colabcctbxsnips.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "source": [
        "# Install the snippet notebook\n",
        "\n",
        "Store the snippet notebook on your Google Drive. Then copy the updated URL to \n",
        "Tools --> Settings --> Site --> Custom snippet notebook URL. Then when you open \n",
        "a new notebook, the snippets will be available.\n",
        "\n",
        "1.   File --> Save Copy in Drive\n",
        "2.   Tools --> Settings --> Site --> Custom snippet notebook URL\n"
      ],
      "metadata": {
        "id": "jda5IgVWoB0v"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Install cctbx (1/2)\n",
        "\n",
        "This prodedure is adapted from Billy Poon's example: \n",
        "https://github.com/phenix-project/Colabs/blob/main/Start_cctbx.ipynb\n",
        "\n",
        "The installation of cctbx involves a two step process:\n",
        "\n",
        "1.   Install condacolab\n",
        "2.   Install cctbx with mamba and move certain libraries to better locations.\n",
        "\n",
        "The module condacolab install conda and mamba. Mamba is faster.\n",
        "A progress bar will be updated as the snippet runs.\n",
        "\n",
        "Completion of the first step will involve the generation of the error message:\n",
        "\n",
        "**Your session crashed for an unknown reason.** \n",
        "\n",
        "Click on the X to close the error message \n",
        "before running **Install cctbx (2/2)**\n"
      ],
      "metadata": {
        "id": "cfsInLhL4n5O"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from IPython.utils import io\n",
        "import tqdm.notebook\n",
        "\n",
        "total = 50\n",
        "with tqdm.notebook.tqdm(total=total) as pbar:\n",
        "    with io.capture_output() as captured:\n",
        "        !pip install -q condacolab\n",
        "        pbar.update(10)\n",
        "\n",
        "        import condacolab\n",
        "        condacolab.install()\n",
        "        pbar.update(40)   "
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "ft3z-TiIKKmM"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Install cctbx (2/2)\n",
        "\n",
        "Use mamba to install cctbx-base."
      ],
      "metadata": {
        "id": "ZEEAGVu-4wfO"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "\n",
        "with tqdm.notebook.tqdm(total=total) as pbar:\n",
        "    with io.capture_output() as captured:\n",
        "        !mamba install -q cctbx-base\n",
        "        pbar.update(10)\n",
        "\n",
        "        # conda installs ${CONDA_PREFIX}/share/cctbx into /usr/local instead of /usr\n",
        "        !cp -af /usr/local/share/cctbx /usr/share/\n",
        "\n",
        "        # Add libraries to the sys.path\n",
        "        import sys\n",
        "        for d in ['/usr/local/lib/python3.7/lib-dynload', '/usr/local/lib']:\n",
        "          if d not in sys.path:\n",
        "            sys.path.insert(0, d)\n",
        "        pbar.update(10)\n",
        "\n",
        "        # Check installation\n",
        "        import os\n",
        "        if os.path.isdir('/usr/local/share/cctbx') \\\n",
        "          and '/usr/local/lib/python3.7/lib-dynload' in sys.path \\\n",
        "          and '/usr/local/lib' in sys.path:\n",
        "          print('Finished installing cctbx-base')\n",
        "        else:\n",
        "          raise RuntimeError('There was an error fixing up the installation of cctbx-base')\n",
        "        pbar.update(30)"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "TFtfP--2Kdnn"
      }
    },
    {
      "cell_type": "markdown",
      "source": [],
      "metadata": {
        "id": "-fqGpICEqWz8"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Test cctbx\n",
        "\n",
        "- The code prints three sets of parameter values below the code block.\n"
      ],
      "metadata": {
        "id": "ZnGPACpx5OM_"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from cctbx import crystal\n",
        "from cctbx import miller\n",
        "\n",
        "ms = miller.build_set(\n",
        "    crystal_symmetry=crystal.symmetry(\n",
        "        space_group_symbol=\"P4\",\n",
        "        unit_cell=(150.8,150.8,250.4,90.0,90.0,90.0)),\n",
        "    anomalous_flag=False,\n",
        "    d_min=3.4)\n",
        "msu = ms.map_to_asu()\n",
        "[print(hkl) for hkl in msu.indices()]\n",
        "print(msu.show_comprehensive_summary())"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "jug2vYAgLpQF"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Copy mtz files from Google Drive\n",
        "\n",
        "Load mtz file(s) that you want to analyze onto Google Drive in a created-folder called `dataFiles` and then mount the Google Drive.\n",
        "\n"
      ],
      "metadata": {
        "id": "FlBXN5gvv4OE"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from google.colab import drive\n",
        "drive.mount(\"/content/drive\")\n",
        "%shell cp ./drive/MyDrive/dataFiles/*.mtz ."
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "DvnoFLjzDv0F"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# iotbx extractCrystalSymmetry\n",
        "\n",
        "- Extract crystal symmetry from mtz file.\n",
        "- To fetch the X-ray data in a cif file and convert to a mtz file, run the following command on your local computer after installing phenix.\n",
        "\n",
        "```bash\n",
        "phenix.fetch_pdb --mtz 3nd4\n",
        "```\n",
        "\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from __future__ import absolute_import, division, print_function\n",
        "from iotbx import mtz\n",
        "from cctbx import crystal\n",
        "\n",
        "def extract_from(file_name):\n",
        "  mtz_object = mtz.object(file_name=file_name)\n",
        "  assert mtz_object.n_symmetry_matrices() > 0\n",
        "  return mtz_object.crystals()[0].crystal_symmetry()\n",
        "  \n",
        " extract_from(file_name=\"${1:3nd4}.mtz\")\n",
        " ```\n",
        "\n"
      ],
      "metadata": {
        "id": "EVQyieZ8qcFD"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from __future__ import absolute_import, division, print_function\n",
        "from iotbx import mtz\n",
        "from cctbx import crystal\n",
        "\n",
        "def extract_from(file_name):\n",
        "  mtz_object = mtz.object(file_name=file_name)\n",
        "  assert mtz_object.n_symmetry_matrices() > 0\n",
        "  return mtz_object.crystals()[0].crystal_symmetry()\n",
        "  \n",
        "extract_from(file_name=\"3nd4.mtz\")\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "kbljp2mmqbWr"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# iotbx fetchAtomcCif\n",
        "\n",
        "- Fetch  atomic coordinates from RCSB in mmCIF format.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"${1:3nd4}\", data_type=\"xray\", mirror=\"rcsb\", format=\"cif\", log=sys.stdout)\n",
        "```"
      ],
      "metadata": {
        "id": "J4rFQzYhsbZ7"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"3nd4\",data_type=\"xray\", mirror=\"rcsb\", format=\"cif\", log=sys.stdout)\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "usgHLXiDtBdG"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "## iotbx fetchFASTA\n",
        "\n",
        "- Fetch fasta file from RCSB.\n",
        "\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"3nd4\",data_type=\"pdb\", mirror=\"rcsb\", format=\"pdb\", log=sys.stdout)\n",
        "```"
      ],
      "metadata": {
        "id": "6_KJwOWbtFtI"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"3nd4\",data_type=\"pdb\", mirror=\"rcsb\", format=\"pdb\", log=sys.stdout)\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "Kzd_FAWmtbOf"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# iotbx fetchPDB\n",
        "\n",
        "- Fetch pdb file from RCSB in PDB format.\n",
        "\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"${1:3nd4}\",data_type=\"pdb\", mirror=\"rcsb\", format=\"pdb\", log=sys.stdout)\n",
        "```"
      ],
      "metadata": {
        "id": "EoQhQqQCtu_3"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"3nd4\",data_type=\"pdb\", mirror=\"rcsb\", format=\"pdb\", log=sys.stdout)\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "V5UBJJ3otoDx"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# iotbx fetchXrayCif\n",
        "\n",
        "- Fetch X-ray data from RCSB in mmCIF format.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"${1:3nd4}\", data_type=\"xray\", mirror=\"rcsb\", format=\"cif\", log=sys.stdout)\n",
        "```"
      ],
      "metadata": {
        "id": "KgeOzIYYuRaW"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.pdb.fetch import get_pdb\n",
        "import sys\n",
        "get_pdb(id=\"3nd4\", data_type=\"xray\", mirror=\"rcsb\", format=\"cif\", log=sys.stdout)\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "WdquvihZuyjJ"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# iotbx symmetryFromPDB\n",
        "\n",
        "- Print the symmetry from a PDB file.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "import iotbx\n",
        "iotbx.pdb.crystal_symmetry_from_pdb.extract_from(\"${1:3nd4}.pdb\")\n",
        "```\n"
      ],
      "metadata": {
        "id": "nKBTJVCgvE7F"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import iotbx\n",
        "iotbx.pdb.crystal_symmetry_from_pdb.extract_from(\"3nd4.pdb\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "nGGXVjP3vvqv"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays changeMtzColumns\n",
        "\n",
        "- Read in mtz file from current directory and write out with fewer columns.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_in = any_reflection_file(\"${1:/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz}\")\n",
        "\n",
        "miller_arrays = hkl_in.as_miller_arrays()\n",
        "\n",
        "i_obs =  miller_arrays[3]\n",
        "r_free_flags = miller_arrays[0]\n",
        "f_obs = i_obs.f_sq_as_f()\n",
        "\n",
        "mtz_dataset = i_obs.as_mtz_dataset(column_root_label=\"I\")\n",
        "mtz_dataset.add_miller_array(f_obs, column_root_label=\"F\")\n",
        "mtz_dataset.add_miller_array(r_free_flags,column_root_label=\"${2:FreeR_flag}\")\n",
        "mtz_dataset.mtz_object().write(\"${3:loxodata.mtz}\")\n",
        "```"
      ],
      "metadata": {
        "id": "6vkkOUG45LqT"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_in = any_reflection_file(\"ret_blu.mtz\")\n",
        "\n",
        "miller_arrays = hkl_in.as_miller_arrays()\n",
        "\n",
        "i_obs =  miller_arrays[3]\n",
        "r_free_flags = miller_arrays[0]\n",
        "f_obs = i_obs.f_sq_as_f()\n",
        "\n",
        "mtz_dataset = i_obs.as_mtz_dataset(column_root_label=\"I\")\n",
        "mtz_dataset.add_miller_array(f_obs, column_root_label=\"F\")\n",
        "mtz_dataset.add_miller_array(r_free_flags,column_root_label=\"FreeR_flag\")\n",
        "mtz_dataset.mtz_object().write(\"loxodata.mtz\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "4Tpz8bxQ6NGh"
      }
    },
    {
      "cell_type": "markdown",
      "source": [],
      "metadata": {
        "id": "y7fMKwcPAQCf"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays CNS2mtz\n",
        "\n",
        "- Convert CNS reflection file into an mtz file.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx import reflection_file_reader\n",
        "import os\n",
        "reflection_file = reflection_file_reader.any_reflection_file(file_name=os.path.expandvars(\"${1:\\$CNS_SOLVE/doc/html/tutorial/data/pen/scale.hkl}\"))\n",
        "from cctbx import crystal\n",
        "crystal_symmetry = crystal.symmetry( unit_cell=(${2:97.37, 46.64, 65.47, 90, 115.4, 90}), space_group_symbol=\"${3:C2}\")\n",
        "miller_arrays = reflection_file.as_miller_arrays( crystal_symmetry=crystal_symmetry)\n",
        "mtz_dataset = None\n",
        "for miller_array in miller_arrays:\n",
        "    if (mtz_dataset is None):\n",
        "        mtz_dataset = miller_array.as_mtz_dataset(\n",
        "            column_root_label=miller_array.info().labels[0]) \n",
        "    else:\n",
        "        mtz_dataset.add_miller_array(\n",
        "            miller_array=miller_array, \n",
        "            column_root_label=miller_array.info().labels[0])\n",
        "mtz_object = mtz_dataset.mtz_object() \n",
        "mtz_object.show_summary()\n",
        "```"
      ],
      "metadata": {
        "id": "PqqXarYqAR-e"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx import reflection_file_reader\n",
        "import os\n",
        "reflection_file = reflection_file_reader.any_reflection_file(file_name=os.path.expandvars(\"\\$CNS_SOLVE/doc/html/tutorial/data/pen/scale.hkl\"))\n",
        "from cctbx import crystal\n",
        "crystal_symmetry = crystal.symmetry( unit_cell=(97.37, 46.64, 65.47, 90, 115.4, 90), space_group_symbol=\"C2\")\n",
        "miller_arrays = reflection_file.as_miller_arrays( crystal_symmetry=crystal_symmetry)\n",
        "mtz_dataset = None\n",
        "for miller_array in miller_arrays:\n",
        "    if (mtz_dataset is None):\n",
        "        mtz_dataset = miller_array.as_mtz_dataset(\n",
        "            column_root_label=miller_array.info().labels[0]) \n",
        "    else:\n",
        "        mtz_dataset.add_miller_array(\n",
        "            miller_array=miller_array, \n",
        "            column_root_label=miller_array.info().labels[0])\n",
        "mtz_object = mtz_dataset.mtz_object() \n",
        "mtz_object.show_summary()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "Y3FcAnzXAQel"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays computeAllPossibleMillerIndices\n",
        "\n",
        "- Compute all possible Miller indices.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from cctbx import miller\n",
        "\n",
        "def generate_reflection_indices(uc, dmin):\n",
        "    maxh, maxk, maxl = uc.max_miller_indices(dmin)\n",
        "    indices = []\n",
        "    for h in range(-maxh, maxh + 1):\n",
        "        for k in range(-maxk, maxk + 1):\n",
        "            for l in range(-maxl, maxl + 1):\n",
        "                if h == 0 and k == 0 and l == 0:\n",
        "                    continue\n",
        "                if uc.d((h, k, l)) < dmin:\n",
        "                    continue\n",
        "        indices.append((h, k, l))\n",
        "    return indices\n",
        "    \n",
        "uc=(${1:5.4307,5.4307,5.4307,90.00,90.0,90.00})\n",
        "dmin=${2:1.0}\n",
        "```"
      ],
      "metadata": {
        "id": "K-PdaFeqMflX"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from cctbx import miller\n",
        "\n",
        "def generate_reflection_indices(uc, dmin):\n",
        "    maxh, maxk, maxl = uc.max_miller_indices(dmin)\n",
        "\n",
        "    indices = []\n",
        "    for h in range(-maxh, maxh + 1):\n",
        "        for k in range(-maxk, maxk + 1):\n",
        "            for l in range(-maxl, maxl + 1):\n",
        "                if h == 0 and k == 0 and l == 0:\n",
        "                    continue\n",
        "                if uc.d((h, k, l)) < dmin:\n",
        "                    continue\n",
        "        indices.append((h, k, l))\n",
        "    return indices\n",
        "    \n",
        "uc=(5.4307,5.4307,5.4307,90.00,90.0,90.00)\n",
        "dmin=1.0\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "VKTWj4MAMgVW"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays computeMillerIndicesInASU \n",
        "\n",
        "- Compute all possible Miller indices in the asymmetric (ASU).\n",
        "\n",
        "- The `$`'s below marks a site for editing.\n",
        "\n",
        "```bash\n",
        "from cctbx import miller\n",
        "import cctbx\n",
        "from cctbx import crystal\n",
        "\n",
        "ms = miller.build_set(\n",
        "    crystal_symmetry=crystal.symmetry(\n",
        "        space_group_symbol=\"${1:I432}\",\n",
        "        unit_cell=(\"2:{54.4,54.4,54.4,90.00,90.0,90.00}\") ),\n",
        "    anomalous_flag=${3:False},\n",
        "    d_min=${4:0.4})\n",
        "\n",
        "# map the reflections to the asu and print\n",
        "  \n",
        "msu = ms.map_to_asu()\n",
        "[print(hkl2) for hkl2 in msu.indices()]\n",
        "```"
      ],
      "metadata": {
        "id": "ccemjjFlNhnO"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from cctbx import miller\n",
        "import cctbx\n",
        "from cctbx import crystal\n",
        "\n",
        "ms = miller.build_set(\n",
        "    crystal_symmetry=crystal.symmetry(\n",
        "        space_group_symbol=\"I432\",\n",
        "        unit_cell=(\"54.4,54.4,54.4,90.00,90.0,90.00\") ),\n",
        "    anomalous_flag=False,\n",
        "    d_min=5.0)\n",
        "\n",
        "for hkl in ms.indices():\n",
        "    print(hkl)\n",
        "\n",
        "# map the reflections to the asu and print\n",
        "msu = ms.map_to_asu()\n",
        "[print(hkl2) for hkl2 in msu.indices()]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "xofyYtthONwE"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays IndicesInUnitCell\n",
        "\n",
        "- Build miller indices given unit cell and resolution limit.\n",
        "\n",
        "- The `$` below marks a site for editing."
      ],
      "metadata": {
        "id": "zRKyAaf7RfyL"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from cctbx import crystal\n",
        "from cctbx import miller\n",
        "\n",
        "ms = miller.build_set(\n",
        "    crystal_symmetry=crystal.symmetry(\n",
        "        space_group_symbol=\"P4\",\n",
        "        unit_cell=(150.8,150.8,250.4,90.0,90.0,90.0)),\n",
        "    anomalous_flag=False,\n",
        "    d_min=10.4)\n",
        "msu = ms.map_to_asu()\n",
        "[print(hkl) for hkl in msu.indices()]\n",
        "print(msu.show_comprehensive_summary())"
      ],
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
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            "(2, 5, 21)\n",
            "(2, 5, 22)\n",
            "(2, 6, 0)\n",
            "(2, 6, 1)\n",
            "(2, 6, 2)\n",
            "(2, 6, 3)\n",
            "(2, 6, 4)\n",
            "(2, 6, 5)\n",
            "(2, 6, 6)\n",
            "(2, 6, 7)\n",
            "(2, 6, 8)\n",
            "(2, 6, 9)\n",
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            "(2, 6, 11)\n",
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            "(2, 6, 16)\n",
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            "(2, 6, 18)\n",
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            "(2, 7, 0)\n",
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            "(2, 7, 2)\n",
            "(2, 7, 3)\n",
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            "(2, 7, 6)\n",
            "(2, 7, 7)\n",
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            "(2, 7, 10)\n",
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            "(2, 7, 14)\n",
            "(2, 7, 15)\n",
            "(2, 7, 16)\n",
            "(2, 7, 17)\n",
            "(2, 7, 18)\n",
            "(2, 7, 19)\n",
            "(2, 7, 20)\n",
            "(2, 8, 0)\n",
            "(2, 8, 1)\n",
            "(2, 8, 2)\n",
            "(2, 8, 3)\n",
            "(2, 8, 4)\n",
            "(2, 8, 5)\n",
            "(2, 8, 6)\n",
            "(2, 8, 7)\n",
            "(2, 8, 8)\n",
            "(2, 8, 9)\n",
            "(2, 8, 10)\n",
            "(2, 8, 11)\n",
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            "(2, 8, 13)\n",
            "(2, 8, 14)\n",
            "(2, 8, 15)\n",
            "(2, 8, 16)\n",
            "(2, 8, 17)\n",
            "(2, 8, 18)\n",
            "(2, 8, 19)\n",
            "(2, 9, 0)\n",
            "(2, 9, 1)\n",
            "(2, 9, 2)\n",
            "(2, 9, 3)\n",
            "(2, 9, 4)\n",
            "(2, 9, 5)\n",
            "(2, 9, 6)\n",
            "(2, 9, 7)\n",
            "(2, 9, 8)\n",
            "(2, 9, 9)\n",
            "(2, 9, 10)\n",
            "(2, 9, 11)\n",
            "(2, 9, 12)\n",
            "(2, 9, 13)\n",
            "(2, 9, 14)\n",
            "(2, 9, 15)\n",
            "(2, 9, 16)\n",
            "(2, 9, 17)\n",
            "(2, 9, 18)\n",
            "(2, 10, 0)\n",
            "(2, 10, 1)\n",
            "(2, 10, 2)\n",
            "(2, 10, 3)\n",
            "(2, 10, 4)\n",
            "(2, 10, 5)\n",
            "(2, 10, 6)\n",
            "(2, 10, 7)\n",
            "(2, 10, 8)\n",
            "(2, 10, 9)\n",
            "(2, 10, 10)\n",
            "(2, 10, 11)\n",
            "(2, 10, 12)\n",
            "(2, 10, 13)\n",
            "(2, 10, 14)\n",
            "(2, 10, 15)\n",
            "(2, 10, 16)\n",
            "(2, 10, 17)\n",
            "(2, 11, 0)\n",
            "(2, 11, 1)\n",
            "(2, 11, 2)\n",
            "(2, 11, 3)\n",
            "(2, 11, 4)\n",
            "(2, 11, 5)\n",
            "(2, 11, 6)\n",
            "(2, 11, 7)\n",
            "(2, 11, 8)\n",
            "(2, 11, 9)\n",
            "(2, 11, 10)\n",
            "(2, 11, 11)\n",
            "(2, 11, 12)\n",
            "(2, 11, 13)\n",
            "(2, 11, 14)\n",
            "(2, 11, 15)\n",
            "(2, 12, 0)\n",
            "(2, 12, 1)\n",
            "(2, 12, 2)\n",
            "(2, 12, 3)\n",
            "(2, 12, 4)\n",
            "(2, 12, 5)\n",
            "(2, 12, 6)\n",
            "(2, 12, 7)\n",
            "(2, 12, 8)\n",
            "(2, 12, 9)\n",
            "(2, 12, 10)\n",
            "(2, 12, 11)\n",
            "(2, 12, 12)\n",
            "(2, 12, 13)\n",
            "(2, 13, 0)\n",
            "(2, 13, 1)\n",
            "(2, 13, 2)\n",
            "(2, 13, 3)\n",
            "(2, 13, 4)\n",
            "(2, 13, 5)\n",
            "(2, 13, 6)\n",
            "(2, 13, 7)\n",
            "(2, 13, 8)\n",
            "(2, 13, 9)\n",
            "(2, 13, 10)\n",
            "(2, 14, 0)\n",
            "(2, 14, 1)\n",
            "(2, 14, 2)\n",
            "(2, 14, 3)\n",
            "(2, 14, 4)\n",
            "(2, 14, 5)\n",
            "(3, 1, 0)\n",
            "(3, 1, 1)\n",
            "(3, 1, 2)\n",
            "(3, 1, 3)\n",
            "(3, 1, 4)\n",
            "(3, 1, 5)\n",
            "(3, 1, 6)\n",
            "(3, 1, 7)\n",
            "(3, 1, 8)\n",
            "(3, 1, 9)\n",
            "(3, 1, 10)\n",
            "(3, 1, 11)\n",
            "(3, 1, 12)\n",
            "(3, 1, 13)\n",
            "(3, 1, 14)\n",
            "(3, 1, 15)\n",
            "(3, 1, 16)\n",
            "(3, 1, 17)\n",
            "(3, 1, 18)\n",
            "(3, 1, 19)\n",
            "(3, 1, 20)\n",
            "(3, 1, 21)\n",
            "(3, 1, 22)\n",
            "(3, 1, 23)\n",
            "(3, 2, 0)\n",
            "(3, 2, 1)\n",
            "(3, 2, 2)\n",
            "(3, 2, 3)\n",
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            "(3, 2, 6)\n",
            "(3, 2, 7)\n",
            "(3, 2, 8)\n",
            "(3, 2, 9)\n",
            "(3, 2, 10)\n",
            "(3, 2, 11)\n",
            "(3, 2, 12)\n",
            "(3, 2, 13)\n",
            "(3, 2, 14)\n",
            "(3, 2, 15)\n",
            "(3, 2, 16)\n",
            "(3, 2, 17)\n",
            "(3, 2, 18)\n",
            "(3, 2, 19)\n",
            "(3, 2, 20)\n",
            "(3, 2, 21)\n",
            "(3, 2, 22)\n",
            "(3, 2, 23)\n",
            "(3, 3, 0)\n",
            "(3, 3, 1)\n",
            "(3, 3, 2)\n",
            "(3, 3, 3)\n",
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            "(3, 3, 5)\n",
            "(3, 3, 6)\n",
            "(3, 3, 7)\n",
            "(3, 3, 8)\n",
            "(3, 3, 9)\n",
            "(3, 3, 10)\n",
            "(3, 3, 11)\n",
            "(3, 3, 12)\n",
            "(3, 3, 13)\n",
            "(3, 3, 14)\n",
            "(3, 3, 15)\n",
            "(3, 3, 16)\n",
            "(3, 3, 17)\n",
            "(3, 3, 18)\n",
            "(3, 3, 19)\n",
            "(3, 3, 20)\n",
            "(3, 3, 21)\n",
            "(3, 3, 22)\n",
            "(3, 3, 23)\n",
            "(3, 4, 0)\n",
            "(3, 4, 1)\n",
            "(3, 4, 2)\n",
            "(3, 4, 3)\n",
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            "(3, 4, 5)\n",
            "(3, 4, 6)\n",
            "(3, 4, 7)\n",
            "(3, 4, 8)\n",
            "(3, 4, 9)\n",
            "(3, 4, 10)\n",
            "(3, 4, 11)\n",
            "(3, 4, 12)\n",
            "(3, 4, 13)\n",
            "(3, 4, 14)\n",
            "(3, 4, 15)\n",
            "(3, 4, 16)\n",
            "(3, 4, 17)\n",
            "(3, 4, 18)\n",
            "(3, 4, 19)\n",
            "(3, 4, 20)\n",
            "(3, 4, 21)\n",
            "(3, 4, 22)\n",
            "(3, 5, 0)\n",
            "(3, 5, 1)\n",
            "(3, 5, 2)\n",
            "(3, 5, 3)\n",
            "(3, 5, 4)\n",
            "(3, 5, 5)\n",
            "(3, 5, 6)\n",
            "(3, 5, 7)\n",
            "(3, 5, 8)\n",
            "(3, 5, 9)\n",
            "(3, 5, 10)\n",
            "(3, 5, 11)\n",
            "(3, 5, 12)\n",
            "(3, 5, 13)\n",
            "(3, 5, 14)\n",
            "(3, 5, 15)\n",
            "(3, 5, 16)\n",
            "(3, 5, 17)\n",
            "(3, 5, 18)\n",
            "(3, 5, 19)\n",
            "(3, 5, 20)\n",
            "(3, 5, 21)\n",
            "(3, 5, 22)\n",
            "(3, 6, 0)\n",
            "(3, 6, 1)\n",
            "(3, 6, 2)\n",
            "(3, 6, 3)\n",
            "(3, 6, 4)\n",
            "(3, 6, 5)\n",
            "(3, 6, 6)\n",
            "(3, 6, 7)\n",
            "(3, 6, 8)\n",
            "(3, 6, 9)\n",
            "(3, 6, 10)\n",
            "(3, 6, 11)\n",
            "(3, 6, 12)\n",
            "(3, 6, 13)\n",
            "(3, 6, 14)\n",
            "(3, 6, 15)\n",
            "(3, 6, 16)\n",
            "(3, 6, 17)\n",
            "(3, 6, 18)\n",
            "(3, 6, 19)\n",
            "(3, 6, 20)\n",
            "(3, 6, 21)\n",
            "(3, 7, 0)\n",
            "(3, 7, 1)\n",
            "(3, 7, 2)\n",
            "(3, 7, 3)\n",
            "(3, 7, 4)\n",
            "(3, 7, 5)\n",
            "(3, 7, 6)\n",
            "(3, 7, 7)\n",
            "(3, 7, 8)\n",
            "(3, 7, 9)\n",
            "(3, 7, 10)\n",
            "(3, 7, 11)\n",
            "(3, 7, 12)\n",
            "(3, 7, 13)\n",
            "(3, 7, 14)\n",
            "(3, 7, 15)\n",
            "(3, 7, 16)\n",
            "(3, 7, 17)\n",
            "(3, 7, 18)\n",
            "(3, 7, 19)\n",
            "(3, 7, 20)\n",
            "(3, 8, 0)\n",
            "(3, 8, 1)\n",
            "(3, 8, 2)\n",
            "(3, 8, 3)\n",
            "(3, 8, 4)\n",
            "(3, 8, 5)\n",
            "(3, 8, 6)\n",
            "(3, 8, 7)\n",
            "(3, 8, 8)\n",
            "(3, 8, 9)\n",
            "(3, 8, 10)\n",
            "(3, 8, 11)\n",
            "(3, 8, 12)\n",
            "(3, 8, 13)\n",
            "(3, 8, 14)\n",
            "(3, 8, 15)\n",
            "(3, 8, 16)\n",
            "(3, 8, 17)\n",
            "(3, 8, 18)\n",
            "(3, 8, 19)\n",
            "(3, 9, 0)\n",
            "(3, 9, 1)\n",
            "(3, 9, 2)\n",
            "(3, 9, 3)\n",
            "(3, 9, 4)\n",
            "(3, 9, 5)\n",
            "(3, 9, 6)\n",
            "(3, 9, 7)\n",
            "(3, 9, 8)\n",
            "(3, 9, 9)\n",
            "(3, 9, 10)\n",
            "(3, 9, 11)\n",
            "(3, 9, 12)\n",
            "(3, 9, 13)\n",
            "(3, 9, 14)\n",
            "(3, 9, 15)\n",
            "(3, 9, 16)\n",
            "(3, 9, 17)\n",
            "(3, 9, 18)\n",
            "(3, 10, 0)\n",
            "(3, 10, 1)\n",
            "(3, 10, 2)\n",
            "(3, 10, 3)\n",
            "(3, 10, 4)\n",
            "(3, 10, 5)\n",
            "(3, 10, 6)\n",
            "(3, 10, 7)\n",
            "(3, 10, 8)\n",
            "(3, 10, 9)\n",
            "(3, 10, 10)\n",
            "(3, 10, 11)\n",
            "(3, 10, 12)\n",
            "(3, 10, 13)\n",
            "(3, 10, 14)\n",
            "(3, 10, 15)\n",
            "(3, 10, 16)\n",
            "(3, 11, 0)\n",
            "(3, 11, 1)\n",
            "(3, 11, 2)\n",
            "(3, 11, 3)\n",
            "(3, 11, 4)\n",
            "(3, 11, 5)\n",
            "(3, 11, 6)\n",
            "(3, 11, 7)\n",
            "(3, 11, 8)\n",
            "(3, 11, 9)\n",
            "(3, 11, 10)\n",
            "(3, 11, 11)\n",
            "(3, 11, 12)\n",
            "(3, 11, 13)\n",
            "(3, 11, 14)\n",
            "(3, 12, 0)\n",
            "(3, 12, 1)\n",
            "(3, 12, 2)\n",
            "(3, 12, 3)\n",
            "(3, 12, 4)\n",
            "(3, 12, 5)\n",
            "(3, 12, 6)\n",
            "(3, 12, 7)\n",
            "(3, 12, 8)\n",
            "(3, 12, 9)\n",
            "(3, 12, 10)\n",
            "(3, 12, 11)\n",
            "(3, 12, 12)\n",
            "(3, 13, 0)\n",
            "(3, 13, 1)\n",
            "(3, 13, 2)\n",
            "(3, 13, 3)\n",
            "(3, 13, 4)\n",
            "(3, 13, 5)\n",
            "(3, 13, 6)\n",
            "(3, 13, 7)\n",
            "(3, 13, 8)\n",
            "(3, 13, 9)\n",
            "(3, 14, 0)\n",
            "(3, 14, 1)\n",
            "(3, 14, 2)\n",
            "(3, 14, 3)\n",
            "(4, 1, 0)\n",
            "(4, 1, 1)\n",
            "(4, 1, 2)\n",
            "(4, 1, 3)\n",
            "(4, 1, 4)\n",
            "(4, 1, 5)\n",
            "(4, 1, 6)\n",
            "(4, 1, 7)\n",
            "(4, 1, 8)\n",
            "(4, 1, 9)\n",
            "(4, 1, 10)\n",
            "(4, 1, 11)\n",
            "(4, 1, 12)\n",
            "(4, 1, 13)\n",
            "(4, 1, 14)\n",
            "(4, 1, 15)\n",
            "(4, 1, 16)\n",
            "(4, 1, 17)\n",
            "(4, 1, 18)\n",
            "(4, 1, 19)\n",
            "(4, 1, 20)\n",
            "(4, 1, 21)\n",
            "(4, 1, 22)\n",
            "(4, 1, 23)\n",
            "(4, 2, 0)\n",
            "(4, 2, 1)\n",
            "(4, 2, 2)\n",
            "(4, 2, 3)\n",
            "(4, 2, 4)\n",
            "(4, 2, 5)\n",
            "(4, 2, 6)\n",
            "(4, 2, 7)\n",
            "(4, 2, 8)\n",
            "(4, 2, 9)\n",
            "(4, 2, 10)\n",
            "(4, 2, 11)\n",
            "(4, 2, 12)\n",
            "(4, 2, 13)\n",
            "(4, 2, 14)\n",
            "(4, 2, 15)\n",
            "(4, 2, 16)\n",
            "(4, 2, 17)\n",
            "(4, 2, 18)\n",
            "(4, 2, 19)\n",
            "(4, 2, 20)\n",
            "(4, 2, 21)\n",
            "(4, 2, 22)\n",
            "(4, 3, 0)\n",
            "(4, 3, 1)\n",
            "(4, 3, 2)\n",
            "(4, 3, 3)\n",
            "(4, 3, 4)\n",
            "(4, 3, 5)\n",
            "(4, 3, 6)\n",
            "(4, 3, 7)\n",
            "(4, 3, 8)\n",
            "(4, 3, 9)\n",
            "(4, 3, 10)\n",
            "(4, 3, 11)\n",
            "(4, 3, 12)\n",
            "(4, 3, 13)\n",
            "(4, 3, 14)\n",
            "(4, 3, 15)\n",
            "(4, 3, 16)\n",
            "(4, 3, 17)\n",
            "(4, 3, 18)\n",
            "(4, 3, 19)\n",
            "(4, 3, 20)\n",
            "(4, 3, 21)\n",
            "(4, 3, 22)\n",
            "(4, 4, 0)\n",
            "(4, 4, 1)\n",
            "(4, 4, 2)\n",
            "(4, 4, 3)\n",
            "(4, 4, 4)\n",
            "(4, 4, 5)\n",
            "(4, 4, 6)\n",
            "(4, 4, 7)\n",
            "(4, 4, 8)\n",
            "(4, 4, 9)\n",
            "(4, 4, 10)\n",
            "(4, 4, 11)\n",
            "(4, 4, 12)\n",
            "(4, 4, 13)\n",
            "(4, 4, 14)\n",
            "(4, 4, 15)\n",
            "(4, 4, 16)\n",
            "(4, 4, 17)\n",
            "(4, 4, 18)\n",
            "(4, 4, 19)\n",
            "(4, 4, 20)\n",
            "(4, 4, 21)\n",
            "(4, 4, 22)\n",
            "(4, 5, 0)\n",
            "(4, 5, 1)\n",
            "(4, 5, 2)\n",
            "(4, 5, 3)\n",
            "(4, 5, 4)\n",
            "(4, 5, 5)\n",
            "(4, 5, 6)\n",
            "(4, 5, 7)\n",
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            "(4, 5, 9)\n",
            "(4, 5, 10)\n",
            "(4, 5, 11)\n",
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            "(4, 5, 13)\n",
            "(4, 5, 14)\n",
            "(4, 5, 15)\n",
            "(4, 5, 16)\n",
            "(4, 5, 17)\n",
            "(4, 5, 18)\n",
            "(4, 5, 19)\n",
            "(4, 5, 20)\n",
            "(4, 5, 21)\n",
            "(4, 6, 0)\n",
            "(4, 6, 1)\n",
            "(4, 6, 2)\n",
            "(4, 6, 3)\n",
            "(4, 6, 4)\n",
            "(4, 6, 5)\n",
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            "(4, 6, 10)\n",
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            "(4, 6, 12)\n",
            "(4, 6, 13)\n",
            "(4, 6, 14)\n",
            "(4, 6, 15)\n",
            "(4, 6, 16)\n",
            "(4, 6, 17)\n",
            "(4, 6, 18)\n",
            "(4, 6, 19)\n",
            "(4, 6, 20)\n",
            "(4, 7, 0)\n",
            "(4, 7, 1)\n",
            "(4, 7, 2)\n",
            "(4, 7, 3)\n",
            "(4, 7, 4)\n",
            "(4, 7, 5)\n",
            "(4, 7, 6)\n",
            "(4, 7, 7)\n",
            "(4, 7, 8)\n",
            "(4, 7, 9)\n",
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            "(4, 7, 12)\n",
            "(4, 7, 13)\n",
            "(4, 7, 14)\n",
            "(4, 7, 15)\n",
            "(4, 7, 16)\n",
            "(4, 7, 17)\n",
            "(4, 7, 18)\n",
            "(4, 7, 19)\n",
            "(4, 7, 20)\n",
            "(4, 8, 0)\n",
            "(4, 8, 1)\n",
            "(4, 8, 2)\n",
            "(4, 8, 3)\n",
            "(4, 8, 4)\n",
            "(4, 8, 5)\n",
            "(4, 8, 6)\n",
            "(4, 8, 7)\n",
            "(4, 8, 8)\n",
            "(4, 8, 9)\n",
            "(4, 8, 10)\n",
            "(4, 8, 11)\n",
            "(4, 8, 12)\n",
            "(4, 8, 13)\n",
            "(4, 8, 14)\n",
            "(4, 8, 15)\n",
            "(4, 8, 16)\n",
            "(4, 8, 17)\n",
            "(4, 8, 18)\n",
            "(4, 9, 0)\n",
            "(4, 9, 1)\n",
            "(4, 9, 2)\n",
            "(4, 9, 3)\n",
            "(4, 9, 4)\n",
            "(4, 9, 5)\n",
            "(4, 9, 6)\n",
            "(4, 9, 7)\n",
            "(4, 9, 8)\n",
            "(4, 9, 9)\n",
            "(4, 9, 10)\n",
            "(4, 9, 11)\n",
            "(4, 9, 12)\n",
            "(4, 9, 13)\n",
            "(4, 9, 14)\n",
            "(4, 9, 15)\n",
            "(4, 9, 16)\n",
            "(4, 9, 17)\n",
            "(4, 10, 0)\n",
            "(4, 10, 1)\n",
            "(4, 10, 2)\n",
            "(4, 10, 3)\n",
            "(4, 10, 4)\n",
            "(4, 10, 5)\n",
            "(4, 10, 6)\n",
            "(4, 10, 7)\n",
            "(4, 10, 8)\n",
            "(4, 10, 9)\n",
            "(4, 10, 10)\n",
            "(4, 10, 11)\n",
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            "(4, 10, 13)\n",
            "(4, 10, 14)\n",
            "(4, 10, 15)\n",
            "(4, 10, 16)\n",
            "(4, 11, 0)\n",
            "(4, 11, 1)\n",
            "(4, 11, 2)\n",
            "(4, 11, 3)\n",
            "(4, 11, 4)\n",
            "(4, 11, 5)\n",
            "(4, 11, 6)\n",
            "(4, 11, 7)\n",
            "(4, 11, 8)\n",
            "(4, 11, 9)\n",
            "(4, 11, 10)\n",
            "(4, 11, 11)\n",
            "(4, 11, 12)\n",
            "(4, 11, 13)\n",
            "(4, 11, 14)\n",
            "(4, 12, 0)\n",
            "(4, 12, 1)\n",
            "(4, 12, 2)\n",
            "(4, 12, 3)\n",
            "(4, 12, 4)\n",
            "(4, 12, 5)\n",
            "(4, 12, 6)\n",
            "(4, 12, 7)\n",
            "(4, 12, 8)\n",
            "(4, 12, 9)\n",
            "(4, 12, 10)\n",
            "(4, 12, 11)\n",
            "(4, 13, 0)\n",
            "(4, 13, 1)\n",
            "(4, 13, 2)\n",
            "(4, 13, 3)\n",
            "(4, 13, 4)\n",
            "(4, 13, 5)\n",
            "(4, 13, 6)\n",
            "(4, 13, 7)\n",
            "(4, 13, 8)\n",
            "(5, 1, 0)\n",
            "(5, 1, 1)\n",
            "(5, 1, 2)\n",
            "(5, 1, 3)\n",
            "(5, 1, 4)\n",
            "(5, 1, 5)\n",
            "(5, 1, 6)\n",
            "(5, 1, 7)\n",
            "(5, 1, 8)\n",
            "(5, 1, 9)\n",
            "(5, 1, 10)\n",
            "(5, 1, 11)\n",
            "(5, 1, 12)\n",
            "(5, 1, 13)\n",
            "(5, 1, 14)\n",
            "(5, 1, 15)\n",
            "(5, 1, 16)\n",
            "(5, 1, 17)\n",
            "(5, 1, 18)\n",
            "(5, 1, 19)\n",
            "(5, 1, 20)\n",
            "(5, 1, 21)\n",
            "(5, 1, 22)\n",
            "(5, 2, 0)\n",
            "(5, 2, 1)\n",
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            "(5, 2, 6)\n",
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            "(5, 2, 9)\n",
            "(5, 2, 10)\n",
            "(5, 2, 11)\n",
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            "(5, 2, 13)\n",
            "(5, 2, 14)\n",
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            "(5, 2, 16)\n",
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            "(5, 2, 22)\n",
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            "(5, 4, 1)\n",
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            "(5, 8, 0)\n",
            "(5, 8, 1)\n",
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            "(5, 8, 15)\n",
            "(5, 8, 16)\n",
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            "(5, 9, 0)\n",
            "(5, 9, 1)\n",
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            "(5, 11, 0)\n",
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            "(5, 12, 0)\n",
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            "(5, 13, 0)\n",
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            "(6, 3, 1)\n",
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            "(6, 8, 1)\n",
            "(6, 8, 2)\n",
            "(6, 8, 3)\n",
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            "(6, 8, 6)\n",
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            "(6, 8, 15)\n",
            "(6, 8, 16)\n",
            "(6, 8, 17)\n",
            "(6, 9, 0)\n",
            "(6, 9, 1)\n",
            "(6, 9, 2)\n",
            "(6, 9, 3)\n",
            "(6, 9, 4)\n",
            "(6, 9, 5)\n",
            "(6, 9, 6)\n",
            "(6, 9, 7)\n",
            "(6, 9, 8)\n",
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            "(6, 9, 14)\n",
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            "(6, 9, 16)\n",
            "(6, 10, 0)\n",
            "(6, 10, 1)\n",
            "(6, 10, 2)\n",
            "(6, 10, 3)\n",
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            "(6, 10, 8)\n",
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            "(6, 10, 13)\n",
            "(6, 10, 14)\n",
            "(6, 11, 0)\n",
            "(6, 11, 1)\n",
            "(6, 11, 2)\n",
            "(6, 11, 3)\n",
            "(6, 11, 4)\n",
            "(6, 11, 5)\n",
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            "(6, 11, 8)\n",
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            "(6, 11, 10)\n",
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            "(6, 12, 0)\n",
            "(6, 12, 1)\n",
            "(6, 12, 2)\n",
            "(6, 12, 3)\n",
            "(6, 12, 4)\n",
            "(6, 12, 5)\n",
            "(6, 12, 6)\n",
            "(6, 12, 7)\n",
            "(6, 12, 8)\n",
            "(6, 12, 9)\n",
            "(6, 13, 0)\n",
            "(6, 13, 1)\n",
            "(6, 13, 2)\n",
            "(6, 13, 3)\n",
            "(7, 1, 0)\n",
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            "(7, 1, 2)\n",
            "(7, 1, 3)\n",
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            "(7, 1, 7)\n",
            "(7, 1, 8)\n",
            "(7, 1, 9)\n",
            "(7, 1, 10)\n",
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            "(7, 1, 14)\n",
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            "(7, 1, 16)\n",
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            "(7, 1, 18)\n",
            "(7, 1, 19)\n",
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            "(7, 1, 21)\n",
            "(7, 2, 0)\n",
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            "(7, 2, 8)\n",
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            "(7, 2, 10)\n",
            "(7, 2, 11)\n",
            "(7, 2, 12)\n",
            "(7, 2, 13)\n",
            "(7, 2, 14)\n",
            "(7, 2, 15)\n",
            "(7, 2, 16)\n",
            "(7, 2, 17)\n",
            "(7, 2, 18)\n",
            "(7, 2, 19)\n",
            "(7, 2, 20)\n",
            "(7, 3, 0)\n",
            "(7, 3, 1)\n",
            "(7, 3, 2)\n",
            "(7, 3, 3)\n",
            "(7, 3, 4)\n",
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            "(7, 3, 6)\n",
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            "(7, 3, 8)\n",
            "(7, 3, 9)\n",
            "(7, 3, 10)\n",
            "(7, 3, 11)\n",
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            "(7, 3, 13)\n",
            "(7, 3, 14)\n",
            "(7, 3, 15)\n",
            "(7, 3, 16)\n",
            "(7, 3, 17)\n",
            "(7, 3, 18)\n",
            "(7, 3, 19)\n",
            "(7, 3, 20)\n",
            "(7, 4, 0)\n",
            "(7, 4, 1)\n",
            "(7, 4, 2)\n",
            "(7, 4, 3)\n",
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            "(7, 4, 14)\n",
            "(7, 4, 15)\n",
            "(7, 4, 16)\n",
            "(7, 4, 17)\n",
            "(7, 4, 18)\n",
            "(7, 4, 19)\n",
            "(7, 4, 20)\n",
            "(7, 5, 0)\n",
            "(7, 5, 1)\n",
            "(7, 5, 2)\n",
            "(7, 5, 3)\n",
            "(7, 5, 4)\n",
            "(7, 5, 5)\n",
            "(7, 5, 6)\n",
            "(7, 5, 7)\n",
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            "(7, 5, 9)\n",
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            "(7, 5, 11)\n",
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            "(7, 5, 13)\n",
            "(7, 5, 14)\n",
            "(7, 5, 15)\n",
            "(7, 5, 16)\n",
            "(7, 5, 17)\n",
            "(7, 5, 18)\n",
            "(7, 5, 19)\n",
            "(7, 6, 0)\n",
            "(7, 6, 1)\n",
            "(7, 6, 2)\n",
            "(7, 6, 3)\n",
            "(7, 6, 4)\n",
            "(7, 6, 5)\n",
            "(7, 6, 6)\n",
            "(7, 6, 7)\n",
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            "(7, 6, 10)\n",
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            "(7, 6, 13)\n",
            "(7, 6, 14)\n",
            "(7, 6, 15)\n",
            "(7, 6, 16)\n",
            "(7, 6, 17)\n",
            "(7, 6, 18)\n",
            "(7, 7, 0)\n",
            "(7, 7, 1)\n",
            "(7, 7, 2)\n",
            "(7, 7, 3)\n",
            "(7, 7, 4)\n",
            "(7, 7, 5)\n",
            "(7, 7, 6)\n",
            "(7, 7, 7)\n",
            "(7, 7, 8)\n",
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            "(7, 7, 10)\n",
            "(7, 7, 11)\n",
            "(7, 7, 12)\n",
            "(7, 7, 13)\n",
            "(7, 7, 14)\n",
            "(7, 7, 15)\n",
            "(7, 7, 16)\n",
            "(7, 7, 17)\n",
            "(7, 8, 0)\n",
            "(7, 8, 1)\n",
            "(7, 8, 2)\n",
            "(7, 8, 3)\n",
            "(7, 8, 4)\n",
            "(7, 8, 5)\n",
            "(7, 8, 6)\n",
            "(7, 8, 7)\n",
            "(7, 8, 8)\n",
            "(7, 8, 9)\n",
            "(7, 8, 10)\n",
            "(7, 8, 11)\n",
            "(7, 8, 12)\n",
            "(7, 8, 13)\n",
            "(7, 8, 14)\n",
            "(7, 8, 15)\n",
            "(7, 8, 16)\n",
            "(7, 9, 0)\n",
            "(7, 9, 1)\n",
            "(7, 9, 2)\n",
            "(7, 9, 3)\n",
            "(7, 9, 4)\n",
            "(7, 9, 5)\n",
            "(7, 9, 6)\n",
            "(7, 9, 7)\n",
            "(7, 9, 8)\n",
            "(7, 9, 9)\n",
            "(7, 9, 10)\n",
            "(7, 9, 11)\n",
            "(7, 9, 12)\n",
            "(7, 9, 13)\n",
            "(7, 9, 14)\n",
            "(7, 10, 0)\n",
            "(7, 10, 1)\n",
            "(7, 10, 2)\n",
            "(7, 10, 3)\n",
            "(7, 10, 4)\n",
            "(7, 10, 5)\n",
            "(7, 10, 6)\n",
            "(7, 10, 7)\n",
            "(7, 10, 8)\n",
            "(7, 10, 9)\n",
            "(7, 10, 10)\n",
            "(7, 10, 11)\n",
            "(7, 10, 12)\n",
            "(7, 11, 0)\n",
            "(7, 11, 1)\n",
            "(7, 11, 2)\n",
            "(7, 11, 3)\n",
            "(7, 11, 4)\n",
            "(7, 11, 5)\n",
            "(7, 11, 6)\n",
            "(7, 11, 7)\n",
            "(7, 11, 8)\n",
            "(7, 11, 9)\n",
            "(7, 11, 10)\n",
            "(7, 12, 0)\n",
            "(7, 12, 1)\n",
            "(7, 12, 2)\n",
            "(7, 12, 3)\n",
            "(7, 12, 4)\n",
            "(7, 12, 5)\n",
            "(7, 12, 6)\n",
            "(8, 1, 0)\n",
            "(8, 1, 1)\n",
            "(8, 1, 2)\n",
            "(8, 1, 3)\n",
            "(8, 1, 4)\n",
            "(8, 1, 5)\n",
            "(8, 1, 6)\n",
            "(8, 1, 7)\n",
            "(8, 1, 8)\n",
            "(8, 1, 9)\n",
            "(8, 1, 10)\n",
            "(8, 1, 11)\n",
            "(8, 1, 12)\n",
            "(8, 1, 13)\n",
            "(8, 1, 14)\n",
            "(8, 1, 15)\n",
            "(8, 1, 16)\n",
            "(8, 1, 17)\n",
            "(8, 1, 18)\n",
            "(8, 1, 19)\n",
            "(8, 1, 20)\n",
            "(8, 2, 0)\n",
            "(8, 2, 1)\n",
            "(8, 2, 2)\n",
            "(8, 2, 3)\n",
            "(8, 2, 4)\n",
            "(8, 2, 5)\n",
            "(8, 2, 6)\n",
            "(8, 2, 7)\n",
            "(8, 2, 8)\n",
            "(8, 2, 9)\n",
            "(8, 2, 10)\n",
            "(8, 2, 11)\n",
            "(8, 2, 12)\n",
            "(8, 2, 13)\n",
            "(8, 2, 14)\n",
            "(8, 2, 15)\n",
            "(8, 2, 16)\n",
            "(8, 2, 17)\n",
            "(8, 2, 18)\n",
            "(8, 2, 19)\n",
            "(8, 3, 0)\n",
            "(8, 3, 1)\n",
            "(8, 3, 2)\n",
            "(8, 3, 3)\n",
            "(8, 3, 4)\n",
            "(8, 3, 5)\n",
            "(8, 3, 6)\n",
            "(8, 3, 7)\n",
            "(8, 3, 8)\n",
            "(8, 3, 9)\n",
            "(8, 3, 10)\n",
            "(8, 3, 11)\n",
            "(8, 3, 12)\n",
            "(8, 3, 13)\n",
            "(8, 3, 14)\n",
            "(8, 3, 15)\n",
            "(8, 3, 16)\n",
            "(8, 3, 17)\n",
            "(8, 3, 18)\n",
            "(8, 3, 19)\n",
            "(8, 4, 0)\n",
            "(8, 4, 1)\n",
            "(8, 4, 2)\n",
            "(8, 4, 3)\n",
            "(8, 4, 4)\n",
            "(8, 4, 5)\n",
            "(8, 4, 6)\n",
            "(8, 4, 7)\n",
            "(8, 4, 8)\n",
            "(8, 4, 9)\n",
            "(8, 4, 10)\n",
            "(8, 4, 11)\n",
            "(8, 4, 12)\n",
            "(8, 4, 13)\n",
            "(8, 4, 14)\n",
            "(8, 4, 15)\n",
            "(8, 4, 16)\n",
            "(8, 4, 17)\n",
            "(8, 4, 18)\n",
            "(8, 5, 0)\n",
            "(8, 5, 1)\n",
            "(8, 5, 2)\n",
            "(8, 5, 3)\n",
            "(8, 5, 4)\n",
            "(8, 5, 5)\n",
            "(8, 5, 6)\n",
            "(8, 5, 7)\n",
            "(8, 5, 8)\n",
            "(8, 5, 9)\n",
            "(8, 5, 10)\n",
            "(8, 5, 11)\n",
            "(8, 5, 12)\n",
            "(8, 5, 13)\n",
            "(8, 5, 14)\n",
            "(8, 5, 15)\n",
            "(8, 5, 16)\n",
            "(8, 5, 17)\n",
            "(8, 5, 18)\n",
            "(8, 6, 0)\n",
            "(8, 6, 1)\n",
            "(8, 6, 2)\n",
            "(8, 6, 3)\n",
            "(8, 6, 4)\n",
            "(8, 6, 5)\n",
            "(8, 6, 6)\n",
            "(8, 6, 7)\n",
            "(8, 6, 8)\n",
            "(8, 6, 9)\n",
            "(8, 6, 10)\n",
            "(8, 6, 11)\n",
            "(8, 6, 12)\n",
            "(8, 6, 13)\n",
            "(8, 6, 14)\n",
            "(8, 6, 15)\n",
            "(8, 6, 16)\n",
            "(8, 6, 17)\n",
            "(8, 7, 0)\n",
            "(8, 7, 1)\n",
            "(8, 7, 2)\n",
            "(8, 7, 3)\n",
            "(8, 7, 4)\n",
            "(8, 7, 5)\n",
            "(8, 7, 6)\n",
            "(8, 7, 7)\n",
            "(8, 7, 8)\n",
            "(8, 7, 9)\n",
            "(8, 7, 10)\n",
            "(8, 7, 11)\n",
            "(8, 7, 12)\n",
            "(8, 7, 13)\n",
            "(8, 7, 14)\n",
            "(8, 7, 15)\n",
            "(8, 7, 16)\n",
            "(8, 8, 0)\n",
            "(8, 8, 1)\n",
            "(8, 8, 2)\n",
            "(8, 8, 3)\n",
            "(8, 8, 4)\n",
            "(8, 8, 5)\n",
            "(8, 8, 6)\n",
            "(8, 8, 7)\n",
            "(8, 8, 8)\n",
            "(8, 8, 9)\n",
            "(8, 8, 10)\n",
            "(8, 8, 11)\n",
            "(8, 8, 12)\n",
            "(8, 8, 13)\n",
            "(8, 8, 14)\n",
            "(8, 8, 15)\n",
            "(8, 9, 0)\n",
            "(8, 9, 1)\n",
            "(8, 9, 2)\n",
            "(8, 9, 3)\n",
            "(8, 9, 4)\n",
            "(8, 9, 5)\n",
            "(8, 9, 6)\n",
            "(8, 9, 7)\n",
            "(8, 9, 8)\n",
            "(8, 9, 9)\n",
            "(8, 9, 10)\n",
            "(8, 9, 11)\n",
            "(8, 9, 12)\n",
            "(8, 9, 13)\n",
            "(8, 10, 0)\n",
            "(8, 10, 1)\n",
            "(8, 10, 2)\n",
            "(8, 10, 3)\n",
            "(8, 10, 4)\n",
            "(8, 10, 5)\n",
            "(8, 10, 6)\n",
            "(8, 10, 7)\n",
            "(8, 10, 8)\n",
            "(8, 10, 9)\n",
            "(8, 10, 10)\n",
            "(8, 10, 11)\n",
            "(8, 11, 0)\n",
            "(8, 11, 1)\n",
            "(8, 11, 2)\n",
            "(8, 11, 3)\n",
            "(8, 11, 4)\n",
            "(8, 11, 5)\n",
            "(8, 11, 6)\n",
            "(8, 11, 7)\n",
            "(8, 11, 8)\n",
            "(8, 12, 0)\n",
            "(8, 12, 1)\n",
            "(8, 12, 2)\n",
            "(9, 1, 0)\n",
            "(9, 1, 1)\n",
            "(9, 1, 2)\n",
            "(9, 1, 3)\n",
            "(9, 1, 4)\n",
            "(9, 1, 5)\n",
            "(9, 1, 6)\n",
            "(9, 1, 7)\n",
            "(9, 1, 8)\n",
            "(9, 1, 9)\n",
            "(9, 1, 10)\n",
            "(9, 1, 11)\n",
            "(9, 1, 12)\n",
            "(9, 1, 13)\n",
            "(9, 1, 14)\n",
            "(9, 1, 15)\n",
            "(9, 1, 16)\n",
            "(9, 1, 17)\n",
            "(9, 1, 18)\n",
            "(9, 2, 0)\n",
            "(9, 2, 1)\n",
            "(9, 2, 2)\n",
            "(9, 2, 3)\n",
            "(9, 2, 4)\n",
            "(9, 2, 5)\n",
            "(9, 2, 6)\n",
            "(9, 2, 7)\n",
            "(9, 2, 8)\n",
            "(9, 2, 9)\n",
            "(9, 2, 10)\n",
            "(9, 2, 11)\n",
            "(9, 2, 12)\n",
            "(9, 2, 13)\n",
            "(9, 2, 14)\n",
            "(9, 2, 15)\n",
            "(9, 2, 16)\n",
            "(9, 2, 17)\n",
            "(9, 2, 18)\n",
            "(9, 3, 0)\n",
            "(9, 3, 1)\n",
            "(9, 3, 2)\n",
            "(9, 3, 3)\n",
            "(9, 3, 4)\n",
            "(9, 3, 5)\n",
            "(9, 3, 6)\n",
            "(9, 3, 7)\n",
            "(9, 3, 8)\n",
            "(9, 3, 9)\n",
            "(9, 3, 10)\n",
            "(9, 3, 11)\n",
            "(9, 3, 12)\n",
            "(9, 3, 13)\n",
            "(9, 3, 14)\n",
            "(9, 3, 15)\n",
            "(9, 3, 16)\n",
            "(9, 3, 17)\n",
            "(9, 3, 18)\n",
            "(9, 4, 0)\n",
            "(9, 4, 1)\n",
            "(9, 4, 2)\n",
            "(9, 4, 3)\n",
            "(9, 4, 4)\n",
            "(9, 4, 5)\n",
            "(9, 4, 6)\n",
            "(9, 4, 7)\n",
            "(9, 4, 8)\n",
            "(9, 4, 9)\n",
            "(9, 4, 10)\n",
            "(9, 4, 11)\n",
            "(9, 4, 12)\n",
            "(9, 4, 13)\n",
            "(9, 4, 14)\n",
            "(9, 4, 15)\n",
            "(9, 4, 16)\n",
            "(9, 4, 17)\n",
            "(9, 5, 0)\n",
            "(9, 5, 1)\n",
            "(9, 5, 2)\n",
            "(9, 5, 3)\n",
            "(9, 5, 4)\n",
            "(9, 5, 5)\n",
            "(9, 5, 6)\n",
            "(9, 5, 7)\n",
            "(9, 5, 8)\n",
            "(9, 5, 9)\n",
            "(9, 5, 10)\n",
            "(9, 5, 11)\n",
            "(9, 5, 12)\n",
            "(9, 5, 13)\n",
            "(9, 5, 14)\n",
            "(9, 5, 15)\n",
            "(9, 5, 16)\n",
            "(9, 6, 0)\n",
            "(9, 6, 1)\n",
            "(9, 6, 2)\n",
            "(9, 6, 3)\n",
            "(9, 6, 4)\n",
            "(9, 6, 5)\n",
            "(9, 6, 6)\n",
            "(9, 6, 7)\n",
            "(9, 6, 8)\n",
            "(9, 6, 9)\n",
            "(9, 6, 10)\n",
            "(9, 6, 11)\n",
            "(9, 6, 12)\n",
            "(9, 6, 13)\n",
            "(9, 6, 14)\n",
            "(9, 6, 15)\n",
            "(9, 6, 16)\n",
            "(9, 7, 0)\n",
            "(9, 7, 1)\n",
            "(9, 7, 2)\n",
            "(9, 7, 3)\n",
            "(9, 7, 4)\n",
            "(9, 7, 5)\n",
            "(9, 7, 6)\n",
            "(9, 7, 7)\n",
            "(9, 7, 8)\n",
            "(9, 7, 9)\n",
            "(9, 7, 10)\n",
            "(9, 7, 11)\n",
            "(9, 7, 12)\n",
            "(9, 7, 13)\n",
            "(9, 7, 14)\n",
            "(9, 8, 0)\n",
            "(9, 8, 1)\n",
            "(9, 8, 2)\n",
            "(9, 8, 3)\n",
            "(9, 8, 4)\n",
            "(9, 8, 5)\n",
            "(9, 8, 6)\n",
            "(9, 8, 7)\n",
            "(9, 8, 8)\n",
            "(9, 8, 9)\n",
            "(9, 8, 10)\n",
            "(9, 8, 11)\n",
            "(9, 8, 12)\n",
            "(9, 8, 13)\n",
            "(9, 9, 0)\n",
            "(9, 9, 1)\n",
            "(9, 9, 2)\n",
            "(9, 9, 3)\n",
            "(9, 9, 4)\n",
            "(9, 9, 5)\n",
            "(9, 9, 6)\n",
            "(9, 9, 7)\n",
            "(9, 9, 8)\n",
            "(9, 9, 9)\n",
            "(9, 9, 10)\n",
            "(9, 9, 11)\n",
            "(9, 10, 0)\n",
            "(9, 10, 1)\n",
            "(9, 10, 2)\n",
            "(9, 10, 3)\n",
            "(9, 10, 4)\n",
            "(9, 10, 5)\n",
            "(9, 10, 6)\n",
            "(9, 10, 7)\n",
            "(9, 10, 8)\n",
            "(9, 11, 0)\n",
            "(9, 11, 1)\n",
            "(9, 11, 2)\n",
            "(9, 11, 3)\n",
            "(9, 11, 4)\n",
            "(10, 1, 0)\n",
            "(10, 1, 1)\n",
            "(10, 1, 2)\n",
            "(10, 1, 3)\n",
            "(10, 1, 4)\n",
            "(10, 1, 5)\n",
            "(10, 1, 6)\n",
            "(10, 1, 7)\n",
            "(10, 1, 8)\n",
            "(10, 1, 9)\n",
            "(10, 1, 10)\n",
            "(10, 1, 11)\n",
            "(10, 1, 12)\n",
            "(10, 1, 13)\n",
            "(10, 1, 14)\n",
            "(10, 1, 15)\n",
            "(10, 1, 16)\n",
            "(10, 1, 17)\n",
            "(10, 2, 0)\n",
            "(10, 2, 1)\n",
            "(10, 2, 2)\n",
            "(10, 2, 3)\n",
            "(10, 2, 4)\n",
            "(10, 2, 5)\n",
            "(10, 2, 6)\n",
            "(10, 2, 7)\n",
            "(10, 2, 8)\n",
            "(10, 2, 9)\n",
            "(10, 2, 10)\n",
            "(10, 2, 11)\n",
            "(10, 2, 12)\n",
            "(10, 2, 13)\n",
            "(10, 2, 14)\n",
            "(10, 2, 15)\n",
            "(10, 2, 16)\n",
            "(10, 2, 17)\n",
            "(10, 3, 0)\n",
            "(10, 3, 1)\n",
            "(10, 3, 2)\n",
            "(10, 3, 3)\n",
            "(10, 3, 4)\n",
            "(10, 3, 5)\n",
            "(10, 3, 6)\n",
            "(10, 3, 7)\n",
            "(10, 3, 8)\n",
            "(10, 3, 9)\n",
            "(10, 3, 10)\n",
            "(10, 3, 11)\n",
            "(10, 3, 12)\n",
            "(10, 3, 13)\n",
            "(10, 3, 14)\n",
            "(10, 3, 15)\n",
            "(10, 3, 16)\n",
            "(10, 4, 0)\n",
            "(10, 4, 1)\n",
            "(10, 4, 2)\n",
            "(10, 4, 3)\n",
            "(10, 4, 4)\n",
            "(10, 4, 5)\n",
            "(10, 4, 6)\n",
            "(10, 4, 7)\n",
            "(10, 4, 8)\n",
            "(10, 4, 9)\n",
            "(10, 4, 10)\n",
            "(10, 4, 11)\n",
            "(10, 4, 12)\n",
            "(10, 4, 13)\n",
            "(10, 4, 14)\n",
            "(10, 4, 15)\n",
            "(10, 4, 16)\n",
            "(10, 5, 0)\n",
            "(10, 5, 1)\n",
            "(10, 5, 2)\n",
            "(10, 5, 3)\n",
            "(10, 5, 4)\n",
            "(10, 5, 5)\n",
            "(10, 5, 6)\n",
            "(10, 5, 7)\n",
            "(10, 5, 8)\n",
            "(10, 5, 9)\n",
            "(10, 5, 10)\n",
            "(10, 5, 11)\n",
            "(10, 5, 12)\n",
            "(10, 5, 13)\n",
            "(10, 5, 14)\n",
            "(10, 5, 15)\n",
            "(10, 6, 0)\n",
            "(10, 6, 1)\n",
            "(10, 6, 2)\n",
            "(10, 6, 3)\n",
            "(10, 6, 4)\n",
            "(10, 6, 5)\n",
            "(10, 6, 6)\n",
            "(10, 6, 7)\n",
            "(10, 6, 8)\n",
            "(10, 6, 9)\n",
            "(10, 6, 10)\n",
            "(10, 6, 11)\n",
            "(10, 6, 12)\n",
            "(10, 6, 13)\n",
            "(10, 6, 14)\n",
            "(10, 7, 0)\n",
            "(10, 7, 1)\n",
            "(10, 7, 2)\n",
            "(10, 7, 3)\n",
            "(10, 7, 4)\n",
            "(10, 7, 5)\n",
            "(10, 7, 6)\n",
            "(10, 7, 7)\n",
            "(10, 7, 8)\n",
            "(10, 7, 9)\n",
            "(10, 7, 10)\n",
            "(10, 7, 11)\n",
            "(10, 7, 12)\n",
            "(10, 8, 0)\n",
            "(10, 8, 1)\n",
            "(10, 8, 2)\n",
            "(10, 8, 3)\n",
            "(10, 8, 4)\n",
            "(10, 8, 5)\n",
            "(10, 8, 6)\n",
            "(10, 8, 7)\n",
            "(10, 8, 8)\n",
            "(10, 8, 9)\n",
            "(10, 8, 10)\n",
            "(10, 8, 11)\n",
            "(10, 9, 0)\n",
            "(10, 9, 1)\n",
            "(10, 9, 2)\n",
            "(10, 9, 3)\n",
            "(10, 9, 4)\n",
            "(10, 9, 5)\n",
            "(10, 9, 6)\n",
            "(10, 9, 7)\n",
            "(10, 9, 8)\n",
            "(10, 10, 0)\n",
            "(10, 10, 1)\n",
            "(10, 10, 2)\n",
            "(10, 10, 3)\n",
            "(10, 10, 4)\n",
            "(10, 10, 5)\n",
            "(11, 1, 0)\n",
            "(11, 1, 1)\n",
            "(11, 1, 2)\n",
            "(11, 1, 3)\n",
            "(11, 1, 4)\n",
            "(11, 1, 5)\n",
            "(11, 1, 6)\n",
            "(11, 1, 7)\n",
            "(11, 1, 8)\n",
            "(11, 1, 9)\n",
            "(11, 1, 10)\n",
            "(11, 1, 11)\n",
            "(11, 1, 12)\n",
            "(11, 1, 13)\n",
            "(11, 1, 14)\n",
            "(11, 1, 15)\n",
            "(11, 2, 0)\n",
            "(11, 2, 1)\n",
            "(11, 2, 2)\n",
            "(11, 2, 3)\n",
            "(11, 2, 4)\n",
            "(11, 2, 5)\n",
            "(11, 2, 6)\n",
            "(11, 2, 7)\n",
            "(11, 2, 8)\n",
            "(11, 2, 9)\n",
            "(11, 2, 10)\n",
            "(11, 2, 11)\n",
            "(11, 2, 12)\n",
            "(11, 2, 13)\n",
            "(11, 2, 14)\n",
            "(11, 2, 15)\n",
            "(11, 3, 0)\n",
            "(11, 3, 1)\n",
            "(11, 3, 2)\n",
            "(11, 3, 3)\n",
            "(11, 3, 4)\n",
            "(11, 3, 5)\n",
            "(11, 3, 6)\n",
            "(11, 3, 7)\n",
            "(11, 3, 8)\n",
            "(11, 3, 9)\n",
            "(11, 3, 10)\n",
            "(11, 3, 11)\n",
            "(11, 3, 12)\n",
            "(11, 3, 13)\n",
            "(11, 3, 14)\n",
            "(11, 4, 0)\n",
            "(11, 4, 1)\n",
            "(11, 4, 2)\n",
            "(11, 4, 3)\n",
            "(11, 4, 4)\n",
            "(11, 4, 5)\n",
            "(11, 4, 6)\n",
            "(11, 4, 7)\n",
            "(11, 4, 8)\n",
            "(11, 4, 9)\n",
            "(11, 4, 10)\n",
            "(11, 4, 11)\n",
            "(11, 4, 12)\n",
            "(11, 4, 13)\n",
            "(11, 4, 14)\n",
            "(11, 5, 0)\n",
            "(11, 5, 1)\n",
            "(11, 5, 2)\n",
            "(11, 5, 3)\n",
            "(11, 5, 4)\n",
            "(11, 5, 5)\n",
            "(11, 5, 6)\n",
            "(11, 5, 7)\n",
            "(11, 5, 8)\n",
            "(11, 5, 9)\n",
            "(11, 5, 10)\n",
            "(11, 5, 11)\n",
            "(11, 5, 12)\n",
            "(11, 5, 13)\n",
            "(11, 6, 0)\n",
            "(11, 6, 1)\n",
            "(11, 6, 2)\n",
            "(11, 6, 3)\n",
            "(11, 6, 4)\n",
            "(11, 6, 5)\n",
            "(11, 6, 6)\n",
            "(11, 6, 7)\n",
            "(11, 6, 8)\n",
            "(11, 6, 9)\n",
            "(11, 6, 10)\n",
            "(11, 6, 11)\n",
            "(11, 6, 12)\n",
            "(11, 7, 0)\n",
            "(11, 7, 1)\n",
            "(11, 7, 2)\n",
            "(11, 7, 3)\n",
            "(11, 7, 4)\n",
            "(11, 7, 5)\n",
            "(11, 7, 6)\n",
            "(11, 7, 7)\n",
            "(11, 7, 8)\n",
            "(11, 7, 9)\n",
            "(11, 7, 10)\n",
            "(11, 8, 0)\n",
            "(11, 8, 1)\n",
            "(11, 8, 2)\n",
            "(11, 8, 3)\n",
            "(11, 8, 4)\n",
            "(11, 8, 5)\n",
            "(11, 8, 6)\n",
            "(11, 8, 7)\n",
            "(11, 8, 8)\n",
            "(11, 9, 0)\n",
            "(11, 9, 1)\n",
            "(11, 9, 2)\n",
            "(11, 9, 3)\n",
            "(11, 9, 4)\n",
            "(12, 1, 0)\n",
            "(12, 1, 1)\n",
            "(12, 1, 2)\n",
            "(12, 1, 3)\n",
            "(12, 1, 4)\n",
            "(12, 1, 5)\n",
            "(12, 1, 6)\n",
            "(12, 1, 7)\n",
            "(12, 1, 8)\n",
            "(12, 1, 9)\n",
            "(12, 1, 10)\n",
            "(12, 1, 11)\n",
            "(12, 1, 12)\n",
            "(12, 1, 13)\n",
            "(12, 2, 0)\n",
            "(12, 2, 1)\n",
            "(12, 2, 2)\n",
            "(12, 2, 3)\n",
            "(12, 2, 4)\n",
            "(12, 2, 5)\n",
            "(12, 2, 6)\n",
            "(12, 2, 7)\n",
            "(12, 2, 8)\n",
            "(12, 2, 9)\n",
            "(12, 2, 10)\n",
            "(12, 2, 11)\n",
            "(12, 2, 12)\n",
            "(12, 2, 13)\n",
            "(12, 3, 0)\n",
            "(12, 3, 1)\n",
            "(12, 3, 2)\n",
            "(12, 3, 3)\n",
            "(12, 3, 4)\n",
            "(12, 3, 5)\n",
            "(12, 3, 6)\n",
            "(12, 3, 7)\n",
            "(12, 3, 8)\n",
            "(12, 3, 9)\n",
            "(12, 3, 10)\n",
            "(12, 3, 11)\n",
            "(12, 3, 12)\n",
            "(12, 4, 0)\n",
            "(12, 4, 1)\n",
            "(12, 4, 2)\n",
            "(12, 4, 3)\n",
            "(12, 4, 4)\n",
            "(12, 4, 5)\n",
            "(12, 4, 6)\n",
            "(12, 4, 7)\n",
            "(12, 4, 8)\n",
            "(12, 4, 9)\n",
            "(12, 4, 10)\n",
            "(12, 4, 11)\n",
            "(12, 5, 0)\n",
            "(12, 5, 1)\n",
            "(12, 5, 2)\n",
            "(12, 5, 3)\n",
            "(12, 5, 4)\n",
            "(12, 5, 5)\n",
            "(12, 5, 6)\n",
            "(12, 5, 7)\n",
            "(12, 5, 8)\n",
            "(12, 5, 9)\n",
            "(12, 5, 10)\n",
            "(12, 6, 0)\n",
            "(12, 6, 1)\n",
            "(12, 6, 2)\n",
            "(12, 6, 3)\n",
            "(12, 6, 4)\n",
            "(12, 6, 5)\n",
            "(12, 6, 6)\n",
            "(12, 6, 7)\n",
            "(12, 6, 8)\n",
            "(12, 6, 9)\n",
            "(12, 7, 0)\n",
            "(12, 7, 1)\n",
            "(12, 7, 2)\n",
            "(12, 7, 3)\n",
            "(12, 7, 4)\n",
            "(12, 7, 5)\n",
            "(12, 7, 6)\n",
            "(12, 8, 0)\n",
            "(12, 8, 1)\n",
            "(12, 8, 2)\n",
            "(13, 1, 0)\n",
            "(13, 1, 1)\n",
            "(13, 1, 2)\n",
            "(13, 1, 3)\n",
            "(13, 1, 4)\n",
            "(13, 1, 5)\n",
            "(13, 1, 6)\n",
            "(13, 1, 7)\n",
            "(13, 1, 8)\n",
            "(13, 1, 9)\n",
            "(13, 1, 10)\n",
            "(13, 2, 0)\n",
            "(13, 2, 1)\n",
            "(13, 2, 2)\n",
            "(13, 2, 3)\n",
            "(13, 2, 4)\n",
            "(13, 2, 5)\n",
            "(13, 2, 6)\n",
            "(13, 2, 7)\n",
            "(13, 2, 8)\n",
            "(13, 2, 9)\n",
            "(13, 2, 10)\n",
            "(13, 3, 0)\n",
            "(13, 3, 1)\n",
            "(13, 3, 2)\n",
            "(13, 3, 3)\n",
            "(13, 3, 4)\n",
            "(13, 3, 5)\n",
            "(13, 3, 6)\n",
            "(13, 3, 7)\n",
            "(13, 3, 8)\n",
            "(13, 3, 9)\n",
            "(13, 4, 0)\n",
            "(13, 4, 1)\n",
            "(13, 4, 2)\n",
            "(13, 4, 3)\n",
            "(13, 4, 4)\n",
            "(13, 4, 5)\n",
            "(13, 4, 6)\n",
            "(13, 4, 7)\n",
            "(13, 4, 8)\n",
            "(13, 5, 0)\n",
            "(13, 5, 1)\n",
            "(13, 5, 2)\n",
            "(13, 5, 3)\n",
            "(13, 5, 4)\n",
            "(13, 5, 5)\n",
            "(13, 5, 6)\n",
            "(13, 6, 0)\n",
            "(13, 6, 1)\n",
            "(13, 6, 2)\n",
            "(13, 6, 3)\n",
            "(14, 1, 0)\n",
            "(14, 1, 1)\n",
            "(14, 1, 2)\n",
            "(14, 1, 3)\n",
            "(14, 1, 4)\n",
            "(14, 1, 5)\n",
            "(14, 1, 6)\n",
            "(14, 2, 0)\n",
            "(14, 2, 1)\n",
            "(14, 2, 2)\n",
            "(14, 2, 3)\n",
            "(14, 2, 4)\n",
            "(14, 2, 5)\n",
            "(14, 3, 0)\n",
            "(14, 3, 1)\n",
            "(14, 3, 2)\n",
            "(14, 3, 3)\n",
            "Number of Miller indices: 2761\n",
            "Anomalous flag: False\n",
            "Unit cell: (150.8, 150.8, 250.4, 90, 90, 90)\n",
            "Space group: P 4 (No. 75)\n",
            "Systematic absences: 0\n",
            "Centric reflections: 166\n",
            "Resolution range: 250.4 10.4043\n",
            "Completeness in resolution range: 1\n",
            "Completeness with d_max=infinity: 1\n",
            "Unit cell: (150.8, 150.8, 250.4, 90, 90, 90)\n",
            "Space group: P 4 (No. 75)\n"
          ]
        }
      ],
      "execution_count": 6,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "oJEs1KeCR7iC",
        "outputId": "07e3a436-47b1-4520-a963-387da87f09a0"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays extractReflectionsInShell\n",
        "\n",
        "- Extract the reflections in a shell.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"${1:3nd4}.mtz\")\n",
        "miller_arrays = mtz_obj.as_miller_arrays()\n",
        "for miller_array in miller_arrays:\n",
        "    miller_array_truncated = miller_array.resolution_filter(d_min=${2:2}, d_max=${3:5})\n",
        "print(miller_array_truncated)\n",
        " ```"
      ],
      "metadata": {
        "id": "l1NaO_5LSMWb"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"3nd4.mtz\")\n",
        "miller_arrays = mtz_obj.as_miller_arrays()\n",
        "for miller_array in miller_arrays:\n",
        "    miller_array_truncated = miller_array.resolution_filter(d_min=2, d_max=5)\n",
        "print(miller_array_truncated)\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "GkVVoB6gS1AV"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays allIndicesInUnitCell\n",
        "- Build miller indices given unit cell and resolution limit.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from cctbx import crystal\n",
        "from cctbx import miller\n",
        "\n",
        "ms = miller.build_set(\n",
        "    crystal_symmetry=crystal.symmetry(\n",
        "        space_group_symbol=\"${1:P4}\",\n",
        "        unit_cell=(${2:150.8,150.8,250.4,90.0,90.0,90.0})),\n",
        "    anomalous_flag=${3:False},\n",
        "    d_min=${4:1.4})\n",
        "msu = ms.map_to_asu()\n",
        "[print(hkl) for hkl in msu.indices()]\n",
        "print(msu.show_comprehensive_summary())\n",
        "```"
      ],
      "metadata": {
        "id": "_W4JYSOBaYIe"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from cctbx import crystal\n",
        "from cctbx import miller\n",
        "\n",
        "ms = miller.build_set(\n",
        "    crystal_symmetry=crystal.symmetry(\n",
        "        space_group_symbol=\"P4\",\n",
        "        unit_cell=(150.8,150.8,250.4,90.0,90.0,90.0)),\n",
        "    anomalous_flag=False,\n",
        "    d_min=1.4)\n",
        "msu = ms.map_to_asu()\n",
        "[print(hkl) for hkl in msu.indices()]\n",
        "print(msu.show_comprehensive_summary())"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "1KM7k-dpzQn9"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays printColumnLabelsMillerArray\n",
        "\n",
        "```python\n",
        "[print(f\"Column label: '${1:key[2]}'\")  for key in miller_arrays_dict.keys()]\n",
        "```"
      ],
      "metadata": {
        "id": "z8ZfZAfQzM8J"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(f\"Column label: key[2]\")  for key in miller_arrays_dict.keys()]"
      ],
      "outputs": [
        {
          "output_type": "error",
          "ename": "NameError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
            "Input \u001b[0;32mIn [1]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m [\u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mColumn label: key[2]\u001b[39m\u001b[38;5;124m\"\u001b[39m)  \u001b[38;5;28;01mfor\u001b[39;00m key \u001b[38;5;129;01min\u001b[39;00m \u001b[43mmiller_arrays_dict\u001b[49m\u001b[38;5;241m.\u001b[39mkeys()]\n",
            "\u001b[0;31mNameError\u001b[0m: name 'miller_arrays_dict' is not defined"
          ]
        }
      ],
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 166
        },
        "id": "dEEPNO53Le3P",
        "outputId": "6a664f4a-3f3c-412e-ecef-16bbdbb39c3e"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays generateAllIndices\n",
        "\n",
        "- Compute all possible Miller indices.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from cctbx import miller\n",
        "\n",
        "def generate_reflection_indices(uc, dmin):\n",
        "    maxh, maxk, maxl = uc.max_miller_indices(dmin)\n",
        "\n",
        "    indices = []\n",
        "\n",
        "    for h in range(-maxh, maxh + 1):\n",
        "        for k in range(-maxk, maxk + 1):\n",
        "            for l in range(-maxl, maxl + 1):\n",
        "                if h == 0 and k == 0 and l == 0:\n",
        "                    continue\n",
        "                if uc.d((h, k, l)) < dmin:\n",
        "                    continue\n",
        "        indices.append((h, k, l))\n",
        "    return indices\n",
        "    \n",
        "uc=(${1:5.4307,5.4307,5.4307,90.00,90.0,90.00})\n",
        "dmin=${2:1.0}\n",
        "```\n"
      ],
      "metadata": {
        "id": "ljCDcZi3zNSk"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from cctbx import miller\n",
        "\n",
        "def generate_reflection_indices(uc, dmin):\n",
        "    maxh, maxk, maxl = uc.max_miller_indices(dmin)\n",
        "    indices = []\n",
        "    for h in range(-maxh, maxh + 1):\n",
        "        for k in range(-maxk, maxk + 1):\n",
        "            for l in range(-maxl, maxl + 1):\n",
        "                if h == 0 and k == 0 and l == 0:\n",
        "                    continue\n",
        "                if uc.d((h, k, l)) < dmin:\n",
        "                    continue\n",
        "        indices.append((h, k, l))\n",
        "    return indices\n",
        "    \n",
        "uc=(5.4307,5.4307,5.4307,90.00,90.0,90.00)\n",
        "dmin=1.0\n",
        "generate_reflection_indices(uc=uc,dmin=dmin)\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "vqoTD7UJOZHh"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays iotbx mtz2array\n",
        "\n",
        "- Read in a mtz file into a Miller array with iotbx.file_reader.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.file_reader import any_file\n",
        "mtz_in = any_file(\"${1:data}.mtz\", force_type=\"mtz\")\n",
        "miller_arrays = mtz_in.file_server.miller_arrays\n",
        "```"
      ],
      "metadata": {
        "id": "laKArPEtzNVm"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.file_reader import any_file\n",
        "mtz_in = any_file(\"3nd4.mtz\", force_type=\"mtz\")\n",
        "miller_arrays = mtz_in.file_server.miller_arrays"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "kvZ3yeSTcAuA"
      }
    },
    {
      "cell_type": "markdown",
      "source": [],
      "metadata": {
        "id": "qW-cyRQoQ66-"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays normalizeStructureFactors\n",
        "\n",
        "- Calculate quasi-normalized structure factor.\n",
        "- The `$` below marks a site for editing."
      ],
      "metadata": {
        "id": "0eB254q0zNZn"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "all_e_values = miller_array.quasi_normalize_structure_factors().sort(by_value=\"data\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "i8ZQ8ogpX7v4"
      }
    },
    {
      "cell_type": "markdown",
      "source": [],
      "metadata": {
        "id": "RTW6NpLPQ8C9"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays truncate\n",
        "\n",
        "- Read mtz file into a Miller array, truncate by resolution, and print summary.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"${1:3nd4}.mtz\")\n",
        "miller_arrays = mtz_obj.as_miller_arrays()\n",
        "miller_array_truncated = miller_arrays[0].resolution_filter(d_min=${2:2}, d_max=${3:5})\n",
        "print(miller_array_truncated)\n",
        "miller_array_truncated.show_summary()\n",
        "```"
      ],
      "metadata": {
        "id": "dMbqmLzpzNc3"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"3nd4.mtz\")\n",
        "miller_arrays = mtz_obj.as_miller_arrays()\n",
        "miller_array_truncated = miller_arrays[0].resolution_filter(d_min=2, d_max=5)\n",
        "print(miller_array_truncated)\n",
        "miller_array_truncated.show_summary()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "YrP3HH2OYRfg"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays mtz2array\n",
        "\n",
        "- Read a mtz file into a miller array.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_file = any_reflection_file(\"${1:3hz7.mtz}\")\n",
        "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)\n",
        "```"
      ],
      "metadata": {
        "id": "uPjpz3PNzNgJ"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_file = any_reflection_file(\"3hz7.mtz\")\n",
        "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "WCDLUq1lYhG4"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays printColumnLabels\n",
        "\n",
        "- Print column labels in a Miller array."
      ],
      "metadata": {
        "id": "0wdtxPEzzNjj"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(\"Miller Array %s: %s\" % (i, miller_array.info().labels)) for i, miller_array in list(enumerate(miller_arrays))[:2]]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "f5dejIXVa4m3"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays wavelength\n",
        "\n",
        "- Print wavelengths of each miller array."
      ],
      "metadata": {
        "id": "50f8B2wjzNoN"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(\"Miller Array %s: %s\" % (i, miller_array.info().wavelength)) for i, miller_array in list(enumerate(miller_arrays))]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "Eh6DDiXCbP7w"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays source\n",
        "\n",
        "- Print the source of each miller array."
      ],
      "metadata": {
        "id": "WnYqAFGJzNrm"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "print(\"Miller Array %s: %s\" % (i, miller_array.info().source)) for i, miller_array in list(enumerate(miller_arrays))]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "cQQLu9rpbhXo"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays length\n",
        "\n",
        "- Print length of miller arrays (i.e., the number of datasets in a mtz file)."
      ],
      "metadata": {
        "id": "dxgLWtwmzNso"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "len(miller_arrays)"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "3JnS79gLbyVR"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays symmetry\n",
        "\n",
        "- Print the crystal symmetry of each miller array."
      ],
      "metadata": {
        "id": "7GLt1X59zNxl"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(\"Miller Array %s: %s\" % (i, miller_array.info().crystal_symmetry_from_file)) for i, miller_array in list(enumerate(miller_arrays))]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "UwLRu9bacBDJ"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays printHKLs\n",
        "\n",
        "- Print all of the miller indices for a given Miller array."
      ],
      "metadata": {
        "id": "fKsElrxuzNy7"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(hkl) for hkl in miller_arrays[0].indices()]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "vFqkHfNYcUBK"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays CCone-half\n",
        "\n",
        "- Return CC one-half for a given Miller array. \n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].cc_one_half()\n",
        "```\n"
      ],
      "metadata": {
        "id": "as7L_8TMzN4G"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].cc_one_half()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "Jj9SnIR8oXOq"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays dstar\n",
        "\n",
        "- Return the resolution range in d* in a specified Miller array.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].min_max_d_star_sq()\n",
        "```"
      ],
      "metadata": {
        "id": "ofXkd1wUzN7l"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].min_max_d_star_sq()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "mmIkf6shdHlv"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays DminDmax\n",
        "\n",
        "- Return the resolution range in Angstroms for a Miller array.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].d_max_min()\n",
        "```"
      ],
      "metadata": {
        "id": "u0dtBh-azN8z"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].d_max_min()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "tVss5RcTdiNw"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays IoverSig\n",
        "\n",
        "- Return the I/sig overall for a given Miller array.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].i_over_sig_i()\n",
        "```"
      ],
      "metadata": {
        "id": "NUYdXD53eCRk"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].i_over_sig_i()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "odwipdMCeLUk"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays CConeHalfSigmaTau\n",
        "\n",
        "- Return CC one-half sigma tau for a given Miller array.\n",
        "- The `$` below marks a site for editing.\n",
        "\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].cc_one_half_sigma_tau()\n",
        "```"
      ],
      "metadata": {
        "id": "GSEYaKiTec6l"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].cc_one_half_sigma_tau()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "jv0AVa8MeuLC"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays CConeHalf\n",
        "\n",
        "- Return CC one-half for a given Miller array.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].cc_one_half()\n",
        "```"
      ],
      "metadata": {
        "id": "nkUFihIYms4l"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].cc_one_half()"
      ],
      "outputs": [
        {
          "output_type": "error",
          "ename": "NameError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
            "Input \u001b[0;32mIn [3]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mmiller_arrays\u001b[49m[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mcc_one_half()\n",
            "\u001b[0;31mNameError\u001b[0m: name 'miller_arrays' is not defined"
          ]
        }
      ],
      "execution_count": 3,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 166
        },
        "id": "JWXeRfScnDrd",
        "outputId": "19d14f67-d878-4dda-b09b-8f1bc436209b"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays bijvoetRatios\n",
        "\n",
        "- Print the Bijvoet ratios in a specified Miller array.  May have to average by bin first.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "[print(i) for i in miller_arrays[${1:0}].bijvoet_ratios()]\n",
        "```"
      ],
      "metadata": {
        "id": "qVXI0d2dnRls"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(i) for i in miller_arrays[0].bijvoet_ratios()]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "_P21i4Pu7JBL"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays measurability\n",
        "\n",
        "- Return the `measurability` of the anomalous signal in a specified Miller array.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].measurability()\n",
        "```"
      ],
      "metadata": {
        "id": "-3oQVCL2ncub"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].measurability()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "ND4lacOt7a5C"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays anomalousSignal\n",
        "\n",
        "- Return the anomalous signal in a specified Miller array.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].anomalous_signal()\n",
        "```"
      ],
      "metadata": {
        "id": "b2u_Jslgnd3D"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].anomalous_signal()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "vPEkTpjbnh9x"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays comprehensiveSummary\n",
        "\n",
        "- Show comprehensive summary for a specified Miller array.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].show_comprehensive_summary()\n",
        "```"
      ],
      "metadata": {
        "id": "JtkFFrGonkOo"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].show_comprehensive_summary()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "6GvT6esp8D0x"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays numberBijvoetArrays\n",
        "\n",
        "- Show number of bijvoet pairs for a specified Miller array.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].n_bijvoet_pairs()\n",
        "```"
      ],
      "metadata": {
        "id": "fZMsGl4inlDb"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].n_bijvoet_pairs()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "elx5b1qU8lWR"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays wilsonRatio\n",
        "\n",
        "- Show wilson ratio of miller array for a specified Miller array. \n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "miller_arrays[${1:0}].wilson_ratio()\n",
        "```"
      ],
      "metadata": {
        "id": "S5qy4u3KnlzY"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays[0].wilson_ratio()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "r0ADosOS8w-X"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays IpIn\n",
        "\n",
        "- Unpack into I(+) and I(-) for a specified Miller array. \n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "Iobs = miller_arrays[${1:0}]\n",
        "i_plus, i_minus = Iobs.hemispheres_acentrics()\n",
        "ipd = i_plus.data()\n",
        "ip=list(ipd)\n",
        "imd = i_minus.data()\n",
        "im = list(imd)\n",
        "len(im)\n",
        "Iobs.show_summary()\n",
        "print(Iobs.info())\n",
        "print(Iobs.observation_type())\n",
        "```"
      ],
      "metadata": {
        "id": "OkL_GmUhnqIu"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "Iobs = miller_arrays[0]\n",
        "i_plus, i_minus = Iobs.hemispheres_acentrics()\n",
        "ipd = i_plus.data()\n",
        "ip=list(ipd)\n",
        "imd = i_minus.data()\n",
        "im = list(imd)\n",
        "len(im)\n",
        "Iobs.show_summary()\n",
        "print(Iobs.info())\n",
        "print(Iobs.observation_type())"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "utyc9_xv9KQR"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays printSelectRows\n",
        "\n",
        "- Print five rows of the Iobs for a specified Miller array. \n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "list(Iobs[${1:100:105}])\n",
        "```"
      ],
      "metadata": {
        "id": "FLF6gUo7nqz-"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "list(Iobs[100:105])"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "fHdAcAGd9d3d"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays extractIntensities\n",
        "\n",
        "- Extract just the intensities for a give Miller array and print ten rows of them.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "Iobs = miller_arrays[${1:0}]\n",
        "iobsdata = Iobs.data()\n",
        "list(iobsdata[${1:100:110}])\n",
        "```"
      ],
      "metadata": {
        "id": "KZNVYEWRnrb2"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "Iobs = miller_arrays[0]\n",
        "iobsdata = Iobs.data()\n",
        "list(iobsdata[100:110])"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "hWojAvzb9vXG"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays convert2MTZ\n",
        "\n",
        "- Convert a miller array into a mtz_dataset and write out as a mtz file.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "mtz_dataset = Iobs.as_mtz_dataset(column_root_label=\"${1:I}\")\n",
        "mtz_dataset.mtz_object().write(\"${2:3hz7intensities}.mtz\")\n",
        "```"
      ],
      "metadata": {
        "id": "K1b41D8tnr6U"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "mtz_dataset = Iobs.as_mtz_dataset(column_root_label=\"I\")\n",
        "mtz_dataset.mtz_object().write(\"3hz7intensities.mtz\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "ozXAhvz7-LrN"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays printIntensities\n",
        "\n",
        "- Print all of the intensities for a given Miller array.\n"
      ],
      "metadata": {
        "id": "qYWUWRVKnshU"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "[print(hkl) for hkl in miller_arrays[1].data()]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "E8DE7JSA-ZfM"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays \n",
        "\n",
        "- Read in the mtz file and print its column labels as a sanity check.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "mtz_filename2 = \"${1:3hz7intensities}.mtz\"\n",
        "mtz_file2 = mtz.object(mtz_filename2)\n",
        "mtz_file2.column_labels()\n",
        "```"
      ],
      "metadata": {
        "id": "dkhwYw2fns71"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "mtz_filename2 = \"3hz7intensities.mtz\"\n",
        "mtz_file2 = mtz.object(mtz_filename2)\n",
        "mtz_file2.column_labels()\n"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "Nh0uM-o5-uVT"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays array2Dictionary\n",
        "\n",
        "- Set up the arrays as dictionaries.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"${1:3nd4}.mtz\")\n",
        "# Only works with mtz.object. \n",
        "# Does not work if mtz is read in with iotbx.file_reader.\n",
        "miller_arrays_dict = mtz_obj.as_miller_arrays_dict()\n",
        "```"
      ],
      "metadata": {
        "id": "su6MkKzQntVm"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"3nd4.mtz\")\n",
        "# Only works with mtz.object. \n",
        "# Does not work if mtz is read in with iotbx.file_reader.\n",
        "miller_arrays_dict = mtz_obj.as_miller_arrays_dict()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "USFTyvwL_LJy"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays dictKeys\n",
        "\n",
        "- Print the miller keys() of a miller dictionary.\n"
      ],
      "metadata": {
        "id": "tUHS-bnrnt1Q"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "miller_arrays_dict.keys()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "3fpveeAs_mwV"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays printColumnsMillerDict\n",
        "\n",
        "- Print the column labels of Miller dictionary.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"${1:/Users/blaine/3nd4.mtz}\")\n",
        "# Only works with mtz.object. Does not work if mtz is read in with iotbx.file_reader.\n",
        "miller_arrays_dict = mtz_obj.as_miller_arrays_dict()\n",
        "[print(f\"Column label: {key[2]}\")  for key in miller_arrays_dict.keys()]\n",
        "```"
      ],
      "metadata": {
        "id": "LvBFFqQ7nuUR"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"/Users/blaine/3nd4.mtz\")\n",
        "# Only works with mtz.object. Does not work if mtz is read in with iotbx.file_reader.\n",
        "miller_arrays_dict = mtz_obj.as_miller_arrays_dict()\n",
        "[print(f\"Column label: {key[2]\")  for key in miller_arrays_dict.keys()]"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "jiAj8FGQACCi"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays changeMTZcolumns\n",
        "\n",
        "- Read in mtz file and write out with fewer columns.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_in = any_reflection_file(\"${1:/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz}\")\n",
        "\n",
        "miller_arrays = hkl_in.as_miller_arrays()\n",
        "\n",
        "i_obs =  miller_arrays[3]\n",
        "r_free_flags = miller_arrays[0]\n",
        "f_obs = i_obs.f_sq_as_f()\n",
        "\n",
        "mtz_dataset = i_obs.as_mtz_dataset(column_root_label=\"I\")\n",
        "mtz_dataset.add_miller_array(f_obs, column_root_label=\"F\")\n",
        "mtz_dataset.add_miller_array(r_free_flags,column_root_label=\"${2:FreeR_flag}\")\n",
        "mtz_dataset.mtz_object().write(\"${3:loxodata.mtz}\")\n",
        "```"
      ],
      "metadata": {
        "id": "3k-dvPMpnvDF"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_in = any_reflection_file(\"/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz\")\n",
        "\n",
        "miller_arrays = hkl_in.as_miller_arrays()\n",
        "\n",
        "i_obs =  miller_arrays[3]\n",
        "r_free_flags = miller_arrays[0]\n",
        "f_obs = i_obs.f_sq_as_f()\n",
        "\n",
        "mtz_dataset = i_obs.as_mtz_dataset(column_root_label=\"I\")\n",
        "mtz_dataset.add_miller_array(f_obs, column_root_label=\"F\")\n",
        "mtz_dataset.add_miller_array(r_free_flags,column_root_label=\"FreeR_flag\")\n",
        "mtz_dataset.mtz_object().write(\"loxodata.mtz\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "Uh80vFNKA0U6"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays generateLplot\n",
        "\n",
        "- The $ below marks a site for editing.\n",
        "- Use pandas to read in a hkl file with whitespace separators into a dataframe.\n",
        "- Append to the dataframe a column with F/sigmaF values.\n",
        "- Append to the dataframe a column with the absolute value of the L indices.\n",
        "- Average F/sigmaF by absL index.\n",
        "- Write to absL and F/sigmaF to csv file.\n",
        "\n",
        "```python\n",
        "mtzdata = pd.read_csv(\"${1:1524start}.hkl\", names=[\"H\",\"K\",\"L\",${2:\"F\",\"SIGF\"}], sep=\"\\s+\")\n",
        "mtzdata[\"FovSigF\"] = mtzdata.apply(lambda row: row[\"F\"] / row[\"SIGF\"], axis=1)\n",
        "mtzdata[\"absL\"] = mtzdata.apply(lambda row: abs(row[\"L\"]), axis=1)\n",
        "FovSigFabsL = mtzdata.groupby([mtzdata.absL]).FovSigF.mean()\n",
        "FovSigFabsL.to_csv(\"${3:test2}.csv\")\n",
        "```"
      ],
      "metadata": {
        "id": "yS1rU9KJnvrt"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "mtzdata = pd.read_csv(\"1524start.hkl\", names=[\"H\",\"K\",\"L\",\"F\",\"SIGF\"], sep=\"\\s+\")\n",
        "mtzdata[\"FovSigF\"] = mtzdata.apply(lambda row: row[\"F\"] / row[\"SIGF\"], axis=1)\n",
        "mtzdata[\"absL\"] = mtzdata.apply(lambda row: abs(row[\"L\"]), axis=1)\n",
        "FovSigFabsL = mtzdata.groupby([mtzdata.absL]).FovSigF.mean()\n",
        "FovSigFabsL.to_csv(\"test2.csv\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "tWCNjHx3Bv9W"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# xrayDataPlots IpIn_scatterplot\n",
        "\n",
        "- Scatter plot of I(+) and (I(-). The presence of an anomalous signal is indicated by deviations from x=y.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "%matplotlib inline\n",
        "import matplotlib.pyplot as plt\n",
        "import matplotlib as mpl\n",
        "import matplotlib.ticker as ticker\n",
        "from matplotlib.ticker import MultipleLocator #, FormatStrFormatter\n",
        "from matplotlib.ticker import FuncFormatter\n",
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "\n",
        "# >>> change the mtz file name\n",
        "hkl_file = any_reflection_file(\"${1:3hz7}.mtz\")\n",
        "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)\n",
        "Iobs = miller_arrays[1]\n",
        "i_plus, i_minus = Iobs.hemispheres_acentrics()\n",
        "ipd = i_plus.data()\n",
        "ip=list(ipd)\n",
        "imd = i_minus.data()\n",
        "im = list(imd)\n",
        "len(im)\n",
        "\n",
        "comma_fmt = FuncFormatter(lambda x, p: format(int(x), \",\"))\n",
        "\n",
        "mpl.rcParams[\"savefig.dpi\"] = 600\n",
        "mpl.rcParams[\"figure.dpi\"] = 600\n",
        "\n",
        "# Set to width of a one column on a two-column page.\n",
        "# May want to adjust settings for a slide.\n",
        "fig, ax = plt.subplots(figsize=[3.25, 3.25])\n",
        "ax.scatter(ip,im,c=\"k\",alpha=0.3,s=5.5)\n",
        "ax.set_xlabel(r\"I(+)\",fontsize=12)\n",
        "ax.set_ylabel(r\"I(-)\",fontsize=12)\n",
        "ax.xaxis.set_major_locator(MultipleLocator(50000.))\n",
        "ax.yaxis.set_major_locator(MultipleLocator(50000.))\n",
        "ax.get_xaxis().set_major_formatter(comma_fmt)\n",
        "ax.get_yaxis().set_major_formatter(comma_fmt)\n",
        "\n",
        "plt.xticks(fontsize=12)\n",
        "plt.yticks(fontsize=12)\n",
        "ax.grid(False)\n",
        "\n",
        "# >>> change name of the figure file\n",
        "plt.savefig(\"${1:3hz7}IpIm.pdf\",bbox_inches=\"tight\")\n",
        "```"
      ],
      "metadata": {
        "id": "C-IXE-2onwTn"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "%matplotlib inline\n",
        "import matplotlib.pyplot as plt\n",
        "import matplotlib as mpl\n",
        "import matplotlib.ticker as ticker\n",
        "from matplotlib.ticker import MultipleLocator #, FormatStrFormatter\n",
        "from matplotlib.ticker import FuncFormatter\n",
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "\n",
        "# >>> change the mtz file name\n",
        "hkl_file = any_reflection_file(\"3hz7.mtz\")\n",
        "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)\n",
        "Iobs = miller_arrays[1]\n",
        "i_plus, i_minus = Iobs.hemispheres_acentrics()\n",
        "ipd = i_plus.data()\n",
        "ip=list(ipd)\n",
        "imd = i_minus.data()\n",
        "im = list(imd)\n",
        "len(im)\n",
        "\n",
        "comma_fmt = FuncFormatter(lambda x, p: format(int(x), \",\"))\n",
        "\n",
        "mpl.rcParams[\"savefig.dpi\"] = 600\n",
        "mpl.rcParams[\"figure.dpi\"] = 600\n",
        "\n",
        "# Set to width of a one column on a two-column page.\n",
        "# May want to adjust settings for a slide.\n",
        "fig, ax = plt.subplots(figsize=[3.25, 3.25])\n",
        "ax.scatter(ip,im,c=\"k\",alpha=0.3,s=5.5)\n",
        "ax.set_xlabel(r\"I(+)\",fontsize=12)\n",
        "ax.set_ylabel(r\"I(-)\",fontsize=12)\n",
        "ax.xaxis.set_major_locator(MultipleLocator(50000.))\n",
        "ax.yaxis.set_major_locator(MultipleLocator(50000.))\n",
        "ax.get_xaxis().set_major_formatter(comma_fmt)\n",
        "ax.get_yaxis().set_major_formatter(comma_fmt)\n",
        "\n",
        "plt.xticks(fontsize=12)\n",
        "plt.yticks(fontsize=12)\n",
        "ax.grid(False)\n",
        "\n",
        "# >>> change name of the figure file\n",
        "plt.savefig(\"3hz7IpIm.pdf\",bbox_inches=\"tight\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "nQGA6y26Czsk"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# xrayDataPlot meanIvsDstar\n",
        "\n",
        "- Miller arrays to plot of bin mean intensity over dstar.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "# Description:  Miller arrays to plot of bin mean intensity over dstar\n",
        "# Source:  NA\n",
        "\n",
        "\"\"\"\n",
        "from iotbx.file_reader import any_file\n",
        "import matplotlib.pyplot as plt\n",
        "\n",
        "f = any_file(\"${1:/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz}\")\n",
        "\n",
        "print(f.file_type)\n",
        "f.show_summary()\n",
        "miller_arrays = f.file_server.miller_arrays\n",
        "iobs =  miller_arrays[3]\n",
        "flags = miller_arrays[0]\n",
        "iobs, flags = iobs.common_sets(other=flags)\n",
        "iobsData = iobs.data()\n",
        "list(iobsData[100:110])\n",
        "iobs.show_comprehensive_summary()\n",
        "# iobs.binner()\n",
        "n_bins = ${2:20}\n",
        "binner = iobs.setup_binner(n_bins=n_bins)\n",
        "binner.show_summary()\n",
        "\n",
        "used = list(binner.range_used())\n",
        "selections = [binner.selection(i) for i in used]\n",
        "means = [iobs.select(sel).mean() for sel in selections]\n",
        "\n",
        "from math import log\n",
        "lnmeans = [log(y) for y in means]\n",
        "\n",
        "d_star_power = 1.618034\n",
        "centers = binner.bin_centers(d_star_power)\n",
        "d_centers = list(centers**(-1 / d_star_power))\n",
        "d_centers\n",
        "\n",
        "# plt.ylabel(\"Natural log of the amplitudes squared\")\n",
        "# plt.xlabel(r\"$\\textrm{d^*}$ in $\\textrm{\\AA}$\")\n",
        "# ax.set_xlim(35, 1.5)\n",
        "# plt.scatter(d_centers,lnmeanss)\n",
        "\n",
        "fig, ax = plt.subplots()\n",
        "ax.scatter(d_centers,lnmeans)\n",
        "ax.set_xlim(${3:8}, ${4:1.5})  # decreasing\n",
        "ax.set_xlabel(r\"$d^*$ in $\\AA$\")\n",
        "ax.set_ylabel(\"Natural log of the intensities\")\n",
        "ax.grid(False)\n",
        "plt.savefig(\"${5:iobsvsdstar}.pdf\")\n",
        "```"
      ],
      "metadata": {
        "id": "vCWmdpGEn0hg"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.file_reader import any_file\n",
        "import matplotlib.pyplot as plt\n",
        "\n",
        "f = any_file(\"/Users/blaine/manuscripts/RETkinaseLoxo/ret_blu.mtz\")\n",
        "\n",
        "print(f.file_type)\n",
        "f.show_summary()\n",
        "miller_arrays = f.file_server.miller_arrays\n",
        "iobs =  miller_arrays[3]\n",
        "flags = miller_arrays[0]\n",
        "iobs, flags = iobs.common_sets(other=flags)\n",
        "iobsData = iobs.data()\n",
        "list(iobsData[100:110])\n",
        "iobs.show_comprehensive_summary()\n",
        "# iobs.binner()\n",
        "n_bins = 20\n",
        "binner = iobs.setup_binner(n_bins=n_bins)\n",
        "binner.show_summary()\n",
        "\n",
        "used = list(binner.range_used())\n",
        "selections = [binner.selection(i) for i in used]\n",
        "means = [iobs.select(sel).mean() for sel in selections]\n",
        "\n",
        "from math import log\n",
        "lnmeans = [log(y) for y in means]\n",
        "\n",
        "d_star_power = 1.618034\n",
        "centers = binner.bin_centers(d_star_power)\n",
        "d_centers = list(centers**(-1 / d_star_power))\n",
        "d_centers\n",
        "\n",
        "# plt.ylabel(\"Natural log of the amplitudes squared\")\n",
        "# plt.xlabel(r\"$\\textrm{d^*$ in $\\textrm{\\AA$\")\n",
        "# ax.set_xlim(35, 1.5)\n",
        "# plt.scatter(d_centers,lnmeanss)\n",
        "\n",
        "fig, ax = plt.subplots()\n",
        "ax.scatter(d_centers,lnmeans)\n",
        "ax.set_xlim(8, 1.5)  # decreasing\n",
        "ax.set_xlabel(r\"$d^*$ in $\\AA$\")\n",
        "ax.set_ylabel(\"Natural log of the intensities\")\n",
        "ax.grid(False)"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "LkQVKuKnE2eP"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# xrayDataPlot FcalcsVsResolutionBin\n",
        "\n",
        "- Example of computing Fcalcs and then plotting them by resolution bin. This script uses miller arrays and binner.\n",
        "- The $ below marks a site for editing.\n",
        "- This script reads in a phenix.refine mtz file.\n",
        "- It plots the R-factor by resolution bin.\n",
        "- The plots are made with matplotlib using miller arrays.\n",
        "- It also plots the correlation coefficients.\n",
        "- The plots were made with matplotlib.\n",
        "- This script was adapted from an example script in iotbx:  \n",
        "\n",
        "Source:  https://github.com/cctbx/cctbx_project/blob/master/\n",
        "iotbx/examples/recalculate_phenix_refine_r_factors.py\n",
        "\n",
        "\n",
        "```python\n",
        "# get_ipython().run_line_magic(\"matplotlib\", \"inline\")\n",
        "\n",
        "from __future__ import absolute_import, division, print_function\n",
        "from iotbx.reflection_file_utils import get_r_free_flags_scores\n",
        "from iotbx.file_reader import any_file\n",
        "import matplotlib\n",
        "import matplotlib.pyplot as plt\n",
        "\n",
        "\n",
        "\n",
        "def compute_r_factors(fobs, fmodel, flags):\n",
        "  fmodel, fobs = fmodel.common_sets(other=fobs)\n",
        "  fmodel, flags = fmodel.common_sets(other=flags)\n",
        "  fc_work = fmodel.select(~(flags.data()))\n",
        "  fo_work = fobs.select(~(flags.data()))\n",
        "  fc_test = fmodel.select(flags.data())\n",
        "  fo_test = fobs.select(flags.data())\n",
        "  r_work = fo_work.r1_factor(fc_work)\n",
        "  r_free = fo_test.r1_factor(fc_test)\n",
        "  \n",
        "  print(\"r_work = %.4f\" % r_work)\n",
        "  print(\"r_free = %.4f\" % r_free)\n",
        "  print(\"\")\n",
        "\n",
        "  binner = flags.setup_binner(n_bins=20)\n",
        "  d_star_power = 1.618034\n",
        "  centers = binner.bin_centers(d_star_power)\n",
        "  d_centers = list(centers**(-1 / d_star_power))\n",
        "#   for i in d_centers:\n",
        "#     print(i)\n",
        "    \n",
        "  fo_work.use_binning_of(flags)\n",
        "  fc_work.use_binner_of(fo_work)\n",
        "  fo_test.use_binning_of(fo_work)\n",
        "  fc_test.use_binning_of(fo_work)\n",
        "\n",
        "  r_work_list = []\n",
        "  r_free_list = []\n",
        "  cc_work_list = []\n",
        "  cc_free_list = []\n",
        "  for i_bin in fo_work.binner().range_all():\n",
        "    sel_work = fo_work.binner().selection(i_bin)\n",
        "    sel_test = fo_test.binner().selection(i_bin)\n",
        "    fo_work_bin = fo_work.select(sel_work)\n",
        "    fc_work_bin = fc_work.select(sel_work)\n",
        "    fo_test_bin = fo_test.select(sel_test)\n",
        "    fc_test_bin = fc_test.select(sel_test)\n",
        "    if fc_test_bin.size() == 0 : continue\n",
        "        \n",
        "    r_work_bin = fo_work_bin.r1_factor(other=fc_work_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_work_list.append(r_work_bin)\n",
        "    \n",
        "    r_free_bin = fo_test_bin.r1_factor(other=fc_test_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_free_list.append(r_free_bin)\n",
        "    \n",
        "    cc_work_bin = fo_work_bin.correlation(fc_work_bin).coefficient()\n",
        "    cc_work_list.append(cc_work_bin)\n",
        "    \n",
        "    cc_free_bin = fo_test_bin.correlation(fc_test_bin).coefficient()\n",
        "    cc_free_list.append(cc_free_bin)\n",
        "    \n",
        "    legend = flags.binner().bin_legend(i_bin, show_counts=False)\n",
        "    print(\"%s  %8d %8d  %.4f %.4f  %.3f %.3f\" % (legend, fo_work_bin.size(),\n",
        "      fo_test_bin.size(), r_work_bin, r_free_bin, cc_work_bin, cc_free_bin))\n",
        "    \n",
        "  return d_centers, r_work_list, r_free_list, cc_work_list, cc_free_list\n",
        "\n",
        "\n",
        "def plot_r_factors(d_centers, r_work_list, r_free_list):\n",
        "  plt.scatter(d_centers, r_work_list, label=r\"$\\mathit{R_{work}}$\")\n",
        "  plt.scatter(d_centers, r_free_list, label=r\"$\\mathit{R_{free}}$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA}$)\")\n",
        "  plt.ylabel(r\"R-factor (%)\")\n",
        "  plt.legend(loc=\"upper right\")\n",
        "  plt.savefig(\"Rs.pdf\")\n",
        "  plt.close()\n",
        "\n",
        "\n",
        "def plot_cc(d_centers, cc_work_list, cc_free_list):\n",
        "  plt.scatter(d_centers, cc_work_list, label=r\"$\\mathit{CC_{work}}$\")\n",
        "  plt.scatter(d_centers, cc_free_list, label=r\"$\\mathit{CC_{free}}$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA}$)\")\n",
        "  plt.ylabel(r\"Correlation Coefficeint Fo vs Fc (%)\")\n",
        "  plt.legend(loc=\"lower right\")\n",
        "  plt.savefig(\"CCs.pdf\")\n",
        "\n",
        "\n",
        "def run(input_mtz):\n",
        "  mtz_in = any_file(input_mtz)\n",
        "  ma = mtz_in.file_server.miller_arrays\n",
        "  flags = fmodel = fobs = None\n",
        "  # select the output arrays from phenix.refine.  This could easily be modified\n",
        "  # to handle MTZ files from other programs.\n",
        "  for array in ma :\n",
        "    labels = array.info().label_string()\n",
        "    if labels.startswith(\"R-free-flags\"):\n",
        "      flags = array\n",
        "    elif labels.startswith(\"F-model\"):\n",
        "      fmodel = abs(array)\n",
        "    elif labels.startswith(\"F-obs-filtered\"):\n",
        "      fobs = array\n",
        "  if (None in [flags, fobs, fmodel]):\n",
        "    raise RuntimeError(\"Not a valid phenix.refine output file\")\n",
        "  scores = get_r_free_flags_scores([flags], None)\n",
        "  test_flag_value = scores.test_flag_values[0]\n",
        "  flags = flags.customized_copy(data=flags.data()==test_flag_value)\n",
        "\n",
        "  (d_centers, \n",
        "   r_work_list, \n",
        "   r_free_list, \n",
        "   cc_work_list, \n",
        "   cc_free_list) = compute_r_factors(fobs, fmodel, flags)\n",
        "  plot_r_factors(d_centers, r_work_list, r_free_list)\n",
        "  plot_cc(d_centers, cc_work_list, cc_free_list)\n",
        "\n",
        "\n",
        "if (__name__ == \"__main__\"):\n",
        "  run(input_mtz=\"${1:28molrepEdited_5_refine_001}.mtz\")\n",
        "```"
      ],
      "metadata": {
        "id": "NuQ_TiBHn02b"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "# get_ipython().run_line_magic(\"matplotlib\", \"inline\")\n",
        "\n",
        "from __future__ import absolute_import, division, print_function\n",
        "from iotbx.reflection_file_utils import get_r_free_flags_scores\n",
        "from iotbx.file_reader import any_file\n",
        "import matplotlib\n",
        "import matplotlib.pyplot as plt\n",
        "\n",
        "\n",
        "\n",
        "def compute_r_factors(fobs, fmodel, flags):\n",
        "  fmodel, fobs = fmodel.common_sets(other=fobs)\n",
        "  fmodel, flags = fmodel.common_sets(other=flags)\n",
        "  fc_work = fmodel.select(~(flags.data()))\n",
        "  fo_work = fobs.select(~(flags.data()))\n",
        "  fc_test = fmodel.select(flags.data())\n",
        "  fo_test = fobs.select(flags.data())\n",
        "  r_work = fo_work.r1_factor(fc_work)\n",
        "  r_free = fo_test.r1_factor(fc_test)\n",
        "  \n",
        "  print(\"r_work = %.4f\" % r_work)\n",
        "  print(\"r_free = %.4f\" % r_free)\n",
        "  print(\"\")\n",
        "\n",
        "  binner = flags.setup_binner(n_bins=20)\n",
        "  d_star_power = 1.618034\n",
        "  centers = binner.bin_centers(d_star_power)\n",
        "  d_centers = list(centers**(-1 / d_star_power))\n",
        "#   for i in d_centers:\n",
        "#     print(i)\n",
        "    \n",
        "  fo_work.use_binning_of(flags)\n",
        "  fc_work.use_binner_of(fo_work)\n",
        "  fo_test.use_binning_of(fo_work)\n",
        "  fc_test.use_binning_of(fo_work)\n",
        "\n",
        "  r_work_list = []\n",
        "  r_free_list = []\n",
        "  cc_work_list = []\n",
        "  cc_free_list = []\n",
        "  for i_bin in fo_work.binner().range_all():\n",
        "    sel_work = fo_work.binner().selection(i_bin)\n",
        "    sel_test = fo_test.binner().selection(i_bin)\n",
        "    fo_work_bin = fo_work.select(sel_work)\n",
        "    fc_work_bin = fc_work.select(sel_work)\n",
        "    fo_test_bin = fo_test.select(sel_test)\n",
        "    fc_test_bin = fc_test.select(sel_test)\n",
        "    if fc_test_bin.size() == 0 : continue\n",
        "        \n",
        "    r_work_bin = fo_work_bin.r1_factor(other=fc_work_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_work_list.append(r_work_bin)\n",
        "    \n",
        "    r_free_bin = fo_test_bin.r1_factor(other=fc_test_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_free_list.append(r_free_bin)\n",
        "    \n",
        "    cc_work_bin = fo_work_bin.correlation(fc_work_bin).coefficient()\n",
        "    cc_work_list.append(cc_work_bin)\n",
        "    \n",
        "    cc_free_bin = fo_test_bin.correlation(fc_test_bin).coefficient()\n",
        "    cc_free_list.append(cc_free_bin)\n",
        "    \n",
        "    legend = flags.binner().bin_legend(i_bin, show_counts=False)\n",
        "    print(\"%s  %8d %8d  %.4f %.4f  %.3f %.3f\" % (legend, fo_work_bin.size(),\n",
        "      fo_test_bin.size(), r_work_bin, r_free_bin, cc_work_bin, cc_free_bin))\n",
        "    \n",
        "  return d_centers, r_work_list, r_free_list, cc_work_list, cc_free_list\n",
        "\n",
        "\n",
        "def plot_r_factors(d_centers, r_work_list, r_free_list):\n",
        "  plt.scatter(d_centers, r_work_list, label=r\"$\\mathit{R_{work$\")\n",
        "  plt.scatter(d_centers, r_free_list, label=r\"$\\mathit{R_{free$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA$)\")\n",
        "  plt.ylabel(r\"R-factor (%)\")\n",
        "  plt.legend(loc=\"upper right\")\n",
        "  plt.savefig(\"Rs.pdf\")\n",
        "  plt.close()\n",
        "\n",
        "\n",
        "def plot_cc(d_centers, cc_work_list, cc_free_list):\n",
        "  plt.scatter(d_centers, cc_work_list, label=r\"$\\mathit{CC_{work$\")\n",
        "  plt.scatter(d_centers, cc_free_list, label=r\"$\\mathit{CC_{free$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA$)\")\n",
        "  plt.ylabel(r\"Correlation Coefficeint Fo vs Fc (%)\")\n",
        "  plt.legend(loc=\"lower right\")\n",
        "  plt.savefig(\"CCs.pdf\")\n",
        "\n",
        "\n",
        "def run(input_mtz):\n",
        "  mtz_in = any_file(input_mtz)\n",
        "  ma = mtz_in.file_server.miller_arrays\n",
        "  flags = fmodel = fobs = None\n",
        "  # select the output arrays from phenix.refine.  This could easily be modified\n",
        "  # to handle MTZ files from other programs.\n",
        "  for array in ma :\n",
        "    labels = array.info().label_string()\n",
        "    if labels.startswith(\"R-free-flags\"):\n",
        "      flags = array\n",
        "    elif labels.startswith(\"F-model\"):\n",
        "      fmodel = abs(array)\n",
        "    elif labels.startswith(\"F-obs-filtered\"):\n",
        "      fobs = array\n",
        "  if (None in [flags, fobs, fmodel]):\n",
        "    raise RuntimeError(\"Not a valid phenix.refine output file\")\n",
        "  scores = get_r_free_flags_scores([flags], None)\n",
        "  test_flag_value = scores.test_flag_values[0]\n",
        "  flags = flags.customized_copy(data=flags.data()==test_flag_value)\n",
        "\n",
        "  (d_centers, \n",
        "   r_work_list, \n",
        "   r_free_list, \n",
        "   cc_work_list, \n",
        "   cc_free_list) = compute_r_factors(fobs, fmodel, flags)\n",
        "  plot_r_factors(d_centers, r_work_list, r_free_list)\n",
        "  plot_cc(d_centers, cc_work_list, cc_free_list)\n",
        "\n",
        "\n",
        "if (__name__ == \"__main__\"):\n",
        "  run(input_mtz=\"28molrepEdited_5_refine_001.mtz\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "kvQ96ynp1EoW"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays RfactorByResolutionBin\n",
        "\n",
        "- Read in a phenix.refine mtz file. It plots the work and free R-factors by resolution bin.\n",
        "- The $ below marks a site for editing.\n",
        "- This script reads in a phenix.refine mtz file.\n",
        "- It plots the R-factor by resolution bin.\n",
        "- The plots are made with matplotlib using miller arrays.\n",
        "- It also plots the correlation coefficients.\n",
        "- The plots were made with matplotlib.\n",
        "\n",
        "This script was adapted from an example script in iotbx:  \n",
        "\n",
        "Source:  https://github.com/cctbx/cctbx_project/blob/master/iotbx/examples/recalculate_phenix_refine_r_factors.py\n",
        "\n",
        "\n",
        "```python\n",
        "# get_ipython().run_line_magic(\"matplotlib\", \"inline\")\n",
        "\n",
        "from __future__ import absolute_import, division, print_function\n",
        "from iotbx.reflection_file_utils import get_r_free_flags_scores\n",
        "from iotbx.file_reader import any_file\n",
        "import matplotlib\n",
        "import matplotlib.pyplot as plt\n",
        "\n",
        "\n",
        "\n",
        "def compute_r_factors(fobs, fmodel, flags):\n",
        "  fmodel, fobs = fmodel.common_sets(other=fobs)\n",
        "  fmodel, flags = fmodel.common_sets(other=flags)\n",
        "  fc_work = fmodel.select(~(flags.data()))\n",
        "  fo_work = fobs.select(~(flags.data()))\n",
        "  fc_test = fmodel.select(flags.data())\n",
        "  fo_test = fobs.select(flags.data())\n",
        "  r_work = fo_work.r1_factor(fc_work)\n",
        "  r_free = fo_test.r1_factor(fc_test)\n",
        "  \n",
        "  print(\"r_work = %.4f\" % r_work)\n",
        "  print(\"r_free = %.4f\" % r_free)\n",
        "  print(\"\")\n",
        "\n",
        "  binner = flags.setup_binner(n_bins=20)\n",
        "  d_star_power = 1.618034\n",
        "  centers = binner.bin_centers(d_star_power)\n",
        "  d_centers = list(centers**(-1 / d_star_power))\n",
        "#   for i in d_centers:\n",
        "#     print(i)\n",
        "    \n",
        "  fo_work.use_binning_of(flags)\n",
        "  fc_work.use_binner_of(fo_work)\n",
        "  fo_test.use_binning_of(fo_work)\n",
        "  fc_test.use_binning_of(fo_work)\n",
        "\n",
        "  r_work_list = []\n",
        "  r_free_list = []\n",
        "  cc_work_list = []\n",
        "  cc_free_list = []\n",
        "  for i_bin in fo_work.binner().range_all():\n",
        "    sel_work = fo_work.binner().selection(i_bin)\n",
        "    sel_test = fo_test.binner().selection(i_bin)\n",
        "    fo_work_bin = fo_work.select(sel_work)\n",
        "    fc_work_bin = fc_work.select(sel_work)\n",
        "    fo_test_bin = fo_test.select(sel_test)\n",
        "    fc_test_bin = fc_test.select(sel_test)\n",
        "    if fc_test_bin.size() == 0 : continue\n",
        "        \n",
        "    r_work_bin = fo_work_bin.r1_factor(other=fc_work_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_work_list.append(r_work_bin)\n",
        "    \n",
        "    r_free_bin = fo_test_bin.r1_factor(other=fc_test_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_free_list.append(r_free_bin)\n",
        "    \n",
        "    cc_work_bin = fo_work_bin.correlation(fc_work_bin).coefficient()\n",
        "    cc_work_list.append(cc_work_bin)\n",
        "    \n",
        "    cc_free_bin = fo_test_bin.correlation(fc_test_bin).coefficient()\n",
        "    cc_free_list.append(cc_free_bin)\n",
        "    \n",
        "    legend = flags.binner().bin_legend(i_bin, show_counts=False)\n",
        "    print(\"%s  %8d %8d  %.4f %.4f  %.3f %.3f\" % (legend, fo_work_bin.size(),\n",
        "      fo_test_bin.size(), r_work_bin, r_free_bin, cc_work_bin, cc_free_bin))\n",
        "    \n",
        "  return d_centers, r_work_list, r_free_list, cc_work_list, cc_free_list\n",
        "\n",
        "\n",
        "def plot_r_factors(d_centers, r_work_list, r_free_list):\n",
        "  plt.scatter(d_centers, r_work_list, label=r\"$\\mathit{R_{work}}$\")\n",
        "  plt.scatter(d_centers, r_free_list, label=r\"$\\mathit{R_{free}}$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA}$)\")\n",
        "  plt.ylabel(r\"R-factor (%)\")\n",
        "  plt.legend(loc=\"upper right\")\n",
        "  plt.savefig(\"Rs.pdf\")\n",
        "  plt.close()\n",
        "\n",
        "\n",
        "def plot_cc(d_centers, cc_work_list, cc_free_list):\n",
        "  plt.scatter(d_centers, cc_work_list, label=r\"$\\mathit{CC_{work}}$\")\n",
        "  plt.scatter(d_centers, cc_free_list, label=r\"$\\mathit{CC_{free}}$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA}$)\")\n",
        "  plt.ylabel(r\"Correlation Coefficeint Fo vs Fc (%)\")\n",
        "  plt.legend(loc=\"lower right\")\n",
        "  plt.savefig(\"CCs.pdf\")\n",
        "\n",
        "\n",
        "def run(input_mtz):\n",
        "  mtz_in = any_file(input_mtz)\n",
        "  ma = mtz_in.file_server.miller_arrays\n",
        "  flags = fmodel = fobs = None\n",
        "  # select the output arrays from phenix.refine.  This could easily be modified\n",
        "  # to handle MTZ files from other programs.\n",
        "  for array in ma :\n",
        "    labels = array.info().label_string()\n",
        "    if labels.startswith(\"R-free-flags\"):\n",
        "      flags = array\n",
        "    elif labels.startswith(\"F-model\"):\n",
        "      fmodel = abs(array)\n",
        "    elif labels.startswith(\"F-obs-filtered\"):\n",
        "      fobs = array\n",
        "  if (None in [flags, fobs, fmodel]):\n",
        "    raise RuntimeError(\"Not a valid phenix.refine output file\")\n",
        "  scores = get_r_free_flags_scores([flags], None)\n",
        "  test_flag_value = scores.test_flag_values[0]\n",
        "  flags = flags.customized_copy(data=flags.data()==test_flag_value)\n",
        "\n",
        "  (d_centers, \n",
        "   r_work_list, \n",
        "   r_free_list, \n",
        "   cc_work_list, \n",
        "   cc_free_list) = compute_r_factors(fobs, fmodel, flags)\n",
        "  plot_r_factors(d_centers, r_work_list, r_free_list)\n",
        "  plot_cc(d_centers, cc_work_list, cc_free_list)\n",
        "\n",
        "\n",
        "if (__name__ == \"__main__\"):\n",
        "  run(input_mtz=\"${1:28molrepEdited_5_refine_001}.mtz\")\n",
        "```"
      ],
      "metadata": {
        "id": "gnYSZg-5n1M-"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "# get_ipython().run_line_magic(\"matplotlib\", \"inline\")\n",
        "\n",
        "from __future__ import absolute_import, division, print_function\n",
        "from iotbx.reflection_file_utils import get_r_free_flags_scores\n",
        "from iotbx.file_reader import any_file\n",
        "import matplotlib\n",
        "import matplotlib.pyplot as plt\n",
        "\n",
        "\n",
        "\n",
        "def compute_r_factors(fobs, fmodel, flags):\n",
        "  fmodel, fobs = fmodel.common_sets(other=fobs)\n",
        "  fmodel, flags = fmodel.common_sets(other=flags)\n",
        "  fc_work = fmodel.select(~(flags.data()))\n",
        "  fo_work = fobs.select(~(flags.data()))\n",
        "  fc_test = fmodel.select(flags.data())\n",
        "  fo_test = fobs.select(flags.data())\n",
        "  r_work = fo_work.r1_factor(fc_work)\n",
        "  r_free = fo_test.r1_factor(fc_test)\n",
        "  \n",
        "  print(\"r_work = %.4f\" % r_work)\n",
        "  print(\"r_free = %.4f\" % r_free)\n",
        "  print(\"\")\n",
        "\n",
        "  binner = flags.setup_binner(n_bins=20)\n",
        "  d_star_power = 1.618034\n",
        "  centers = binner.bin_centers(d_star_power)\n",
        "  d_centers = list(centers**(-1 / d_star_power))\n",
        "#   for i in d_centers:\n",
        "#     print(i)\n",
        "    \n",
        "  fo_work.use_binning_of(flags)\n",
        "  fc_work.use_binner_of(fo_work)\n",
        "  fo_test.use_binning_of(fo_work)\n",
        "  fc_test.use_binning_of(fo_work)\n",
        "\n",
        "  r_work_list = []\n",
        "  r_free_list = []\n",
        "  cc_work_list = []\n",
        "  cc_free_list = []\n",
        "  for i_bin in fo_work.binner().range_all():\n",
        "    sel_work = fo_work.binner().selection(i_bin)\n",
        "    sel_test = fo_test.binner().selection(i_bin)\n",
        "    fo_work_bin = fo_work.select(sel_work)\n",
        "    fc_work_bin = fc_work.select(sel_work)\n",
        "    fo_test_bin = fo_test.select(sel_test)\n",
        "    fc_test_bin = fc_test.select(sel_test)\n",
        "    if fc_test_bin.size() == 0 : continue\n",
        "        \n",
        "    r_work_bin = fo_work_bin.r1_factor(other=fc_work_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_work_list.append(r_work_bin)\n",
        "    \n",
        "    r_free_bin = fo_test_bin.r1_factor(other=fc_test_bin,\n",
        "      assume_index_matching=True)\n",
        "    r_free_list.append(r_free_bin)\n",
        "    \n",
        "    cc_work_bin = fo_work_bin.correlation(fc_work_bin).coefficient()\n",
        "    cc_work_list.append(cc_work_bin)\n",
        "    \n",
        "    cc_free_bin = fo_test_bin.correlation(fc_test_bin).coefficient()\n",
        "    cc_free_list.append(cc_free_bin)\n",
        "    \n",
        "    legend = flags.binner().bin_legend(i_bin, show_counts=False)\n",
        "    print(\"%s  %8d %8d  %.4f %.4f  %.3f %.3f\" % (legend, fo_work_bin.size(),\n",
        "      fo_test_bin.size(), r_work_bin, r_free_bin, cc_work_bin, cc_free_bin))\n",
        "    \n",
        "  return d_centers, r_work_list, r_free_list, cc_work_list, cc_free_list\n",
        "\n",
        "\n",
        "def plot_r_factors(d_centers, r_work_list, r_free_list):\n",
        "  plt.scatter(d_centers, r_work_list, label=r\"$\\mathit{R_{work$\")\n",
        "  plt.scatter(d_centers, r_free_list, label=r\"$\\mathit{R_{free$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA$)\")\n",
        "  plt.ylabel(r\"R-factor (%)\")\n",
        "  plt.legend(loc=\"upper right\")\n",
        "  plt.savefig(\"Rs.pdf\")\n",
        "  plt.close()\n",
        "\n",
        "\n",
        "def plot_cc(d_centers, cc_work_list, cc_free_list):\n",
        "  plt.scatter(d_centers, cc_work_list, label=r\"$\\mathit{CC_{work$\")\n",
        "  plt.scatter(d_centers, cc_free_list, label=r\"$\\mathit{CC_{free$\")\n",
        "  plt.xlabel(r\"Resolution ($\\mathrm{\\AA$)\")\n",
        "  plt.ylabel(r\"Correlation Coefficeint Fo vs Fc (%)\")\n",
        "  plt.legend(loc=\"lower right\")\n",
        "  plt.savefig(\"CCs.pdf\")\n",
        "\n",
        "\n",
        "def run(input_mtz):\n",
        "  mtz_in = any_file(input_mtz)\n",
        "  ma = mtz_in.file_server.miller_arrays\n",
        "  flags = fmodel = fobs = None\n",
        "  # select the output arrays from phenix.refine.  This could easily be modified\n",
        "  # to handle MTZ files from other programs.\n",
        "  for array in ma :\n",
        "    labels = array.info().label_string()\n",
        "    if labels.startswith(\"R-free-flags\"):\n",
        "      flags = array\n",
        "    elif labels.startswith(\"F-model\"):\n",
        "      fmodel = abs(array)\n",
        "    elif labels.startswith(\"F-obs-filtered\"):\n",
        "      fobs = array\n",
        "  if (None in [flags, fobs, fmodel]):\n",
        "    raise RuntimeError(\"Not a valid phenix.refine output file\")\n",
        "  scores = get_r_free_flags_scores([flags], None)\n",
        "  test_flag_value = scores.test_flag_values[0]\n",
        "  flags = flags.customized_copy(data=flags.data()==test_flag_value)\n",
        "\n",
        "  (d_centers, \n",
        "   r_work_list, \n",
        "   r_free_list, \n",
        "   cc_work_list, \n",
        "   cc_free_list) = compute_r_factors(fobs, fmodel, flags)\n",
        "  plot_r_factors(d_centers, r_work_list, r_free_list)\n",
        "  plot_cc(d_centers, cc_work_list, cc_free_list)\n",
        "\n",
        "\n",
        "if (__name__ == \"__main__\"):\n",
        "  run(input_mtz=\"28molrepEdited_5_refine_001.mtz\")"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "iIWS6ahp2Dp0"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays dstarsVsMeasurability\n",
        "\n",
        "- Generate the list of dstars and measurability as lists for plotting by matplotlib.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_file = any_reflection_file(\"${1:3hz7}.mtz\")\n",
        "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)\n",
        "\n",
        "Iobs = miller_arrays[1]\n",
        "# Set up the bins\n",
        "n_bins = 50\n",
        "binner = Iobs.setup_binner(n_bins=n_bins)\n",
        "# binner.show_summary()\n",
        "used = list(binner.range_used())\n",
        "selections = [binner.selection(i) for i in used]\n",
        "\n",
        "# make d_centers for the x-axis\n",
        "d_star_power = 1.618034\n",
        "centers = binner.bin_centers(d_star_power)\n",
        "d_centers = list(centers**(-1 / d_star_power))\n",
        "\n",
        "# make list of the measurabilities by resolution bin\n",
        "meas = [Iobs.select(sel).measurability() for sel in selections]\n",
        "\n",
        "%matplotlib inline\n",
        "import matplotlib.pyplot as plt\n",
        "import matplotlib as mpl\n",
        "mpl.rcParams[\"savefig.dpi\"] = 600\n",
        "mpl.rcParams[\"figure.dpi\"] = 600\n",
        "\n",
        "fig, ax = plt.subplots(figsize=[3.25, 2.])\n",
        "ax.scatter(d_centers,lnmeans,c=\"k\",alpha=0.3,s=5.5)\n",
        "\n",
        "ax.set_xlim(8, 1.5) # decreasing time\n",
        "ax.set_xlabel(r\"$d^*$ in $\\AA$\",fontsize=12)\n",
        "ax.set_ylabel(\"ln(I)\",fontsize=12)\n",
        "plt.xticks(fontsize=12)\n",
        "plt.yticks(fontsize=12)\n",
        "ax.grid(False)\n",
        "plt.savefig(\"${1:3hz7}measureability.pdf\",bbox_inches=\"tight\")\n",
        "plt.show()\n",
        "```"
      ],
      "metadata": {
        "id": "8AQYaH3Mn1h_"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx.reflection_file_reader import any_reflection_file\n",
        "hkl_file = any_reflection_file(\"3hz7.mtz\")\n",
        "miller_arrays = hkl_file.as_miller_arrays(merge_equivalents=False)\n",
        "\n",
        "Iobs = miller_arrays[1]\n",
        "# Set up the bins\n",
        "n_bins = 50\n",
        "binner = Iobs.setup_binner(n_bins=n_bins)\n",
        "# binner.show_summary()\n",
        "used = list(binner.range_used())\n",
        "selections = [binner.selection(i) for i in used]\n",
        "\n",
        "# make d_centers for the x-axis\n",
        "d_star_power = 1.618034\n",
        "centers = binner.bin_centers(d_star_power)\n",
        "d_centers = list(centers**(-1 / d_star_power))\n",
        "\n",
        "# make list of the measurabilities by resolution bin\n",
        "meas = [Iobs.select(sel).measurability() for sel in selections]\n",
        "\n",
        "%matplotlib inline\n",
        "import matplotlib.pyplot as plt\n",
        "import matplotlib as mpl\n",
        "mpl.rcParams[\"savefig.dpi\"] = 600\n",
        "mpl.rcParams[\"figure.dpi\"] = 600\n",
        "\n",
        "fig, ax = plt.subplots(figsize=[3.25, 2.])\n",
        "ax.scatter(d_centers,lnmeans,c=\"k\",alpha=0.3,s=5.5)\n",
        "\n",
        "ax.set_xlim(8, 1.5) # decreasing time\n",
        "ax.set_xlabel(r\"$d^*$ in $\\AA$\",fontsize=12)\n",
        "ax.set_ylabel(\"ln(I)\",fontsize=12)\n",
        "plt.xticks(fontsize=12)\n",
        "plt.yticks(fontsize=12)\n",
        "ax.grid(False)\n",
        "plt.savefig(\"3hz7measureability.pdf\",bbox_inches=\"tight\")\n",
        "plt.show()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "SY6gYI2h2l3M"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# millerArrays dstarsLogMeans\n",
        "\n",
        "- Generate the list of dstars and logMeans as lists for plotting by matplotlib.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "used = list(binner.range_used())\n",
        "selections = [binner.selection(i) for i in used]\n",
        "\n",
        "# make means of the intensities by bin\n",
        "means = [Iobs.select(sel).mean() for sel in selections]\n",
        "from math import log\n",
        "lnmeans = [log(y) for y in means]\n",
        "\n",
        "# meansBR = [Iobs.bijvoet_ratios().select(sel).mean() for sel in selections]\n",
        "\n",
        "# make d_centers\n",
        "d_star_power = 1.618034\n",
        "centers = binner.bin_centers(d_star_power)\n",
        "d_centers = list(centers**(-1 / d_star_power))\n",
        "\n",
        "%matplotlib inline\n",
        "import matplotlib.pyplot as plt\n",
        "import matplotlib as mpl\n",
        "mpl.rcParams[\"savefig.dpi\"] = 600\n",
        "mpl.rcParams[\"figure.dpi\"] = 600\n",
        "\n",
        "fig, ax = plt.subplots(figsize=[3.25, 2.])\n",
        "ax.scatter(d_centers,lnmeans,c=\"k\",alpha=0.3,s=5.5)\n",
        "\n",
        "ax.set_xlim(${1:8, 1.5}) # decreasing time\n",
        "ax.set_xlabel(r\"$d^*$ in $\\AA$\",fontsize=12)\n",
        "ax.set_ylabel(\"ln(I)\",fontsize=12)\n",
        "plt.xticks(fontsize=12)\n",
        "plt.yticks(fontsize=12)\n",
        "ax.grid(False)\n",
        "plt.savefig(\"${2:3hz7}iobsvsdstar.pdf\",bbox_inches=\"tight\")\n",
        "plt.show()\n",
        "\n",
        "```"
      ],
      "metadata": {
        "id": "smfr1XU9n12C"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# eigenValues \n",
        "\n",
        "- The commands to find the eigenvalues and eigenvectors on a tensor. \n",
        "- The code is from a post to cctbxbb on 10 December 2020 by Richard Gildea in a reply to Robert Oeffner about code in cctbx for finding eigenvalues and eigenvectors. Robert was requesting the analog in cctbx to scipy.linalg.eig.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from scitbx.array_family import flex;\n",
        "from scitbx.linalg import eigensystem;\n",
        "m = flex.double((${1:-2, -4, 2, -2, 1, 2, 4, 2, 5}));\n",
        "m.reshape(flex.grid(3,3));\n",
        "es = eigensystem.real_symmetric(m);\n",
        "list(es.values());\n",
        "list(es.vectors());\n",
        "```"
      ],
      "metadata": {
        "id": "VP2O5X7Qn2MM"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from scitbx.array_family import flex;\n",
        "from scitbx.linalg import eigensystem;\n",
        "m = flex.double((-2, -4, 2, -2, 1, 2, 4, 2, 5));\n",
        "m.reshape(flex.grid(3,3));\n",
        "es = eigensystem.real_symmetric(m);\n",
        "list(es.values());\n",
        "list(es.vectors());"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "BDE4axwd5wAk"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# iotbx  \n",
        "\n",
        "- Read mtz file into a mtz object and print summary.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"/Users/blaine/${1:3nd4}.mtz\")\n",
        "mtz_obj.show_summary()\n",
        "```"
      ],
      "metadata": {
        "id": "TOCq7ZJhn2ha"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from iotbx import mtz\n",
        "mtz_obj = mtz.object(file_name=\"/Users/blaine/3nd4.mtz\")\n",
        "mtz_obj.show_summary()"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "QlW3wl-n6L3V"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# install CCTBX in PyMOL\n",
        "\n",
        "- Install cctbx inside PyMOL. This protocol worked on a Mac OS.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "# At the PyMOL prompt in the PyMOL GUI paste the following:\n",
        "conda install conda-forge::cctbx-base conda-forge::jupyter \n",
        "conda install conda-forge::jupyterlab=2.2.0\n",
        "conda install conda-forge::cctbx-base\n",
        "# In a terminal\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter serverextension enable --py jupyterlab --user\n",
        "/Applications/PyMOL.app/Contents/bin/ipython kernel install --name pymol --user\n",
        "/Applications/PyMOL.app/Contents/bin/pip install jupyterlab-snippets-multimenus\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter lab build\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter lab clean\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter --path # select the top option under Data for storing the libraries\n",
        "cd ~.local/share/jupyter # change as per output from prior line\n",
        "mkdir multimenus_snippets\n",
        "cd multimenus_snippets\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolcctbx.git cctbx\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolcctbxplus.git cctbx+\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolpysnips.git pymol\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolpysnipsplus.git pymol+\n",
        "/Applications/PyMOL.app/Contents/bin/ipython kernel install --name pymol37 --user\n",
        "```"
      ],
      "metadata": {
        "id": "sgnKMC5on209"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "# At the PyMOL prompt in the PyMOL GUI paste the following:\n",
        "conda install conda-forge::cctbx-base conda-forge::jupyter \n",
        "conda install conda-forge::jupyterlab=2.2.0\n",
        "conda install conda-forge::cctbx-base\n",
        "# In a terminal\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter serverextension enable --py jupyterlab --user\n",
        "/Applications/PyMOL.app/Contents/bin/ipython kernel install --name pymol --user\n",
        "/Applications/PyMOL.app/Contents/bin/pip install jupyterlab-snippets-multimenus\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter lab build\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter lab clean\n",
        "/Applications/PyMOL.app/Contents/bin/jupyter --path # select the top option under Data for storing the libraries\n",
        "cd ~.local/share/jupyter # change as per output from prior line\n",
        "mkdir multimenus_snippets\n",
        "cd multimenus_snippets\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolcctbx.git cctbx\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolcctbxplus.git cctbx+\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolpysnips.git pymol\n",
        "git clone https://github.com/MooersLab/juptyerlabpymolpysnipsplus.git pymol+\n",
        "/Applications/PyMOL.app/Contents/bin/ipython kernel install --name pymol37 --user"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "IMTnmC5i6kIw"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# mmtbx makeMaps\n",
        "\n",
        "- Read in mtz and pdb file and write map coefficients to a separate mtz file.\n",
        "- The $ below marks a site for editing.\n",
        "\n",
        "```python\n",
        "from mmtbx.maps.utils import create_map_from_pdb_and_mtz\n",
        "'''The phenix.maps commandline tool is the recommended approach.'''\n",
        "id=\"${1:3nd4}\"\n",
        "create_map_from_pdb_and_mtz(\n",
        "          pdb_file=\"%s.pdb\" % id,\n",
        "          mtz_file=\"%s.mtz\" % id,\n",
        "          output_file=\"%s_maps.mtz\" % id,\n",
        "          fill=False,\n",
        "          out=None,\n",
        "          llg_map=False,\n",
        "          remove_unknown_scatterering_type=True,\n",
        "          assume_pdb_data=False)\n",
        "```"
      ],
      "metadata": {
        "id": "DMBvceCon3N5"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from mmtbx.maps.utils import create_map_from_pdb_and_mtz\n",
        "'''The phenix.maps commandline tool is the recommended approach.'''\n",
        "id=\"3nd4\"\n",
        "create_map_from_pdb_and_mtz(\n",
        "          pdb_file=\"%s.pdb\" % id,\n",
        "          mtz_file=\"%s.mtz\" % id,\n",
        "          output_file=\"%s_maps.mtz\" % id,\n",
        "          fill=False,\n",
        "          out=None,\n",
        "          llg_map=False,\n",
        "          remove_unknown_scatterering_type=True,\n",
        "          assume_pdb_data=False)"
      ],
      "outputs": [],
      "execution_count": null,
      "metadata": {
        "id": "qJ37ZXi27ADa"
      }
    }
  ],
  "metadata": {
    "colab": {
      "name": "Copy of colabcctbxsnips.ipynb",
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