02_mdtraj_atomselection.ipynb

{
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  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "authorship_tag": "ABX9TyMj2IrYDpUEaYS0wE1n/chj",
      "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/matsunagalab/tutorial_analyzingMDdata/blob/main/02_mdtraj_atomselection.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# MDTraj atom selection"
      ],
      "metadata": {
        "id": "0X69xW8MAEgT"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "## MDTrajのインストール"
      ],
      "metadata": {
        "id": "gc7BWdXBq4wn"
      }
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "lPrxEpnrqCxY",
        "outputId": "599760df-7f54-4d11-9699-453c578afc66"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "⏬ Downloading https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-Linux-x86_64.sh...\n",
            "📦 Installing...\n",
            "📌 Adjusting configuration...\n",
            "🩹 Patching environment...\n",
            "⏲ Done in 0:00:15\n",
            "🔁 Restarting kernel...\n"
          ]
        }
      ],
      "source": [
        "!pip install -q condacolab\n",
        "import condacolab\n",
        "condacolab.install()"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!conda install -c conda-forge mdtraj"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "rnl67WvV_Ya7",
        "outputId": "21b97827-6c41-4c0f-8c1a-1ee0e614869b"
      },
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Channels:\n",
            " - conda-forge\n",
            "Platform: linux-64\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\bdone\n",
            "Solving environment: | \b\b/ \b\b- \b\b\\ \b\bdone\n",
            "\n",
            "\n",
            "==> WARNING: A newer version of conda exists. <==\n",
            "    current version: 23.11.0\n",
            "    latest version: 24.7.1\n",
            "\n",
            "Please update conda by running\n",
            "\n",
            "    $ conda update -n base -c conda-forge conda\n",
            "\n",
            "\n",
            "\n",
            "# All requested packages already installed.\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## T4 LysozymeのMDデータの取得\n",
        "\n",
        "`wildtype.pdb` と `wildtype.dcd` をダウンロードする。"
      ],
      "metadata": {
        "id": "kAul5GDHq8PP"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!gdown 1Lu22Z7ARKSws77sBaYr84iCcQsnTHId9\n",
        "!gdown 1Eh0SSSxgAmv7LI2NvAY43tLMLI63lSa-"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "7xrlhSPFqFjc",
        "outputId": "aeee89be-d229-4b93-ff5f-ca10281f8d0a"
      },
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Downloading...\n",
            "From: https://drive.google.com/uc?id=1Lu22Z7ARKSws77sBaYr84iCcQsnTHId9\n",
            "To: /content/wildtype.pdb\n",
            "100% 214k/214k [00:00<00:00, 77.2MB/s]\n",
            "Downloading...\n",
            "From (original): https://drive.google.com/uc?id=1Eh0SSSxgAmv7LI2NvAY43tLMLI63lSa-\n",
            "From (redirected): https://drive.google.com/uc?id=1Eh0SSSxgAmv7LI2NvAY43tLMLI63lSa-&confirm=t&uuid=56fdff72-6469-4049-b4a0-d93bfa10a6c6\n",
            "To: /content/wildtype.dcd\n",
            "100% 318M/318M [00:03<00:00, 104MB/s]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## MDTrajでの原子選択\n",
        "\n",
        "以下の文書は主に MDTrajのドキュメント https://www.mdtraj.org/1.9.5/examples/atom-selection.html を日本語訳したものです。\n",
        "\n",
        "MDTrajでの原子と残基の選択の基本について説明します。まず、例のトラジェクトリをロードします。"
      ],
      "metadata": {
        "id": "CqrKHWP_AQCm"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import mdtraj as md\n",
        "import numpy as np\n",
        "\n",
        "# DCDファイルからトラジェクトリを読み込み、対応するPDBトポロジーファイルを使用する\n",
        "# トラジェクトリオブジェクト traj が作成される\n",
        "traj = md.load('/content/wildtype.dcd', top='/content/wildtype.pdb')\n",
        "\n",
        "# traj の中身を出力する\n",
        "print(traj)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "evnqDlrYspzP",
        "outputId": "67da212a-83fd-4d74-a1af-6a5129e06d6c"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "<mdtraj.Trajectory with 10000 frames, 2643 atoms, 164 residues, and unitcells>\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "traj.n_atoms や traj.n_residues を使用して、より直接的に原子数や残基数を確認することもできます。"
      ],
      "metadata": {
        "id": "cefbXOesMffK"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print('原子は何個？ %s' % traj.n_atoms)\n",
        "print('残基は何個？ %s' % traj.n_residues)"
      ],
      "metadata": {
        "id": "QD2u1WU_sPCd",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "86b21f21-f3c8-43c0-94b0-50ffa44f248f"
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "原子は何個？ 2643\n",
            "残基は何個？ 164\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "また、traj.xyz を操作することで原子の位置を操作することもできます。これは、各原子のxyz座標を含むNumPy配列で、次元は(n_frames, n_atoms, 3)です。5フレーム目の10番目の原子の3D座標を探してみましょう。"
      ],
      "metadata": {
        "id": "Cal-bvJrMnsH"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "frame_idx = 4 # ゼロから始まるフレーム番号\n",
        "atom_idx = 9 # ゼロから始まる原子インデックス\n",
        "print('10フレーム目の5番目の原子はどこにある？')\n",
        "print('x: %s\\ty: %s\\tz: %s' % tuple(traj.xyz[frame_idx, atom_idx,:]))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "XQJXR0z7GPct",
        "outputId": "b7d93e28-d445-4064-ecaf-ae762412e739"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "10フレーム目の5番目の原子はどこにある？\n",
            "x: 5.22431\ty: 0.44880342\tz: 0.6664297\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "トポロジーオブジェクト、すべてのTrajectoryオブジェクトにはTopologyが含まれています。TrajectoryのTopologyには、系（分子）の結合情報や特定のChain, Residue(残基), Atom情報が含まれています。"
      ],
      "metadata": {
        "id": "aHG6Ijd4RGnQ"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "topology = traj.topology\n",
        "print(topology)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "3Mopsz4kGWtW",
        "outputId": "4ac85fa2-3dd7-4e09-86e8-1fc7e0584b35"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "<mdtraj.Topology with 1 chains, 164 residues, 2643 atoms, 2663 bonds>\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "トポロジーオブジェクトを使用すれば、特定の原子を選択したり、すべての原子をループしたりすることができます。 (注意: zero-based indexです)"
      ],
      "metadata": {
        "id": "XCo_FevPRb8p"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print('5番目の原子: %s' % topology.atom(4))\n",
        "print('すべての原子: %s' % [atom for atom in topology.atoms])"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ICthR7d6Gg52",
        "outputId": "1d301e88-1dde-4441-824e-0748f42a694c"
      },
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "5番目の原子: MET1-CA\n",
            "すべての原子: [MET1-N, MET1-H, MET1-H2, MET1-H3, MET1-CA, MET1-HA, MET1-C, MET1-O, MET1-CB, MET1-HB2, MET1-HB3, MET1-CG, MET1-HG2, MET1-HG3, MET1-SD, MET1-CE, MET1-HE1, MET1-HE2, MET1-HE3, ASN2-N, ASN2-H, ASN2-CA, ASN2-HA, ASN2-C, ASN2-O, ASN2-CB, ASN2-HB2, ASN2-HB3, ASN2-CG, ASN2-OD1, ASN2-ND2, ASN2-HD21, ASN2-HD22, ILE3-N, ILE3-H, ILE3-CA, ILE3-HA, ILE3-C, ILE3-O, ILE3-CB, ILE3-HB, ILE3-CG1, ILE3-HG12, ILE3-HG13, ILE3-CG2, ILE3-HG21, ILE3-HG22, ILE3-HG23, ILE3-CD1, ILE3-HD11, ILE3-HD12, ILE3-HD13, PHE4-N, PHE4-H, PHE4-CA, PHE4-HA, PHE4-C, PHE4-O, PHE4-CB, PHE4-HB2, PHE4-HB3, PHE4-CG, PHE4-CD1, PHE4-HD1, PHE4-CD2, PHE4-HD2, PHE4-CE1, PHE4-HE1, PHE4-CE2, PHE4-HE2, PHE4-CZ, PHE4-HZ, GLU5-N, GLU5-H, GLU5-CA, GLU5-HA, GLU5-C, GLU5-O, GLU5-CB, GLU5-HB2, GLU5-HB3, GLU5-CG, GLU5-HG2, GLU5-HG3, GLU5-CD, GLU5-OE1, GLU5-OE2, MET6-N, MET6-H, MET6-CA, MET6-HA, MET6-C, MET6-O, MET6-CB, MET6-HB2, MET6-HB3, MET6-CG, MET6-HG2, MET6-HG3, MET6-SD, MET6-CE, MET6-HE1, MET6-HE2, MET6-HE3, LEU7-N, LEU7-H, LEU7-CA, LEU7-HA, LEU7-C, LEU7-O, LEU7-CB, LEU7-HB2, LEU7-HB3, LEU7-CG, LEU7-HG, LEU7-CD1, LEU7-HD11, LEU7-HD12, LEU7-HD13, LEU7-CD2, LEU7-HD21, LEU7-HD22, LEU7-HD23, ARG8-N, ARG8-H, ARG8-CA, ARG8-HA, ARG8-C, ARG8-O, ARG8-CB, ARG8-HB2, ARG8-HB3, ARG8-CG, ARG8-HG2, ARG8-HG3, ARG8-CD, ARG8-HD2, ARG8-HD3, ARG8-NE, ARG8-HE, ARG8-CZ, ARG8-NH1, ARG8-HH11, ARG8-HH12, ARG8-NH2, ARG8-HH21, ARG8-HH22, ILE9-N, ILE9-H, ILE9-CA, ILE9-HA, ILE9-C, ILE9-O, ILE9-CB, ILE9-HB, ILE9-CG1, ILE9-HG12, ILE9-HG13, ILE9-CG2, ILE9-HG21, ILE9-HG22, ILE9-HG23, ILE9-CD1, ILE9-HD11, ILE9-HD12, ILE9-HD13, ASP10-N, ASP10-H, ASP10-CA, ASP10-HA, ASP10-C, ASP10-O, ASP10-CB, ASP10-HB2, ASP10-HB3, ASP10-CG, ASP10-OD1, ASP10-OD2, GLU11-N, GLU11-H, GLU11-CA, GLU11-HA, GLU11-C, GLU11-O, GLU11-CB, GLU11-HB2, GLU11-HB3, GLU11-CG, GLU11-HG2, GLU11-HG3, GLU11-CD, GLU11-OE1, GLU11-OE2, GLY12-N, GLY12-H, GLY12-CA, GLY12-HA2, GLY12-HA3, GLY12-C, GLY12-O, LEU13-N, LEU13-H, LEU13-CA, LEU13-HA, LEU13-C, LEU13-O, LEU13-CB, LEU13-HB2, LEU13-HB3, LEU13-CG, LEU13-HG, LEU13-CD1, LEU13-HD11, LEU13-HD12, LEU13-HD13, LEU13-CD2, LEU13-HD21, LEU13-HD22, LEU13-HD23, ARG14-N, ARG14-H, ARG14-CA, ARG14-HA, ARG14-C, ARG14-O, ARG14-CB, ARG14-HB2, ARG14-HB3, ARG14-CG, ARG14-HG2, ARG14-HG3, ARG14-CD, ARG14-HD2, ARG14-HD3, ARG14-NE, ARG14-HE, ARG14-CZ, ARG14-NH1, ARG14-HH11, ARG14-HH12, ARG14-NH2, ARG14-HH21, ARG14-HH22, LEU15-N, LEU15-H, LEU15-CA, LEU15-HA, LEU15-C, LEU15-O, LEU15-CB, LEU15-HB2, LEU15-HB3, LEU15-CG, LEU15-HG, LEU15-CD1, LEU15-HD11, LEU15-HD12, LEU15-HD13, LEU15-CD2, LEU15-HD21, LEU15-HD22, LEU15-HD23, LYS16-N, LYS16-H, LYS16-CA, LYS16-HA, LYS16-C, LYS16-O, LYS16-CB, LYS16-HB2, LYS16-HB3, LYS16-CG, LYS16-HG2, LYS16-HG3, LYS16-CD, LYS16-HD2, LYS16-HD3, LYS16-CE, LYS16-HE2, LYS16-HE3, LYS16-NZ, LYS16-HZ1, LYS16-HZ2, LYS16-HZ3, ILE17-N, ILE17-H, ILE17-CA, ILE17-HA, ILE17-C, ILE17-O, ILE17-CB, ILE17-HB, ILE17-CG1, ILE17-HG12, ILE17-HG13, ILE17-CG2, ILE17-HG21, ILE17-HG22, ILE17-HG23, ILE17-CD1, ILE17-HD11, ILE17-HD12, ILE17-HD13, TYR18-N, TYR18-H, TYR18-CA, TYR18-HA, TYR18-C, TYR18-O, TYR18-CB, TYR18-HB2, TYR18-HB3, TYR18-CG, TYR18-CD1, TYR18-HD1, TYR18-CD2, TYR18-HD2, TYR18-CE1, TYR18-HE1, TYR18-CE2, TYR18-HE2, TYR18-CZ, TYR18-OH, TYR18-HH, LYS19-N, LYS19-H, LYS19-CA, LYS19-HA, LYS19-C, LYS19-O, LYS19-CB, LYS19-HB2, LYS19-HB3, LYS19-CG, LYS19-HG2, LYS19-HG3, LYS19-CD, LYS19-HD2, LYS19-HD3, LYS19-CE, LYS19-HE2, LYS19-HE3, LYS19-NZ, LYS19-HZ1, LYS19-HZ2, LYS19-HZ3, ASP20-N, ASP20-H, ASP20-CA, ASP20-HA, ASP20-C, ASP20-O, ASP20-CB, ASP20-HB2, ASP20-HB3, ASP20-CG, ASP20-OD1, ASP20-OD2, THR21-N, THR21-H, THR21-CA, THR21-HA, THR21-C, THR21-O, THR21-CB, THR21-HB, THR21-OG1, THR21-HG1, THR21-CG2, THR21-HG21, THR21-HG22, THR21-HG23, GLU22-N, GLU22-H, GLU22-CA, GLU22-HA, GLU22-C, GLU22-O, GLU22-CB, GLU22-HB2, GLU22-HB3, GLU22-CG, GLU22-HG2, GLU22-HG3, GLU22-CD, GLU22-OE1, GLU22-OE2, GLY23-N, GLY23-H, GLY23-CA, GLY23-HA2, GLY23-HA3, GLY23-C, GLY23-O, TYR24-N, TYR24-H, TYR24-CA, TYR24-HA, TYR24-C, TYR24-O, TYR24-CB, TYR24-HB2, TYR24-HB3, TYR24-CG, TYR24-CD1, TYR24-HD1, TYR24-CD2, TYR24-HD2, TYR24-CE1, TYR24-HE1, TYR24-CE2, TYR24-HE2, TYR24-CZ, TYR24-OH, TYR24-HH, TYR25-N, TYR25-H, TYR25-CA, TYR25-HA, TYR25-C, TYR25-O, TYR25-CB, TYR25-HB2, TYR25-HB3, TYR25-CG, TYR25-CD1, TYR25-HD1, TYR25-CD2, TYR25-HD2, TYR25-CE1, TYR25-HE1, TYR25-CE2, TYR25-HE2, TYR25-CZ, TYR25-OH, TYR25-HH, THR26-N, THR26-H, THR26-CA, THR26-HA, THR26-C, THR26-O, THR26-CB, THR26-HB, THR26-OG1, THR26-HG1, THR26-CG2, THR26-HG21, THR26-HG22, THR26-HG23, ILE27-N, ILE27-H, ILE27-CA, ILE27-HA, ILE27-C, ILE27-O, ILE27-CB, ILE27-HB, ILE27-CG1, ILE27-HG12, ILE27-HG13, ILE27-CG2, ILE27-HG21, ILE27-HG22, ILE27-HG23, ILE27-CD1, ILE27-HD11, ILE27-HD12, ILE27-HD13, GLY28-N, GLY28-H, GLY28-CA, GLY28-HA2, GLY28-HA3, GLY28-C, GLY28-O, ILE29-N, ILE29-H, ILE29-CA, ILE29-HA, ILE29-C, ILE29-O, ILE29-CB, ILE29-HB, ILE29-CG1, ILE29-HG12, ILE29-HG13, ILE29-CG2, ILE29-HG21, ILE29-HG22, ILE29-HG23, ILE29-CD1, ILE29-HD11, ILE29-HD12, ILE29-HD13, GLY30-N, GLY30-H, GLY30-CA, GLY30-HA2, GLY30-HA3, GLY30-C, GLY30-O, HIS31-N, HIS31-H, HIS31-CA, HIS31-HA, HIS31-C, HIS31-O, HIS31-CB, HIS31-HB2, HIS31-HB3, HIS31-CG, HIS31-ND1, HIS31-HD1, HIS31-CD2, HIS31-HD2, HIS31-CE1, HIS31-HE1, HIS31-NE2, LEU32-N, LEU32-H, LEU32-CA, LEU32-HA, LEU32-C, LEU32-O, LEU32-CB, LEU32-HB2, LEU32-HB3, LEU32-CG, LEU32-HG, LEU32-CD1, LEU32-HD11, LEU32-HD12, LEU32-HD13, LEU32-CD2, LEU32-HD21, LEU32-HD22, LEU32-HD23, LEU33-N, LEU33-H, LEU33-CA, LEU33-HA, LEU33-C, LEU33-O, LEU33-CB, LEU33-HB2, LEU33-HB3, LEU33-CG, LEU33-HG, LEU33-CD1, LEU33-HD11, LEU33-HD12, LEU33-HD13, LEU33-CD2, LEU33-HD21, LEU33-HD22, LEU33-HD23, THR34-N, THR34-H, THR34-CA, THR34-HA, THR34-C, THR34-O, THR34-CB, THR34-HB, THR34-OG1, THR34-HG1, THR34-CG2, THR34-HG21, THR34-HG22, THR34-HG23, LYS35-N, LYS35-H, LYS35-CA, LYS35-HA, LYS35-C, LYS35-O, LYS35-CB, LYS35-HB2, LYS35-HB3, LYS35-CG, LYS35-HG2, LYS35-HG3, LYS35-CD, LYS35-HD2, LYS35-HD3, LYS35-CE, LYS35-HE2, LYS35-HE3, LYS35-NZ, LYS35-HZ1, LYS35-HZ2, LYS35-HZ3, SER36-N, SER36-H, SER36-CA, SER36-HA, SER36-C, SER36-O, SER36-CB, SER36-HB2, SER36-HB3, SER36-OG, SER36-HG, PRO37-N, PRO37-CA, PRO37-HA, PRO37-C, PRO37-O, PRO37-CB, PRO37-HB2, PRO37-HB3, PRO37-CG, PRO37-HG2, PRO37-HG3, PRO37-CD, PRO37-HD2, PRO37-HD3, SER38-N, SER38-H, SER38-CA, SER38-HA, SER38-C, SER38-O, SER38-CB, SER38-HB2, SER38-HB3, SER38-OG, SER38-HG, LEU39-N, LEU39-H, LEU39-CA, LEU39-HA, LEU39-C, LEU39-O, LEU39-CB, LEU39-HB2, LEU39-HB3, LEU39-CG, LEU39-HG, LEU39-CD1, LEU39-HD11, LEU39-HD12, LEU39-HD13, LEU39-CD2, LEU39-HD21, LEU39-HD22, LEU39-HD23, ASN40-N, ASN40-H, ASN40-CA, ASN40-HA, ASN40-C, ASN40-O, ASN40-CB, ASN40-HB2, ASN40-HB3, ASN40-CG, ASN40-OD1, ASN40-ND2, ASN40-HD21, ASN40-HD22, ALA41-N, ALA41-H, ALA41-CA, ALA41-HA, ALA41-C, ALA41-O, ALA41-CB, ALA41-HB1, ALA41-HB2, ALA41-HB3, ALA42-N, ALA42-H, ALA42-CA, ALA42-HA, ALA42-C, ALA42-O, ALA42-CB, ALA42-HB1, ALA42-HB2, ALA42-HB3, LYS43-N, LYS43-H, LYS43-CA, LYS43-HA, LYS43-C, LYS43-O, LYS43-CB, LYS43-HB2, LYS43-HB3, LYS43-CG, LYS43-HG2, LYS43-HG3, LYS43-CD, LYS43-HD2, LYS43-HD3, LYS43-CE, LYS43-HE2, LYS43-HE3, LYS43-NZ, LYS43-HZ1, LYS43-HZ2, LYS43-HZ3, SER44-N, SER44-H, SER44-CA, SER44-HA, SER44-C, SER44-O, SER44-CB, SER44-HB2, SER44-HB3, SER44-OG, SER44-HG, GLU45-N, GLU45-H, GLU45-CA, GLU45-HA, GLU45-C, GLU45-O, GLU45-CB, GLU45-HB2, GLU45-HB3, GLU45-CG, GLU45-HG2, GLU45-HG3, GLU45-CD, GLU45-OE1, GLU45-OE2, LEU46-N, LEU46-H, LEU46-CA, LEU46-HA, LEU46-C, LEU46-O, LEU46-CB, LEU46-HB2, LEU46-HB3, LEU46-CG, LEU46-HG, LEU46-CD1, LEU46-HD11, LEU46-HD12, LEU46-HD13, LEU46-CD2, LEU46-HD21, LEU46-HD22, LEU46-HD23, ASP47-N, ASP47-H, ASP47-CA, ASP47-HA, ASP47-C, ASP47-O, ASP47-CB, ASP47-HB2, ASP47-HB3, ASP47-CG, ASP47-OD1, ASP47-OD2, LYS48-N, LYS48-H, LYS48-CA, LYS48-HA, LYS48-C, LYS48-O, LYS48-CB, LYS48-HB2, LYS48-HB3, LYS48-CG, LYS48-HG2, LYS48-HG3, LYS48-CD, LYS48-HD2, LYS48-HD3, LYS48-CE, LYS48-HE2, LYS48-HE3, LYS48-NZ, LYS48-HZ1, LYS48-HZ2, LYS48-HZ3, ALA49-N, ALA49-H, ALA49-CA, ALA49-HA, ALA49-C, ALA49-O, ALA49-CB, ALA49-HB1, ALA49-HB2, ALA49-HB3, ILE50-N, ILE50-H, ILE50-CA, ILE50-HA, ILE50-C, ILE50-O, ILE50-CB, ILE50-HB, ILE50-CG1, ILE50-HG12, ILE50-HG13, ILE50-CG2, ILE50-HG21, ILE50-HG22, ILE50-HG23, ILE50-CD1, ILE50-HD11, ILE50-HD12, ILE50-HD13, GLY51-N, GLY51-H, GLY51-CA, GLY51-HA2, GLY51-HA3, GLY51-C, GLY51-O, ARG52-N, ARG52-H, ARG52-CA, ARG52-HA, ARG52-C, ARG52-O, ARG52-CB, ARG52-HB2, ARG52-HB3, ARG52-CG, ARG52-HG2, ARG52-HG3, ARG52-CD, ARG52-HD2, ARG52-HD3, ARG52-NE, ARG52-HE, ARG52-CZ, ARG52-NH1, ARG52-HH11, ARG52-HH12, ARG52-NH2, ARG52-HH21, ARG52-HH22, ASN53-N, ASN53-H, ASN53-CA, ASN53-HA, ASN53-C, ASN53-O, ASN53-CB, ASN53-HB2, ASN53-HB3, ASN53-CG, ASN53-OD1, ASN53-ND2, ASN53-HD21, ASN53-HD22, CYS54-N, CYS54-H, CYS54-CA, CYS54-HA, CYS54-C, CYS54-O, CYS54-CB, CYS54-HB2, CYS54-HB3, CYS54-SG, CYS54-HG, ASN55-N, ASN55-H, ASN55-CA, ASN55-HA, ASN55-C, ASN55-O, ASN55-CB, ASN55-HB2, ASN55-HB3, ASN55-CG, ASN55-OD1, ASN55-ND2, ASN55-HD21, ASN55-HD22, GLY56-N, GLY56-H, GLY56-CA, GLY56-HA2, GLY56-HA3, GLY56-C, GLY56-O, VAL57-N, VAL57-H, VAL57-CA, VAL57-HA, VAL57-C, VAL57-O, VAL57-CB, VAL57-HB, VAL57-CG1, VAL57-HG11, VAL57-HG12, VAL57-HG13, VAL57-CG2, VAL57-HG21, VAL57-HG22, VAL57-HG23, ILE58-N, ILE58-H, ILE58-CA, ILE58-HA, ILE58-C, ILE58-O, ILE58-CB, ILE58-HB, ILE58-CG1, ILE58-HG12, ILE58-HG13, ILE58-CG2, ILE58-HG21, ILE58-HG22, ILE58-HG23, ILE58-CD1, ILE58-HD11, ILE58-HD12, ILE58-HD13, THR59-N, THR59-H, THR59-CA, THR59-HA, THR59-C, THR59-O, THR59-CB, THR59-HB, THR59-OG1, THR59-HG1, THR59-CG2, THR59-HG21, THR59-HG22, THR59-HG23, LYS60-N, LYS60-H, LYS60-CA, LYS60-HA, LYS60-C, LYS60-O, LYS60-CB, LYS60-HB2, LYS60-HB3, LYS60-CG, LYS60-HG2, LYS60-HG3, LYS60-CD, LYS60-HD2, LYS60-HD3, LYS60-CE, LYS60-HE2, LYS60-HE3, LYS60-NZ, LYS60-HZ1, LYS60-HZ2, LYS60-HZ3, ASP61-N, ASP61-H, ASP61-CA, ASP61-HA, ASP61-C, ASP61-O, ASP61-CB, ASP61-HB2, ASP61-HB3, ASP61-CG, ASP61-OD1, ASP61-OD2, GLU62-N, GLU62-H, GLU62-CA, GLU62-HA, GLU62-C, GLU62-O, GLU62-CB, GLU62-HB2, GLU62-HB3, GLU62-CG, GLU62-HG2, GLU62-HG3, GLU62-CD, GLU62-OE1, GLU62-OE2, ALA63-N, ALA63-H, ALA63-CA, ALA63-HA, ALA63-C, ALA63-O, ALA63-CB, ALA63-HB1, ALA63-HB2, ALA63-HB3, GLU64-N, GLU64-H, GLU64-CA, GLU64-HA, GLU64-C, GLU64-O, GLU64-CB, GLU64-HB2, GLU64-HB3, GLU64-CG, GLU64-HG2, GLU64-HG3, GLU64-CD, GLU64-OE1, GLU64-OE2, LYS65-N, LYS65-H, LYS65-CA, LYS65-HA, LYS65-C, LYS65-O, LYS65-CB, LYS65-HB2, LYS65-HB3, LYS65-CG, LYS65-HG2, LYS65-HG3, LYS65-CD, LYS65-HD2, LYS65-HD3, LYS65-CE, LYS65-HE2, LYS65-HE3, LYS65-NZ, LYS65-HZ1, LYS65-HZ2, LYS65-HZ3, LEU66-N, LEU66-H, LEU66-CA, LEU66-HA, LEU66-C, LEU66-O, LEU66-CB, LEU66-HB2, LEU66-HB3, LEU66-CG, LEU66-HG, LEU66-CD1, LEU66-HD11, LEU66-HD12, LEU66-HD13, LEU66-CD2, LEU66-HD21, LEU66-HD22, LEU66-HD23, PHE67-N, PHE67-H, PHE67-CA, PHE67-HA, PHE67-C, PHE67-O, PHE67-CB, PHE67-HB2, PHE67-HB3, PHE67-CG, PHE67-CD1, PHE67-HD1, PHE67-CD2, PHE67-HD2, PHE67-CE1, PHE67-HE1, PHE67-CE2, PHE67-HE2, PHE67-CZ, PHE67-HZ, ASN68-N, ASN68-H, ASN68-CA, ASN68-HA, ASN68-C, ASN68-O, ASN68-CB, ASN68-HB2, ASN68-HB3, ASN68-CG, ASN68-OD1, ASN68-ND2, ASN68-HD21, ASN68-HD22, GLN69-N, GLN69-H, GLN69-CA, GLN69-HA, GLN69-C, GLN69-O, GLN69-CB, GLN69-HB2, GLN69-HB3, GLN69-CG, GLN69-HG2, GLN69-HG3, GLN69-CD, GLN69-OE1, GLN69-NE2, GLN69-HE21, GLN69-HE22, ASP70-N, ASP70-H, ASP70-CA, ASP70-HA, ASP70-C, ASP70-O, ASP70-CB, ASP70-HB2, ASP70-HB3, ASP70-CG, ASP70-OD1, ASP70-OD2, VAL71-N, VAL71-H, VAL71-CA, VAL71-HA, VAL71-C, VAL71-O, VAL71-CB, VAL71-HB, VAL71-CG1, VAL71-HG11, VAL71-HG12, VAL71-HG13, VAL71-CG2, VAL71-HG21, VAL71-HG22, VAL71-HG23, ASP72-N, ASP72-H, ASP72-CA, ASP72-HA, ASP72-C, ASP72-O, ASP72-CB, ASP72-HB2, ASP72-HB3, ASP72-CG, ASP72-OD1, ASP72-OD2, ALA73-N, ALA73-H, ALA73-CA, ALA73-HA, ALA73-C, ALA73-O, ALA73-CB, ALA73-HB1, ALA73-HB2, ALA73-HB3, ALA74-N, ALA74-H, ALA74-CA, ALA74-HA, ALA74-C, ALA74-O, ALA74-CB, ALA74-HB1, ALA74-HB2, ALA74-HB3, VAL75-N, VAL75-H, VAL75-CA, VAL75-HA, VAL75-C, VAL75-O, VAL75-CB, VAL75-HB, VAL75-CG1, VAL75-HG11, VAL75-HG12, VAL75-HG13, VAL75-CG2, VAL75-HG21, VAL75-HG22, VAL75-HG23, ARG76-N, ARG76-H, ARG76-CA, ARG76-HA, ARG76-C, ARG76-O, ARG76-CB, ARG76-HB2, ARG76-HB3, ARG76-CG, ARG76-HG2, ARG76-HG3, ARG76-CD, ARG76-HD2, ARG76-HD3, ARG76-NE, ARG76-HE, ARG76-CZ, ARG76-NH1, ARG76-HH11, ARG76-HH12, ARG76-NH2, ARG76-HH21, ARG76-HH22, GLY77-N, GLY77-H, GLY77-CA, GLY77-HA2, GLY77-HA3, GLY77-C, GLY77-O, ILE78-N, ILE78-H, ILE78-CA, ILE78-HA, ILE78-C, ILE78-O, ILE78-CB, ILE78-HB, ILE78-CG1, ILE78-HG12, ILE78-HG13, ILE78-CG2, ILE78-HG21, ILE78-HG22, ILE78-HG23, ILE78-CD1, ILE78-HD11, ILE78-HD12, ILE78-HD13, LEU79-N, LEU79-H, LEU79-CA, LEU79-HA, LEU79-C, LEU79-O, LEU79-CB, LEU79-HB2, LEU79-HB3, LEU79-CG, LEU79-HG, LEU79-CD1, LEU79-HD11, LEU79-HD12, LEU79-HD13, LEU79-CD2, LEU79-HD21, LEU79-HD22, LEU79-HD23, ARG80-N, ARG80-H, ARG80-CA, ARG80-HA, ARG80-C, ARG80-O, ARG80-CB, ARG80-HB2, ARG80-HB3, ARG80-CG, ARG80-HG2, ARG80-HG3, ARG80-CD, ARG80-HD2, ARG80-HD3, ARG80-NE, ARG80-HE, ARG80-CZ, ARG80-NH1, ARG80-HH11, ARG80-HH12, ARG80-NH2, ARG80-HH21, ARG80-HH22, ASN81-N, ASN81-H, ASN81-CA, ASN81-HA, ASN81-C, ASN81-O, ASN81-CB, ASN81-HB2, ASN81-HB3, ASN81-CG, ASN81-OD1, ASN81-ND2, ASN81-HD21, ASN81-HD22, ALA82-N, ALA82-H, ALA82-CA, ALA82-HA, ALA82-C, ALA82-O, ALA82-CB, ALA82-HB1, ALA82-HB2, ALA82-HB3, LYS83-N, LYS83-H, LYS83-CA, LYS83-HA, LYS83-C, LYS83-O, LYS83-CB, LYS83-HB2, LYS83-HB3, LYS83-CG, LYS83-HG2, LYS83-HG3, LYS83-CD, LYS83-HD2, LYS83-HD3, LYS83-CE, LYS83-HE2, LYS83-HE3, LYS83-NZ, LYS83-HZ1, LYS83-HZ2, LYS83-HZ3, LEU84-N, LEU84-H, LEU84-CA, LEU84-HA, LEU84-C, LEU84-O, LEU84-CB, LEU84-HB2, LEU84-HB3, LEU84-CG, LEU84-HG, LEU84-CD1, LEU84-HD11, LEU84-HD12, LEU84-HD13, LEU84-CD2, LEU84-HD21, LEU84-HD22, LEU84-HD23, LYS85-N, LYS85-H, LYS85-CA, LYS85-HA, LYS85-C, LYS85-O, LYS85-CB, LYS85-HB2, LYS85-HB3, LYS85-CG, LYS85-HG2, LYS85-HG3, LYS85-CD, LYS85-HD2, LYS85-HD3, LYS85-CE, LYS85-HE2, LYS85-HE3, LYS85-NZ, LYS85-HZ1, LYS85-HZ2, LYS85-HZ3, PRO86-N, PRO86-CA, PRO86-HA, PRO86-C, PRO86-O, PRO86-CB, PRO86-HB2, PRO86-HB3, PRO86-CG, PRO86-HG2, PRO86-HG3, PRO86-CD, PRO86-HD2, PRO86-HD3, VAL87-N, VAL87-H, VAL87-CA, VAL87-HA, VAL87-C, VAL87-O, VAL87-CB, VAL87-HB, VAL87-CG1, VAL87-HG11, VAL87-HG12, VAL87-HG13, VAL87-CG2, VAL87-HG21, VAL87-HG22, VAL87-HG23, TYR88-N, TYR88-H, TYR88-CA, TYR88-HA, TYR88-C, TYR88-O, TYR88-CB, TYR88-HB2, TYR88-HB3, TYR88-CG, TYR88-CD1, TYR88-HD1, TYR88-CD2, TYR88-HD2, TYR88-CE1, TYR88-HE1, TYR88-CE2, TYR88-HE2, TYR88-CZ, TYR88-OH, TYR88-HH, ASP89-N, ASP89-H, ASP89-CA, ASP89-HA, ASP89-C, ASP89-O, ASP89-CB, ASP89-HB2, ASP89-HB3, ASP89-CG, ASP89-OD1, ASP89-OD2, SER90-N, SER90-H, SER90-CA, SER90-HA, SER90-C, SER90-O, SER90-CB, SER90-HB2, SER90-HB3, SER90-OG, SER90-HG, LEU91-N, LEU91-H, LEU91-CA, LEU91-HA, LEU91-C, LEU91-O, LEU91-CB, LEU91-HB2, LEU91-HB3, LEU91-CG, LEU91-HG, LEU91-CD1, LEU91-HD11, LEU91-HD12, LEU91-HD13, LEU91-CD2, LEU91-HD21, LEU91-HD22, LEU91-HD23, ASP92-N, ASP92-H, ASP92-CA, ASP92-HA, ASP92-C, ASP92-O, ASP92-CB, ASP92-HB2, ASP92-HB3, ASP92-CG, ASP92-OD1, ASP92-OD2, ALA93-N, ALA93-H, ALA93-CA, ALA93-HA, ALA93-C, ALA93-O, ALA93-CB, ALA93-HB1, ALA93-HB2, ALA93-HB3, VAL94-N, VAL94-H, VAL94-CA, VAL94-HA, VAL94-C, VAL94-O, VAL94-CB, VAL94-HB, VAL94-CG1, VAL94-HG11, VAL94-HG12, VAL94-HG13, VAL94-CG2, VAL94-HG21, VAL94-HG22, VAL94-HG23, ARG95-N, ARG95-H, ARG95-CA, ARG95-HA, ARG95-C, ARG95-O, ARG95-CB, ARG95-HB2, ARG95-HB3, ARG95-CG, ARG95-HG2, ARG95-HG3, ARG95-CD, ARG95-HD2, ARG95-HD3, ARG95-NE, ARG95-HE, ARG95-CZ, ARG95-NH1, ARG95-HH11, ARG95-HH12, ARG95-NH2, ARG95-HH21, ARG95-HH22, ARG96-N, ARG96-H, ARG96-CA, ARG96-HA, ARG96-C, ARG96-O, ARG96-CB, ARG96-HB2, ARG96-HB3, ARG96-CG, ARG96-HG2, ARG96-HG3, ARG96-CD, ARG96-HD2, ARG96-HD3, ARG96-NE, ARG96-HE, ARG96-CZ, ARG96-NH1, ARG96-HH11, ARG96-HH12, ARG96-NH2, ARG96-HH21, ARG96-HH22, CYS97-N, CYS97-H, CYS97-CA, CYS97-HA, CYS97-C, CYS97-O, CYS97-CB, CYS97-HB2, CYS97-HB3, CYS97-SG, CYS97-HG, ALA98-N, ALA98-H, ALA98-CA, ALA98-HA, ALA98-C, ALA98-O, ALA98-CB, ALA98-HB1, ALA98-HB2, ALA98-HB3, LEU99-N, LEU99-H, LEU99-CA, LEU99-HA, LEU99-C, LEU99-O, LEU99-CB, LEU99-HB2, LEU99-HB3, LEU99-CG, LEU99-HG, LEU99-CD1, LEU99-HD11, LEU99-HD12, LEU99-HD13, LEU99-CD2, LEU99-HD21, LEU99-HD22, LEU99-HD23, ILE100-N, ILE100-H, ILE100-CA, ILE100-HA, ILE100-C, ILE100-O, ILE100-CB, ILE100-HB, ILE100-CG1, ILE100-HG12, ILE100-HG13, ILE100-CG2, ILE100-HG21, ILE100-HG22, ILE100-HG23, ILE100-CD1, ILE100-HD11, ILE100-HD12, ILE100-HD13, ASN101-N, ASN101-H, ASN101-CA, ASN101-HA, ASN101-C, ASN101-O, ASN101-CB, ASN101-HB2, ASN101-HB3, ASN101-CG, ASN101-OD1, ASN101-ND2, ASN101-HD21, ASN101-HD22, MET102-N, MET102-H, MET102-CA, MET102-HA, MET102-C, MET102-O, MET102-CB, MET102-HB2, MET102-HB3, MET102-CG, MET102-HG2, MET102-HG3, MET102-SD, MET102-CE, MET102-HE1, MET102-HE2, MET102-HE3, VAL103-N, VAL103-H, VAL103-CA, VAL103-HA, VAL103-C, VAL103-O, VAL103-CB, VAL103-HB, VAL103-CG1, VAL103-HG11, VAL103-HG12, VAL103-HG13, VAL103-CG2, VAL103-HG21, VAL103-HG22, VAL103-HG23, PHE104-N, PHE104-H, PHE104-CA, PHE104-HA, PHE104-C, PHE104-O, PHE104-CB, PHE104-HB2, PHE104-HB3, PHE104-CG, PHE104-CD1, PHE104-HD1, PHE104-CD2, PHE104-HD2, PHE104-CE1, PHE104-HE1, PHE104-CE2, PHE104-HE2, PHE104-CZ, PHE104-HZ, GLN105-N, GLN105-H, GLN105-CA, GLN105-HA, GLN105-C, GLN105-O, GLN105-CB, GLN105-HB2, GLN105-HB3, GLN105-CG, GLN105-HG2, GLN105-HG3, GLN105-CD, GLN105-OE1, GLN105-NE2, GLN105-HE21, GLN105-HE22, MET106-N, MET106-H, MET106-CA, MET106-HA, MET106-C, MET106-O, MET106-CB, MET106-HB2, MET106-HB3, MET106-CG, MET106-HG2, MET106-HG3, MET106-SD, MET106-CE, MET106-HE1, MET106-HE2, MET106-HE3, GLY107-N, GLY107-H, GLY107-CA, GLY107-HA2, GLY107-HA3, GLY107-C, GLY107-O, GLU108-N, GLU108-H, GLU108-CA, GLU108-HA, GLU108-C, GLU108-O, GLU108-CB, GLU108-HB2, GLU108-HB3, GLU108-CG, GLU108-HG2, GLU108-HG3, GLU108-CD, GLU108-OE1, GLU108-OE2, THR109-N, THR109-H, THR109-CA, THR109-HA, THR109-C, THR109-O, THR109-CB, THR109-HB, THR109-OG1, THR109-HG1, THR109-CG2, THR109-HG21, THR109-HG22, THR109-HG23, GLY110-N, GLY110-H, GLY110-CA, GLY110-HA2, GLY110-HA3, GLY110-C, GLY110-O, VAL111-N, VAL111-H, VAL111-CA, VAL111-HA, VAL111-C, VAL111-O, VAL111-CB, VAL111-HB, VAL111-CG1, VAL111-HG11, VAL111-HG12, VAL111-HG13, VAL111-CG2, VAL111-HG21, VAL111-HG22, VAL111-HG23, ALA112-N, ALA112-H, ALA112-CA, ALA112-HA, ALA112-C, ALA112-O, ALA112-CB, ALA112-HB1, ALA112-HB2, ALA112-HB3, GLY113-N, GLY113-H, GLY113-CA, GLY113-HA2, GLY113-HA3, GLY113-C, GLY113-O, PHE114-N, PHE114-H, PHE114-CA, PHE114-HA, PHE114-C, PHE114-O, PHE114-CB, PHE114-HB2, PHE114-HB3, PHE114-CG, PHE114-CD1, PHE114-HD1, PHE114-CD2, PHE114-HD2, PHE114-CE1, PHE114-HE1, PHE114-CE2, PHE114-HE2, PHE114-CZ, PHE114-HZ, THR115-N, THR115-H, THR115-CA, THR115-HA, THR115-C, THR115-O, THR115-CB, THR115-HB, THR115-OG1, THR115-HG1, THR115-CG2, THR115-HG21, THR115-HG22, THR115-HG23, ASN116-N, ASN116-H, ASN116-CA, ASN116-HA, ASN116-C, ASN116-O, ASN116-CB, ASN116-HB2, ASN116-HB3, ASN116-CG, ASN116-OD1, ASN116-ND2, ASN116-HD21, ASN116-HD22, SER117-N, SER117-H, SER117-CA, SER117-HA, SER117-C, SER117-O, SER117-CB, SER117-HB2, SER117-HB3, SER117-OG, SER117-HG, LEU118-N, LEU118-H, LEU118-CA, LEU118-HA, LEU118-C, LEU118-O, LEU118-CB, LEU118-HB2, LEU118-HB3, LEU118-CG, LEU118-HG, LEU118-CD1, LEU118-HD11, LEU118-HD12, LEU118-HD13, LEU118-CD2, LEU118-HD21, LEU118-HD22, LEU118-HD23, ARG119-N, ARG119-H, ARG119-CA, ARG119-HA, ARG119-C, ARG119-O, ARG119-CB, ARG119-HB2, ARG119-HB3, ARG119-CG, ARG119-HG2, ARG119-HG3, ARG119-CD, ARG119-HD2, ARG119-HD3, ARG119-NE, ARG119-HE, ARG119-CZ, ARG119-NH1, ARG119-HH11, ARG119-HH12, ARG119-NH2, ARG119-HH21, ARG119-HH22, MET120-N, MET120-H, MET120-CA, MET120-HA, MET120-C, MET120-O, MET120-CB, MET120-HB2, MET120-HB3, MET120-CG, MET120-HG2, MET120-HG3, MET120-SD, MET120-CE, MET120-HE1, MET120-HE2, MET120-HE3, LEU121-N, LEU121-H, LEU121-CA, LEU121-HA, LEU121-C, LEU121-O, LEU121-CB, LEU121-HB2, LEU121-HB3, LEU121-CG, LEU121-HG, LEU121-CD1, LEU121-HD11, LEU121-HD12, LEU121-HD13, LEU121-CD2, LEU121-HD21, LEU121-HD22, LEU121-HD23, GLN122-N, GLN122-H, GLN122-CA, GLN122-HA, GLN122-C, GLN122-O, GLN122-CB, GLN122-HB2, GLN122-HB3, GLN122-CG, GLN122-HG2, GLN122-HG3, GLN122-CD, GLN122-OE1, GLN122-NE2, GLN122-HE21, GLN122-HE22, GLN123-N, GLN123-H, GLN123-CA, GLN123-HA, GLN123-C, GLN123-O, GLN123-CB, GLN123-HB2, GLN123-HB3, GLN123-CG, GLN123-HG2, GLN123-HG3, GLN123-CD, GLN123-OE1, GLN123-NE2, GLN123-HE21, GLN123-HE22, LYS124-N, LYS124-H, LYS124-CA, LYS124-HA, LYS124-C, LYS124-O, LYS124-CB, LYS124-HB2, LYS124-HB3, LYS124-CG, LYS124-HG2, LYS124-HG3, LYS124-CD, LYS124-HD2, LYS124-HD3, LYS124-CE, LYS124-HE2, LYS124-HE3, LYS124-NZ, LYS124-HZ1, LYS124-HZ2, LYS124-HZ3, ARG125-N, ARG125-H, ARG125-CA, ARG125-HA, ARG125-C, ARG125-O, ARG125-CB, ARG125-HB2, ARG125-HB3, ARG125-CG, ARG125-HG2, ARG125-HG3, ARG125-CD, ARG125-HD2, ARG125-HD3, ARG125-NE, ARG125-HE, ARG125-CZ, ARG125-NH1, ARG125-HH11, ARG125-HH12, ARG125-NH2, ARG125-HH21, ARG125-HH22, TRP126-N, TRP126-H, TRP126-CA, TRP126-HA, TRP126-C, TRP126-O, TRP126-CB, TRP126-HB2, TRP126-HB3, TRP126-CG, TRP126-CD1, TRP126-HD1, TRP126-CD2, TRP126-NE1, TRP126-HE1, TRP126-CE2, TRP126-CE3, TRP126-HE3, TRP126-CZ2, TRP126-HZ2, TRP126-CZ3, TRP126-HZ3, TRP126-CH2, TRP126-HH2, ASP127-N, ASP127-H, ASP127-CA, ASP127-HA, ASP127-C, ASP127-O, ASP127-CB, ASP127-HB2, ASP127-HB3, ASP127-CG, ASP127-OD1, ASP127-OD2, GLU128-N, GLU128-H, GLU128-CA, GLU128-HA, GLU128-C, GLU128-O, GLU128-CB, GLU128-HB2, GLU128-HB3, GLU128-CG, GLU128-HG2, GLU128-HG3, GLU128-CD, GLU128-OE1, GLU128-OE2, ALA129-N, ALA129-H, ALA129-CA, ALA129-HA, ALA129-C, ALA129-O, ALA129-CB, ALA129-HB1, ALA129-HB2, ALA129-HB3, ALA130-N, ALA130-H, ALA130-CA, ALA130-HA, ALA130-C, ALA130-O, ALA130-CB, ALA130-HB1, ALA130-HB2, ALA130-HB3, VAL131-N, VAL131-H, VAL131-CA, VAL131-HA, VAL131-C, VAL131-O, VAL131-CB, VAL131-HB, VAL131-CG1, VAL131-HG11, VAL131-HG12, VAL131-HG13, VAL131-CG2, VAL131-HG21, VAL131-HG22, VAL131-HG23, ASN132-N, ASN132-H, ASN132-CA, ASN132-HA, ASN132-C, ASN132-O, ASN132-CB, ASN132-HB2, ASN132-HB3, ASN132-CG, ASN132-OD1, ASN132-ND2, ASN132-HD21, ASN132-HD22, LEU133-N, LEU133-H, LEU133-CA, LEU133-HA, LEU133-C, LEU133-O, LEU133-CB, LEU133-HB2, LEU133-HB3, LEU133-CG, LEU133-HG, LEU133-CD1, LEU133-HD11, LEU133-HD12, LEU133-HD13, LEU133-CD2, LEU133-HD21, LEU133-HD22, LEU133-HD23, ALA134-N, ALA134-H, ALA134-CA, ALA134-HA, ALA134-C, ALA134-O, ALA134-CB, ALA134-HB1, ALA134-HB2, ALA134-HB3, LYS135-N, LYS135-H, LYS135-CA, LYS135-HA, LYS135-C, LYS135-O, LYS135-CB, LYS135-HB2, LYS135-HB3, LYS135-CG, LYS135-HG2, LYS135-HG3, LYS135-CD, LYS135-HD2, LYS135-HD3, LYS135-CE, LYS135-HE2, LYS135-HE3, LYS135-NZ, LYS135-HZ1, LYS135-HZ2, LYS135-HZ3, SER136-N, SER136-H, SER136-CA, SER136-HA, SER136-C, SER136-O, SER136-CB, SER136-HB2, SER136-HB3, SER136-OG, SER136-HG, ARG137-N, ARG137-H, ARG137-CA, ARG137-HA, ARG137-C, ARG137-O, ARG137-CB, ARG137-HB2, ARG137-HB3, ARG137-CG, ARG137-HG2, ARG137-HG3, ARG137-CD, ARG137-HD2, ARG137-HD3, ARG137-NE, ARG137-HE, ARG137-CZ, ARG137-NH1, ARG137-HH11, ARG137-HH12, ARG137-NH2, ARG137-HH21, ARG137-HH22, TRP138-N, TRP138-H, TRP138-CA, TRP138-HA, TRP138-C, TRP138-O, TRP138-CB, TRP138-HB2, TRP138-HB3, TRP138-CG, TRP138-CD1, TRP138-HD1, TRP138-CD2, TRP138-NE1, TRP138-HE1, TRP138-CE2, TRP138-CE3, TRP138-HE3, TRP138-CZ2, TRP138-HZ2, TRP138-CZ3, TRP138-HZ3, TRP138-CH2, TRP138-HH2, TYR139-N, TYR139-H, TYR139-CA, TYR139-HA, TYR139-C, TYR139-O, TYR139-CB, TYR139-HB2, TYR139-HB3, TYR139-CG, TYR139-CD1, TYR139-HD1, TYR139-CD2, TYR139-HD2, TYR139-CE1, TYR139-HE1, TYR139-CE2, TYR139-HE2, TYR139-CZ, TYR139-OH, TYR139-HH, ASN140-N, ASN140-H, ASN140-CA, ASN140-HA, ASN140-C, ASN140-O, ASN140-CB, ASN140-HB2, ASN140-HB3, ASN140-CG, ASN140-OD1, ASN140-ND2, ASN140-HD21, ASN140-HD22, GLN141-N, GLN141-H, GLN141-CA, GLN141-HA, GLN141-C, GLN141-O, GLN141-CB, GLN141-HB2, GLN141-HB3, GLN141-CG, GLN141-HG2, GLN141-HG3, GLN141-CD, GLN141-OE1, GLN141-NE2, GLN141-HE21, GLN141-HE22, THR142-N, THR142-H, THR142-CA, THR142-HA, THR142-C, THR142-O, THR142-CB, THR142-HB, THR142-OG1, THR142-HG1, THR142-CG2, THR142-HG21, THR142-HG22, THR142-HG23, PRO143-N, PRO143-CA, PRO143-HA, PRO143-C, PRO143-O, PRO143-CB, PRO143-HB2, PRO143-HB3, PRO143-CG, PRO143-HG2, PRO143-HG3, PRO143-CD, PRO143-HD2, PRO143-HD3, ASN144-N, ASN144-H, ASN144-CA, ASN144-HA, ASN144-C, ASN144-O, ASN144-CB, ASN144-HB2, ASN144-HB3, ASN144-CG, ASN144-OD1, ASN144-ND2, ASN144-HD21, ASN144-HD22, ARG145-N, ARG145-H, ARG145-CA, ARG145-HA, ARG145-C, ARG145-O, ARG145-CB, ARG145-HB2, ARG145-HB3, ARG145-CG, ARG145-HG2, ARG145-HG3, ARG145-CD, ARG145-HD2, ARG145-HD3, ARG145-NE, ARG145-HE, ARG145-CZ, ARG145-NH1, ARG145-HH11, ARG145-HH12, ARG145-NH2, ARG145-HH21, ARG145-HH22, ALA146-N, ALA146-H, ALA146-CA, ALA146-HA, ALA146-C, ALA146-O, ALA146-CB, ALA146-HB1, ALA146-HB2, ALA146-HB3, LYS147-N, LYS147-H, LYS147-CA, LYS147-HA, LYS147-C, LYS147-O, LYS147-CB, LYS147-HB2, LYS147-HB3, LYS147-CG, LYS147-HG2, LYS147-HG3, LYS147-CD, LYS147-HD2, LYS147-HD3, LYS147-CE, LYS147-HE2, LYS147-HE3, LYS147-NZ, LYS147-HZ1, LYS147-HZ2, LYS147-HZ3, ARG148-N, ARG148-H, ARG148-CA, ARG148-HA, ARG148-C, ARG148-O, ARG148-CB, ARG148-HB2, ARG148-HB3, ARG148-CG, ARG148-HG2, ARG148-HG3, ARG148-CD, ARG148-HD2, ARG148-HD3, ARG148-NE, ARG148-HE, ARG148-CZ, ARG148-NH1, ARG148-HH11, ARG148-HH12, ARG148-NH2, ARG148-HH21, ARG148-HH22, VAL149-N, VAL149-H, VAL149-CA, VAL149-HA, VAL149-C, VAL149-O, VAL149-CB, VAL149-HB, VAL149-CG1, VAL149-HG11, VAL149-HG12, VAL149-HG13, VAL149-CG2, VAL149-HG21, VAL149-HG22, VAL149-HG23, ILE150-N, ILE150-H, ILE150-CA, ILE150-HA, ILE150-C, ILE150-O, ILE150-CB, ILE150-HB, ILE150-CG1, ILE150-HG12, ILE150-HG13, ILE150-CG2, ILE150-HG21, ILE150-HG22, ILE150-HG23, ILE150-CD1, ILE150-HD11, ILE150-HD12, ILE150-HD13, THR151-N, THR151-H, THR151-CA, THR151-HA, THR151-C, THR151-O, THR151-CB, THR151-HB, THR151-OG1, THR151-HG1, THR151-CG2, THR151-HG21, THR151-HG22, THR151-HG23, THR152-N, THR152-H, THR152-CA, THR152-HA, THR152-C, THR152-O, THR152-CB, THR152-HB, THR152-OG1, THR152-HG1, THR152-CG2, THR152-HG21, THR152-HG22, THR152-HG23, PHE153-N, PHE153-H, PHE153-CA, PHE153-HA, PHE153-C, PHE153-O, PHE153-CB, PHE153-HB2, PHE153-HB3, PHE153-CG, PHE153-CD1, PHE153-HD1, PHE153-CD2, PHE153-HD2, PHE153-CE1, PHE153-HE1, PHE153-CE2, PHE153-HE2, PHE153-CZ, PHE153-HZ, ARG154-N, ARG154-H, ARG154-CA, ARG154-HA, ARG154-C, ARG154-O, ARG154-CB, ARG154-HB2, ARG154-HB3, ARG154-CG, ARG154-HG2, ARG154-HG3, ARG154-CD, ARG154-HD2, ARG154-HD3, ARG154-NE, ARG154-HE, ARG154-CZ, ARG154-NH1, ARG154-HH11, ARG154-HH12, ARG154-NH2, ARG154-HH21, ARG154-HH22, THR155-N, THR155-H, THR155-CA, THR155-HA, THR155-C, THR155-O, THR155-CB, THR155-HB, THR155-OG1, THR155-HG1, THR155-CG2, THR155-HG21, THR155-HG22, THR155-HG23, GLY156-N, GLY156-H, GLY156-CA, GLY156-HA2, GLY156-HA3, GLY156-C, GLY156-O, THR157-N, THR157-H, THR157-CA, THR157-HA, THR157-C, THR157-O, THR157-CB, THR157-HB, THR157-OG1, THR157-HG1, THR157-CG2, THR157-HG21, THR157-HG22, THR157-HG23, TRP158-N, TRP158-H, TRP158-CA, TRP158-HA, TRP158-C, TRP158-O, TRP158-CB, TRP158-HB2, TRP158-HB3, TRP158-CG, TRP158-CD1, TRP158-HD1, TRP158-CD2, TRP158-NE1, TRP158-HE1, TRP158-CE2, TRP158-CE3, TRP158-HE3, TRP158-CZ2, TRP158-HZ2, TRP158-CZ3, TRP158-HZ3, TRP158-CH2, TRP158-HH2, ASP159-N, ASP159-H, ASP159-CA, ASP159-HA, ASP159-C, ASP159-O, ASP159-CB, ASP159-HB2, ASP159-HB3, ASP159-CG, ASP159-OD1, ASP159-OD2, ALA160-N, ALA160-H, ALA160-CA, ALA160-HA, ALA160-C, ALA160-O, ALA160-CB, ALA160-HB1, ALA160-HB2, ALA160-HB3, TYR161-N, TYR161-H, TYR161-CA, TYR161-HA, TYR161-C, TYR161-O, TYR161-CB, TYR161-HB2, TYR161-HB3, TYR161-CG, TYR161-CD1, TYR161-HD1, TYR161-CD2, TYR161-HD2, TYR161-CE1, TYR161-HE1, TYR161-CE2, TYR161-HE2, TYR161-CZ, TYR161-OH, TYR161-HH, LYS162-N, LYS162-H, LYS162-CA, LYS162-HA, LYS162-C, LYS162-O, LYS162-CB, LYS162-HB2, LYS162-HB3, LYS162-CG, LYS162-HG2, LYS162-HG3, LYS162-CD, LYS162-HD2, LYS162-HD3, LYS162-CE, LYS162-HE2, LYS162-HE3, LYS162-NZ, LYS162-HZ1, LYS162-HZ2, LYS162-HZ3, ASN163-N, ASN163-H, ASN163-CA, ASN163-HA, ASN163-C, ASN163-O, ASN163-CB, ASN163-HB2, ASN163-HB3, ASN163-CG, ASN163-OD1, ASN163-ND2, ASN163-HD21, ASN163-HD22, LEU164-N, LEU164-H, LEU164-CA, LEU164-HA, LEU164-C, LEU164-O, LEU164-CB, LEU164-HB2, LEU164-HB3, LEU164-CG, LEU164-HG, LEU164-CD1, LEU164-HD11, LEU164-HD12, LEU164-HD13, LEU164-CD2, LEU164-HD21, LEU164-HD22, LEU164-HD23, LEU164-OXT]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Residue(残基)についても同じことが言えます。"
      ],
      "metadata": {
        "id": "WA4HwPQPM0xX"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print('2番目の残基: %s' % traj.topology.residue(1))\n",
        "print('すべての残基: %s' % [residue for residue in traj.topology.residues])"
      ],
      "metadata": {
        "id": "v7xYIW1yGoxi",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "5f07b907-2e76-4d84-c133-cc70a0c21980"
      },
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "2番目の残基: ASN2\n",
            "すべての残基: [MET1, ASN2, ILE3, PHE4, GLU5, MET6, LEU7, ARG8, ILE9, ASP10, GLU11, GLY12, LEU13, ARG14, LEU15, LYS16, ILE17, TYR18, LYS19, ASP20, THR21, GLU22, GLY23, TYR24, TYR25, THR26, ILE27, GLY28, ILE29, GLY30, HIS31, LEU32, LEU33, THR34, LYS35, SER36, PRO37, SER38, LEU39, ASN40, ALA41, ALA42, LYS43, SER44, GLU45, LEU46, ASP47, LYS48, ALA49, ILE50, GLY51, ARG52, ASN53, CYS54, ASN55, GLY56, VAL57, ILE58, THR59, LYS60, ASP61, GLU62, ALA63, GLU64, LYS65, LEU66, PHE67, ASN68, GLN69, ASP70, VAL71, ASP72, ALA73, ALA74, VAL75, ARG76, GLY77, ILE78, LEU79, ARG80, ASN81, ALA82, LYS83, LEU84, LYS85, PRO86, VAL87, TYR88, ASP89, SER90, LEU91, ASP92, ALA93, VAL94, ARG95, ARG96, CYS97, ALA98, LEU99, ILE100, ASN101, MET102, VAL103, PHE104, GLN105, MET106, GLY107, GLU108, THR109, GLY110, VAL111, ALA112, GLY113, PHE114, THR115, ASN116, SER117, LEU118, ARG119, MET120, LEU121, GLN122, GLN123, LYS124, ARG125, TRP126, ASP127, GLU128, ALA129, ALA130, VAL131, ASN132, LEU133, ALA134, LYS135, SER136, ARG137, TRP138, TYR139, ASN140, GLN141, THR142, PRO143, ASN144, ARG145, ALA146, LYS147, ARG148, VAL149, ILE150, THR151, THR152, PHE153, ARG154, THR155, GLY156, THR157, TRP158, ASP159, ALA160, TYR161, LYS162, ASN163, LEU164]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "さらに、すべての原子と残基もオブジェクトであり、それぞれが独自のpropertyを持っています。以下は、そのうちのいくつかを説明するシンプルな例です。"
      ],
      "metadata": {
        "id": "EUdR5t_qU0lq"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "atom = topology.atom(10)\n",
        "print('''こんにちは！私は %s 番目の原子で、名前は %s です。\n",
        "私は %s 原子で、%s 個の結合を持っています。\n",
        "私は %s 残基の一部です。''' % (atom.index, atom.name, atom.element.name, atom.n_bonds, atom.residue.name))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "VzRnRE_GUwh-",
        "outputId": "d17b3e11-672d-4d84-ba32-aca2669f2554"
      },
      "execution_count": 9,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "こんにちは！私は 10 番目の原子で、名前は HB3 です。\n",
            "私は hydrogen 原子で、1 個の結合を持っています。\n",
            "私は MET 残基の一部です。\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "また、atom.is_sidechainやresidue.is_proteinのようなより複雑なプロパティもあります。これらを利用することで、よりパワフルな選択が可能になります。"
      ],
      "metadata": {
        "id": "M8lupifvVSK6"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "これらのプロパティをPythonのフィルタリスト機能と組み合わせると強力です。たとえば、分子の側鎖にあるすべての Carbon atom のインデックスを求めたいとしましょう。こんな感じで実現できます。"
      ],
      "metadata": {
        "id": "jDbS6henW0Uq"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print([atom.index for atom in topology.atoms if atom.element.symbol == 'C' and atom.is_sidechain])"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "VOvvXd31U_Ci",
        "outputId": "f6c2bf28-8579-4c47-e285-9aaec3ad25ab"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[6, 9, 13, 23, 26, 37, 39, 43, 46, 56, 59, 60, 62, 64, 66, 68, 76, 79, 82, 91, 94, 98, 108, 111, 113, 117, 127, 130, 133, 138, 151, 153, 157, 160, 170, 173, 182, 185, 188, 204, 207, 209, 213, 223, 226, 229, 234, 247, 250, 252, 256, 266, 269, 272, 275, 288, 290, 294, 297, 307, 310, 311, 313, 315, 318, 320, 328, 331, 334, 337, 350, 353, 362, 366, 376, 379, 382, 398, 401, 402, 404, 406, 409, 411, 419, 422, 423, 425, 427, 430, 432, 440, 444, 454, 456, 460, 463, 480, 482, 486, 489, 506, 511, 512, 515, 523, 526, 528, 532, 542, 545, 547, 551, 561, 565, 575, 578, 581, 584, 597, 605, 610, 613, 622, 633, 636, 638, 642, 652, 655, 666, 676, 686, 689, 692, 695, 708, 719, 722, 725, 734, 737, 739, 743, 753, 756, 765, 768, 771, 774, 787, 797, 799, 803, 806, 823, 826, 829, 834, 847, 850, 861, 872, 875, 893, 895, 899, 909, 911, 915, 918, 928, 932, 942, 945, 948, 951, 964, 967, 976, 979, 982, 991, 1001, 1004, 1007, 1016, 1019, 1022, 1025, 1038, 1041, 1043, 1047, 1057, 1060, 1061, 1063, 1065, 1067, 1069, 1077, 1080, 1091, 1094, 1097, 1108, 1111, 1120, 1122, 1126, 1136, 1139, 1148, 1158, 1168, 1170, 1174, 1184, 1187, 1190, 1195, 1215, 1217, 1221, 1224, 1234, 1237, 1239, 1243, 1253, 1256, 1259, 1264, 1277, 1280, 1291, 1301, 1304, 1307, 1310, 1323, 1326, 1328, 1332, 1342, 1345, 1348, 1351, 1361, 1366, 1369, 1378, 1380, 1384, 1394, 1397, 1398, 1400, 1402, 1405, 1407, 1415, 1418, 1427, 1438, 1441, 1443, 1447, 1457, 1460, 1469, 1479, 1481, 1485, 1495, 1498, 1501, 1506, 1519, 1522, 1525, 1530, 1543, 1554, 1564, 1567, 1569, 1573, 1583, 1585, 1589, 1592, 1602, 1605, 1616, 1619, 1623, 1633, 1635, 1639, 1649, 1652, 1653, 1655, 1657, 1659, 1661, 1669, 1672, 1675, 1686, 1689, 1693, 1710, 1713, 1716, 1725, 1729, 1746, 1748, 1752, 1762, 1779, 1782, 1783, 1785, 1787, 1789, 1791, 1799, 1803, 1813, 1816, 1827, 1838, 1841, 1843, 1847, 1857, 1860, 1863, 1868, 1881, 1884, 1888, 1898, 1901, 1903, 1907, 1917, 1920, 1923, 1934, 1937, 1940, 1951, 1954, 1957, 1960, 1973, 1976, 1979, 1984, 1997, 2000, 2001, 2005, 2006, 2007, 2009, 2011, 2013, 2021, 2024, 2033, 2036, 2039, 2048, 2058, 2068, 2070, 2074, 2084, 2087, 2098, 2101, 2103, 2107, 2117, 2127, 2130, 2133, 2136, 2149, 2160, 2163, 2166, 2171, 2184, 2187, 2188, 2192, 2193, 2194, 2196, 2198, 2200, 2208, 2211, 2212, 2214, 2216, 2219, 2221, 2229, 2232, 2243, 2246, 2249, 2260, 2264, 2271, 2276, 2279, 2288, 2291, 2302, 2305, 2308, 2313, 2326, 2336, 2339, 2342, 2345, 2358, 2361, 2364, 2369, 2382, 2384, 2388, 2398, 2400, 2404, 2407, 2417, 2421, 2431, 2435, 2445, 2448, 2449, 2451, 2453, 2455, 2457, 2465, 2468, 2471, 2476, 2489, 2493, 2510, 2514, 2524, 2527, 2528, 2532, 2533, 2534, 2536, 2538, 2540, 2548, 2551, 2560, 2570, 2573, 2574, 2576, 2578, 2581, 2583, 2591, 2594, 2597, 2600, 2613, 2616, 2627, 2630, 2632, 2636]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "または、最初の Chain のすべての 偶数インデックスの Residue (残基) を求めることもできます（ただし、この例では1つの鎖しかありません）"
      ],
      "metadata": {
        "id": "Zdf8-DhvXIhj"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print([residue for residue in topology.chain(0).residues if residue.index % 2 == 0])"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ke4_W8fSXA-M",
        "outputId": "d0a65bd7-6042-4b9c-effc-9dc0ecdb713c"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[MET1, ILE3, GLU5, LEU7, ILE9, GLU11, LEU13, LEU15, ILE17, LYS19, THR21, GLY23, TYR25, ILE27, ILE29, HIS31, LEU33, LYS35, PRO37, LEU39, ALA41, LYS43, GLU45, ASP47, ALA49, GLY51, ASN53, ASN55, VAL57, THR59, ASP61, ALA63, LYS65, PHE67, GLN69, VAL71, ALA73, VAL75, GLY77, LEU79, ASN81, LYS83, LYS85, VAL87, ASP89, LEU91, ALA93, ARG95, CYS97, LEU99, ASN101, VAL103, GLN105, GLY107, THR109, VAL111, GLY113, THR115, SER117, ARG119, LEU121, GLN123, ARG125, ASP127, ALA129, VAL131, LEU133, LYS135, ARG137, TYR139, GLN141, PRO143, ARG145, LYS147, VAL149, THR151, PHE153, THR155, THR157, ASP159, TYR161, ASN163]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "上記のようなフィルタリストのプログラミングに迷っている場合、MDTrajはPyMolやVMDに似た豊富な原子選択言語も提供しています。これには、topology.selectを使用してアクセスできます。最後の2つの残基のすべての原子を探してみましょう。\n",
        "\n",
        "原子選択構文の詳細については、[ドキュメント](https://www.mdtraj.org/1.9.7/atom_selection.html)をご覧ください。"
      ],
      "metadata": {
        "id": "ADiayc9pXote"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print(topology.select('resid 1 to 2'))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "2pgEZ3UXXmdJ",
        "outputId": "1058f492-bde4-4099-b8e2-f328579ab322"
      },
      "execution_count": 12,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42\n",
            " 43 44 45 46 47 48 49 50 51]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "より複雑な選択も可能です。以下では、主鎖のすべての Nitrogen atom を選択します。"
      ],
      "metadata": {
        "id": "YzbM-88GXvli"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print(topology.select('name N and backbone'))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "G0zRE6byXsN2",
        "outputId": "ffc8c567-7b61-4b38-e14c-700211756db8"
      },
      "execution_count": 13,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[   0   19   33   52   72   87  104  123  147  166  178  193  200  219\n",
            "  243  262  284  303  324  346  358  372  387  394  415  436  450  469\n",
            "  476  495  502  519  538  557  571  593  604  618  629  648  662  672\n",
            "  682  704  715  730  749  761  783  793  812  819  843  857  868  882\n",
            "  889  905  924  938  960  972  987  997 1012 1034 1053 1073 1087 1104\n",
            " 1116 1132 1144 1154 1164 1180 1204 1211 1230 1249 1273 1287 1297 1319\n",
            " 1338 1360 1374 1390 1411 1423 1434 1453 1465 1475 1491 1515 1539 1550\n",
            " 1560 1579 1598 1612 1629 1645 1665 1682 1699 1706 1721 1735 1742 1758\n",
            " 1768 1775 1795 1809 1823 1834 1853 1877 1894 1913 1930 1947 1969 1993\n",
            " 2017 2029 2044 2054 2064 2080 2094 2113 2123 2145 2156 2180 2204 2225\n",
            " 2239 2256 2270 2284 2298 2322 2332 2354 2378 2394 2413 2427 2441 2461\n",
            " 2485 2499 2506 2520 2544 2556 2566 2587 2609 2623]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "これらの結果を生成するコードを見たい場合は、select_expressionを使用できます。これは、atom selection コードの文字列表現を返します。"
      ],
      "metadata": {
        "id": "iYFaXVIYX7hE"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "selection = topology.select_expression('name CA and resid 1 to 2')\n",
        "print(selection)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "dSPlam1LX3TT",
        "outputId": "21c707bb-49bb-412e-9007-11150f4bdb1e"
      },
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[atom.index for atom in topology.atoms if ((atom.name == 'CA') and (1 <= atom.residue.index <= 2))\n",
            "]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "uCkupK9HYBSn"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}