{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/af/examples/af_single_sequential.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "id": "-AXy0s_4cKaK"
      },
      "outputs": [],
      "source": [
        "#@title af_single_sequential\n",
        "#@markdown implementing [@MartinPacesa](https://twitter.com/MartinPacesa/status/1640005299124707328)'s idea\n",
        "import os\n",
        "if not os.path.isdir(\"params\"):\n",
        "  print(\"installing AlphaFold...\")\n",
        "  # get code\n",
        "  os.system(\"pip -q install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1\")\n",
        "  # for debugging\n",
        "  os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/colabdesign colabdesign\")\n",
        "  print(\"downloading AlphaFold params...\")\n",
        "  # download params\n",
        "  os.system(\"mkdir params\")\n",
        "  os.system(\"apt-get install aria2 -qq\")\n",
        "  os.system(\"aria2c -q -x 16 https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar\")\n",
        "  os.system(\"tar -xf alphafold_params_2022-03-02.tar -C params\")\n",
        "\n",
        "import os\n",
        "from colabdesign import mk_afdesign_model, clear_mem\n",
        "from IPython.display import HTML\n",
        "from google.colab import files\n",
        "import numpy as np\n",
        "import tqdm.notebook\n",
        "TQDM_BAR_FORMAT = '{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} remaining: {remaining}]'\n",
        "def get_pdb(pdb_code=\"\"):\n",
        "  if pdb_code is None or pdb_code == \"\":\n",
        "    upload_dict = files.upload()\n",
        "    pdb_string = upload_dict[list(upload_dict.keys())[0]]\n",
        "    with open(\"tmp.pdb\",\"wb\") as out: out.write(pdb_string)\n",
        "    return \"tmp.pdb\"\n",
        "  elif os.path.isfile(pdb_code):\n",
        "    return pdb_code\n",
        "  elif len(pdb_code) == 4:\n",
        "    os.system(f\"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb\")\n",
        "    return f\"{pdb_code}.pdb\"\n",
        "  else:\n",
        "    os.system(f\"wget -qnc https://alphafold.ebi.ac.uk/files/AF-{pdb_code}-F1-model_v3.pdb\")\n",
        "    return f\"AF-{pdb_code}-F1-model_v3.pdb\"\n",
        "\n",
        "#@markdown Specify either pdb/pdb_chain or sequence:\n",
        "pdb = \"6D0T\" #@param {type:\"string\"}\n",
        "pdb_chain = \"A\" #@param {type:\"string\"}\n",
        "sequence = \"\" #@param {type:\"string\"}\n",
        "num_recycles = 0 #@param [\"0\", \"1\", \"2\", \"4\", \"8\", \"16\"] {type:\"raw\"}\n",
        "clear_mem()\n",
        "if sequence == \"\":\n",
        "  pdb_filename = get_pdb(pdb)\n",
        "  af_model = mk_afdesign_model(protocol=\"fixbb\")\n",
        "  af_model.prep_inputs(pdb_filename=pdb_filename, chain=pdb_chain)\n",
        "  af_model.set_seq(mode=\"wildtype\")\n",
        "  mode = \"pdb\"\n",
        "else:\n",
        "  af_model = mk_afdesign_model(protocol=\"hallucination\")\n",
        "  af_model.prep_inputs(length=len(sequence))\n",
        "  af_model.set_seq(sequence)\n",
        "  mode = \"free\"\n",
        "\n",
        "import random, string\n",
        "path = ''.join(random.choices(string.ascii_lowercase + string.digits, k=5))\n",
        "while os.path.isdir(path):\n",
        "  path = ''.join(random.choices(string.ascii_lowercase + string.digits, k=5))\n",
        "\n",
        "seq = af_model._params[\"seq\"].copy()\n",
        "os.makedirs(path, exist_ok=True)\n",
        "with tqdm.notebook.tqdm(total=af_model._len, bar_format=TQDM_BAR_FORMAT) as pbar:\n",
        "  for n in range(1,af_model._len+1):\n",
        "  \n",
        "    # replace sequence (this is just for visualization)\n",
        "    af_model._params[\"seq\"] = seq.copy()\n",
        "    af_model._params[\"seq\"][:,n:] = 0\n",
        "    \n",
        "    # mask part of the input features\n",
        "    af_model._inputs[\"seq_mask\"] = (np.arange(af_model._len) < n).astype(float)\n",
        "    af_model.predict(verbose=False, hard=False, num_recycles=num_recycles)\n",
        "    af_model._save_results(verbose=False)\n",
        "    af_model.save_current_pdb(f\"{path}/{n:04d}.pdb\")\n",
        "    pbar.update(1)"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "HTML(af_model.animate(dpi=100))"
      ],
      "metadata": {
        "id": "lphWx8wkEpwP"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "af_model.plot_pdb()"
      ],
      "metadata": {
        "id": "9h1uXK44TygM"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#@title Package and download results\n",
        "#@markdown If you are having issues downloading the result archive, \n",
        "#@markdown try disabling your adblocker and run this cell again. \n",
        "#@markdown  If that fails click on the little folder icon to the \n",
        "#@markdown  left, navigate to file: `name.result.zip`, \n",
        "#@markdown  right-click and select \\\"Download\\\" \n",
        "#@markdown (see [screenshot](https://pbs.twimg.com/media/E6wRW2lWUAEOuoe?format=jpg&name=small)).\n",
        "from google.colab import files\n",
        "!zip -r {path}.result.zip {path}/*\n",
        "files.download(f\"{path}.result.zip\")"
      ],
      "metadata": {
        "id": "zGE1CJxuTzyQ",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": []
    }
  ],
  "metadata": {
    "accelerator": "GPU",
    "colab": {
      "collapsed_sections": [
        "q4qiU9I0QHSz"
      ],
      "provenance": [],
      "include_colab_link": true
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    },
    "gpuClass": "standard"
  },
  "nbformat": 4,
  "nbformat_minor": 0
}