Bio2Byte_Pymol_scripting.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "Bio2Byte - Pymol scripting",
      "private_outputs": true,
      "provenance": [],
      "collapsed_sections": [],
      "authorship_tag": "ABX9TyNvlj5VUoZMZCAv+t263kLH",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/Bio2Byte/public_notebooks/blob/main/Bio2Byte_Pymol_scripting.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Setting up"
      ],
      "metadata": {
        "id": "Q9n0ja60re6i"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 1. Preparing the online environment\n",
        "#@markdown This cell will set up this online environment to run PyMol scripts.\n",
        "#@markdown ## Notes\n",
        "#@markdown It may be required to restart the Kernel, do not worry, it is normal.\n",
        "\n",
        "%%capture\n",
        "\n",
        "!pip install -q condacolab\n",
        "import condacolab\n",
        "condacolab.install()"
      ],
      "metadata": {
        "cellView": "form",
        "id": "rgH0UiGgmt6b"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "id": "C7yqkXGjmeqn"
      },
      "outputs": [],
      "source": [
        "#@title 2. Installing PyMol library\n",
        "#@markdown This cell will install the PyMol library and its dependencies. This \n",
        "#@markdown step may take a long while to finish.\n",
        "\n",
        "%%capture\n",
        "!conda install schrodinger::pymol"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 3. Creating the results directory\n",
        "#@markdown This cell will create a directory to store all the files generated by\n",
        "#@markdown PyMol\n",
        "%%capture\n",
        "\n",
        "import os\n",
        "\n",
        "if not os.path.exists(\"/content/results\"):\n",
        "    os.mkdir(\"/content/results\")"
      ],
      "metadata": {
        "cellView": "form",
        "id": "G9WTvYvgs8Ii"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# PyMol scripting"
      ],
      "metadata": {
        "id": "pisYVs7ZrXr7"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 4. PDB input\n",
        "#@markdown Type here the name of the PDB of interest.\n",
        "import os \n",
        "\n",
        "pdb_name = '6s7o' #@param {type:\"string\"}\n",
        "\n",
        "image_filename        = \"/content/results/{0}.png\".format(pdb_name)\n",
        "animation_filename    = \"/content/results/{0}.gif\".format(pdb_name)\n",
        "animation_temp_prefix = \"/tmp/{0}/\".format(pdb_name)\n",
        "\n",
        "if not os.path.exists(animation_temp_prefix):\n",
        "    os.mkdir(animation_temp_prefix)"
      ],
      "metadata": {
        "id": "p3oQXE4TwGiS"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 5.a Creating a static image of the 3D structure \n",
        "%%capture\n",
        "\n",
        "from pymol import cmd\n",
        "from IPython import display\n",
        "\n",
        "# 1. Load a PDB file of your choice\n",
        "cmd.fetch(pdb_name)\n",
        "cmd.show_as(\"cartoon\")\n",
        "cmd.center()\n",
        "\n",
        "# 2. Export the image as PNG\n",
        "cmd.exporting.save(filename=image_filename, format=\"png\")"
      ],
      "metadata": {
        "cellView": "form",
        "id": "jgRwKikvm52K"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 5.b Rendering the static image of the 3D structure \n",
        "\n",
        "display.Image(image_filename, format='png', width='400')"
      ],
      "metadata": {
        "cellView": "form",
        "id": "LgVrKc375KQF"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 6.a Rotating 360 degrees the 3D structure \n",
        "%%capture\n",
        "\n",
        "import os\n",
        "import imageio\n",
        "\n",
        "# Number of degrees to rotate each frame\n",
        "step = 10\n",
        "\n",
        "# Vector to hold images\n",
        "images = []\n",
        "\n",
        "for a in range(0, 360, step):\n",
        "  cmd.rotate(\"y\", float(step)) # Rotate around Y-axis\n",
        "  # cmd.ray(256,256) # Raytrace 256x256 image\n",
        "  \n",
        "  filename = os.path.join(animation_temp_prefix, \"{0}.png\".format(a))\n",
        "  cmd.exporting.save(filename, format=\"png\")\n",
        "\n",
        "  images.append(imageio.imread(filename))\n",
        "\n",
        "# Create gif animation from images\n",
        "imageio.mimsave(animation_filename, images)"
      ],
      "metadata": {
        "cellView": "form",
        "id": "NnvbYlqQ0HHU"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 6.b Rendering the 360-degree rotated 3D structure \n",
        "\n",
        "from IPython.core.interactiveshell import InteractiveShell\n",
        "InteractiveShell.ast_node_interactivity = \"all\"\n",
        "from IPython import display\n",
        "\n",
        "display.Image(open(animation_filename,'rb').read())"
      ],
      "metadata": {
        "cellView": "form",
        "id": "TUsnaltL4Iit"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 7. Download the results\n",
        "#@markdown This step will export all the results stored inside `/content/results` directory. \n",
        "\n",
        "from google.colab import files\n",
        "\n",
        "!zip -r /content/pymol-results.zip /content/results\n",
        "\n",
        "files.download(\"/content/pymol-results.zip\")"
      ],
      "metadata": {
        "cellView": "form",
        "id": "X6KLmVxWsDf8"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}