notebooks/pka_prediction.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "colab_type": "text",
        "id": "view-in-github"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/mayrf/pkasolver/blob/main/notebooks/pka_prediction.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "YEGEu0gXoNzD"
      },
      "source": [
        "# Calculate microstate pKa values\n",
        "\n",
        "Code and more documentation at:\n",
        "https://github.com/mayrf/pkasolver"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "BrnGvVB1lZ6Y",
        "outputId": "8fcc5491-5389-4053-edcd-90a60aae86c0"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "⏬ Downloading https://github.com/jaimergp/miniforge/releases/latest/download/Mambaforge-colab-Linux-x86_64.sh...\n",
            "📦 Installing...\n",
            "📌 Adjusting configuration...\n",
            "🩹 Patching environment...\n",
            "⏲ Done in 0:00:31\n",
            "🔁 Restarting kernel...\n"
          ]
        }
      ],
      "source": [
        "# @title Initializing Condacolab\n",
        "!pip install -q condacolab\n",
        "import condacolab\n",
        "condacolab.install()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "cg5NTzCefRRX",
        "outputId": "ba7174e7-28a7-444f-eb22-39459e3970fd"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "✨🍰✨ Everything looks OK!\n"
          ]
        }
      ],
      "source": [
        "# @title Check that everything is fine\n",
        "\n",
        "import condacolab\n",
        "condacolab.check()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "4TZCXZ_IJXCz",
        "outputId": "bd23921a-e1d6-4fd7-faf5-ba85214e69cd"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "📦 Installing dependencies ...\n",
            "🔥 Installing PyTorch and PyG ...\n",
            "✔️ Installing pkasolver package ...\n",
            "🎉 Done!\n"
          ]
        }
      ],
      "source": [
        "# @title Installing dependencies and pkasolver package (this might take up to 5 minutes)\n",
        "\n",
        "print('📦 Installing dependencies ...')\n",
        "!mamba install -c conda-forge rdkit > /dev/null\n",
        "print('🔥 Installing PyTorch and PyG ...')\n",
        "!pip install torch==1.13.1+cpu -f https://download.pytorch.org/whl/cpu/torch_stable.html > /dev/null\n",
        "!pip install torch-scatter -f https://data.pyg.org/whl/torch-1.13.1+cpu.html > /dev/null\n",
        "!pip install torch-sparse -f https://data.pyg.org/whl/torch-1.13.1+cpu.html > /dev/null\n",
        "!pip install torch-spline-conv torch-geometric==2.0.1 -f https://data.pyg.org/whl/torch-1.13.1+cpu.html > /dev/null\n",
        "!pip install cairosvg svgutils molvs > /dev/null\n",
        "print('✔️ Installing pkasolver package ...')\n",
        "!pip install -q git+https://github.com/mayrf/pkasolver.git > /dev/null\n",
        "print(\"🎉 Done!\")"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "id": "aw-6bqsym4hX",
        "outputId": "0cf8e792-7e9c-4fbf-9e01-1665c9da94dc"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "🔮 Predicting...\n"
          ]
        },
        {
          "name": "stderr",
          "output_type": "stream",
          "text": [
            "[query.py:297 - calculate_microstate_pka_values()] Using dimorphite-dl to identify protonation sites.\n"
          ]
        },
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "Proposed mol at pH 7.4: CC(Cc1ccccc1)NC(=O)C([NH3+])CCCC[NH3+]\n",
            "📸 Visualizing ...\n"
          ]
        },
        {
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L 771.7 830.6 L 771.7 817.5 \" fill=\"#0000FF\"/>\n<path class=\"atom-13\" d=\"M 782.6 830.1 Q 782.9 829.3, 783.7 828.9 Q 784.5 828.4, 785.5 828.4 Q 786.8 828.4, 787.6 829.1 Q 788.3 829.8, 788.3 831.1 Q 788.3 832.4, 787.3 833.6 Q 786.4 834.8, 784.4 836.2 L 788.4 836.2 L 788.4 837.2 L 782.6 837.2 L 782.6 836.3 Q 784.2 835.2, 785.2 834.3 Q 786.1 833.5, 786.6 832.7 Q 787.1 831.9, 787.1 831.1 Q 787.1 830.3, 786.7 829.8 Q 786.2 829.4, 785.5 829.4 Q 784.8 829.4, 784.4 829.7 Q 783.9 829.9, 783.6 830.6 L 782.6 830.1 \" fill=\"#0000FF\"/>\n<path class=\"atom-18\" d=\"M 529.8 827.2 L 531.6 827.2 L 531.6 832.8 L 538.3 832.8 L 538.3 827.2 L 540.1 827.2 L 540.1 840.3 L 538.3 840.3 L 538.3 834.3 L 531.6 834.3 L 531.6 840.3 L 529.8 840.3 L 529.8 827.2 \" fill=\"#0000FF\"/>\n<path class=\"atom-18\" d=\"M 540.7 839.9 Q 541.1 839.0, 541.8 838.6 Q 542.6 838.1, 543.6 838.1 Q 544.9 838.1, 545.7 838.8 Q 546.4 839.5, 546.4 840.8 Q 546.4 842.1, 545.5 843.3 Q 544.5 844.5, 542.6 845.9 L 546.6 845.9 L 546.6 846.9 L 540.7 846.9 L 540.7 846.1 Q 542.3 844.9, 543.3 844.0 Q 544.3 843.2, 544.7 842.4 Q 545.2 841.7, 545.2 840.9 Q 545.2 840.0, 544.8 839.6 Q 544.4 839.1, 543.6 839.1 Q 542.9 839.1, 542.5 839.4 Q 542.0 839.7, 541.7 840.3 L 540.7 839.9 \" fill=\"#0000FF\"/>\n<path class=\"atom-18\" d=\"M 550.2 827.2 L 554.5 834.1 Q 554.9 834.8, 555.6 836.1 Q 556.3 837.3, 556.3 837.4 L 556.3 827.2 L 558.1 827.2 L 558.1 840.3 L 556.3 840.3 L 551.6 832.7 Q 551.1 831.8, 550.5 830.8 Q 550.0 829.8, 549.8 829.5 L 549.8 840.3 L 548.1 840.3 L 548.1 827.2 L 550.2 827.2 \" fill=\"#0000FF\"/>\n<text fill=\"black\" font-family=\"sans-serif\" font-size=\"14\" font-weight=\"normal\" letter-spacing=\"0\" text-anchor=\"middle\" x=\"500\" y=\"240\">pka_0 = 2.46 (stddev: 1.42)</text><path d=\"M450.0 120.0 L550.0 120.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M550.0 120.0 L535.0 115.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 130.0 L550.0 130.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 130.0 L465.0 135.0\" stroke=\"black\" stroke-width=\"2\"/><text fill=\"black\" font-family=\"sans-serif\" font-size=\"14\" font-weight=\"normal\" letter-spacing=\"0\" text-anchor=\"middle\" x=\"500\" y=\"490\">pka_1 = 7.80 (stddev: 0.23)</text><path d=\"M450.0 370.0 L550.0 370.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M550.0 370.0 L535.0 365.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 380.0 L550.0 380.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 380.0 L465.0 385.0\" stroke=\"black\" stroke-width=\"2\"/><text fill=\"black\" font-family=\"sans-serif\" font-size=\"14\" font-weight=\"normal\" letter-spacing=\"0\" text-anchor=\"middle\" x=\"500\" y=\"740\">pka_2 = 10.21 (stddev: 0.10)</text><path d=\"M450.0 620.0 L550.0 620.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M550.0 620.0 L535.0 615.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 630.0 L550.0 630.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 630.0 L465.0 635.0\" stroke=\"black\" stroke-width=\"2\"/><text fill=\"black\" font-family=\"sans-serif\" font-size=\"14\" font-weight=\"normal\" letter-spacing=\"0\" text-anchor=\"middle\" x=\"500\" y=\"990\">pka_3 = 13.23 (stddev: 0.46)</text><path d=\"M450.0 870.0 L550.0 870.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M550.0 870.0 L535.0 865.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 880.0 L550.0 880.0\" stroke=\"black\" stroke-width=\"2\"/><path d=\"M450.0 880.0 L465.0 885.0\" stroke=\"black\" stroke-width=\"2\"/></svg>",
            "text/plain": [
              "<IPython.core.display.SVG object>"
            ]
          },
          "metadata": {},
          "output_type": "display_data"
        }
      ],
      "source": [
        "# @title Predict pKa values\n",
        "from pkasolver.query import QueryModel\n",
        "from pkasolver.ml_architecture import GINPairV1\n",
        "import pickle \n",
        "import pkasolver\n",
        "import torch\n",
        "from os import path\n",
        "from rdkit import Chem\n",
        "from pkasolver.query import calculate_microstate_pka_values, draw_pka_reactions\n",
        "from IPython.display import display\n",
        "\n",
        "# load trained model\n",
        "base_path = path.dirname(pkasolver.__file__)\n",
        "# get input\n",
        "print(\"🔮 Predicting...\")\n",
        "smiles = \"CC(CC1=CC=CC=C1)NC(=O)C(CCCCN)N\"  # @param {type:\"string\"}\n",
        "# convert from Smiles to rdkit mol\n",
        "mol = Chem.MolFromSmiles(smiles)\n",
        "################################################\n",
        "################################################\n",
        "# calculate microstate pka values\n",
        "protonation_states = calculate_microstate_pka_values(mol, only_dimorphite=False)\n",
        "################################################\n",
        "print(\"📸 Visualizing ...\")\n",
        "# draw the micostate pka values\n",
        "calc = draw_pka_reactions(protonation_states)\n",
        "display(calc)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "cellView": "form",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "BehVZ0to5AKU",
        "outputId": "0962d2d7-434b-454a-da1c-3ef37e604d1f"
      },
      "outputs": [
        {
          "name": "stdout",
          "output_type": "stream",
          "text": [
            "😀################################😀\n",
            "CC(Cc1ccccc1)[NH2+]C(=O)C([NH3+])CCCC[NH3+] CC(Cc1ccccc1)NC(=O)C([NH3+])CCCC[NH3+]\n",
            "2.461258141994476\n",
            "CC(Cc1ccccc1)NC(=O)C([NH3+])CCCC[NH3+] CC(Cc1ccccc1)NC(=O)C(N)CCCC[NH3+]\n",
            "7.804567699432373\n",
            "CC(Cc1ccccc1)NC(=O)C(N)CCCC[NH3+] CC(Cc1ccccc1)NC(=O)C(N)CCCCN\n",
            "10.212386016845704\n",
            "CC(Cc1ccccc1)NC(=O)C(N)CCCCN CC(Cc1ccccc1)[N-]C(=O)C(N)CCCCN\n",
            "13.233402290344237\n",
            "😀################################😀\n"
          ]
        }
      ],
      "source": [
        "# @title Report SMILE list with pKa values\n",
        "\n",
        "print(\"😀################################😀\")\n",
        "for i in range(len(protonation_states)):\n",
        "    state = protonation_states[i]\n",
        "    print(\n",
        "        Chem.MolToSmiles(state.protonated_mol),\n",
        "        Chem.MolToSmiles(state.deprotonated_mol),\n",
        "    )\n",
        "    print(state.pka)\n",
        "print(\"😀################################😀\")\n"
      ]
    }
  ],
  "metadata": {
    "colab": {
      "collapsed_sections": [],
      "include_colab_link": true,
      "name": "pka_prediction.ipynb",
      "provenance": []
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}