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    "# Visualizing Zeolite Framework Classifications\n",
    "\n",
    "Find all zeolite topologies that fit certain criteria:\n",
    "\n",
    "- largest channel is an 8 MR\n",
    "- largest channel is a 10 MR\n",
    "- largest channel is a 12 MR\n",
    "- realizable as AlPO\n",
    "- split plots by dimensionality of the channels, 0D, 1D, 2D, 3D\n",
    "\n",
    "### First some important imports "
   ]
  },
  {
   "cell_type": "code",
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   "source": [
    "import math\n",
    "import pandas as pd\n",
    "\n",
    "from bokeh.io import output_notebook\n",
    "from bokeh.plotting import figure, show, output_file\n",
    "from bokeh.charts import Bar\n",
    "from bokeh.charts.attributes import cat\n",
    "from bokeh.models import HoverTool, ColumnDataSource, FixedTicker\n",
    "from bokeh.palettes import Category10, Set1, Spectral\n",
    "\n",
    "output_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Obtain the data\n",
    "\n",
    "The data is accessed from the [``zefram``](https://bitbucket.org/lukaszmentel/zefram) package that has a collection of [IZA](http://www.iza-structure.org/databases/) and [ZEOMICS](http://helios.princeton.edu/zeomics/) databases accessible from Python."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from zefram import get_session, get_table, framework, Framework, RingSize"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The data is retrieved as ``pandas.DataFrame`` allowing convenient manipulations and vizualiztions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 229 entries, 0 to 228\n",
      "Data columns (total 45 columns):\n",
      "id                          229 non-null int64\n",
      "code                        229 non-null object\n",
      "atoms                       204 non-null float64\n",
      "cages                       204 non-null float64\n",
      "channels                    204 non-null float64\n",
      "connections                 204 non-null float64\n",
      "junctions                   204 non-null float64\n",
      "lcd                         204 non-null float64\n",
      "name                        204 non-null object\n",
      "pld                         201 non-null float64\n",
      "portals                     204 non-null float64\n",
      "tpw_abs                     204 non-null float64\n",
      "tpw_pct                     204 non-null float64\n",
      "url_zeomics                 204 non-null object\n",
      "a                           229 non-null float64\n",
      "b                           229 non-null float64\n",
      "c                           229 non-null float64\n",
      "alpha                       229 non-null float64\n",
      "beta                        229 non-null float64\n",
      "gamma                       229 non-null float64\n",
      "accessible_area             225 non-null float64\n",
      "accessible_area_m2pg        225 non-null float64\n",
      "accessible_volume           225 non-null float64\n",
      "accessible_volume_pct       225 non-null float64\n",
      "channel_dim                 229 non-null int64\n",
      "cif                         229 non-null object\n",
      "framework_density           229 non-null float64\n",
      "isdisordered                229 non-null bool\n",
      "isinterrupted               229 non-null bool\n",
      "maxdsd_a                    225 non-null float64\n",
      "maxdsd_b                    225 non-null float64\n",
      "maxdsd_c                    225 non-null float64\n",
      "maxdsi                      225 non-null float64\n",
      "occupiable_area             225 non-null float64\n",
      "occupiable_area_m2pg        225 non-null float64\n",
      "occupiable_volume           225 non-null float64\n",
      "occupiable_volume_pct       225 non-null float64\n",
      "rdls                        224 non-null float64\n",
      "sbu                         229 non-null object\n",
      "specific_accessible_area    225 non-null float64\n",
      "specific_occupiable_area    225 non-null float64\n",
      "td10                        229 non-null float64\n",
      "topological_density         176 non-null float64\n",
      "url_iza                     229 non-null object\n",
      "_spacegroup_id              229 non-null int64\n",
      "dtypes: bool(2), float64(34), int64(3), object(6)\n",
      "memory usage: 77.5+ KB\n"
     ]
    }
   ],
   "source": [
    "df = get_table('frameworks')\n",
    "df.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def assign_label(rings):\n",
    "    '''\n",
    "    assign string labels to a list of ints\n",
    "    matching the usual zeolite pore size labels\n",
    "    '''\n",
    "\n",
    "    if max(rings) == 8:\n",
    "        return 's'\n",
    "    elif max(rings) == 10:\n",
    "        if 8 in rings:\n",
    "            return 'ms'\n",
    "        else:\n",
    "            return 'm'\n",
    "    elif max(rings) == 12:\n",
    "        if 10 in rings and 8 in rings:\n",
    "            return 'lms'\n",
    "        elif 10 in rings:\n",
    "            return 'lm'\n",
    "        elif 8 in rings:\n",
    "            return 'ls'\n",
    "        else:\n",
    "            return 'l'\n",
    "        \n",
    "    else:\n",
    "        return None\n",
    "    \n",
    "def are_all_even(lst):\n",
    "    'check if all the elements of a list are even numbers'\n",
    "\n",
    "    return all(x % 2 == 0 for x in lst)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "df.loc[:, 'Rings'] = [[r.size for r in framework(row['code']).ring_sizes] for i, row in df.iterrows()]\n",
    "# get the largest ring\n",
    "df.loc[:, 'max_ring'] = df['Rings'].apply(max)\n",
    "# assign a string label\n",
    "df.loc[:, 'ring_label'] = df.Rings.apply(assign_label)\n",
    "df.loc[:, 'alpo_possible'] = df.Rings.apply(are_all_even)\n",
    "df.rename(columns={'lcd': 'Largest cavity dia.', 'pld': 'Pore limiting dia.',\n",
    "                   'maxdsi': 'Max dia. of inc. sphere'}, inplace=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Histogram\n",
    "\n",
    "Now we can plot a histogram depicting the distirubtion of frameworks depneding on the largest channel."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
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       "            var render_items = [{\"docid\":\"19a11c57-91d3-47cb-bc74-1c8a87eac861\",\"elementid\":\"078e6a8e-3ab8-4175-b63a-b526e9cf831c\",\"modelid\":\"691c2ac2-4420-4e9b-be78-61529994790b\"}];\n",
       "            \n",
       "            Bokeh.embed.embed_items(docs_json, render_items);\n",
       "          };\n",
       "          if (document.readyState != \"loading\") fn();\n",
       "          else document.addEventListener(\"DOMContentLoaded\", fn);\n",
       "        })();\n",
       "      },\n",
       "      function(Bokeh) {\n",
       "      }\n",
       "    ];\n",
       "  \n",
       "    function run_inline_js() {\n",
       "      \n",
       "      if ((window.Bokeh !== undefined) || (force === true)) {\n",
       "        for (var i = 0; i < inline_js.length; i++) {\n",
       "          inline_js[i](window.Bokeh);\n",
       "        }if (force === true) {\n",
       "          display_loaded();\n",
       "        }} else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(run_inline_js, 100);\n",
       "      } else if (!window._bokeh_failed_load) {\n",
       "        console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
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     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "p = Bar(df, 'max_ring', values='max_ring', agg='count', group='channel_dim',\n",
    "        xlabel='Largest channel [#T atoms]', ylabel='Number of frameworks',\n",
    "        legend='top_right', plot_width=760)\n",
    "show(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "gencols = ['code', 'channel_dim', 'Largest cavity dia.', 'Pore limiting dia.',\n",
    "           'Max dia. of inc. sphere', 'Rings', 'ring_label', 'alpo_possible']\n",
    "df0d = df.loc[df['channel_dim'] == 0, gencols].copy()\n",
    "df1d = df.loc[df['channel_dim'] == 1, gencols].copy()\n",
    "df2d = df.loc[df['channel_dim'] == 2, gencols].copy()\n",
    "df3d = df.loc[df['channel_dim'] == 3, gencols].copy()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plotting function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from sklearn.utils.extmath import cartesian\n",
    "\n",
    "def show_plot(dataframe, width=750, height=300,radius=0.4, alpha=0.6, title=None, showit=True):\n",
    "\n",
    "    df = dataframe.copy()\n",
    "\n",
    "    colors = {'s': Spectral[4][0], 'm': Spectral[4][1], 'l': Spectral[4][2], 'alpo': Spectral[4][3]}\n",
    "\n",
    "    ncols = 10\n",
    "    nitems = df.shape[0]\n",
    "\n",
    "    if nitems % ncols == 0:\n",
    "        nrows = nitems / ncols\n",
    "    else:\n",
    "        nrows = nitems // ncols + 1\n",
    "\n",
    "    xy = cartesian([np.arange(nrows), np.arange(ncols)])\n",
    "\n",
    "    df.loc[:, 'x'] = xy[:nitems, 1]\n",
    "    df.loc[:, 'y'] = xy[:nitems, 0]\n",
    "\n",
    "    source = ColumnDataSource(data=df)\n",
    "\n",
    "    hover = HoverTool(\n",
    "        tooltips=[\n",
    "            (\"Pore limiting diameter\", \"@Pore limiting dia.\"),\n",
    "            (\"Largest cavity D.\", \"@Largest cavity dia.\"),\n",
    "            (\"Max. D. Sph. I.\", \"@maxdsi\"),\n",
    "            (\"Dimensionality\", \"@channel_dim\"),\n",
    "            (\"Rings\", \"@rings\")\n",
    "        ]\n",
    "    )\n",
    "\n",
    "    p = figure(title=title,\n",
    "                x_range = (df.x.min() - 0.5, df.x.max() + 0.5),\n",
    "                y_range = (df.y.max() + 0.5, df.y.min() - 0.5),\n",
    "                plot_width=width, plot_height=height, tools='save')\n",
    "\n",
    "    # empty circles\n",
    "    x = df.loc[df.ring_label.str.len().isnull(), 'x'].values\n",
    "    y = df.loc[df.ring_label.str.len().isnull(), 'y'].values\n",
    "    p.circle(x, y, radius=radius, color='#ffffff', fill_alpha=1.0, line_color='#888888')\n",
    "    \n",
    "    # full circles\n",
    "    mask = df.ring_label.str.len() == 1\n",
    "    x = df.loc[mask, 'x'].values\n",
    "    y = df.loc[mask, 'y'].values\n",
    "    c = [colors[k] for k in df.loc[mask, 'ring_label']]\n",
    "    p.circle(x, y, radius=radius, color=c, fill_alpha=alpha, line_color='#888888')\n",
    "    \n",
    "    # half circles/wedges\n",
    "    mask = df.ring_label.str.len() == 2 \n",
    "    x = df.loc[mask, 'x'].values\n",
    "    y = df.loc[mask, 'y'].values\n",
    "    c1 = [colors[k] for k in df.loc[mask, 'ring_label'].str[0]]\n",
    "    c2 = [colors[k] for k in df.loc[mask, 'ring_label'].str[1]]\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/4, end_angle=5*math.pi/4,\n",
    "            color=c1, alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=5*math.pi/4, end_angle=math.pi/4,\n",
    "            color=c2, alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    # third circles/wedges\n",
    "    mask = df.ring_label.str.len() == 3\n",
    "    x = df.loc[mask, 'x'].values\n",
    "    y = df.loc[mask, 'y'].values\n",
    "    p.wedge(x, y, radius=radius, start_angle=math.pi/2, end_angle=7*math.pi/6,\n",
    "            color=colors['s'], alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=7*math.pi/6, end_angle=11*math.pi/6,\n",
    "            color=colors['m'], alpha=alpha, direction=\"anticlock\")\n",
    "    p.wedge(x, y, radius=radius, start_angle=11*math.pi/6, end_angle=math.pi/2,\n",
    "            color=colors['l'], alpha=alpha, direction=\"anticlock\")\n",
    "    \n",
    "    x = df.loc[df.alpo_possible, 'x'].values\n",
    "    y = df.loc[df.alpo_possible, 'y'].values\n",
    "    p.circle(x, y, radius=radius + 0.02, color='#ffffff', fill_alpha=0.0,\n",
    "             line_color=colors['alpo'], line_width=5.0, line_alpha=0.6)\n",
    "    \n",
    "    maxx = df['x'].max()\n",
    "    maxy = df['y'].max()\n",
    "    p.circle([maxx-3.2, maxx-2.2, maxx-1.2, maxx-0.2], [maxy] * 4,\n",
    "             color=[colors['s'], colors['m'], colors['l'], colors['alpo']], radius=0.1, alpha=alpha)\n",
    "    p.text([maxx-3, maxx-2, maxx-1, maxx-0.05], [maxy] * 4, text=['8', '10', '12', 'AlPO'],\n",
    "          text_alpha=0.7, text_align='left', text_baseline='middle')\n",
    "\n",
    "    text_props = {\n",
    "            \"text_font\": \"times\",\n",
    "            \"text_font_style\": \"bold\",\n",
    "            \"text_font_size\": \"13pt\",\n",
    "            \"source\": source,\n",
    "            \"angle\": 0,\n",
    "            \"color\": \"black\",\n",
    "            \"text_alpha\": 0.7,\n",
    "            \"text_align\": \"center\",\n",
    "            \"text_baseline\": \"middle\"\n",
    "        }\n",
    "\n",
    "    p.text(x=\"x\", y=\"y\", text=\"code\", **text_props)\n",
    "    p.grid.grid_line_color = None\n",
    "\n",
    "    p.axis[0].ticker.num_minor_ticks = 0\n",
    "    p.axis[1].ticker.num_minor_ticks = 0\n",
    "    p.axis.major_label_text_font_size = '0pt'\n",
    "    p.axis.major_tick_line_color = None\n",
    "\n",
    "    p.border_fill_color = 'white'\n",
    "    p.outline_line_width = 0\n",
    "    p.axis.visible = False\n",
    "    \n",
    "    \n",
    "    \n",
    "    p.legend.location = \"bottom_right\"\n",
    "    p.legend.orientation = \"horizontal\"\n",
    "\n",
    "    if showit:\n",
    "        show(p)\n",
    "    else:\n",
    "        return p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
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   "source": [
    "show_plot(df3d, width=760, height=750,radius=0.44, title='Tridirectional Zeolite Topologies')"
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   "metadata": {},
   "source": [
    "# Bar charts with pore sizes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
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   "outputs": [],
   "source": [
    "def diameters_bar_plot(data, category, title=None, showit=True):\n",
    "    '''\n",
    "    plot a bar chart for a given category\n",
    "    \n",
    "    Args:\n",
    "        data (pd.DataFrame) :\n",
    "        \n",
    "        category (str) : 's', 'm', 'l', 'ms',...\n",
    "\n",
    "    '''\n",
    "\n",
    "    mask = data.ring_label == category\n",
    "    cols = ['code', 'Max dia. of inc. sphere', 'Largest cavity dia.', 'Pore limiting dia.']\n",
    "    melted = pd.melt(data.loc[mask, cols].sort_values(by='Largest cavity dia.'),\n",
    "                     id_vars=['code'], value_vars=cols[1:])\n",
    "\n",
    "    p = Bar(melted, label=cat('code', sort=False), values=\"value\", group=\"variable\",\n",
    "            legend=\"top_left\", xlabel='Framwork code', ylabel='Length [Angstrom]',\n",
    "            plot_width=750, title=title)\n",
    "    \n",
    "    if showit:\n",
    "        show(p)\n",
    "    else:\n",
    "        return p"
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   "cell_type": "code",
   "execution_count": 14,
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   "source": [
    "diameters_bar_plot(df, 's', title='Small pore frameworks (8MR)')"
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  },
  {
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   "execution_count": 15,
   "metadata": {},
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    "diameters_bar_plot(df, 'm', title='Medium pore frameworks (10MR)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
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   "source": [
    "diameters_bar_plot(df, 'l', title='Large pore frameworks (12MR)')"
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   "source": [
    "diameters_bar_plot(df, 'lm', title='Medium-large pore frameworks (10 and 12 MR)')"
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   "source": [
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       "        })();\n",
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       "      function(Bokeh) {\n",
       "      }\n",
       "    ];\n",
       "  \n",
       "    function run_inline_js() {\n",
       "      \n",
       "      if ((window.Bokeh !== undefined) || (force === true)) {\n",
       "        for (var i = 0; i < inline_js.length; i++) {\n",
       "          inline_js[i](window.Bokeh);\n",
       "        }if (force === true) {\n",
       "          display_loaded();\n",
       "        }} else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(run_inline_js, 100);\n",
       "      } else if (!window._bokeh_failed_load) {\n",
       "        console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "        window._bokeh_failed_load = true;\n",
       "      } else if (force !== true) {\n",
       "        var cell = $(document.getElementById(\"5e70564c-16aa-45fc-ab7e-7706a85024d8\")).parents('.cell').data().cell;\n",
       "        cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "      }\n",
       "  \n",
       "    }\n",
       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
       "    } else {\n",
       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "        run_inline_js();\n",
       "      });\n",
       "    }\n",
       "  }(this));\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "diameters_bar_plot(df, 'lms', title='Small-medium-large pore frameworks (8, 10 and 12 MR)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/json": {
       "Software versions": [
        {
         "module": "Python",
         "version": "3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]"
        },
        {
         "module": "IPython",
         "version": "6.0.0"
        },
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         "module": "OS",
         "version": "Linux 3.16.0 4 amd64 x86_64 with debian 8.7"
        },
        {
         "module": "bokeh",
         "version": "0.12.5"
        },
        {
         "module": "pandas",
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        },
        {
         "module": "numpy",
         "version": "1.12.1"
        },
        {
         "module": "zefram",
         "version": "0.1.2"
        }
       ]
      },
      "text/html": [
       "<table><tr><th>Software</th><th>Version</th></tr><tr><td>Python</td><td>3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]</td></tr><tr><td>IPython</td><td>6.0.0</td></tr><tr><td>OS</td><td>Linux 3.16.0 4 amd64 x86_64 with debian 8.7</td></tr><tr><td>bokeh</td><td>0.12.5</td></tr><tr><td>pandas</td><td>0.19.2</td></tr><tr><td>numpy</td><td>1.12.1</td></tr><tr><td>zefram</td><td>0.1.2</td></tr><tr><td colspan='2'>Mon May 08 00:27:01 2017 CEST</td></tr></table>"
      ],
      "text/latex": [
       "\\begin{tabular}{|l|l|}\\hline\n",
       "{\\bf Software} & {\\bf Version} \\\\ \\hline\\hline\n",
       "Python & 3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] \\\\ \\hline\n",
       "IPython & 6.0.0 \\\\ \\hline\n",
       "OS & Linux 3.16.0 4 amd64 x86\\_64 with debian 8.7 \\\\ \\hline\n",
       "bokeh & 0.12.5 \\\\ \\hline\n",
       "pandas & 0.19.2 \\\\ \\hline\n",
       "numpy & 1.12.1 \\\\ \\hline\n",
       "zefram & 0.1.2 \\\\ \\hline\n",
       "\\hline \\multicolumn{2}{|l|}{Mon May 08 00:27:01 2017 CEST} \\\\ \\hline\n",
       "\\end{tabular}\n"
      ],
      "text/plain": [
       "Software versions\n",
       "Python 3.6.1 64bit [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]\n",
       "IPython 6.0.0\n",
       "OS Linux 3.16.0 4 amd64 x86_64 with debian 8.7\n",
       "bokeh 0.12.5\n",
       "pandas 0.19.2\n",
       "numpy 1.12.1\n",
       "zefram 0.1.2\n",
       "Mon May 08 00:27:01 2017 CEST"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%version_information bokeh, pandas, numpy, zefram"
   ]
  }
 ],
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