crystal_system_classification.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "from dotenv import load_dotenv\n",
    "from openai import OpenAI\n",
    "from pydantic import BaseModel\n",
    "\n",
    "load_dotenv(override=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "nanozymes_df = pd.read_excel(\"nanozymes.xlsx\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "syngony_dict = {\n",
    "    \"amorphous\": 0,\n",
    "    \"triclinic\": 1,\n",
    "    \"monoclinic\": 2,\n",
    "    \"orthorhombic\": 3,\n",
    "    \"tetragonal\": 4,\n",
    "    \"trigonal\": 5,\n",
    "    \"hexagonal\": 6,\n",
    "    \"cubic\": 7,\n",
    "}\n",
    "\n",
    "syngony_dict_reversed = {\n",
    "    0: \"amorphous\",\n",
    "    1: \"triclinic\",\n",
    "    2: \"monoclinic\",\n",
    "    3: \"orthorhombic\",\n",
    "    4: \"tetragonal\",\n",
    "    5: \"trigonal\",\n",
    "    6: \"hexagonal\",\n",
    "    7: \"cubic\",\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "nanozymes_df[\"syngony\"] = nanozymes_df[\"Syngony\"].map(syngony_dict_reversed)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "main_cs = ['amorphous', 'triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'trigonal', 'hexagonal', 'cubic']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "not_in_main_cs = nanozymes_df[~nanozymes_df['syngony'].isin(main_cs)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "nanozymes_df.drop(not_in_main_cs.index, axis=0, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "nanozymes_df.reset_index(inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "class Response(BaseModel):\n",
    "    syngony: str\n",
    "\n",
    "client = OpenAI()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "prompt = \"\"\"You are an expert in the field of nanozymes. Your task is to analyze formulas of nanomaterials and provide the crystal system (syngony) for each. The syngony should be one of the following: ['amorphous', 'triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'trigonal', 'hexagonal', 'cubic']\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "nanozymes_df['predicted_syngony'] = ''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_sampled = nanozymes_df.sample(100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_sampled.reset_index(inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
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       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>level_0</th>\n",
       "      <th>index</th>\n",
       "      <th>formula</th>\n",
       "      <th>activity</th>\n",
       "      <th>Syngony</th>\n",
       "      <th>length, nm</th>\n",
       "      <th>width, nm</th>\n",
       "      <th>depth, nm</th>\n",
       "      <th>surface</th>\n",
       "      <th>pol</th>\n",
       "      <th>...</th>\n",
       "      <th>ReactionType</th>\n",
       "      <th>C min, mM</th>\n",
       "      <th>C max, mM</th>\n",
       "      <th>C(const), mM</th>\n",
       "      <th>Ccat(mg/mL)</th>\n",
       "      <th>ph</th>\n",
       "      <th>temp, °C</th>\n",
       "      <th>link</th>\n",
       "      <th>syngony</th>\n",
       "      <th>predicted_syngony</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>318</td>\n",
       "      <td>329</td>\n",
       "      <td>Pt</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>4.40</td>\n",
       "      <td>4.40</td>\n",
       "      <td>4.40</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>TMB + H2O2</td>\n",
       "      <td>0.0625</td>\n",
       "      <td>0.5</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>https://doi.org/10.1016/j.snb.2017.07.108</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>868</td>\n",
       "      <td>1017</td>\n",
       "      <td>Fe2O3</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>5.0</td>\n",
       "      <td>30.00</td>\n",
       "      <td>30.00</td>\n",
       "      <td>30.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>TMB + H2O2</td>\n",
       "      <td>0.0100</td>\n",
       "      <td>1.0</td>\n",
       "      <td>700</td>\n",
       "      <td>0.0625</td>\n",
       "      <td>3.5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1021/acsami.7b13835</td>\n",
       "      <td>trigonal</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>78</td>\n",
       "      <td>78</td>\n",
       "      <td>Fe3O4</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>246.60</td>\n",
       "      <td>246.60</td>\n",
       "      <td>246.60</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>TMB + H2O2</td>\n",
       "      <td>0.0500</td>\n",
       "      <td>0.3</td>\n",
       "      <td>20</td>\n",
       "      <td>0.166243</td>\n",
       "      <td>4.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>https://doi.org/10.1016/j.procbio.2019.05.014</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>463</td>\n",
       "      <td>494</td>\n",
       "      <td>CoS</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>6.0</td>\n",
       "      <td>3000.00</td>\n",
       "      <td>3000.00</td>\n",
       "      <td>3000.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>H2O2 + TMB</td>\n",
       "      <td>0.0010</td>\n",
       "      <td>20.0</td>\n",
       "      <td>0.15</td>\n",
       "      <td>0.5</td>\n",
       "      <td>3.5</td>\n",
       "      <td>25.0</td>\n",
       "      <td>https://doi.org/10.1039/C6RA16619A</td>\n",
       "      <td>hexagonal</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>610</td>\n",
       "      <td>665</td>\n",
       "      <td>ZnS</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>10.00</td>\n",
       "      <td>10.00</td>\n",
       "      <td>10.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>TMB + H2O2</td>\n",
       "      <td>0.0010</td>\n",
       "      <td>1.0</td>\n",
       "      <td>10</td>\n",
       "      <td>0.00625</td>\n",
       "      <td>4.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>https://doi.org/10.1021/acssuschemeng.9b04043</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>870</td>\n",
       "      <td>1019</td>\n",
       "      <td>Fe2O3</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>5.0</td>\n",
       "      <td>33.00</td>\n",
       "      <td>33.00</td>\n",
       "      <td>33.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>TMB + H2O2</td>\n",
       "      <td>0.0100</td>\n",
       "      <td>1.0</td>\n",
       "      <td>700</td>\n",
       "      <td>0.0625</td>\n",
       "      <td>3.5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1021/acsami.7b13835</td>\n",
       "      <td>trigonal</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>419</td>\n",
       "      <td>448</td>\n",
       "      <td>Co4N</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>2500.00</td>\n",
       "      <td>80.00</td>\n",
       "      <td>80.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>H2O2 + TMB</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>80.0</td>\n",
       "      <td>0.8</td>\n",
       "      <td>0.015</td>\n",
       "      <td>4.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>https://doi.org/10.1021/acsami.7b09861</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>61</td>\n",
       "      <td>61</td>\n",
       "      <td>Co3O4/CeO2</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>2000.00</td>\n",
       "      <td>200.00</td>\n",
       "      <td>200.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>poly(N-Vinylpyrrolidone)</td>\n",
       "      <td>...</td>\n",
       "      <td>TMB + H2O2</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.2</td>\n",
       "      <td>3</td>\n",
       "      <td>6.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>https://doi.org/10.1016/j.snb.2019.01.068</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>673</td>\n",
       "      <td>751</td>\n",
       "      <td>NiS</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>320.00</td>\n",
       "      <td>320.00</td>\n",
       "      <td>320.00</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>H2O2 + TMB</td>\n",
       "      <td>0.6000</td>\n",
       "      <td>20.0</td>\n",
       "      <td>0.25</td>\n",
       "      <td>0.025</td>\n",
       "      <td>4.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>https://doi.org/10.1007/s00216-018-1423-x</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99</th>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>WO2.92</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1.33</td>\n",
       "      <td>1.33</td>\n",
       "      <td>1.33</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>ABTS + H2O2</td>\n",
       "      <td>0.0010</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4</td>\n",
       "      <td>0.35</td>\n",
       "      <td>6.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>https://doi.org/10.1016/j.aca.2017.09.011</td>\n",
       "      <td>cubic</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>100 rows × 24 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    level_0  index     formula    activity  Syngony  length, nm  width, nm  \\\n",
       "0       318    329          Pt  peroxidase      7.0        4.40       4.40   \n",
       "1       868   1017       Fe2O3  peroxidase      5.0       30.00      30.00   \n",
       "2        78     78       Fe3O4  peroxidase      7.0      246.60     246.60   \n",
       "3       463    494         CoS  peroxidase      6.0     3000.00    3000.00   \n",
       "4       610    665         ZnS  peroxidase      7.0       10.00      10.00   \n",
       "..      ...    ...         ...         ...      ...         ...        ...   \n",
       "95      870   1019       Fe2O3  peroxidase      5.0       33.00      33.00   \n",
       "96      419    448        Co4N  peroxidase      7.0     2500.00      80.00   \n",
       "97       61     61  Co3O4/CeO2  peroxidase      7.0     2000.00     200.00   \n",
       "98      673    751         NiS  peroxidase      7.0      320.00     320.00   \n",
       "99       90     90      WO2.92  peroxidase      7.0        1.33       1.33   \n",
       "\n",
       "    depth, nm surface                       pol  ... ReactionType  C min, mM  \\\n",
       "0        4.40   naked                         0  ...   TMB + H2O2     0.0625   \n",
       "1       30.00   naked                         0  ...   TMB + H2O2     0.0100   \n",
       "2      246.60   naked                         0  ...   TMB + H2O2     0.0500   \n",
       "3     3000.00   naked                         0  ...   H2O2 + TMB     0.0010   \n",
       "4       10.00   naked                         0  ...   TMB + H2O2     0.0010   \n",
       "..        ...     ...                       ...  ...          ...        ...   \n",
       "95      33.00   naked                         0  ...   TMB + H2O2     0.0100   \n",
       "96      80.00   naked                         0  ...   H2O2 + TMB     1.0000   \n",
       "97     200.00   naked  poly(N-Vinylpyrrolidone)  ...   TMB + H2O2     1.0000   \n",
       "98     320.00   naked                         0  ...   H2O2 + TMB     0.6000   \n",
       "99       1.33   naked                         0  ...  ABTS + H2O2     0.0010   \n",
       "\n",
       "   C max, mM C(const), mM Ccat(mg/mL)   ph  temp, °C  \\\n",
       "0        0.5            1         NaN  4.0      35.0   \n",
       "1        1.0          700      0.0625  3.5       NaN   \n",
       "2        0.3           20    0.166243  4.0      40.0   \n",
       "3       20.0         0.15         0.5  3.5      25.0   \n",
       "4        1.0           10     0.00625  4.0      40.0   \n",
       "..       ...          ...         ...  ...       ...   \n",
       "95       1.0          700      0.0625  3.5       NaN   \n",
       "96      80.0          0.8       0.015  4.0      25.0   \n",
       "97       3.0          1.2           3  6.0      30.0   \n",
       "98      20.0         0.25       0.025  4.0      25.0   \n",
       "99       4.0            4        0.35  6.0      37.0   \n",
       "\n",
       "                                             link    syngony  \\\n",
       "0     https://doi.org/10.1016/j.snb.2017.07.108        cubic   \n",
       "1          https://doi.org/10.1021/acsami.7b13835   trigonal   \n",
       "2   https://doi.org/10.1016/j.procbio.2019.05.014      cubic   \n",
       "3              https://doi.org/10.1039/C6RA16619A  hexagonal   \n",
       "4   https://doi.org/10.1021/acssuschemeng.9b04043      cubic   \n",
       "..                                            ...        ...   \n",
       "95         https://doi.org/10.1021/acsami.7b13835   trigonal   \n",
       "96         https://doi.org/10.1021/acsami.7b09861      cubic   \n",
       "97      https://doi.org/10.1016/j.snb.2019.01.068      cubic   \n",
       "98      https://doi.org/10.1007/s00216-018-1423-x      cubic   \n",
       "99      https://doi.org/10.1016/j.aca.2017.09.011      cubic   \n",
       "\n",
       "    predicted_syngony  \n",
       "0                      \n",
       "1                      \n",
       "2                      \n",
       "3                      \n",
       "4                      \n",
       "..                ...  \n",
       "95                     \n",
       "96                     \n",
       "97                     \n",
       "98                     \n",
       "99                     \n",
       "\n",
       "[100 rows x 24 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_sampled"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(df_sampled.shape[0]):\n",
    "    formula = df_sampled.loc[i, 'formula']\n",
    "    completion = client.beta.chat.completions.parse(\n",
    "        model=\"gpt-4o-2024-08-06\",\n",
    "        messages=[\n",
    "            {\"role\": \"system\", \"content\": prompt},\n",
    "            {\"role\": \"user\", \"content\": f\"Formula: {formula}\"},\n",
    "        ],\n",
    "        response_format=Response,\n",
    "    )\n",
    "    message = completion.choices[0].message\n",
    "    if not message.parsed:\n",
    "        print(i, df_sampled.loc[i, 'formula'], message.refusal)\n",
    "        continue\n",
    "    # print(f\"Real: {df_sampled.loc[i, 'syngony']}, predicted: {message.parsed.syngony}, equal: {df_sampled.loc[i, 'syngony']==message.parsed.syngony}\")\n",
    "    df_sampled.loc[i, 'predicted_syngony'] = message.parsed.syngony"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_sampled['equal'] = df_sampled['syngony'] == df_sampled['predicted_syngony']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.86\n"
     ]
    }
   ],
   "source": [
    "sum(df_sampled['equal']) / len(df_sampled)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>level_0</th>\n",
       "      <th>index</th>\n",
       "      <th>formula</th>\n",
       "      <th>activity</th>\n",
       "      <th>Syngony</th>\n",
       "      <th>length, nm</th>\n",
       "      <th>width, nm</th>\n",
       "      <th>depth, nm</th>\n",
       "      <th>surface</th>\n",
       "      <th>pol</th>\n",
       "      <th>...</th>\n",
       "      <th>C min, mM</th>\n",
       "      <th>C max, mM</th>\n",
       "      <th>C(const), mM</th>\n",
       "      <th>Ccat(mg/mL)</th>\n",
       "      <th>ph</th>\n",
       "      <th>temp, °C</th>\n",
       "      <th>link</th>\n",
       "      <th>syngony</th>\n",
       "      <th>predicted_syngony</th>\n",
       "      <th>equal</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>88</th>\n",
       "      <td>59</td>\n",
       "      <td>59</td>\n",
       "      <td>CoO/CeO2</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1500.0</td>\n",
       "      <td>100.0</td>\n",
       "      <td>100.0</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.300</td>\n",
       "      <td>3.00</td>\n",
       "      <td>0.1</td>\n",
       "      <td>0.083333</td>\n",
       "      <td>3.6</td>\n",
       "      <td>25.0</td>\n",
       "      <td>https://doi.org/10.1016/j.apmt.2019.03.009</td>\n",
       "      <td>cubic</td>\n",
       "      <td>cubic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>474</td>\n",
       "      <td>505</td>\n",
       "      <td>ZnS</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.5</td>\n",
       "      <td>7.5</td>\n",
       "      <td>7.5</td>\n",
       "      <td>Tetrakis(4-carboxyphenyl)porphine</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.040</td>\n",
       "      <td>0.10</td>\n",
       "      <td>250</td>\n",
       "      <td>0.04</td>\n",
       "      <td>3.8</td>\n",
       "      <td>25.0</td>\n",
       "      <td>https://doi.org/10.1016/j.snb.2017.05.069</td>\n",
       "      <td>cubic</td>\n",
       "      <td>cubic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>485</td>\n",
       "      <td>516</td>\n",
       "      <td>CoS</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>6.0</td>\n",
       "      <td>130.0</td>\n",
       "      <td>130.0</td>\n",
       "      <td>130.0</td>\n",
       "      <td>naked</td>\n",
       "      <td>dextran</td>\n",
       "      <td>...</td>\n",
       "      <td>0.001</td>\n",
       "      <td>1000.00</td>\n",
       "      <td>10</td>\n",
       "      <td>0.02</td>\n",
       "      <td>7.4</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1002/cbic.202000066</td>\n",
       "      <td>hexagonal</td>\n",
       "      <td>hexagonal</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>662</td>\n",
       "      <td>740</td>\n",
       "      <td>Fe3O4</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>650.0</td>\n",
       "      <td>650.0</td>\n",
       "      <td>650.0</td>\n",
       "      <td>histidine</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.005</td>\n",
       "      <td>0.80</td>\n",
       "      <td>900</td>\n",
       "      <td>0.002</td>\n",
       "      <td>4.5</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1039/C6CC08542C</td>\n",
       "      <td>cubic</td>\n",
       "      <td>cubic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>827</td>\n",
       "      <td>952</td>\n",
       "      <td>Fe2O3</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>38.8</td>\n",
       "      <td>38.8</td>\n",
       "      <td>38.8</td>\n",
       "      <td>naked</td>\n",
       "      <td>poly(N-Vinylpyrrolidone)</td>\n",
       "      <td>...</td>\n",
       "      <td>0.185</td>\n",
       "      <td>0.37</td>\n",
       "      <td>390</td>\n",
       "      <td>0.003</td>\n",
       "      <td>3.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1088/1361-6528/aaddc2</td>\n",
       "      <td>cubic</td>\n",
       "      <td>trigonal</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>946</td>\n",
       "      <td>1108</td>\n",
       "      <td>Fe2O3</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.080</td>\n",
       "      <td>0.32</td>\n",
       "      <td>987</td>\n",
       "      <td>0.1</td>\n",
       "      <td>4.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1039/C6RA00963H</td>\n",
       "      <td>cubic</td>\n",
       "      <td>trigonal</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>87</th>\n",
       "      <td>923</td>\n",
       "      <td>1083</td>\n",
       "      <td>Hg0.01Pt</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>2.5</td>\n",
       "      <td>2.5</td>\n",
       "      <td>2.5</td>\n",
       "      <td>citric acid</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>https://doi.org/10.1021/ac503544w</td>\n",
       "      <td>cubic</td>\n",
       "      <td>cubic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>600</td>\n",
       "      <td>645</td>\n",
       "      <td>Ce2(WO4)3</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>2.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>50.0</td>\n",
       "      <td>naked</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.000</td>\n",
       "      <td>25.00</td>\n",
       "      <td>0.8</td>\n",
       "      <td>0.07</td>\n",
       "      <td>4.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>https://doi.org/10.1016/j.saa.2020.118499</td>\n",
       "      <td>monoclinic</td>\n",
       "      <td>monoclinic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>279</td>\n",
       "      <td>290</td>\n",
       "      <td>CeO2</td>\n",
       "      <td>oxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>poly(acrylic acid)</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.300</td>\n",
       "      <td>1.50</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>7.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>https://doi.org/10.1002/anie.200805279</td>\n",
       "      <td>cubic</td>\n",
       "      <td>cubic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>779</td>\n",
       "      <td>896</td>\n",
       "      <td>Pd@Pt-Ru</td>\n",
       "      <td>peroxidase</td>\n",
       "      <td>7.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>naked</td>\n",
       "      <td>poly(N-Vinylpyrrolidone)</td>\n",
       "      <td>...</td>\n",
       "      <td>0.050</td>\n",
       "      <td>1.00</td>\n",
       "      <td>0.8</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>https://doi.org/10.1039/D2NR01375D</td>\n",
       "      <td>cubic</td>\n",
       "      <td>cubic</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>100 rows × 25 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    level_0  index    formula    activity  Syngony  length, nm  width, nm  \\\n",
       "88       59     59   CoO/CeO2  peroxidase      7.0      1500.0      100.0   \n",
       "26      474    505        ZnS  peroxidase      7.0         7.5        7.5   \n",
       "28      485    516        CoS  peroxidase      6.0       130.0      130.0   \n",
       "5       662    740      Fe3O4  peroxidase      7.0       650.0      650.0   \n",
       "58      827    952      Fe2O3  peroxidase      7.0        38.8       38.8   \n",
       "..      ...    ...        ...         ...      ...         ...        ...   \n",
       "22      946   1108      Fe2O3  peroxidase      7.0        35.0       35.0   \n",
       "87      923   1083   Hg0.01Pt  peroxidase      7.0         2.5        2.5   \n",
       "48      600    645  Ce2(WO4)3  peroxidase      2.0       500.0      500.0   \n",
       "8       279    290       CeO2     oxidase      7.0         5.0        5.0   \n",
       "29      779    896   Pd@Pt-Ru  peroxidase      7.0        18.0       18.0   \n",
       "\n",
       "    depth, nm                            surface                       pol  \\\n",
       "88      100.0                              naked                         0   \n",
       "26        7.5  Tetrakis(4-carboxyphenyl)porphine                         0   \n",
       "28      130.0                              naked                   dextran   \n",
       "5       650.0                          histidine                         0   \n",
       "58       38.8                              naked  poly(N-Vinylpyrrolidone)   \n",
       "..        ...                                ...                       ...   \n",
       "22       35.0                              naked                         0   \n",
       "87        2.5                        citric acid                         0   \n",
       "48       50.0                              naked                         0   \n",
       "8         5.0                 poly(acrylic acid)                         0   \n",
       "29       18.0                              naked  poly(N-Vinylpyrrolidone)   \n",
       "\n",
       "    ... C min, mM  C max, mM C(const), mM Ccat(mg/mL)   ph  temp, °C  \\\n",
       "88  ...     0.300       3.00          0.1    0.083333  3.6      25.0   \n",
       "26  ...     0.040       0.10          250        0.04  3.8      25.0   \n",
       "28  ...     0.001    1000.00           10        0.02  7.4       NaN   \n",
       "5   ...     0.005       0.80          900       0.002  4.5       NaN   \n",
       "58  ...     0.185       0.37          390       0.003  3.0       NaN   \n",
       "..  ...       ...        ...          ...         ...  ...       ...   \n",
       "22  ...     0.080       0.32          987         0.1  4.0       NaN   \n",
       "87  ...       NaN        NaN          NaN         NaN  NaN       NaN   \n",
       "48  ...     1.000      25.00          0.8        0.07  4.0      25.0   \n",
       "8   ...     0.300       1.50            0         NaN  7.0      37.0   \n",
       "29  ...     0.050       1.00          0.8         NaN  4.0      55.0   \n",
       "\n",
       "                                          link     syngony predicted_syngony  \\\n",
       "88  https://doi.org/10.1016/j.apmt.2019.03.009       cubic             cubic   \n",
       "26   https://doi.org/10.1016/j.snb.2017.05.069       cubic             cubic   \n",
       "28      https://doi.org/10.1002/cbic.202000066   hexagonal         hexagonal   \n",
       "5           https://doi.org/10.1039/C6CC08542C       cubic             cubic   \n",
       "58    https://doi.org/10.1088/1361-6528/aaddc2       cubic          trigonal   \n",
       "..                                         ...         ...               ...   \n",
       "22          https://doi.org/10.1039/C6RA00963H       cubic          trigonal   \n",
       "87           https://doi.org/10.1021/ac503544w       cubic             cubic   \n",
       "48   https://doi.org/10.1016/j.saa.2020.118499  monoclinic        monoclinic   \n",
       "8       https://doi.org/10.1002/anie.200805279       cubic             cubic   \n",
       "29          https://doi.org/10.1039/D2NR01375D       cubic             cubic   \n",
       "\n",
       "    equal  \n",
       "88   True  \n",
       "26   True  \n",
       "28   True  \n",
       "5    True  \n",
       "58  False  \n",
       "..    ...  \n",
       "22  False  \n",
       "87   True  \n",
       "48   True  \n",
       "8    True  \n",
       "29   True  \n",
       "\n",
       "[100 rows x 25 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_sampled"
   ]
  }
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