaml.clib   conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py38h1de0b5d_1 None\n",
            "  tqdm               conda-forge/noarch::tqdm-4.65.0-pyhd8ed1ab_1 None\n",
            "\n",
            "The following packages will be UPDATED:\n",
            "\n",
            "  ca-certificates                      2022.9.24-ha878542_0 --> 2022.12.7-ha878542_0 None\n",
            "  certifi                            2022.9.24-pyhd8ed1ab_0 --> 2022.12.7-pyhd8ed1ab_0 None\n",
            "  conda                               22.9.0-py38h578d9bd_2 --> 23.1.0-py38h578d9bd_0 None\n",
            "  openssl                                  3.0.7-h0b41bf4_1 --> 3.0.8-h0b41bf4_0 None\n",
            "\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "ruamel.yaml-0.17.21  | 172 KB    | : 100% 1.0/1 [00:00<00:00,  4.19it/s]\n",
            "tqdm-4.65.0          | 86 KB     | : 100% 1.0/1 [00:00<00:00, 11.21it/s]\n",
            "cudatoolkit-11.8.0   | 635.9 MB  | : 100% 1.0/1 [00:19<00:00, 19.10s/it]               \n",
            "libopenblas-0.3.21   | 10.1 MB   | : 100% 1.0/1 [00:02<00:00,  2.74s/it]               \n",
            "libcblas-3.9.0       | 13 KB     | : 100% 1.0/1 [00:00<00:00, 26.98it/s]\n",
            "liblapack-3.9.0      | 13 KB     | : 100% 1.0/1 [00:00<00:00, 26.44it/s]\n",
            "libgfortran-ng-12.2. | 22 KB     | : 100% 1.0/1 [00:00<00:00, 23.80it/s]\n",
            "ruamel.yaml.clib-0.2 | 143 KB    | : 100% 1.0/1 [00:00<00:00,  2.43it/s]                \n",
            "conda-23.1.0         | 907 KB    | : 100% 1.0/1 [00:00<00:00,  4.54it/s]\n",
            "ca-certificates-2022 | 143 KB    | : 100% 1.0/1 [00:00<00:00, 28.13it/s]\n",
            "numpy-1.24.2         | 6.3 MB    | : 100% 1.0/1 [00:00<00:00,  1.25it/s]\n",
            "openssl-3.0.8        | 2.5 MB    | : 100% 1.0/1 [00:00<00:00,  6.84it/s]\n",
            "openmm-8.0.0         | 10.7 MB   | : 100% 1.0/1 [00:00<00:00,  1.39it/s]               \n",
            "libgfortran5-12.2.0  | 1.8 MB    | : 100% 1.0/1 [00:00<00:00,  1.88it/s]\n",
            "ocl-icd-2.3.1        | 119 KB    | : 100% 1.0/1 [00:00<00:00, 10.63it/s]\n",
            "certifi-2022.12.7    | 147 KB    | : 100% 1.0/1 [00:00<00:00, 27.27it/s]\n",
            "colorama-0.4.6       | 25 KB     | : 100% 1.0/1 [00:00<00:00, 25.68it/s]\n",
            "ocl-icd-system-1.0.0 | 4 KB      | : 100% 1.0/1 [00:00<00:00, 26.53it/s]\n",
            "pluggy-1.0.0         | 16 KB     | : 100% 1.0/1 [00:00<00:00, 22.42it/s]\n",
            "libblas-3.9.0        | 13 KB     | : 100% 1.0/1 [00:00<00:00, 20.72it/s]\n",
            "Preparing transaction: - \b\b\\ \b\bdone\n",
            "Verifying transaction: / \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/ By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html\n",
            "\n",
            "\b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\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",
            "Retrieving notices: ...working... done\n",
            "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\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",
            "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\bdone\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - pdbfixer\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
            "    pdbfixer-1.8.1             |     pyh6c4a22f_0         498 KB  conda-forge\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:         498 KB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "  pdbfixer           conda-forge/noarch::pdbfixer-1.8.1-pyh6c4a22f_0 \n",
            "\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "                                                                        \n",
            "Preparing transaction: | \b\bdone\n",
            "Verifying transaction: - \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\bdone\n",
            "\n",
            "ResolvePackageNotFound: \n",
            "  - conda==22.9.0\n",
            "\n"
          ]
        }
      ],
      "source": [
        "!conda install -c conda-forge openmm -y\n",
        "!conda install -c conda-forge pdbfixer -y\n",
        "!yes|conda install -c conda-forge pymol-open-source 2>&1 1>/dev/null\n",
        "!conda install -c rdkit rdkit -y 2>&1 1>/dev/null\n",
        "!conda install -q -y -c openbabel openbabel 2>&1 1>/dev/null\n",
        "!conda install -c conda-forge mdanalysis 2>&1 1>/dev/null\n",
        "!conda install -c conda-forge prolif 2>&1 1>/dev/null"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "! conda install conda==22.9.0 "
      ],
      "metadata": {
        "id": "NWgRsIIAUF9Z",
        "outputId": "caa2afec-279d-4325-bf58-9574af6d83cd",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\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",
            "Solving environment: / \b\bfailed with initial frozen solve. Retrying with flexible solve.\n",
            "Collecting package metadata (repodata.json): \\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\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",
            "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\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\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",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - conda==22.9.0\n",
            "\n",
            "\n",
            "The following packages will be DOWNGRADED:\n",
            "\n",
            "  conda                               23.1.0-py38h578d9bd_0 --> 22.9.0-py38h578d9bd_2 \n",
            "\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "\n",
            "Preparing transaction: - \b\bdone\n",
            "Verifying transaction: | \b\bdone\n",
            "Executing transaction: - \b\bdone\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!conda install -c conda-forge pymol-open-source"
      ],
      "metadata": {
        "id": "Bu5GuAAvTrxr",
        "outputId": "137fd17f-3fce-493a-8d79-fe620305ffbd",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Collecting package metadata (current_repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\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",
            "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\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\bfailed with initial frozen solve. Retrying with flexible solve.\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| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bfailed with repodata from current_repodata.json, will retry with next repodata source.\n",
            "Collecting package metadata (repodata.json): \\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\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",
            "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\bdone\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - pymol-open-source\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
            "    alsa-lib-1.2.8             |       h166bdaf_0         578 KB  conda-forge\n",
            "    attr-2.5.1                 |       h166bdaf_1          69 KB  conda-forge\n",
            "    dbus-1.13.6                |       h5008d03_3         604 KB  conda-forge\n",
            "    fftw-3.3.10                |nompi_hf0379b8_106         2.1 MB  conda-forge\n",
            "    glew-2.1.0                 |       h9c3ff4c_2         647 KB  conda-forge\n",
            "    glib-2.74.1                |       h6239696_1         474 KB  conda-forge\n",
            "    glib-tools-2.74.1          |       h6239696_1         107 KB  conda-forge\n",
            "    glm-0.9.9.4                |       h924138e_2         204 KB  conda-forge\n",
            "    graphite2-1.3.13           |    h58526e2_1001         102 KB  conda-forge\n",
            "    gst-plugins-base-1.22.0    |       h4243ec0_0         2.6 MB  conda-forge\n",
            "    gstreamer-1.22.0           |       h25f0c4b_0         1.9 MB  conda-forge\n",
            "    gstreamer-orc-0.4.33       |       h166bdaf_0         299 KB  conda-forge\n",
            "    harfbuzz-6.0.0             |       h8e241bc_0         1.2 MB  conda-forge\n",
            "    jack-1.9.22                |       h11f4161_0         453 KB  conda-forge\n",
            "    lame-3.100                 |    h166bdaf_1003         496 KB  conda-forge\n",
            "    libcap-2.66                |       ha37c62d_0          97 KB  conda-forge\n",
            "    libclang-15.0.7            |default_had23c3d_1         130 KB  conda-forge\n",
            "    libclang13-15.0.7          |default_h3e3d535_1         9.1 MB  conda-forge\n",
            "    libcups-2.3.3              |       h36d4200_3         4.3 MB  conda-forge\n",
            "    libdb-6.2.32               |       h9c3ff4c_0        23.3 MB  conda-forge\n",
            "    libevent-2.1.10            |       h28343ad_4         1.1 MB  conda-forge\n",
            "    libflac-1.4.2              |       h27087fc_0         411 KB  conda-forge\n",
            "    libgcrypt-1.10.1           |       h166bdaf_0         703 KB  conda-forge\n",
            "    libglu-9.0.0               |    he1b5a44_1001         413 KB  conda-forge\n",
            "    libgpg-error-1.46          |       h620e276_0         252 KB  conda-forge\n",
            "    libllvm15-15.0.7           |       hadd5161_0        31.5 MB  conda-forge\n",
            "    libogg-1.3.4               |       h7f98852_1         206 KB  conda-forge\n",
            "    libopus-1.3.1              |       h7f98852_1         255 KB  conda-forge\n",
            "    libpq-15.2                 |       hb675445_0         2.3 MB  conda-forge\n",
            "    libsndfile-1.2.0           |       hb75c966_0         342 KB  conda-forge\n",
            "    libsystemd0-252            |       h2a991cd_0         384 KB  conda-forge\n",
            "    libtool-2.4.7              |       h27087fc_0         402 KB  conda-forge\n",
            "    libudev1-253               |       h0b41bf4_0         116 KB  conda-forge\n",
            "    libvorbis-1.3.7            |       h9c3ff4c_0         280 KB  conda-forge\n",
            "    libxkbcommon-1.5.0         |       h79f4944_0         549 KB  conda-forge\n",
            "    mpg123-1.31.2              |       hcb278e6_0         474 KB  conda-forge\n",
            "    mysql-common-8.0.32        |       ha901b37_0         727 KB  conda-forge\n",
            "    mysql-libs-8.0.32          |       hd7da12d_0         1.5 MB  conda-forge\n",
            "    nspr-4.35                  |       h27087fc_0         222 KB  conda-forge\n",
            "    nss-3.88                   |       he45b914_0         1.9 MB  conda-forge\n",
            "    ply-3.11                   |             py_1          44 KB  conda-forge\n",
            "    pmw-2.0.1                  |py38h578d9bd_1007         510 KB  conda-forge\n",
            "    pulseaudio-16.1            |       ha8d29e2_1         1.5 MB  conda-forge\n",
            "    pymol-open-source-2.5.0    |   py38h88c765f_6         6.0 MB  conda-forge\n",
            "    pyqt-5.15.7                |   py38ha0d8c90_3         5.0 MB  conda-forge\n",
            "    pyqt5-sip-12.11.0          |   py38h8dc9893_3          83 KB  conda-forge\n",
            "    qt-main-5.15.8             |       h5d23da1_6        50.0 MB  conda-forge\n",
            "    sip-6.7.7                  |   py38h8dc9893_0         473 KB  conda-forge\n",
            "    toml-0.10.2                |     pyhd8ed1ab_0          18 KB  conda-forge\n",
            "    xcb-util-0.4.0             |       h166bdaf_0          20 KB  conda-forge\n",
            "    xcb-util-image-0.4.0       |       h166bdaf_0          24 KB  conda-forge\n",
            "    xcb-util-keysyms-0.4.0     |       h166bdaf_0          12 KB  conda-forge\n",
            "    xcb-util-renderutil-0.3.9  |       h166bdaf_0          15 KB  conda-forge\n",
            "    xcb-util-wm-0.4.1          |       h166bdaf_0          55 KB  conda-forge\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:       156.2 MB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "  alsa-lib           conda-forge/linux-64::alsa-lib-1.2.8-h166bdaf_0 None\n",
            "  attr               conda-forge/linux-64::attr-2.5.1-h166bdaf_1 None\n",
            "  dbus               conda-forge/linux-64::dbus-1.13.6-h5008d03_3 None\n",
            "  fftw               conda-forge/linux-64::fftw-3.3.10-nompi_hf0379b8_106 None\n",
            "  glew               conda-forge/linux-64::glew-2.1.0-h9c3ff4c_2 None\n",
            "  glib               conda-forge/linux-64::glib-2.74.1-h6239696_1 None\n",
            "  glib-tools         conda-forge/linux-64::glib-tools-2.74.1-h6239696_1 None\n",
            "  glm                conda-forge/linux-64::glm-0.9.9.4-h924138e_2 None\n",
            "  graphite2          conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001 None\n",
            "  gst-plugins-base   conda-forge/linux-64::gst-plugins-base-1.22.0-h4243ec0_0 None\n",
            "  gstreamer          conda-forge/linux-64::gstreamer-1.22.0-h25f0c4b_0 None\n",
            "  gstreamer-orc      conda-forge/linux-64::gstreamer-orc-0.4.33-h166bdaf_0 None\n",
            "  harfbuzz           conda-forge/linux-64::harfbuzz-6.0.0-h8e241bc_0 None\n",
            "  jack               conda-forge/linux-64::jack-1.9.22-h11f4161_0 None\n",
            "  lame               conda-forge/linux-64::lame-3.100-h166bdaf_1003 None\n",
            "  libcap             conda-forge/linux-64::libcap-2.66-ha37c62d_0 None\n",
            "  libclang           conda-forge/linux-64::libclang-15.0.7-default_had23c3d_1 None\n",
            "  libclang13         conda-forge/linux-64::libclang13-15.0.7-default_h3e3d535_1 None\n",
            "  libcups            conda-forge/linux-64::libcups-2.3.3-h36d4200_3 None\n",
            "  libdb              conda-forge/linux-64::libdb-6.2.32-h9c3ff4c_0 None\n",
            "  libevent           conda-forge/linux-64::libevent-2.1.10-h28343ad_4 None\n",
            "  libflac            conda-forge/linux-64::libflac-1.4.2-h27087fc_0 None\n",
            "  libgcrypt          conda-forge/linux-64::libgcrypt-1.10.1-h166bdaf_0 None\n",
            "  libglu             conda-forge/linux-64::libglu-9.0.0-he1b5a44_1001 None\n",
            "  libgpg-error       conda-forge/linux-64::libgpg-error-1.46-h620e276_0 None\n",
            "  libllvm15          conda-forge/linux-64::libllvm15-15.0.7-hadd5161_0 None\n",
            "  libogg             conda-forge/linux-64::libogg-1.3.4-h7f98852_1 None\n",
            "  libopus            conda-forge/linux-64::libopus-1.3.1-h7f98852_1 None\n",
            "  libpq              conda-forge/linux-64::libpq-15.2-hb675445_0 None\n",
            "  libsndfile         conda-forge/linux-64::libsndfile-1.2.0-hb75c966_0 None\n",
            "  libsystemd0        conda-forge/linux-64::libsystemd0-252-h2a991cd_0 None\n",
            "  libtool            conda-forge/linux-64::libtool-2.4.7-h27087fc_0 None\n",
            "  libudev1           conda-forge/linux-64::libudev1-253-h0b41bf4_0 None\n",
            "  libvorbis          conda-forge/linux-64::libvorbis-1.3.7-h9c3ff4c_0 None\n",
            "  libxkbcommon       conda-forge/linux-64::libxkbcommon-1.5.0-h79f4944_0 None\n",
            "  mpg123             conda-forge/linux-64::mpg123-1.31.2-hcb278e6_0 None\n",
            "  mysql-common       conda-forge/linux-64::mysql-common-8.0.32-ha901b37_0 None\n",
            "  mysql-libs         conda-forge/linux-64::mysql-libs-8.0.32-hd7da12d_0 None\n",
            "  nspr               conda-forge/linux-64::nspr-4.35-h27087fc_0 None\n",
            "  nss                conda-forge/linux-64::nss-3.88-he45b914_0 None\n",
            "  ply                conda-forge/noarch::ply-3.11-py_1 None\n",
            "  pmw                conda-forge/linux-64::pmw-2.0.1-py38h578d9bd_1007 None\n",
            "  pulseaudio         conda-forge/linux-64::pulseaudio-16.1-ha8d29e2_1 None\n",
            "  pymol-open-source  conda-forge/linux-64::pymol-open-source-2.5.0-py38h88c765f_6 None\n",
            "  pyqt               conda-forge/linux-64::pyqt-5.15.7-py38ha0d8c90_3 None\n",
            "  pyqt5-sip          conda-forge/linux-64::pyqt5-sip-12.11.0-py38h8dc9893_3 None\n",
            "  qt-main            conda-forge/linux-64::qt-main-5.15.8-h5d23da1_6 None\n",
            "  sip                conda-forge/linux-64::sip-6.7.7-py38h8dc9893_0 None\n",
            "  toml               conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0 None\n",
            "  xcb-util           conda-forge/linux-64::xcb-util-0.4.0-h166bdaf_0 None\n",
            "  xcb-util-image     conda-forge/linux-64::xcb-util-image-0.4.0-h166bdaf_0 None\n",
            "  xcb-util-keysyms   conda-forge/linux-64::xcb-util-keysyms-0.4.0-h166bdaf_0 None\n",
            "  xcb-util-renderut~ conda-forge/linux-64::xcb-util-renderutil-0.3.9-h166bdaf_0 None\n",
            "  xcb-util-wm        conda-forge/linux-64::xcb-util-wm-0.4.1-h166bdaf_0 None\n",
            "\n",
            "The following packages will be UPDATED:\n",
            "\n",
            "  conda                               22.9.0-py38h578d9bd_2 --> 23.1.0-py38h578d9bd_0 None\n",
            "\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages\n",
            "glm-0.9.9.4          | 204 KB    | : 100% 1.0/1 [00:00<00:00,  1.05it/s]\n",
            "lame-3.100           | 496 KB    | : 100% 1.0/1 [00:00<00:00,  6.72it/s]\n",
            "glib-2.74.1          | 474 KB    | : 100% 1.0/1 [00:00<00:00,  3.30it/s]\n",
            "xcb-util-renderutil- | 15 KB     | : 100% 1.0/1 [00:00<00:00,  3.38it/s]\n",
            "libcap-2.66          | 97 KB     | : 100% 1.0/1 [00:00<00:00, 14.15it/s]\n",
            "gst-plugins-base-1.2 | 2.6 MB    | : 100% 1.0/1 [00:00<00:00,  4.29it/s]\n",
            "sip-6.7.7            | 473 KB    | : 100% 1.0/1 [00:00<00:00,  8.37it/s]\n",
            "gstreamer-1.22.0     | 1.9 MB    | : 100% 1.0/1 [00:00<00:00,  5.64it/s]\n",
            "libclang-15.0.7      | 130 KB    | : 100% 1.0/1 [00:00<00:00, 21.64it/s]\n",
            "attr-2.5.1           | 69 KB     | : 100% 1.0/1 [00:00<00:00, 15.58it/s]\n",
            "graphite2-1.3.13     | 102 KB    | : 100% 1.0/1 [00:00<00:00, 21.89it/s]\n",
            "nspr-4.35            | 222 KB    | : 100% 1.0/1 [00:00<00:00, 18.93it/s]\n",
            "libclang13-15.0.7    | 9.1 MB    | : 100% 1.0/1 [00:00<00:00,  3.54it/s]\n",
            "libdb-6.2.32         | 23.3 MB   | : 100% 1.0/1 [00:09<00:00,  9.76s/it]               \n",
            "libopus-1.3.1        | 255 KB    | : 100% 1.0/1 [00:00<00:00, 10.76it/s]\n",
            "pulseaudio-16.1      | 1.5 MB    | : 100% 1.0/1 [00:01<00:00,  1.34s/it]\n",
            "libxkbcommon-1.5.0   | 549 KB    | : 100% 1.0/1 [00:00<00:00, 14.10it/s]\n",
            "pymol-open-source-2. | 6.0 MB    | : 100% 1.0/1 [00:01<00:00,  1.90s/it]\n",
            "libcups-2.3.3        | 4.3 MB    | : 100% 1.0/1 [00:01<00:00,  1.45s/it]\n",
            "glew-2.1.0           | 647 KB    | : 100% 1.0/1 [00:00<00:00,  3.48it/s]\n",
            "qt-main-5.15.8       | 50.0 MB   | : 100% 1.0/1 [00:08<00:00,  8.27s/it]              \n",
            "ply-3.11             | 44 KB     | : 100% 1.0/1 [00:00<00:00, 21.58it/s]\n",
            "libpq-15.2           | 2.3 MB    | : 100% 1.0/1 [00:00<00:00,  2.23it/s]\n",
            "nss-3.88             | 1.9 MB    | : 100% 1.0/1 [00:00<00:00,  4.75it/s]\n",
            "xcb-util-wm-0.4.1    | 55 KB     | : 100% 1.0/1 [00:00<00:00, 10.31it/s]\n",
            "dbus-1.13.6          | 604 KB    | : 100% 1.0/1 [00:00<00:00,  4.75it/s]\n",
            "libsndfile-1.2.0     | 342 KB    | : 100% 1.0/1 [00:00<00:00, 18.79it/s]\n",
            "pyqt5-sip-12.11.0    | 83 KB     | : 100% 1.0/1 [00:00<00:00, 26.39it/s]\n",
            "libtool-2.4.7        | 402 KB    | : 100% 1.0/1 [00:00<00:00, 13.82it/s]\n",
            "toml-0.10.2          | 18 KB     | : 100% 1.0/1 [00:00<00:00, 28.08it/s]\n",
            "mpg123-1.31.2        | 474 KB    | : 100% 1.0/1 [00:00<00:00, 17.21it/s]\n",
            "glib-tools-2.74.1    | 107 KB    | : 100% 1.0/1 [00:00<00:00, 19.42it/s]\n",
            "libflac-1.4.2        | 411 KB    | : 100% 1.0/1 [00:00<00:00,  7.88it/s]\n",
            "pmw-2.0.1            | 510 KB    | : 100% 1.0/1 [00:00<00:00,  3.27it/s]\n",
            "libevent-2.1.10      | 1.1 MB    | : 100% 1.0/1 [00:00<00:00,  1.23it/s]\n",
            "jack-1.9.22          | 453 KB    | : 100% 1.0/1 [00:00<00:00, 15.37it/s]\n",
            "libogg-1.3.4         | 206 KB    | : 100% 1.0/1 [00:00<00:00, 10.98it/s]\n",
            "fftw-3.3.10          | 2.1 MB    | : 100% 1.0/1 [00:00<00:00,  9.71it/s]\n",
            "libllvm15-15.0.7     | 31.5 MB   | : 100% 1.0/1 [00:01<00:00,  1.16s/it]               \n",
            "xcb-util-image-0.4.0 | 24 KB     | : 100% 1.0/1 [00:00<00:00, 22.46it/s]\n",
            "harfbuzz-6.0.0       | 1.2 MB    | : 100% 1.0/1 [00:00<00:00, 10.35it/s]\n",
            "libvorbis-1.3.7      | 280 KB    | : 100% 1.0/1 [00:00<00:00, 11.27it/s]\n",
            "libglu-9.0.0         | 413 KB    | : 100% 1.0/1 [00:00<00:00,  8.21it/s]\n",
            "pyqt-5.15.7          | 5.0 MB    | : 100% 1.0/1 [00:00<00:00,  1.67it/s]\n",
            "gstreamer-orc-0.4.33 | 299 KB    | : 100% 1.0/1 [00:00<00:00,  8.82it/s]\n",
            "libgcrypt-1.10.1     | 703 KB    | : 100% 1.0/1 [00:00<00:00,  6.42it/s]\n",
            "xcb-util-keysyms-0.4 | 12 KB     | : 100% 1.0/1 [00:00<00:00, 28.87it/s]\n",
            "libsystemd0-252      | 384 KB    | : 100% 1.0/1 [00:00<00:00, 10.11it/s]\n",
            "libgpg-error-1.46    | 252 KB    | : 100% 1.0/1 [00:00<00:00, 18.60it/s]\n",
            "mysql-common-8.0.32  | 727 KB    | : 100% 1.0/1 [00:00<00:00,  7.10it/s]\n",
            "mysql-libs-8.0.32    | 1.5 MB    | : 100% 1.0/1 [00:00<00:00, 13.76it/s]\n",
            "xcb-util-0.4.0       | 20 KB     | : 100% 1.0/1 [00:00<00:00, 28.57it/s]\n",
            "alsa-lib-1.2.8       | 578 KB    | : 100% 1.0/1 [00:00<00:00,  4.95it/s]\n",
            "libudev1-253         | 116 KB    | : 100% 1.0/1 [00:00<00:00, 23.86it/s]\n",
            "Preparing transaction: / \b\b- \b\b\\ \b\b| \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\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\bdone\n",
            "Retrieving notices: ...working... done\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import sys\n",
        "import os\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",
        "print(rdBase.rdkitVersion)\n",
        "from openbabel import pybel\n",
        "import MDAnalysis as mda\n",
        "import prolif as plf"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ZddkDoYUbYQf",
        "outputId": "db43a723-c433-4940-fd02-40d4d07f7bbc"
      },
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "2022.09.4\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Input"
      ],
      "metadata": {
        "id": "fN0Z7Mjm5g75"
      }
    },
    {
      "cell_type": "code",
      "execution_count": 28,
      "metadata": {
        "cellView": "form",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "s5B8su8nB0mS",
        "outputId": "92675c7f-4109-4a00-ac1d-634b5b092194"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2023-03-06 05:21:50--  https://files.rcsb.org/download/3HTB.pdb\n",
            "Resolving files.rcsb.org (files.rcsb.org)... 132.249.210.134\n",
            "Connecting to files.rcsb.org (files.rcsb.org)|132.249.210.134|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: unspecified [application/octet-stream]\n",
            "Saving to: ‘3HTB.pdb’\n",
            "\n",
            "3HTB.pdb                [  <=>               ] 161.13K   408KB/s    in 0.4s    \n",
            "\n",
            "2023-03-06 05:21:51 (408 KB/s) - ‘3HTB.pdb’ saved [164997]\n",
            "\n"
          ]
        }
      ],
      "source": [
        "#@title Input expected from the user\n",
        "PDB_ID = \"3HTB\" #@param {type:\"string\"}\n",
        "pdb = PDB_ID + \".pdb\"\n",
        "! wget https://files.rcsb.org/download/$pdb\n",
        "#@title Ligand three-letter name\n",
        "Ligand = \"JZ4\" #@param {type:\"string\"}\n"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# 🍸You can run all the rest at one time."
      ],
      "metadata": {
        "id": "RC8za6t19f_g"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Pymol script to split protein and ligand\n",
        "Only Chain A retained"
      ],
      "metadata": {
        "id": "oSy3j1SjzSCq"
      }
    },
    {
      "cell_type": "code",
      "execution_count": 29,
      "metadata": {
        "id": "nbHM8p20i7pD"
      },
      "outputs": [],
      "source": [
        "#@title Write out a script for pymol\n",
        "com_file = open('split.pml','w')\n",
        "com_file.write('''\n",
        "load 3HTB.pdb\n",
        "remove not chain A\n",
        "remove resn HOH\n",
        "h_add elem O or elem N\n",
        "select 3HTB-JZ4, resn JZ4 #Create a selection called 1OYT-FSN from the ligand\n",
        "select 3HTB-receptor, 3HTB and not 3HTB-JZ4 #Select all that is not the ligand\n",
        "save 3HTB-JZ4.pdb, 3HTB-JZ4\n",
        "save 3HTB-receptor.pdb, 3HTB-receptor    \n",
        "''')\n",
        "com_file.close()"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Correct the script with right PDB ID and ligand name\n",
        "!sed -i 's/3HTB/{PDB_ID}/g' split.pml\n",
        "!sed 's/JZ4/{Ligand}/g' split.pml\n",
        "!sed -i 's/JZ4/{Ligand}/g' split.pml"
      ],
      "metadata": {
        "id": "Gpjf85fDeTf5",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "7955672c-bbcb-45b2-9295-bd1ac9c755d7"
      },
      "execution_count": 30,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\n",
            "load 3HTB.pdb\n",
            "remove not chain A\n",
            "remove resn HOH\n",
            "h_add elem O or elem N\n",
            "select 3HTB-JZ4, resn JZ4 #Create a selection called 1OYT-FSN from the ligand\n",
            "select 3HTB-receptor, 3HTB and not 3HTB-JZ4 #Select all that is not the ligand\n",
            "save 3HTB-JZ4.pdb, 3HTB-JZ4\n",
            "save 3HTB-receptor.pdb, 3HTB-receptor    \n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 31,
      "metadata": {
        "id": "scOeFAqYi7pD",
        "outputId": "133b8968-1f58-48dc-8338-64a648774a28",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            " PyMOL(TM) Molecular Graphics System, Version 2.5.0.\n",
            " Copyright (c) Schrodinger, LLC.\n",
            " All Rights Reserved.\n",
            " \n",
            "    Created by Warren L. DeLano, Ph.D. \n",
            " \n",
            "    PyMOL is user-supported open-source software.  Although some versions\n",
            "    are freely available, PyMOL is not in the public domain.\n",
            " \n",
            "    If PyMOL is helpful in your work or study, then please volunteer \n",
            "    support for our ongoing efforts to create open and affordable scientific\n",
            "    software by purchasing a PyMOL Maintenance and/or Support subscription.\n",
            "\n",
            "    More information can be found at \"http://www.pymol.org\".\n",
            " \n",
            "    Enter \"help\" for a list of commands.\n",
            "    Enter \"help <command-name>\" for information on a specific command.\n",
            "\n",
            " Hit ESC anytime to toggle between text and graphics.\n",
            "\n",
            " Detected 2 CPU cores.  Enabled multithreaded rendering.\n",
            "PyMOL>load 3HTB.pdb\n",
            "HEADER    HYDROLASE                               11-JUN-09   3HTB\n",
            "TITLE     2-PROPYLPHENOL IN COMPLEX WITH T4 LYSOZYME L99A/M102Q\n",
            "COMPND    MOL_ID: 1;\n",
            "COMPND   2 MOLECULE: LYSOZYME;\n",
            "COMPND   3 CHAIN: A;\n",
            "COMPND   4 SYNONYM: LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN;\n",
            "COMPND   5 EC: 3.2.1.17;\n",
            "COMPND   6 ENGINEERED: YES;\n",
            "COMPND   7 MUTATION: YES\n",
            " ObjectMolecule: Read secondary structure assignments.\n",
            " ObjectMolecule: Read crystal symmetry information.\n",
            " CmdLoad: \"\" loaded as \"3HTB\".\n",
            "PyMOL>remove not chain A\n",
            "PyMOL>remove resn HOH\n",
            " Remove: eliminated 220 atoms in model \"3HTB\".\n",
            "PyMOL>h_add elem O or elem N\n",
            "PyMOL>select 3HTB-JZ4, resn JZ4 #Create a selection called 1OYT-FSN from the ligand\n",
            " Selector: selection \"3HTB-JZ4\" defined with 11 atoms.\n",
            "PyMOL>select 3HTB-receptor, 3HTB and not 3HTB-JZ4 #Select all that is not the ligand\n",
            " Selector: selection \"3HTB-receptor\" defined with 1722 atoms.\n",
            "PyMOL>save 3HTB-JZ4.pdb, 3HTB-JZ4\n",
            " Save: wrote \"3HTB-JZ4.pdb\".\n",
            "PyMOL>save 3HTB-receptor.pdb, 3HTB-receptor\n",
            " Save: wrote \"3HTB-receptor.pdb\".\n"
          ]
        }
      ],
      "source": [
        "#@title Run pymol to split protein and native ligand\n",
        "!pymol -c split.pml"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Split protein and ligand are allocated to 2 variables, respectively"
      ],
      "metadata": {
        "id": "lm4nqzovy9-I"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "Protein_PDB_file_name = PDB_ID + '-receptor.pdb'\n",
        "ligand_name = PDB_ID + '-' + Ligand + '.pdb'"
      ],
      "metadata": {
        "id": "-JvvUwiNrsQB"
      },
      "execution_count": 32,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# ligand name is to changed to LIG inside the ligand file"
      ],
      "metadata": {
        "id": "H7wLZN6qvmx8"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!sed -i 's/{Ligand}/LIG/g' {ligand_name}"
      ],
      "metadata": {
        "id": "jpwPxgOMu7nn"
      },
      "execution_count": 33,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Prepare the protein"
      ],
      "metadata": {
        "id": "XG7x0Ti8x--3"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from pdbfixer import PDBFixer\n",
        "from openmm.app import PDBFile\n",
        "fixer = PDBFixer(filename=Protein_PDB_file_name)\n",
        "fixer.findMissingResidues()\n",
        "fixer.findNonstandardResidues()\n",
        "fixer.replaceNonstandardResidues()\n",
        "fixer.removeHeterogens(True)\n",
        "fixer.findMissingAtoms()\n",
        "fixer.addMissingAtoms()\n",
        "fixer.addMissingHydrogens(7.0)\n",
        "fixer.addSolvent(fixer.topology.getUnitCellDimensions())\n",
        "PDBFile.writeFile(fixer.topology, fixer.positions, open('output.pdb', 'w'))"
      ],
      "metadata": {
        "id": "cs1lB2W8YGni"
      },
      "execution_count": 34,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Prepare the ligand\n",
        "This give the ligand correct H atoms since they do not exist in PDB bank, also give ligand correct charges"
      ],
      "metadata": {
        "id": "MZ-MieIqyFPW"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "m=Chem.MolFromPDBFile(ligand_name)\n",
        "Draw.MolToImage(m)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 317
        },
        "id": "gfJPH3rWbBCs",
        "outputId": "95bdcf7c-72c2-4a1c-d073-dd5c827c0a5d"
      },
      "execution_count": 35,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=300x300 at 0x7F2F8937C190>"
            ],
            "image/png": 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\n"
          },
          "metadata": {},
          "execution_count": 35
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!obabel -ipdb {ligand_name} -omol2 -O ligand.mol2 -h"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "k76ASzZ-cEwk",
        "outputId": "b8b1bf90-214d-4873-964c-2340dd114a4b"
      },
      "execution_count": 36,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "1 molecule converted\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "m=Chem.MolFromMol2File('ligand.mol2',sanitize=False)\n",
        "Draw.MolToImage(m)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 317
        },
        "id": "j0ANIjfzcXnd",
        "outputId": "b879d8af-0414-48ec-b4b4-ec822e975245"
      },
      "execution_count": 37,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=300x300 at 0x7F2F85ED5F10>"
            ],
            "image/png": 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i0tPTmzVrJrUOw4YNM6l9I4KysrILFy4wWD0ZYQgZRiYnzp0717Nnzw4dOtQ2BF+nlJSU/fv3c7ncUDVYq52QkMDn84cMGbJ3796mTZvWvKC0tNTf35+iqJUrV37xxRc1L4iPjx87dmyHDh0ka9aYZWRkNG7cuHHjxuXn5+/cuVNqMwgAO3bscKx9vdGHDx8whBrvxYsX58+fNzc3T0hI8PX1BYAmTZp0/Ju3t7fsPaUlS5ZUVFRMnTq1rRqs1V63bt2gQYNoRjuDg4Pfvn1bc4UaAFAUtXXr1sWLF5eXl+vp6RUVFSm1qtbW1sFquQ8yDQyhooqLi69cuXL+/PnXr1+npqaamJjw+fzWrVs3bNgwNjb23bt3kZGRkZGR5GJnZ+eOHTt26NCB/K+NjY3UMmNjY8+ePWtkZKQmf58sLCxoEhgbG7tt2zYul3vo0KFqK9Ryc3MnT578v//9DwAmTJiwd+9emrtBnYUhlFNycvKZM2f+/PPPxMTE9PT0yspKa2vrESNGVFZWHjt2bNasWTNmzBCJRK9evXryt5iYmNTU1NTU1HPnzpFCqraTnTt3trOzI68vWLBALBbPmTOH5t5JTYhEoqlTpwqFwnnz5lWb9rh169bEiROzs7MbNWp0+PBhyQBvy5YtJ0+eDAAdOnSgL7xfv37k3sHKykoptVcTqlwZoOlKSkouX77s5+fn4eFRrbPXokWLEydOUBTVunVrAIiOjpZaQlZW1qVLl4KDg4cMGdKwxo69TZo0GTJkyPfffw8AFhYW+fn5jP8K5NkiOzs7+ssuXrxIqlTn6p+NGzcCgJOTE5/Pl7woFAqDg4PJVHufPn0yMzMZqLoC1HzFDLaEdUtOTj5+/Pjdu3eTk5NJo1f1XS6X26FDh1OnTn3xxReFhYWJiYnGxsYeHh5Si7K3t7e3t5e0CdnZ2ZJ2Mioqity7kreKiorc3d3btm3r5uZGmkoGO4cVFRW///47zQXx8fGylJOWlrZy5UoA2Llzp2TYMzU11c/P78GDB/r6+suXL1++fHnVuUQkhSoTr0FKSkouXboktdGrytLScsKECeXl5eRTV65cAYAePXrI96VZWVnz588HACMjI2tr62rf1aBBg27dus2ePTs8PDw+Pl4sFsvxFaQllB19S0g6in5+fpJXzp49S24dnZyc7t27J0cNlQFbQhYUFhaSjS5tbW1rG/wg0tLS+Hw+ALi4uPB4vPj4+PDw8CdPnmRkZKSmptIfOejs7BwcHDxp0iTJK48ePQIFFkzZ2NiQ2fBdu3ZNmTKlajv56NGj3Nzc+/fvS6abrays2rZtK+lSurm5qXhC//jx45GRkZIVanw+f8aMGWRx9qhRow4cOCD39IzOUWXiVebQoUPkt1u9ejX9lf379ydXvnnzpqysTMaBED09vU6dOiUmJlYrjTw78+uvv8pX7R07dgCAq6urUCis+W7V/mTNqQ5LS0tZ2knSEtrY2CTR2rdvHym2tpYwLy+P1CE8PJyiqL/++otMzRkbG2/dulW+X195sCXUGIaGhgMGDDhw4AD9ZRYWFj4+PidPnqx2a0dR1OPHj0HelrDOtdo0/cm//vrrw4cPVdtJCwuLdu3aSdrJNm3aSJ5IAAAulyt1Sl0iISGBvrZkhVrv3r3Hjx+/bdu2hQsXVlRUuLu7nzp1yt3dvV6/uAoEBgaSHZxqDoZVZWFhQf71kQxTq4gqE68y8rWEFEXl5eW1aNGC5o+rWbNmO3bskFoU2WDT0dFRvjqTKcEuXbrI19mr2k7W/DtkYWFB2kmy74aCo6O3b9/mcDjGxsYPHz4kj/xxOJzZs2eXlZXJUXOELeG/WFtb9+3bNzk5ueZbHA7Hw8MjPDy8tqfmyfYq8jWDiq/VpmknX7x4kZycXLWd/PDhQ/fu3WtrJ+lJVqj5+fmNGDHi3bt3NjY2R44cGTx4sBzVRoCT9TWtXbv21q1b1XJoamrar1+/EydO0Cz4IKMy3t7ecnwpWas9fPhwptZqV8tkQUFBQkLCkydPAgMDRSIRRVFVM2lmZubp6SnJpKurK03JISEhb9++tbW1PXz4sFgs7tu379GjR+3t7Rmpto5iuylWCrlvRwl/f/+qf0SOjo7r1q2r80tJC3n37t361jY5OZnH43G53Pj4+Pp+tr5IP7Zx48Z3797dunXrhAkTag6rmpmZtWnThvz8n//8RzIBQ1FUbGyspL+qr68fHBxMIo0UgSGUEsK8vDzJ04Du7u5Pnjyp8xuLi4v19fUNDAxKSkrqW9vvvvsOAKZOnVrfD8pB6oqZnJycq1evhoaGjhw5stpz9ABgYmLy1VdfzZw589ChQ5LTF52dne/fv6+CCusCDKGUEFIU5e/vb2xsPHTo0KqrsWjcuXMHADp16lTfqsbExOjp6RkZGdGPnjNFlmVrhYWFa9euJX8sDRs2rNpOkvXZY8eOLSoqUkFtdYSW9wnfvXv39OlTmgvITH1Na9eu9fLymj59uoxfJN+oTHl5eVBQkFgsnj17tvqs1ba0tHRzcyM/T5w4ccWKFU+ePHn69CkZ45k0aRLZwwIxRctDuGvXrl27dsnxQWtra9kTCHKNyggEghEjRly7ds3a2nrBggX1rqJcHBwcBAKBra0t/WXGxsbkzrNBgwYNGjTw9fUlj0e6u7v7+PiooqK6RMtDqDL1bQlLSkqGDx9+8+ZNANDT01PZgezkCPg69evXT+qxnhYWFmfPnm3fvj3T9dJpWh7CmTNnTp06leaC6dOnR0VFKfgtqamp79+/t7a2pl+GIvHp06dBgwY9ePDA2to6Pz+/tr0Y1JCZmZkqTiPWMVoeQjs7O7IXaG3Mzc0V/xbSDHbt2lWWefaCgoKBAwc+evTIyclp5syZCxYsqDkgqbb09PTS0tLEYrHsk/uoTvhHyQDZO4RkveWjR49cXFzu3r1LDsHUoBByOJysrKyqp5QhxWEIGSBjh/D9+/c+Pj7Pnz9v06bNnTt3HB0dU1NTQdNCyOfzz549y3ZFtAqGUFHl5eXPnj3T09Pr3LkzzWVpaWk9evRISEho3779H3/8QdZ5aWIIQakHoeokDKGinj17Vl5e7ubmZmlpWds1KSkpffr0SUpK6tSp040bNyTPGWtoCEm3kO26aA8MoaLqvBd99epV9+7dU1JSevTocevWLcm+FSKRKDMzk8PhqM80fZ1ICDMzM58/f852XbQHhlBR9KMyMTExPXv2zM7O7t2795UrVywsLCRvZWZmCoVCe3t7IyMjFdVVYWRQFLuFzMIQKoqmJXzy5Imvr29ubu7gwYOvXr1a7RgGjbsXhb9bQgCgXwyI6kU75wl5PB5pc+psZExNTcmV8m3Ll5OTk5qaam5uLnn2R+LevXuDBw8uKioaM2bMiRMnqm1NDbWHMCUlRSQScblc+nOdBAJBVlYWAFhaWtJvZsUgSQjT09NxtpAxbK8g12zk/BBfX99qr9+5c4e0e2PHjpW6axNFUeQ896VLl1Z7nXQaLS0t6b/6xo0b5L/gtGnT5K1+vUmOmrKwsIiJiVHZ92o3/JdMIVL3OLxy5crAgQOLi4v9/f2PHz9e2wm7aWlpAODk5KSCejJF0hIWFRVht5ApGEKFkA5h1VGZS5cujRw5sqys7Kefftq3bx/NDZtG9wkBu4XMwRDKTyQSRUdHA8CXX35JXjl16tSoUaPKy8sXLly4e/du+qWkKSkpoGkhrPpvCs4WMgVDKL+4uLji4uKWLVuSbXAPHDgwfvz4ysrKoKCg9evX03+2srIyMzNTT0+vWbNmKqksM6r+s5KVlSXjkRWIHoZQflUnJ/bs2fPf//6XoqiwsLB169bV+dnMzMzKykp7e3tDQ0OlV5Q5VUNYVFR05swZFiujNTCE8pNM02/YsGH69OkURW3dulXGrR80sUMI/w4hYLeQIRhCOp8+fXr9+rVIJJL6LmkJX79+HRQUxOVyDx48OHv2bBlL1o4QYreQEdo5Wc+U69ev/+c//xkxYsT58+ervUWOItTX19+5cyeXyz18+PDEiRNlL7nOEIrFYrKvfm3S09Nl/zqmVBvsJd3C2g5jRDLCENIhT69KPZ0zKipKLBaLxWIej3fq1KmRI0fWq+Q6Jwn5fD6Dp4IypVpLSGYLMYQKwhDSIc8KtGvXruZbd+7c4fF4YrH4t99+I4ei1It23I4CdguZgCGkQ0JY8wSY0tLSX375RSQS/fLLL3IkEGQIoZmZ2fXr12lKiI6Olr0LypSaIUxLS6MoSsXnk2oZDGGtCgsL09PTjY2NW7ZsWe2tgwcP5ubment7jx8/vraPZ2Rk7Nq1y8vLi+xyX5VkkpDmSUIul9u1a1ea6pWUlMjwSzCs5gKgzMzM+Ph4qTcLSEY4Olqr58+fUxTl7u5e7QELoVBIDoheunQpzcfj4uLWr19/5MiRmm9p6CQhSAshLiJVHIawVuRetOaow4kTJ9LS0tq0aUN/Ih/NDaeGdgihlge+yNo9JDcMYa2khpCsiQGApUuX0j9NpzshJEfZqL4yWgNDWCupIbxw4UJCQkLz5s2//fZb+o/XGUL6Z3bVk9QQkm6h6iujNTCE0onF4oSEBKgxP7Fx40YAWLBgQW1PCUrUGULNepKQkPpbY7dQQRhC6d6+fVtcXOzo6CjZHA0Abt68+fDhQ1tb20mTJtVZglbejtZ2B47dQkVgCKUja2Wq3YuSozMDAgLIUZs0SkpKcnNzjYyM7Ozsar5bM4TPnz8fM2aMQCBQtN5KVttOPNgtVASGULq4uDj4dwj/+uuv27dvW1hY/Pjjj3V+XHLDWXMWu7KyMisrq+ok4d27d3v16vXrr7+SpxANDQ15PF6dsxd6eno8Ho/H49XcQkp5arsJz8zMJHfvSA44WS9dzZZwzZo1ADBz5kwrK6s6P05zw5mRkVFZWeno6Mjj8QDg8uXL3377rUAgGD58+KJFiwCA7KFWJx8fn/LyclmuZFBtLSHpFrq7u6u4PtoBW0Lpqg2Nvnr16tKlS0ZGRrNmzZLl4zJ2CI8ePTpy5EiBQDB58uSIiAj13wWYZmNI7BbKDUMoBZ/PT01NNTQ0dHFxIa+sXbtWLBb/8MMPUvt4NckSwm3btk2aNIlsh3H48OE6h1vVAU0lySJSVVZGa2jAf3jVkyxYI3/nMjIyTp8+bWBgIONT8wAwYcIEV1dXyQZQVZGHmN6+fXvs2DEOh7Np06Z58+YxWHmlqtb/5PF4DRs2NDMzs7KyMjc3Ly0tNTU1ZatumgtDKEW1DuGGDRsqKiomTpwo+6SCh4dHbU/ZkU3WHjx4wOPxwsPDay7vVmetWrXq2bNno0aNGjdu7O7u3qFDB2dn5yZNmrBdL82GIZSi6tBofn7+kSNHOBzOggULGCmcJNzY2PjixYv9+vVjpEyVGTVq1KhRo9iuhbbBPqEUVVvCLVu2lJSUDBs2jJGhv/j4+Li4OCcnp2vXrmlcApGSYEtYHUVRkgVrfD5/9+7dAMBUMxgaGioWi4cNG9ajRw9GClQlsuEVh8OhX7lOURTZ/UlPTw8f9pUFtoTVJScnFxUV2dvb29jY7Nmzp6CgoE+fPl999ZXiJSclJUVERPB4PNkHeNSHUCjU19fX19evc+cbcvyGvr7+ypUrVVM3TYchrE6ypUV5efm2bdsAYPHixYyUvGrVKpFINGXKFM3adRspG4awOkmH8MiRI9nZ2V5eXr6+vooXm5ycfPLkSQMDg4ULFypeGtImGMLqyNCou7v7pk2bAGDZsmWMdGzWrl1bWVk5YcIETXyMECkVhrA60hJmZ2cnJSW1bt1aciymIjIyMo4ePcrlcoOCghQvDWkZDOG/lJSUpKSkkP18ASAoKIiRE6HXrVtXUVExduxYyTo4hCQwhP/y/PlzsVjs4OAQExPj4ODg5+eneJnv378/cuSInp4eNoNIKgzhv5Ch0eLiYgCYP38+edpIQevXrxcIBKNHj8YnfZBUOFn/LySEOTk51tbWU6dOVbzAvLy8gwcPcjgc+k1KNQhFUfQ7AAiFQpVVRjtgCP+FhBAA5syZY2ZmpniBGzduLC4uHj58uNacmvL69WsTExO2a6FV8Hb0HxRFkaFRExOT6dOnK17gx48f9+zZAwBLlixRvDSkrbAl/EdaWhqfzweA6dOnV91kTW5btmzh8/mDBg3q3Lmz4qWpCXt7e7LvY23u3btH/ulBMsIQ/uPatWsAoKenFxAQoHhpnz592rlzJ2hdM2hhYTFu3DiaC0QiEYawXvB29B8HDhwAAHd3d3t7e8VL2759e2Fhoa+vb7du3RQvDWkxDOFn79+/j4mJAQCa085kV1JSsn37dgBYvny54qUh7YYh/Gzjxo3kebn+/fsrXtrOnTvz8vK++uqrnj17Kl4a0m4YQgCAjx8/7t+/HwD09fXbtGmjYGmlpaXkAEN8oA7JAkMIALBjxw6ySsbNzU3xVTL79u3Lycnx9vZm5BkopPUwhFBaWrpr1y7ys+JT6uXl5eQZqBUrVihaM6QbMISwf//+3Nxcsquv4iE8ePBgVlZW+/btBw4cyETtkPbT9RAKhcItW7YAQKNGjUDhEAqFQjKRvWLFCtzjCMlI1yfrjx07lp6e7uHhkZGRAQqH8JdffklLS2vbtu0333zDUAXVhYGBATmpps5DoEaPHt23b18AMDc3V0XNtAClw0QikZubGwCQOT0bGxtFSqusrGzVqhUAnDlzhqkaIl2g07ej58+ff/HiRYsWLcj2Z56enoqUdvz48Tdv3ri6uo4ePZqhCiKdoNMhJIdyLly4MD4+HhS7FxWJROQc36VLlzKyIwbSHbr71+X69evR0dG2trYTJ06seS5vfZ09e/b169dffPGFZh3wgtSB7oaQNFyBgYHGxsZST6iXHUVRpLQlS5ZoxDGDSK1wKJ082PHx48fe3t6WlpZpaWk8Hs/c3JzD4fD5fPnOyj137tzo0aObNWv25s0bRralQTpFR1vC0NBQAJg1a5alpWVCQoJIJGrdurXcp1WTZnDx4sWYQCQHXQzhy5cvIyMjTUxMZs+eDVUOn5CvtMuXLz958qRJkyaTJk1isJJId+hiCNesWUMOoLexsYG/Q9iuXTv5Slu9ejUALFq0SO6GFOk4nQthenr6mTNnDAwMJCfFK9ISXrt27fHjx7a2tj/88AOTtUS6ROdCuH79eqFQ6Ofn5+TkRF5RZH6C9C3nz5+PuwAiuenW6GhOTo6zs3NZWVlcXBw57DIzM9PR0bFhw4b5+fn1Le3OnTs+Pj7W1tYpKSm4ThLJTbdawi1btggEghEjRkiOm1XkXnTVqlUAMG/ePEwgUoQOhbCoqGjv3r3w7wPo5Q5hVFTUnTt3LC0tGdkmGOkyHQrh7t27CwsL+/bt26VLF8mLcg+Nkv1j5s6da2VlxVwdkS7SlT5hWVlZixYt3r17d/PmTfK0G+Hu7p6QkBAdHd2xY0fZS3v69GmnTp1MTU1TUlLI08AIyU1XWsLDhw+/e/euc+fOVRNYXl6emJjI5XLJU4WyCwkJoShq1qxZmECkOJ0IoUgkInsQLl68uOrrCQkJQqHQxcXF2NhY9tJiY2MjIyNNTU3nzp3LbD2RbtKJEJ46dert27eurq7Dhg2r+jrpENZ3hnDVqlUURf33v/9t3Lgxk7VEukr7Q0hRFHl4d9GiRdUet5UjhC9fvrxw4YKRkZFkwQ1CCtL+EF6+fDk+Pt7R0XHs2LHV3pIjhKtWrRKLxf7+/owcGoMQ6EIISTO4YMGCms8ZkQVrsk8SJiUlRUREGBgYBAYGMltJpMu0PIRHjx6NjY21sbGpeQD9u3fvcnJyrKysHBwcZCxt9erVlZWVU6ZMkaw7RUhx2hzC6Ohof3//0tLSkSNH1lxgTba08PT0lHGX3rS0tJMnTxoYGAQFBTFfV6TDtDaESUlJQ4YMqaiooCjKx8en5gX17RCGhoYKhcLx48c3b96cyYoinaedIczOzu7Xr9+HDx/Ig7ZeXl41rxGJRNbW1jIuWMvIyAgPD+dyuYsWLWK2qghp4Q7chYWFJHVkJZqpqalIJKrt4srKSlnKnDFjBgD4+fkxV02EPtO2llAgEAwdOjQmJsbNzY0cVe3h4UGzGy+Xy62zzPfv3x8+fFhPTw+bQaQM2hbCH3744e7du46OjteuXXv79i0ovLk9AGzYsEEgEIwaNcrd3Z2JOiL0L9oWwoCAAFdX12vXrjk4OEjGPxUpMC8v78CBAxwOB5tBpCTqG8Iff/yxbdu2bdu2JYeW1aaoqIhc9u233wJAp06d4uPjybnzJIRSR2VkFxYWVlxcPHTo0A4dOihSDkK1Ud8921NTU1+8eAEA5eXlNJeJRCJymeRJCNLNq6ioePnypZ6eHv095OnTp1+8ePHzzz9Lfffjx4+7d+8GgGXLlsn1SyBUN/UNoYJevnxZUVHh4uJiZmZW2zXbt28PCAgQi8X9+vXr0aNHzQu2bt3K5/MHDBjQuXNnZVYW6TT1vR1VUExMDNR+L0pRVEhIyJw5cyiKCg4OlprAoqKinTt3AsDSpUuVWFGk87S2JaQZlRGJRNOnT9+/fz+Xy927d29t+/Zu3769oKDAx8ene/fuyq0r0m26GEKxWJyenm5iYnL27NnBgwdL/XhJSQk5Q5tMNiKkPFobQrI0VOrtqIGBQURERGJiIs2A5+rVq3Nzc7t37967d2+l1REhAG3tE2ZkZOTl5VlbWzdt2lTqBWZmZjQJPHLkyIYNG5o3b06ObUJIqbQzhIrMEIaEhEyZMkUsFqekpPTs2ZPhmiFUgwbcjvr6+hoYGNT2rlgsrvkiGRqt71oZkUg0c+bMvXv3crlckUhkbGyMWzkhFdCAEKalpdX3I3IsWCsvL584ceLZs2cNDQ3XrFkTGBjo7Ows4/O+CClCA0L4448/0mw1X15evnXr1mov1vd2tLi4eOTIkTdu3LCysrp06VJhYSEAODs7y1FbhOpLA0I4f/78li1b1vZuQUFBtRCWlJS8ffuWx+O5urrKUv779+8HDhwYExPTpEmTq1evenp67tixAzCESFU0IIT1FRsbKxaL3dzcam6vVlNycvLXX3+dlJREnr1o1qwZ/H0DjLs5IdXQwtFR2e9Fo6Oju3btmpSU1Llz5z///JMkEABSU1MBW0KkKlobwjpHZW7fvt23b9+cnBxfX99bt27Z2NhI3sIQIlXSwhDKMj9x/vz5wYMHFxUVjR8//sqVK9WO2sUQIlXSthCKxeKEhASg3ctwx44dY8aMKSsrmz17dnh4eLVJSD6fn5+fj5OESGW0LYRv3rwpLi5u1qyZtbV1zXfJE0yzZ8+mKGrdunXbtm2ruQeUpBnESUKkGto2OkpzLyoSiX766acDBw7o6+vv3bu35sb4BN6LIhXTthDWNjRaXl7u5+d37tw5U1PTs2fPDho0qLYSMIRIxdQ3hKGhoQEBAQBAfwiZubn51atXAcDS0hJqGRotKCj45ptv7t2717Bhw8uXL3/11Vc0BeIkIVIx9Q1hp06dZLlMX19/wIABkv9b83b03bt3AwYMeP78ub29/f/93//Vue89toRIxbRqYCY/Pz87O9vc3LxFixbklZcvX3bp0uX58+dubm4PHz6U5eQJDCFSMfVtCeXw7NkzqLLv/ePHjwcPHpyXl+ft7R0ZGdmoUSNZCvn666/t7Ozw6CWkMloVwqr3ojdv3hw5ciSfzx86dOiZM2cku5LWKTQ0VHk1RKgmrQqhZFTm2LFjU6dOFQqFEydOPHTokL5+9V/z1q1bubm5ADB8+HByfJpUZWVlv/32GwA0btxY6iGHCDGA1TOhGEa6fPPmzSO3o7NnzxaLxVKvlOximJWVRVNgVlYWuaxHjx7KqTJCWnQ0Wnl5+atXrzgczubNmymKCgsL27ZtG656QepPe25H4+PjhUIhAPB4vKNHj5LzYRBSf9rTEl6+fNnJyYnH4128eBETiDSIlrSEhYWFZNf6kydPVp27R0j9aUlLuG7duoKCgl69eo0dO5btuiBUP9oQwuzs7B07dnA4nHXr1rFdF4TqTRtCuHLlytLS0lGjRnXp0oXtuiBUbxrfJ0xMTDxy5AiXy63ttF16ERERNJuakg1IEVIqjQ/h0qVLhULhtGnTyDn19TV37lyma4RQ/Wj27Wh0dPS5c+eMjIzwTHmkuTQ7hIsXL6Yoas6cOY6OjvKVkJ6eLqxdeno6sxVGqCYNvh29cePGzZs3raysFi5cKHchXC635vLuqu/KXTJCMtLUlpCiKHKQ9aJFixo2bMh2dRCSn6aGMCIi4tGjR/b29rNmzWK7LggpRCNDKBKJgoODASA4ONjExITt6iCkEI0M4cGDB1+9euXi4jJ58mS264KQojQvhAKBYPXq1QAQGhpKc4w2QppC80K4devWzMzMTp06jRo1iu26IMQADQthYWFhWFgYAKxduxafmkfaQcPmCdesWfPx48d+/fr5+voqUo6HhwdFUQBgaGhIc5mhoWG3bt2A9ownhBTEIX8XNUJ2dnarVq0EAkFUVJS3tzfb1UGIGZp0OxocHFxaWjpmzBhMINImGtMSJiYmtm3blqKo+Ph4V1dXtquDEGM0piVcsmRJZWXlDz/8gAlEWkYzWsK//vrL29vbyMgoMTHRwcGB7eogxCTNaAnJI0tz587FBCLtowEt4bVr1wYMGGBlZfX27Vt8YAJpH3VvCSmKWrp0KQAsWbIEE4i0krq3hKdPnx47dqy9vf2bN2/wgQmkldS6JRQKheTJ3ZUrV2ICkbZS6xAePHgwKSnJxcVl0qRJbNcFIWVR39tRgUDQqlWrrKysX3/9FR+YQFpMfVvCLVu2ZGVlde7ceeTIkWzXBSElUtOWsKCg4IsvvigoKLh582bfvn3Zrg5CSqSmLeHu3bsLCgr69++PCURaT02fJ1y4cGGDBg26du3KdkUQUjo1vR1FSHeo9HZ05syZvXv37t27d0FBAc1lubm55LKAgACV1Q0htqj0dvTp06dRUVEAUFFRQXNZWVnZH3/8AQC4iwzSBWo6MIOQ7sAQIsQyDCFCLMMQIsQyDCFCLMMQIsQyDCFCLGNn2dqQIUNoDlSin0VESMuwE8Lo6GhWvhchNcROCMeNG2dkZFTbuyUlJWfOnFFlfRBiETsh3Lx5s62tbW3vZmRkYAiR7sCBGYRYhiFEiGUYQoRYhiFEiGUYQoRYhiFEiGUYQoRYhiFEiGUqnawPDg7OyckBAEtLS5rLrK2tjx49CgB2dnYqqhlC7MEtDxFiGd6OIsQyDCFCLMMQIsQyDCFCLMMQIsQyDCFCLMMQIsQyDCFCLMMQIsQyDCFCLMMQIsQyDCFCLPt/nsXQo0kTGNMAAAAASUVORK5CYII=\n"
          },
          "metadata": {},
          "execution_count": 37
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#mol= [m for m in pybel.readfile(filename='ligand.mol2',format='mol2')][0]\n",
        "#mol.addh()\n",
        "#out=pybel.Outputfile(filename='ligand2.mol2',format='mol2',overwrite=True)\n",
        "#out.write(mol)\n",
        "#out.close()"
      ],
      "metadata": {
        "id": "17renKy9YbR0"
      },
      "execution_count": 38,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#m=Chem.MolFromMol2File('ligand2.mol2',sanitize=False)\n",
        "#Draw.MolToImage(m)"
      ],
      "metadata": {
        "id": "Pg7ibNSFd-SN"
      },
      "execution_count": 39,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!obabel -imol2 ligand.mol2 -opdb -O ligand2.pdb -h"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "4wFaiEgxe9Rh",
        "outputId": "595391c0-5202-4585-ab3b-e620ab6ca2c7"
      },
      "execution_count": 40,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "1 molecule converted\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "m=Chem.MolFromPDBFile('ligand2.pdb')\n",
        "Draw.MolToImage(m)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 317
        },
        "id": "R22q7xekfMv2",
        "outputId": "5ee8dd3f-177f-43b1-e105-dd44e8a01489"
      },
      "execution_count": 41,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=300x300 at 0x7F2F87F6F190>"
            ],
            "image/png": 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\n"
          },
          "metadata": {},
          "execution_count": 41
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Save the ligand and prepared protein together"
      ],
      "metadata": {
        "id": "YH9gy8LZeJXV"
      },
      "execution_count": 42,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Merge the prepared protein and ligand"
      ],
      "metadata": {
        "id": "ksUEI76nyNZv"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Write out a script for pymol\n",
        "com_file = open('merge.pml','w')\n",
        "com_file.write('''\n",
        "load output.pdb\n",
        "load ligand2.pdb\n",
        "h_add elem O or elem N\n",
        "save complex_prepared.pdb, all   \n",
        "''')\n",
        "com_file.close()"
      ],
      "metadata": {
        "id": "yAj07OH6eJeF"
      },
      "execution_count": 43,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!pymol -c merge.pml"
      ],
      "metadata": {
        "id": "95QFba_ceJnN",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "a68f0118-4c15-4be7-ae95-3fb041964b06"
      },
      "execution_count": 44,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            " PyMOL(TM) Molecular Graphics System, Version 2.5.0.\n",
            " Copyright (c) Schrodinger, LLC.\n",
            " All Rights Reserved.\n",
            " \n",
            "    Created by Warren L. DeLano, Ph.D. \n",
            " \n",
            "    PyMOL is user-supported open-source software.  Although some versions\n",
            "    are freely available, PyMOL is not in the public domain.\n",
            " \n",
            "    If PyMOL is helpful in your work or study, then please volunteer \n",
            "    support for our ongoing efforts to create open and affordable scientific\n",
            "    software by purchasing a PyMOL Maintenance and/or Support subscription.\n",
            "\n",
            "    More information can be found at \"http://www.pymol.org\".\n",
            " \n",
            "    Enter \"help\" for a list of commands.\n",
            "    Enter \"help <command-name>\" for information on a specific command.\n",
            "\n",
            " Hit ESC anytime to toggle between text and graphics.\n",
            "\n",
            " Detected 2 CPU cores.  Enabled multithreaded rendering.\n",
            "PyMOL>load output.pdb\n",
            " ObjectMolecule: Read crystal symmetry information.\n",
            " CmdLoad: \"\" loaded as \"output\".\n",
            "PyMOL>load ligand2.pdb\n",
            "COMPND    3HTB-JZ4.pdb\n",
            " CmdLoad: \"\" loaded as \"ligand2\".\n",
            "PyMOL>h_add elem O or elem N\n",
            "PyMOL>save complex_prepared.pdb, all\n",
            " Save: wrote \"complex_prepared.pdb\".\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Read the merged complex into MDAnalysis as an python object\n",
        "Allocate two Rdkit variables to ligand and protein, respectively"
      ],
      "metadata": {
        "id": "_DKWhnMVyTB9"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import numpy as np\n",
        "# load topology\n",
        "u = mda.Universe('complex_prepared.pdb')\n",
        "lig = u.select_atoms(\"resname LIG\")\n",
        "prot = u.select_atoms(\"protein\")"
      ],
      "metadata": {
        "id": "-aZJe8mAimF4"
      },
      "execution_count": 45,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Draw a 2D ligand\n",
        "This is done with Rdkit"
      ],
      "metadata": {
        "id": "Qajver0Uyoju"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from rdkit import Chem\n",
        "from rdkit.Chem import Draw\n",
        "\n",
        "# create a molecule from the MDAnalysis selection\n",
        "lmol = plf.Molecule.from_mda(lig)\n",
        "# cleanup before drawing\n",
        "mol = Chem.RemoveHs(lmol)\n",
        "mol.RemoveAllConformers()\n",
        "Draw.MolToImage(mol, size=(400, 200))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 217
        },
        "id": "JNcvWmG8kEmT",
        "outputId": "5d024b30-a622-4735-a1be-f768512bfa25"
      },
      "execution_count": 46,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=400x200 at 0x7F2F84DA3B20>"
            ],
            "image/png": 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\n"
          },
          "metadata": {},
          "execution_count": 46
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Draw the 2D interaction between protein and ligand\n",
        "This is done by ProLif"
      ],
      "metadata": {
        "id": "9kujsuMGyvCu"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from prolif.plotting.network import LigNetwork\n",
        "\n",
        "fp = plf.Fingerprint()\n",
        "fp.run(u.trajectory[::10], lig, prot)\n",
        "df = fp.to_dataframe(return_atoms=True)\n",
        "\n",
        "net = LigNetwork.from_ifp(\n",
        "    df,\n",
        "    lmol,\n",
        "    # replace with `kind=\"frame\", frame=0` for the other depiction\n",
        "    kind=\"aggregate\",\n",
        "    threshold=0.3,\n",
        "    rotation=270,\n",
        ")\n",
        "net.display()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 449,
          "referenced_widgets": [
            "c5ba706aac0f4d95aba9015bee3105f2",
            "268adf5c9970490baf19a35127f84905",
            "92f7adb76d4c47bba6bd45436e772ac3",
            "9cfae131f4bd4b3e999a40abd22b09dc",
            "1fe2398807494cbd85f801dd50ca94d5",
            "e99a490d65444b23a9ddbe9ba3d88a17",
            "157ecd93c0e04fa3b528adc32187f8f2",
            "bfd2824ee3c3472ca4bc94e5a37445bf",
            "5c893ae625984e35ab66d019bbc013cd",
            "4625f1affc7b4a76843958568ae96dad",
            "50d24e5331b04dae955bc60b59dd9438"
          ]
        },
        "id": "4aVukh4EimKF",
        "outputId": "1c4b8d3e-7184-4cc9-aa5c-3871c7cc4422"
      },
      "execution_count": 47,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "  0%|          | 0/1 [00:00<?, ?it/s]"
            ],
            "application/vnd.jupyter.widget-view+json": {
              "version_major": 2,
              "version_minor": 0,
              "model_id": "c5ba706aac0f4d95aba9015bee3105f2"
            }
          },
          "metadata": {}
        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "/usr/lib/python3.8/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps\n",
            "  cls(buf, protocol).dump(obj)\n"
          ]
        },
        {
          "output_type": "error",
          "ename": "ValueError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-47-6643ba83afde>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mdf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto_dataframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mreturn_atoms\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 7\u001b[0;31m net = LigNetwork.from_ifp(\n\u001b[0m\u001b[1;32m      8\u001b[0m     \u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      9\u001b[0m     \u001b[0mlmol\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.8/site-packages/prolif/plotting/network.py\u001b[0m in \u001b[0;36mfrom_ifp\u001b[0;34m(cls, ifp, lig, kind, frame, threshold, **kwargs)\u001b[0m\n\u001b[1;32m    290\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mkind\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"aggregate\"\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    291\u001b[0m             data = (\n\u001b[0;32m--> 292\u001b[0;31m                 pd.get_dummies(\n\u001b[0m\u001b[1;32m    293\u001b[0m                     \u001b[0mifp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapplymap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobject\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprefix_sep\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\", \"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    294\u001b[0m                 )\n",
            "\u001b[0;32m/usr/local/lib/python3.8/site-packages/pandas/core/reshape/encoding.py\u001b[0m in \u001b[0;36mget_dummies\u001b[0;34m(data, prefix, prefix_sep, dummy_na, columns, sparse, drop_first, dtype)\u001b[0m\n\u001b[1;32m    200\u001b[0m             )\n\u001b[1;32m    201\u001b[0m             \u001b[0mwith_dummies\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdummy\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 202\u001b[0;31m         \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconcat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwith_dummies\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    203\u001b[0m     \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    204\u001b[0m         result = _get_dummies_1d(\n",
            "\u001b[0;32m/usr/local/lib/python3.8/site-packages/pandas/util/_decorators.py\u001b[0m in \u001b[0;36mwrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    329\u001b[0m                     \u001b[0mstacklevel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfind_stack_level\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    330\u001b[0m                 )\n\u001b[0;32m--> 331\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    332\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    333\u001b[0m         \u001b[0;31m# error: \"Callable[[VarArg(Any), KwArg(Any)], Any]\" has no\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.8/site-packages/pandas/core/reshape/concat.py\u001b[0m in \u001b[0;36mconcat\u001b[0;34m(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)\u001b[0m\n\u001b[1;32m    366\u001b[0m     \u001b[0;36m1\u001b[0m   \u001b[0;36m3\u001b[0m   \u001b[0;36m4\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    367\u001b[0m     \"\"\"\n\u001b[0;32m--> 368\u001b[0;31m     op = _Concatenator(\n\u001b[0m\u001b[1;32m    369\u001b[0m         \u001b[0mobjs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    370\u001b[0m         \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.8/site-packages/pandas/core/reshape/concat.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)\u001b[0m\n\u001b[1;32m    423\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    424\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobjs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 425\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"No objects to concatenate\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    426\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    427\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mkeys\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mValueError\u001b[0m: No objects to concatenate"
          ]
        }
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    },
    {
      "cell_type": "code",
      "source": [
        "#@title 2. 👋 Write pymol script\n",
        "com_file = open('image.pml','w')\n",
        "com_file.write('''\n",
        "load output.pdb, tmp\n",
        "load Docked1.pdb, docked\n",
        "#select the surrounding then set it to an object \n",
        "# find 5 angstroms around ligand\n",
        "select resn UNL\n",
        "select res, byres sele around 5\n",
        "#set the ligand to an lig object\n",
        "select lig, resn UNL\n",
        "# Select all to hide\n",
        "select all\n",
        "# hide everythong\n",
        "hide\n",
        "# show the ligand and surroundings\n",
        "show sticks, lig|res\n",
        "# hide the H atom on the sticks\n",
        "hide sticks, h.\n",
        "# zoon on lig and res, background faded\n",
        "zoom lig|res\n",
        "# Color ligand carbon atom yellow\n",
        "color yellow, lig&name C*\n",
        "# Color ligand carbon atom yellow\n",
        "color cyan, res&name C*\n",
        "# Set label and font size\n",
        "# note you still have to click \"residues\" form L dropdown menue to show the label\n",
        "set label_size, 28\n",
        "set label_font_id, 8\n",
        "set label_color, grey\n",
        "# We also define some hydrophobic interaction style\n",
        "set sphere_scale, 0.35\n",
        "set sphere_transparency, 0.3\n",
        "set sphere_color, cyan\n",
        "# Define some hydrogen bond. interaciton style\n",
        "set dash_length, 0.3\n",
        "set dash_radius, 0.08\n",
        "set dash_gap, 0.3\n",
        "# set backgroud white\n",
        "bg_color white\n",
        "show cartoon\n",
        "set cartoon_transparency, 0.3\n",
        "bg_color white\n",
        "set ray_trace_mode, 1\n",
        "png binding_pocket.png\n",
        "save pre_pymol.pse\n",
        "''')\n",
        "com_file.close()\n"
      ],
      "metadata": {
        "id": "5BD3JUREW_Qe"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 4.👋 Generate a pymol session pse file that 70% quality of publication, please download to polish it more.\n",
        "!pymol -c image.pml"
      ],
      "metadata": {
        "id": "4sMwMN3hW_aQ"
      },
      "execution_count": null,
      "outputs": []
    },
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