MaskedProteinEnT-colab-example.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "source": [
        "author Sergey Lyskov\n",
        "\n",
        "Minimal example of running https://github.com/Graylab/MaskedProteinEnT examples inside Colab notebook"
      ],
      "metadata": {
        "id": "S0sOPVOLo8fU"
      }
    },
    {
      "cell_type": "code",
      "execution_count": 2,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "OGLQ4BJUfrVg",
        "outputId": "8945e64c-f5d7-4b4b-cfc6-f71c679b5107"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "fatal: destination path 'MaskedProteinEnT' already exists and is not an empty directory.\n",
            "Looking in links: https://download.pytorch.org/whl/torch_stable.html\n",
            "Requirement already satisfied: torch in /usr/local/lib/python3.10/dist-packages (2.3.1+cu121)\n",
            "Requirement already satisfied: torchvision in /usr/local/lib/python3.10/dist-packages (0.18.1+cu121)\n",
            "Requirement already satisfied: torchaudio in /usr/local/lib/python3.10/dist-packages (2.3.1+cu121)\n",
            "Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from torch) (3.15.4)\n",
            "Requirement already satisfied: typing-extensions>=4.8.0 in /usr/local/lib/python3.10/dist-packages (from torch) (4.12.2)\n",
            "Requirement already satisfied: sympy in /usr/local/lib/python3.10/dist-packages (from torch) (1.13.2)\n",
            "Requirement already satisfied: networkx in /usr/local/lib/python3.10/dist-packages (from torch) (3.3)\n",
            "Requirement already satisfied: jinja2 in /usr/local/lib/python3.10/dist-packages (from torch) (3.1.4)\n",
            "Requirement already satisfied: fsspec in /usr/local/lib/python3.10/dist-packages (from torch) (2024.6.1)\n",
            "Requirement already satisfied: nvidia-cuda-nvrtc-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch) (12.1.105)\n",
            "Requirement already satisfied: nvidia-cuda-runtime-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch) (12.1.105)\n",
            "Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch) (12.1.105)\n",
            "Requirement already satisfied: nvidia-cudnn-cu12==8.9.2.26 in /usr/local/lib/python3.10/dist-packages (from torch) (8.9.2.26)\n",
            "Requirement already satisfied: nvidia-cublas-cu12==12.1.3.1 in /usr/local/lib/python3.10/dist-packages (from torch) (12.1.3.1)\n",
            "Requirement already satisfied: nvidia-cufft-cu12==11.0.2.54 in /usr/local/lib/python3.10/dist-packages (from torch) (11.0.2.54)\n",
            "Requirement already satisfied: nvidia-curand-cu12==10.3.2.106 in /usr/local/lib/python3.10/dist-packages (from torch) (10.3.2.106)\n",
            "Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in /usr/local/lib/python3.10/dist-packages (from torch) (11.4.5.107)\n",
            "Requirement already satisfied: nvidia-cusparse-cu12==12.1.0.106 in /usr/local/lib/python3.10/dist-packages (from torch) (12.1.0.106)\n",
            "Requirement already satisfied: nvidia-nccl-cu12==2.20.5 in /usr/local/lib/python3.10/dist-packages (from torch) (2.20.5)\n",
            "Requirement already satisfied: nvidia-nvtx-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch) (12.1.105)\n",
            "Requirement already satisfied: triton==2.3.1 in /usr/local/lib/python3.10/dist-packages (from torch) (2.3.1)\n",
            "Requirement already satisfied: nvidia-nvjitlink-cu12 in /usr/local/lib/python3.10/dist-packages (from nvidia-cusolver-cu12==11.4.5.107->torch) (12.6.20)\n",
            "Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from torchvision) (1.26.4)\n",
            "Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in /usr/local/lib/python3.10/dist-packages (from torchvision) (9.4.0)\n",
            "Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from jinja2->torch) (2.1.5)\n",
            "Requirement already satisfied: mpmath<1.4,>=1.1.0 in /usr/local/lib/python3.10/dist-packages (from sympy->torch) (1.3.0)\n",
            "Collecting pytorch-lightning (from -r MaskedProteinEnT/requirements.txt (line 1))\n",
            "  Downloading pytorch_lightning-2.4.0-py3-none-any.whl.metadata (21 kB)\n",
            "Collecting biopython (from -r MaskedProteinEnT/requirements.txt (line 2))\n",
            "  Downloading biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)\n",
            "Requirement already satisfied: certifi in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 3)) (2024.7.4)\n",
            "Requirement already satisfied: einops in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 4)) (0.8.0)\n",
            "Requirement already satisfied: h5py in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 5)) (3.11.0)\n",
            "Collecting logomaker (from -r MaskedProteinEnT/requirements.txt (line 6))\n",
            "  Downloading logomaker-0.8-py2.py3-none-any.whl.metadata (1.0 kB)\n",
            "Requirement already satisfied: matplotlib in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 7)) (3.7.1)\n",
            "Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 8)) (1.26.4)\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 9)) (2.1.4)\n",
            "Collecting pytorch-ranger (from -r MaskedProteinEnT/requirements.txt (line 10))\n",
            "  Downloading pytorch_ranger-0.1.1-py3-none-any.whl.metadata (509 bytes)\n",
            "Collecting rotary-embedding-torch (from -r MaskedProteinEnT/requirements.txt (line 11))\n",
            "  Downloading rotary_embedding_torch-0.6.5-py3-none-any.whl.metadata (678 bytes)\n",
            "Collecting scanpy (from -r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading scanpy-1.10.2-py3-none-any.whl.metadata (9.3 kB)\n",
            "Requirement already satisfied: scikit-learn in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 13)) (1.3.2)\n",
            "Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 14)) (1.13.1)\n",
            "Requirement already satisfied: seaborn in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 15)) (0.13.1)\n",
            "Collecting torch-optimizer (from -r MaskedProteinEnT/requirements.txt (line 16))\n",
            "  Downloading torch_optimizer-0.3.0-py3-none-any.whl.metadata (55 kB)\n",
            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m55.9/55.9 kB\u001b[0m \u001b[31m2.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hRequirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 17)) (4.66.5)\n",
            "Requirement already satisfied: typing-extensions in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 18)) (4.12.2)\n",
            "Collecting umap-learn (from -r MaskedProteinEnT/requirements.txt (line 19))\n",
            "  Downloading umap_learn-0.5.6-py3-none-any.whl.metadata (21 kB)\n",
            "Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (from -r MaskedProteinEnT/requirements.txt (line 20)) (2.32.3)\n",
            "Requirement already satisfied: torch>=2.1.0 in /usr/local/lib/python3.10/dist-packages (from pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (2.3.1+cu121)\n",
            "Requirement already satisfied: PyYAML>=5.4 in /usr/local/lib/python3.10/dist-packages (from pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (6.0.2)\n",
            "Requirement already satisfied: fsspec>=2022.5.0 in /usr/local/lib/python3.10/dist-packages (from fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (2024.6.1)\n",
            "Collecting torchmetrics>=0.7.0 (from pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1))\n",
            "  Downloading torchmetrics-1.4.1-py3-none-any.whl.metadata (20 kB)\n",
            "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (24.1)\n",
            "Collecting lightning-utilities>=0.10.0 (from pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1))\n",
            "  Downloading lightning_utilities-0.11.6-py3-none-any.whl.metadata (5.2 kB)\n",
            "Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (1.2.1)\n",
            "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (0.12.1)\n",
            "Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (4.53.1)\n",
            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (1.4.5)\n",
            "Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (9.4.0)\n",
            "Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (3.1.2)\n",
            "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (2.8.2)\n",
            "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->-r MaskedProteinEnT/requirements.txt (line 9)) (2024.1)\n",
            "Requirement already satisfied: tzdata>=2022.1 in /usr/local/lib/python3.10/dist-packages (from pandas->-r MaskedProteinEnT/requirements.txt (line 9)) (2024.1)\n",
            "Collecting anndata>=0.8 (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading anndata-0.10.8-py3-none-any.whl.metadata (6.6 kB)\n",
            "Requirement already satisfied: joblib in /usr/local/lib/python3.10/dist-packages (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (1.4.2)\n",
            "Collecting legacy-api-wrap>=1.4 (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading legacy_api_wrap-1.4-py3-none-any.whl.metadata (1.8 kB)\n",
            "Requirement already satisfied: natsort in /usr/local/lib/python3.10/dist-packages (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (8.4.0)\n",
            "Requirement already satisfied: networkx>=2.7 in /usr/local/lib/python3.10/dist-packages (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (3.3)\n",
            "Requirement already satisfied: numba>=0.56 in /usr/local/lib/python3.10/dist-packages (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (0.60.0)\n",
            "Requirement already satisfied: patsy in /usr/local/lib/python3.10/dist-packages (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (0.5.6)\n",
            "Collecting pynndescent>=0.5 (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading pynndescent-0.5.13-py3-none-any.whl.metadata (6.8 kB)\n",
            "Collecting session-info (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading session_info-1.0.0.tar.gz (24 kB)\n",
            "  Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "Requirement already satisfied: statsmodels>=0.13 in /usr/local/lib/python3.10/dist-packages (from scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (0.14.2)\n",
            "Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->-r MaskedProteinEnT/requirements.txt (line 13)) (3.5.0)\n",
            "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests->-r MaskedProteinEnT/requirements.txt (line 20)) (3.3.2)\n",
            "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests->-r MaskedProteinEnT/requirements.txt (line 20)) (3.7)\n",
            "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests->-r MaskedProteinEnT/requirements.txt (line 20)) (2.0.7)\n",
            "Collecting array-api-compat!=1.5,>1.4 (from anndata>=0.8->scanpy->-r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading array_api_compat-1.8-py3-none-any.whl.metadata (1.5 kB)\n",
            "Requirement already satisfied: exceptiongroup in /usr/local/lib/python3.10/dist-packages (from anndata>=0.8->scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (1.2.2)\n",
            "Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /usr/local/lib/python3.10/dist-packages (from fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (3.10.5)\n",
            "Requirement already satisfied: setuptools in /usr/local/lib/python3.10/dist-packages (from lightning-utilities>=0.10.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (71.0.4)\n",
            "Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /usr/local/lib/python3.10/dist-packages (from numba>=0.56->scanpy->-r MaskedProteinEnT/requirements.txt (line 12)) (0.43.0)\n",
            "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.7->matplotlib->-r MaskedProteinEnT/requirements.txt (line 7)) (1.16.0)\n",
            "Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (3.15.4)\n",
            "Requirement already satisfied: sympy in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (1.13.2)\n",
            "Requirement already satisfied: jinja2 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (3.1.4)\n",
            "Requirement already satisfied: nvidia-cuda-nvrtc-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.1.105)\n",
            "Requirement already satisfied: nvidia-cuda-runtime-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.1.105)\n",
            "Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.1.105)\n",
            "Requirement already satisfied: nvidia-cudnn-cu12==8.9.2.26 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (8.9.2.26)\n",
            "Requirement already satisfied: nvidia-cublas-cu12==12.1.3.1 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.1.3.1)\n",
            "Requirement already satisfied: nvidia-cufft-cu12==11.0.2.54 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (11.0.2.54)\n",
            "Requirement already satisfied: nvidia-curand-cu12==10.3.2.106 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (10.3.2.106)\n",
            "Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (11.4.5.107)\n",
            "Requirement already satisfied: nvidia-cusparse-cu12==12.1.0.106 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.1.0.106)\n",
            "Requirement already satisfied: nvidia-nccl-cu12==2.20.5 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (2.20.5)\n",
            "Requirement already satisfied: nvidia-nvtx-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.1.105)\n",
            "Requirement already satisfied: triton==2.3.1 in /usr/local/lib/python3.10/dist-packages (from torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (2.3.1)\n",
            "Requirement already satisfied: nvidia-nvjitlink-cu12 in /usr/local/lib/python3.10/dist-packages (from nvidia-cusolver-cu12==11.4.5.107->torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (12.6.20)\n",
            "Collecting stdlib_list (from session-info->scanpy->-r MaskedProteinEnT/requirements.txt (line 12))\n",
            "  Downloading stdlib_list-0.10.0-py3-none-any.whl.metadata (3.3 kB)\n",
            "Requirement already satisfied: aiohappyeyeballs>=2.3.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (2.4.0)\n",
            "Requirement already satisfied: aiosignal>=1.1.2 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (1.3.1)\n",
            "Requirement already satisfied: attrs>=17.3.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (24.2.0)\n",
            "Requirement already satisfied: frozenlist>=1.1.1 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (1.4.1)\n",
            "Requirement already satisfied: multidict<7.0,>=4.5 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (6.0.5)\n",
            "Requirement already satisfied: yarl<2.0,>=1.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (1.9.4)\n",
            "Requirement already satisfied: async-timeout<5.0,>=4.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (4.0.3)\n",
            "Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from jinja2->torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (2.1.5)\n",
            "Requirement already satisfied: mpmath<1.4,>=1.1.0 in /usr/local/lib/python3.10/dist-packages (from sympy->torch>=2.1.0->pytorch-lightning->-r MaskedProteinEnT/requirements.txt (line 1)) (1.3.0)\n",
            "Downloading pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m815.2/815.2 kB\u001b[0m \u001b[31m14.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.2/3.2 MB\u001b[0m \u001b[31m58.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading logomaker-0.8-py2.py3-none-any.whl (11.8 MB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m11.8/11.8 MB\u001b[0m \u001b[31m27.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading pytorch_ranger-0.1.1-py3-none-any.whl (14 kB)\n",
            "Downloading rotary_embedding_torch-0.6.5-py3-none-any.whl (5.5 kB)\n",
            "Downloading scanpy-1.10.2-py3-none-any.whl (2.1 MB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m2.1/2.1 MB\u001b[0m \u001b[31m56.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading torch_optimizer-0.3.0-py3-none-any.whl (61 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m61.9/61.9 kB\u001b[0m \u001b[31m3.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading umap_learn-0.5.6-py3-none-any.whl (85 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m85.7/85.7 kB\u001b[0m \u001b[31m5.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading anndata-0.10.8-py3-none-any.whl (124 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m124.4/124.4 kB\u001b[0m \u001b[31m8.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading legacy_api_wrap-1.4-py3-none-any.whl (15 kB)\n",
            "Downloading lightning_utilities-0.11.6-py3-none-any.whl (26 kB)\n",
            "Downloading pynndescent-0.5.13-py3-none-any.whl (56 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m56.9/56.9 kB\u001b[0m \u001b[31m4.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading torchmetrics-1.4.1-py3-none-any.whl (866 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m866.2/866.2 kB\u001b[0m \u001b[31m37.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading array_api_compat-1.8-py3-none-any.whl (38 kB)\n",
            "Downloading stdlib_list-0.10.0-py3-none-any.whl (79 kB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m79.8/79.8 kB\u001b[0m \u001b[31m5.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hBuilding wheels for collected packages: session-info\n",
            "  Building wheel for session-info (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8023 sha256=e00dead63aea6800101c8a3169692565298b718aecba52deb6313f4a33fc470e\n",
            "  Stored in directory: /root/.cache/pip/wheels/6a/aa/b9/eb5d4031476ec10802795b97ccf937b9bd998d68a9b268765a\n",
            "Successfully built session-info\n",
            "Installing collected packages: array-api-compat, stdlib_list, lightning-utilities, legacy-api-wrap, biopython, session-info, pynndescent, logomaker, anndata, umap-learn, torchmetrics, rotary-embedding-torch, pytorch-ranger, torch-optimizer, scanpy, pytorch-lightning\n",
            "Successfully installed anndata-0.10.8 array-api-compat-1.8 biopython-1.84 legacy-api-wrap-1.4 lightning-utilities-0.11.6 logomaker-0.8 pynndescent-0.5.13 pytorch-lightning-2.4.0 pytorch-ranger-0.1.1 rotary-embedding-torch-0.6.5 scanpy-1.10.2 session-info-1.0.0 stdlib_list-0.10.0 torch-optimizer-0.3.0 torchmetrics-1.4.1 umap-learn-0.5.6\n"
          ]
        }
      ],
      "source": [
        "!git clone https://github.com/Graylab/MaskedProteinEnT.git\n",
        "!pip install torch torchvision torchaudio -f https://download.pytorch.org/whl/torch_stable.html\n",
        "!pip install -r MaskedProteinEnT/requirements.txt"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://zenodo.org/records/8313466/files/model.tar.gz"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "U1HpYBMrj9KA",
        "outputId": "5f4e040b-eaa9-4bfb-d5dc-2e1326f362e5"
      },
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2024-08-26 16:45:27--  https://zenodo.org/records/8313466/files/model.tar.gz\n",
            "Resolving zenodo.org (zenodo.org)... 188.184.98.238, 188.185.79.172, 188.184.103.159, ...\n",
            "Connecting to zenodo.org (zenodo.org)|188.184.98.238|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 971894729 (927M) [application/octet-stream]\n",
            "Saving to: ‘model.tar.gz’\n",
            "\n",
            "model.tar.gz        100%[===================>] 926.87M  25.6MB/s    in 37s     \n",
            "\n",
            "2024-08-26 16:46:05 (24.8 MB/s) - ‘model.tar.gz’ saved [971894729/971894729]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!cd MaskedProteinEnT && tar -xvzf ../model.tar.gz\n",
        "!ls"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "PUUZLk0EkVU3",
        "outputId": "e8e9c5e2-92f1-49f3-b028-b40885867af5"
      },
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "models/\n",
            "models/ProtAbPlusAbAgEnT_backup.ckpt\n",
            "models/ProtEnT_backup.ckpt\n",
            "models/ProtAbPlusAbAgCDRPPIEnT_backup.ckpt\n",
            "models/ProtPPIEnT_backup.ckpt\n",
            "models/ProtAbPlusEnT_backup.ckpt\n",
            "models/AbPlusAbAgEnT_backup.ckpt\n",
            "models/AbAgEnT_backup.ckpt\n",
            "models/ProtAbAgEnT_backup.ckpt\n",
            "models/AbAbAgEnT_backup.ckpt\n",
            "models/AbEnT_backup.ckpt\n",
            "models/ProtPPIAbAgEnT_backup.ckpt\n",
            "models/PPIEnT_backup.ckpt\n",
            "models/ProtAbPlusAbAgCDREnT_backup.ckpt\n",
            "models/AbPlusEnT_backup.ckpt\n",
            "models/PPIAbAgEnT_backup.ckpt\n",
            " MaskedProteinEnT   model.tar.gz  'model.tar.gz?download=1'   sample_data\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!cd MaskedProteinEnT && python3 ProteinSequenceSampler.py  \\\n",
        "\t--output_dir ./sampled_sequences \\\n",
        "\t--model models/ProtEnT_backup.ckpt \\\n",
        "\t--from_pdb data/proteins \\\n",
        "\t--sample_temperatures 0.2,0.5 \\\n",
        "\t--num_samples 100"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "0tRzeMSvmFe3",
        "outputId": "6c05b83d-7c79-43e9-99bc-42ed23ba1030"
      },
      "execution_count": 17,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Lightning automatically upgraded your loaded checkpoint from v1.5.0 to v2.4.0. To apply the upgrade to your files permanently, run `python -m pytorch_lightning.utilities.upgrade_checkpoint models/ProtEnT_backup.ckpt`\n",
            "Found 1 files.\n",
            "[0.2, 0.5] [100]\n",
            "1ahs_trunc\n",
            "1ahs_trunc 0.30952380952380953\n",
            "1ahs_trunc\n",
            "1ahs_trunc 0.30952380952380953\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!ls MaskedProteinEnT/sampled_sequences"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "g-W_i-vcmvsH",
        "outputId": "26733526-fb74-400b-a27c-894264ea8a96"
      },
      "execution_count": 19,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "1ahs_trunc  argmax_colab  sequence_recovery_argmax.json\n"
          ]
        }
      ]
    }
  ]
}