notebooks/inspect_orderly_data.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Inspect ORD file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ord_schema\n",
    "from ord_schema import message_helpers, validations\n",
    "from ord_schema.proto import dataset_pb2\n",
    "import os\n",
    "import fnmatch"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'[S:1](=[O:4])(=[O:3])=[O:2].[S:5](=[O:9])(=[O:8])([OH:7])[OH:6]>>[OH:8][S:5]([OH:9])(=[O:7])=[O:6].[O:2]=[S:1](=[O:4])=[O:3] |f:2.3|'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Inspect raw ORD file\n",
    "# Find the schema here\n",
    "# https://github.com/open-reaction-database/ord-schema/blob/main/ord_schema/proto/reaction.proto\n",
    "\n",
    "\n",
    "# Load Dataset message\n",
    "pb = \"../data/ord/02/ord_dataset-02ee2261663048188cf6d85d2cc96e3f.pb.gz\"\n",
    "data = message_helpers.load_message(pb, dataset_pb2.Dataset)\n",
    "\n",
    "# Inspect a reaction identifier\n",
    "data.reactions[0].identifiers[0].value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'uspto-grants-1993_09'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Can also find ORD file just given the hash:\n",
    "def open_ord(ord_hash):\n",
    "    folder_path = '/Users/danielwigh/projects_local/ORDerly_project/ORDerly/data/ord'\n",
    "    # look for files within that folder path or deeper for a file that contains the ord_hash\n",
    "    for root, dirs, files in os.walk(folder_path):\n",
    "        for file in files:\n",
    "            if fnmatch.fnmatch(file, f'*{ord_hash}*'):\n",
    "                filepath = os.path.join(root, file)\n",
    "                data = message_helpers.load_message(filepath, dataset_pb2.Dataset)\n",
    "                return data\n",
    "    raise FileNotFoundError(f\"No file found containing {ord_hash} in the name.\")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'uspto-grants-1986_09'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data = open_ord('ord_dataset-0b70410902ae4139bd5d334881938f69')\n",
    "data.name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/danielwigh/projects_local/ORDerly_project/ORDerly/notebooks'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Inspect extracted data from ORD file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = \"../data/orderly/uspto_no_trust/extracted_ords/uspto-grants-1986_09.parquet\"\n",
    "df = pd.read_parquet(path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "277    C(OC([N:11]1[CH2:23][CH2:22][CH2:21][C@H:12]1[...\n",
       "279    C(OC([N:11]1[CH2:15][CH2:14][CH2:13][C@H:12]1[...\n",
       "582    [CH3:1][C:2]1[O:3][C:4](=[O:14])[C:5](=[CH:7][...\n",
       "Name: rxn_str, dtype: object"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# find df['rxn_str'] which contains [Pd] and [C]\n",
    "\n",
    "filtered_df = df[df['rxn_str'].str.contains('[H][H]', regex=False) & df['rxn_str'].str.contains('\\[C\\]')]\n",
    "filtered_df['rxn_str']\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'C(OC([N:11]1[CH2:23][CH2:22][CH2:21][C@H:12]1[C:13]([N:15]1[CH2:20][CH2:19][O:18][CH2:17][CH2:16]1)=[O:14])=O)C1C=CC=CC=1.[H][H]>C(O)C.[C].[Pd]>[NH:11]1[CH2:23][CH2:22][CH2:21][C@H:12]1[C:13]([N:15]1[CH2:20][CH2:19][O:18][CH2:17][CH2:16]1)=[O:14]'"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.loc[277]['rxn_str']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "'C(OC([N:11]1[CH2:23][CH2:22][CH2:21][C@H:12]1[C:13]([N:15]1[CH2:20][CH2:19][O:18][CH2:17][CH2:16]1)=[O:14])=O)C1C=CC=CC=1.[H][H]>C(O)C.[C].[Pd]>[NH:11]1[CH2:23][CH2:22][CH2:21][C@H:12]1[C:13]([N:15]1[CH2:20][CH2:19][O:18][CH2:17][CH2:16]1)=[O:14]'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "98.7"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.loc[277]['yield_000']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "99.7"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.loc[262]['yield_000']\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CO.[C].[Pd]'"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ag"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Inspect cleaned data from ORD file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = \"../data/orderly/datasets/orderly_no_trust_no_map_train.parquet\"\n",
    "df = pd.read_parquet(path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'[Cl:1][C:2]1[N:3]=[CH:4][C:5]2[C:10]([CH:11]=1)=[C:9]([N+:12]([O-])=O)[CH:8]=[CH:7][CH:6]=2.O.[OH-].[Na+]>C(O)(=O)C.[Fe]>[Cl:1][C:2]1[N:3]=[CH:4][C:5]2[C:10]([CH:11]=1)=[C:9]([NH2:12])[CH:8]=[CH:7][CH:6]=2'"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df['rxn_str'][0]"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Download ORD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloading benchmark from https://figshare.com/ndownloader/articles/23298467/versions/2 to orderly_benchmark.zip\n",
      "Unzipping benchmark\n"
     ]
    }
   ],
   "source": [
    "import pathlib\n",
    "import zipfile\n",
    "\n",
    "import pandas as pd\n",
    "import requests\n",
    "\n",
    "\n",
    "def download_benchmark(\n",
    "    benchmark_zip_file=\"orderly_benchmark.zip\",\n",
    "    benchmark_directory=\"orderly_benchmark/\",\n",
    "    version=2,\n",
    "):\n",
    "    figshare_url = (\n",
    "        f\"https://figshare.com/ndownloader/articles/23298467/versions/{version}\"\n",
    "    )\n",
    "    print(f\"Downloading benchmark from {figshare_url} to {benchmark_zip_file}\")\n",
    "    r = requests.get(figshare_url, allow_redirects=True)\n",
    "    with open(benchmark_zip_file, \"wb\") as f:\n",
    "        f.write(r.content)\n",
    "\n",
    "    print(\"Unzipping benchmark\")\n",
    "    benchmark_directory = pathlib.Path(benchmark_directory)\n",
    "    benchmark_directory.mkdir(parents=True, exist_ok=True)\n",
    "    with zipfile.ZipFile(benchmark_zip_file, \"r\") as zip_ref:\n",
    "        zip_ref.extractall(benchmark_directory)\n",
    "\n",
    "\n",
    "download_benchmark()\n",
    "train_df = pd.read_parquet(\"orderly_benchmark/orderly_benchmark_train.parquet\")\n",
    "test_df = pd.read_parquet(\"orderly_benchmark/orderly_benchmark_test.parquet\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\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>agent_000</th>\n",
       "      <th>agent_001</th>\n",
       "      <th>agent_002</th>\n",
       "      <th>date_of_experiment</th>\n",
       "      <th>extracted_from_file</th>\n",
       "      <th>grant_date</th>\n",
       "      <th>is_mapped</th>\n",
       "      <th>procedure_details</th>\n",
       "      <th>product_000</th>\n",
       "      <th>reactant_000</th>\n",
       "      <th>reactant_001</th>\n",
       "      <th>rxn_str</th>\n",
       "      <th>rxn_time</th>\n",
       "      <th>solvent_000</th>\n",
       "      <th>solvent_001</th>\n",
       "      <th>temperature</th>\n",
       "      <th>yield_000</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>332116</th>\n",
       "      <td>[OH-]</td>\n",
       "      <td>[Na+]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-bcc0b01d4f58457a8733b10a099f43ba</td>\n",
       "      <td>2015-01-01 00:10:00</td>\n",
       "      <td>True</td>\n",
       "      <td>To N-[6-(1-tert-butyloxycarbonylpiperidin-4-yl...</td>\n",
       "      <td>Cc1c(C(=O)Nc2ccc(C3CCNCC3)nc2)cnn1-c1ccc(C(F)(...</td>\n",
       "      <td>Cc1c(C(=O)Nc2ccc(C3CCN(C(=O)OC(C)(C)C)CC3)nc2)...</td>\n",
       "      <td>NULL</td>\n",
       "      <td>C(OC([N:8]1[CH2:13][CH2:12][CH:11]([C:14]2[N:1...</td>\n",
       "      <td>2.50</td>\n",
       "      <td>O=C(O)C(F)(F)F</td>\n",
       "      <td>ClCCl</td>\n",
       "      <td>25.0</td>\n",
       "      <td>89.4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109219</th>\n",
       "      <td>[OH-]</td>\n",
       "      <td>[Pd+2]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-e967d076b4894c2c854795f019ed3c39</td>\n",
       "      <td>2002-01-01 00:06:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A solution of 240 mg (0.50 mmol) of 3-bromo-4-...</td>\n",
       "      <td>CN1C(=O)CC(c2c(CCCCc3cc4ccccc4[nH]3)[nH]c3cccc...</td>\n",
       "      <td>CN1C(=O)C(Br)=C(c2c(CCCCc3cc4ccccc4[nH]3)[nH]c...</td>\n",
       "      <td>NULL</td>\n",
       "      <td>Br[C:2]1[C:3](=[O:31])[N:4]([CH3:30])[C:5](=[O...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CO</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>212362</th>\n",
       "      <td>c1ccc(P(c2ccccc2)c2ccccc2)cc1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-3af92aec23dc4810b92eb0d8c60023ee</td>\n",
       "      <td>2011-01-01 00:03:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A solution of triphenylphosphine (469 mg, 1.79...</td>\n",
       "      <td>BrCc1cc2ccccc2cc1I</td>\n",
       "      <td>BrC(Br)(Br)Br</td>\n",
       "      <td>OCc1cc2ccccc2cc1I</td>\n",
       "      <td>C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.[C:20](...</td>\n",
       "      <td>4.00</td>\n",
       "      <td>ClCCl</td>\n",
       "      <td>None</td>\n",
       "      <td>25.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>198710</th>\n",
       "      <td>[Fe]</td>\n",
       "      <td>Cl</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-f886e51ba1484c76a94bce1482f1eab9</td>\n",
       "      <td>2010-01-01 00:07:00</td>\n",
       "      <td>True</td>\n",
       "      <td>To a solution of methyl N-methyl-N-[(4′-nitro-...</td>\n",
       "      <td>COC(=O)[C@H](C(C)C)N(C)C(=O)c1ccc(-c2ccc(N)cc2...</td>\n",
       "      <td>COC(=O)[C@H](C(C)C)N(C)C(=O)c1ccc(-c2ccc([N+](...</td>\n",
       "      <td>NULL</td>\n",
       "      <td>[CH3:1][N:2]([C:11]([C:13]1[CH:18]=[CH:17][C:1...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCO</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>75.8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>243552</th>\n",
       "      <td>CC(C)OC(=O)/N=N/C(=O)OC(C)C</td>\n",
       "      <td>c1ccc(P(c2ccccc2)c2ccccc2)cc1</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-9cd817a75dfc4fe7ad19d4232772d5ff</td>\n",
       "      <td>2012-01-01 00:07:00</td>\n",
       "      <td>True</td>\n",
       "      <td>DIAD (23.95 ml, 123 mmol) was added dropwise t...</td>\n",
       "      <td>COC(=O)c1cccc(OC)c1OCCNC(=O)OC(C)(C)C</td>\n",
       "      <td>CC(C)(C)OC(=O)NCCO</td>\n",
       "      <td>COC(=O)c1cccc(OC)c1O</td>\n",
       "      <td>CC(OC(/N=N/C(OC(C)C)=O)=O)C.[OH:15][CH2:16][CH...</td>\n",
       "      <td>0.50</td>\n",
       "      <td>C1CCOC1</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>232549</th>\n",
       "      <td>[Li]CCCC</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-aaeaab5f3720492494c1cbbdd0ed2820</td>\n",
       "      <td>2012-01-01 00:02:00</td>\n",
       "      <td>True</td>\n",
       "      <td>To a solution of DIPA (15.5 mL) in THF (300 mL...</td>\n",
       "      <td>COc1ccc2ncc(F)c(C=O)c2c1</td>\n",
       "      <td>CN(C)C=O</td>\n",
       "      <td>COc1ccc2ncc(F)cc2c1</td>\n",
       "      <td>[Li]CCCC.[F:6][C:7]1[CH:8]=[N:9][C:10]2[C:15](...</td>\n",
       "      <td>0.08</td>\n",
       "      <td>C1CCOC1</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>52.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208488</th>\n",
       "      <td>[Na+]</td>\n",
       "      <td>[BH3-]C#N</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-136cfada6ce247b4919085a57363459e</td>\n",
       "      <td>2011-01-01 00:01:00</td>\n",
       "      <td>True</td>\n",
       "      <td>To a cold solution of methyl indole-5-carboxyl...</td>\n",
       "      <td>COC(=O)c1ccc2c(c1)CCN2</td>\n",
       "      <td>COC(=O)c1ccc2[nH]ccc2c1</td>\n",
       "      <td>NULL</td>\n",
       "      <td>[NH:1]1[C:9]2[C:4](=[CH:5][C:6]([C:10]([O:12][...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CC(=O)O</td>\n",
       "      <td>None</td>\n",
       "      <td>25.0</td>\n",
       "      <td>80.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>222435</th>\n",
       "      <td>Cl</td>\n",
       "      <td>[Na+]</td>\n",
       "      <td>[OH-]</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-52a37d876ddb453e86de0c15fa233d29</td>\n",
       "      <td>2011-01-01 00:09:00</td>\n",
       "      <td>True</td>\n",
       "      <td>Before the start of the reaction, the loop rea...</td>\n",
       "      <td>CC(C)(C)OOC(=O)c1ccccc1</td>\n",
       "      <td>CC(C)(C)OO</td>\n",
       "      <td>O=C(Cl)c1ccccc1</td>\n",
       "      <td>[C:1]([O:5][OH:6])([CH3:4])([CH3:3])[CH3:2].[O...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>O</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>95.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>225524</th>\n",
       "      <td>Cc1ccc(S(=O)(=O)[O-])cc1</td>\n",
       "      <td>c1cc[nH+]cc1</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-375a420ee9b042918ddca20f02df37d3</td>\n",
       "      <td>2011-01-01 00:11:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A solution of N-{3-[1,1-Dimethyl-2-(tetrahydro...</td>\n",
       "      <td>CC(C)(CO)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2CCOCC2)on1</td>\n",
       "      <td>CC(C)(COC1CCCCO1)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2...</td>\n",
       "      <td>NULL</td>\n",
       "      <td>[CH3:1][C:2]([C:12]1[CH:16]=[C:15]([NH:17][C:1...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCO</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>81.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>225523</th>\n",
       "      <td>Cc1ccc(S(=O)(=O)O)cc1</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-375a420ee9b042918ddca20f02df37d3</td>\n",
       "      <td>2011-01-01 00:11:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A solution of 98 g (0.21 mol) of N-{3-[1,1-dim...</td>\n",
       "      <td>CC(C)(CO)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2CCOCC2)on1</td>\n",
       "      <td>CC(C)(COC1CCCCO1)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2...</td>\n",
       "      <td>NULL</td>\n",
       "      <td>[CH3:1][C:2]([C:12]1[CH:16]=[C:15]([NH:17][C:1...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>ClCCl</td>\n",
       "      <td>CCO</td>\n",
       "      <td>NaN</td>\n",
       "      <td>82.7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>322976 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                            agent_000                      agent_001  \\\n",
       "332116                          [OH-]                          [Na+]   \n",
       "109219                          [OH-]                         [Pd+2]   \n",
       "212362  c1ccc(P(c2ccccc2)c2ccccc2)cc1                           None   \n",
       "198710                           [Fe]                             Cl   \n",
       "243552    CC(C)OC(=O)/N=N/C(=O)OC(C)C  c1ccc(P(c2ccccc2)c2ccccc2)cc1   \n",
       "...                               ...                            ...   \n",
       "232549                       [Li]CCCC                           None   \n",
       "208488                          [Na+]                      [BH3-]C#N   \n",
       "222435                             Cl                          [Na+]   \n",
       "225524       Cc1ccc(S(=O)(=O)[O-])cc1                   c1cc[nH+]cc1   \n",
       "225523          Cc1ccc(S(=O)(=O)O)cc1                           None   \n",
       "\n",
       "       agent_002 date_of_experiment  \\\n",
       "332116      None                NaT   \n",
       "109219      None                NaT   \n",
       "212362      None                NaT   \n",
       "198710      None                NaT   \n",
       "243552      None                NaT   \n",
       "...          ...                ...   \n",
       "232549      None                NaT   \n",
       "208488      None                NaT   \n",
       "222435     [OH-]                NaT   \n",
       "225524      None                NaT   \n",
       "225523      None                NaT   \n",
       "\n",
       "                                 extracted_from_file          grant_date  \\\n",
       "332116  ord_dataset-bcc0b01d4f58457a8733b10a099f43ba 2015-01-01 00:10:00   \n",
       "109219  ord_dataset-e967d076b4894c2c854795f019ed3c39 2002-01-01 00:06:00   \n",
       "212362  ord_dataset-3af92aec23dc4810b92eb0d8c60023ee 2011-01-01 00:03:00   \n",
       "198710  ord_dataset-f886e51ba1484c76a94bce1482f1eab9 2010-01-01 00:07:00   \n",
       "243552  ord_dataset-9cd817a75dfc4fe7ad19d4232772d5ff 2012-01-01 00:07:00   \n",
       "...                                              ...                 ...   \n",
       "232549  ord_dataset-aaeaab5f3720492494c1cbbdd0ed2820 2012-01-01 00:02:00   \n",
       "208488  ord_dataset-136cfada6ce247b4919085a57363459e 2011-01-01 00:01:00   \n",
       "222435  ord_dataset-52a37d876ddb453e86de0c15fa233d29 2011-01-01 00:09:00   \n",
       "225524  ord_dataset-375a420ee9b042918ddca20f02df37d3 2011-01-01 00:11:00   \n",
       "225523  ord_dataset-375a420ee9b042918ddca20f02df37d3 2011-01-01 00:11:00   \n",
       "\n",
       "        is_mapped                                  procedure_details  \\\n",
       "332116       True  To N-[6-(1-tert-butyloxycarbonylpiperidin-4-yl...   \n",
       "109219       True  A solution of 240 mg (0.50 mmol) of 3-bromo-4-...   \n",
       "212362       True  A solution of triphenylphosphine (469 mg, 1.79...   \n",
       "198710       True  To a solution of methyl N-methyl-N-[(4′-nitro-...   \n",
       "243552       True  DIAD (23.95 ml, 123 mmol) was added dropwise t...   \n",
       "...           ...                                                ...   \n",
       "232549       True  To a solution of DIPA (15.5 mL) in THF (300 mL...   \n",
       "208488       True  To a cold solution of methyl indole-5-carboxyl...   \n",
       "222435       True  Before the start of the reaction, the loop rea...   \n",
       "225524       True  A solution of N-{3-[1,1-Dimethyl-2-(tetrahydro...   \n",
       "225523       True  A solution of 98 g (0.21 mol) of N-{3-[1,1-dim...   \n",
       "\n",
       "                                              product_000  \\\n",
       "332116  Cc1c(C(=O)Nc2ccc(C3CCNCC3)nc2)cnn1-c1ccc(C(F)(...   \n",
       "109219  CN1C(=O)CC(c2c(CCCCc3cc4ccccc4[nH]3)[nH]c3cccc...   \n",
       "212362                                 BrCc1cc2ccccc2cc1I   \n",
       "198710  COC(=O)[C@H](C(C)C)N(C)C(=O)c1ccc(-c2ccc(N)cc2...   \n",
       "243552              COC(=O)c1cccc(OC)c1OCCNC(=O)OC(C)(C)C   \n",
       "...                                                   ...   \n",
       "232549                           COc1ccc2ncc(F)c(C=O)c2c1   \n",
       "208488                             COC(=O)c1ccc2c(c1)CCN2   \n",
       "222435                            CC(C)(C)OOC(=O)c1ccccc1   \n",
       "225524   CC(C)(CO)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2CCOCC2)on1   \n",
       "225523   CC(C)(CO)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2CCOCC2)on1   \n",
       "\n",
       "                                             reactant_000  \\\n",
       "332116  Cc1c(C(=O)Nc2ccc(C3CCN(C(=O)OC(C)(C)C)CC3)nc2)...   \n",
       "109219  CN1C(=O)C(Br)=C(c2c(CCCCc3cc4ccccc4[nH]3)[nH]c...   \n",
       "212362                                      BrC(Br)(Br)Br   \n",
       "198710  COC(=O)[C@H](C(C)C)N(C)C(=O)c1ccc(-c2ccc([N+](...   \n",
       "243552                                 CC(C)(C)OC(=O)NCCO   \n",
       "...                                                   ...   \n",
       "232549                                           CN(C)C=O   \n",
       "208488                            COC(=O)c1ccc2[nH]ccc2c1   \n",
       "222435                                         CC(C)(C)OO   \n",
       "225524  CC(C)(COC1CCCCO1)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2...   \n",
       "225523  CC(C)(COC1CCCCO1)c1cc(NC(=O)C(C)(C)S(=O)(=O)C2...   \n",
       "\n",
       "                reactant_001  \\\n",
       "332116                  NULL   \n",
       "109219                  NULL   \n",
       "212362     OCc1cc2ccccc2cc1I   \n",
       "198710                  NULL   \n",
       "243552  COC(=O)c1cccc(OC)c1O   \n",
       "...                      ...   \n",
       "232549   COc1ccc2ncc(F)cc2c1   \n",
       "208488                  NULL   \n",
       "222435       O=C(Cl)c1ccccc1   \n",
       "225524                  NULL   \n",
       "225523                  NULL   \n",
       "\n",
       "                                                  rxn_str  rxn_time  \\\n",
       "332116  C(OC([N:8]1[CH2:13][CH2:12][CH:11]([C:14]2[N:1...      2.50   \n",
       "109219  Br[C:2]1[C:3](=[O:31])[N:4]([CH3:30])[C:5](=[O...       NaN   \n",
       "212362  C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.[C:20](...      4.00   \n",
       "198710  [CH3:1][N:2]([C:11]([C:13]1[CH:18]=[CH:17][C:1...       NaN   \n",
       "243552  CC(OC(/N=N/C(OC(C)C)=O)=O)C.[OH:15][CH2:16][CH...      0.50   \n",
       "...                                                   ...       ...   \n",
       "232549  [Li]CCCC.[F:6][C:7]1[CH:8]=[N:9][C:10]2[C:15](...      0.08   \n",
       "208488  [NH:1]1[C:9]2[C:4](=[CH:5][C:6]([C:10]([O:12][...       NaN   \n",
       "222435  [C:1]([O:5][OH:6])([CH3:4])([CH3:3])[CH3:2].[O...       NaN   \n",
       "225524  [CH3:1][C:2]([C:12]1[CH:16]=[C:15]([NH:17][C:1...       NaN   \n",
       "225523  [CH3:1][C:2]([C:12]1[CH:16]=[C:15]([NH:17][C:1...       NaN   \n",
       "\n",
       "           solvent_000 solvent_001  temperature  yield_000  \n",
       "332116  O=C(O)C(F)(F)F       ClCCl         25.0       89.4  \n",
       "109219              CO        None          NaN        NaN  \n",
       "212362           ClCCl        None         25.0        NaN  \n",
       "198710             CCO        None          NaN       75.8  \n",
       "243552         C1CCOC1        None          NaN        NaN  \n",
       "...                ...         ...          ...        ...  \n",
       "232549         C1CCOC1        None          0.0       52.0  \n",
       "208488         CC(=O)O        None         25.0       80.2  \n",
       "222435               O        None          NaN       95.3  \n",
       "225524             CCO        None          NaN       81.0  \n",
       "225523           ClCCl         CCO          NaN       82.7  \n",
       "\n",
       "[322976 rows x 17 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "train_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "train_2_df = pd.read_parquet(\"/Users/dsw46/Projects_local/orderly_reproduce/data/orderly/orderly_ord_train.parquet\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
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       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>agent_000</th>\n",
       "      <th>agent_001</th>\n",
       "      <th>agent_002</th>\n",
       "      <th>date_of_experiment</th>\n",
       "      <th>extracted_from_file</th>\n",
       "      <th>grant_date</th>\n",
       "      <th>is_mapped</th>\n",
       "      <th>procedure_details</th>\n",
       "      <th>product_000</th>\n",
       "      <th>product_001</th>\n",
       "      <th>...</th>\n",
       "      <th>rxn_str</th>\n",
       "      <th>rxn_time</th>\n",
       "      <th>solvent_000</th>\n",
       "      <th>solvent_001</th>\n",
       "      <th>temperature</th>\n",
       "      <th>yield_000</th>\n",
       "      <th>yield_001</th>\n",
       "      <th>yield_002</th>\n",
       "      <th>yield_003</th>\n",
       "      <th>yield_004</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>79574</th>\n",
       "      <td>[Pd]</td>\n",
       "      <td>[C]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-a6643d22de674f30a85ba57198b82644</td>\n",
       "      <td>1995-01-01 00:03:00</td>\n",
       "      <td>True</td>\n",
       "      <td>In a mixture of 18 ml of ethanol and 9 ml of N...</td>\n",
       "      <td>Nc1ccccc1Oc1cccc(-c2nnn[nH]2)c1</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[N+:1]([C:4]1[CH:21]=[CH:20][CH:19]=[CH:18][C:...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCO</td>\n",
       "      <td>CN(C)C=O</td>\n",
       "      <td>NaN</td>\n",
       "      <td>96.9</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>148136</th>\n",
       "      <td>CCN=C=NCCCN(C)C</td>\n",
       "      <td>Cl</td>\n",
       "      <td>On1nnc2ccccc21</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-82e842e611ef4a05b6e7f9ea0a46d52d</td>\n",
       "      <td>2003-01-01 00:07:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A mixture of 5-[5-(2,6-dichloro-phenylmethanes...</td>\n",
       "      <td>Cc1[nH]c(/C=C2\\C(=O)Nc3ccc(S(=O)(=O)Cc4c(Cl)cc...</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([Cl:8])[...</td>\n",
       "      <td>72.0</td>\n",
       "      <td>CN(C)C=O</td>\n",
       "      <td>None</td>\n",
       "      <td>40.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>79634</th>\n",
       "      <td>[Na+]</td>\n",
       "      <td>[O-][I+3]([O-])([O-])[O-]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-a6643d22de674f30a85ba57198b82644</td>\n",
       "      <td>1995-01-01 00:03:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A solution of sodium periodate (0.214 g.; 0.00...</td>\n",
       "      <td>COc1ccc2c(c1)C(CC(=O)O)=C(C)C2=Cc1ccc(S(C)=O)cc1</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>I([O-])(=O)(=O)=O.[Na+].[OH2:7].[CH3:8][O:9][C...</td>\n",
       "      <td>8.0</td>\n",
       "      <td>CC(C)=O</td>\n",
       "      <td>CO</td>\n",
       "      <td>25.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>329451</th>\n",
       "      <td>c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2...</td>\n",
       "      <td>O=C([O-])[O-]</td>\n",
       "      <td>[K+]</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-cfad8b3f00044bcda60a96b019f09872</td>\n",
       "      <td>2013-01-01 00:08:00</td>\n",
       "      <td>True</td>\n",
       "      <td>As depicted in Reaction 5, 15 g (46 mmol) of 3...</td>\n",
       "      <td>c1ccc(-c2ccc3[nH]c4ccc(-c5ccccc5)cc4c3c2)cc1</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>Br[C:2]1[CH:3]=[CH:4][C:5]2[NH:6][C:7]3[C:12](...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Cc1ccccc1</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>73.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>359709</th>\n",
       "      <td>[H-]</td>\n",
       "      <td>[Na+]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-a86112d52cd54525a5e36d41f18aced2</td>\n",
       "      <td>2014-01-01 00:07:00</td>\n",
       "      <td>True</td>\n",
       "      <td>Sodium hydride (60% in oil, 19.41 mg, 0.485 mm...</td>\n",
       "      <td>CC(C)(C)OC(=O)CN1C[C@@H]2COCCN2c2nc(Cl)ncc21</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[H-].[Na+].[Cl:3][C:4]1[N:13]=[CH:12][C:11]2[N...</td>\n",
       "      <td>0.5</td>\n",
       "      <td>CN(C)C=O</td>\n",
       "      <td>O</td>\n",
       "      <td>25.0</td>\n",
       "      <td>67.2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</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>182938</th>\n",
       "      <td>[H-]</td>\n",
       "      <td>[Na+]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-844a22e1fcab44a5b59c5e2922b2855a</td>\n",
       "      <td>2007-01-01 00:01:00</td>\n",
       "      <td>True</td>\n",
       "      <td>In DMF (8.0 ml) was suspended sodium hydride (...</td>\n",
       "      <td>CCn1cc(C(=O)OC)c2ccccc21</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[H-].[Na+].[NH:3]1[C:11]2[C:6](=[CH:7][CH:8]=[...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CN(C)C=O</td>\n",
       "      <td>O</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>123321</th>\n",
       "      <td>[Na+]</td>\n",
       "      <td>[OH-]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-18e9ed24dbd44e98b33bdc22aa7580a8</td>\n",
       "      <td>2001-01-01 00:04:00</td>\n",
       "      <td>True</td>\n",
       "      <td>A mixture of 6-benzyloxy-1,3-benzoxathiol-2-on...</td>\n",
       "      <td>Oc1cc(OCc2ccccc2)ccc1S</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[CH2:1]([O:8][C:9]1[CH:18]=[CH:17][C:12]2[S:13...</td>\n",
       "      <td>16.0</td>\n",
       "      <td>CO</td>\n",
       "      <td>None</td>\n",
       "      <td>25.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35293</th>\n",
       "      <td>CC1(C)C2CCC1(CS(=O)(=O)O)C(=O)C2</td>\n",
       "      <td>CCCC[N+](CCCC)(CCCC)CCCC</td>\n",
       "      <td>other</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-1895fe091c3f47afa1ee96a41a250de4</td>\n",
       "      <td>1986-01-01 00:05:00</td>\n",
       "      <td>True</td>\n",
       "      <td>To a stirred solution of 3.58 g of (3S)-2-oxo-...</td>\n",
       "      <td>Oc1cccc2ccc[nH+]c12</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>C([N+](CCCC)(CCCC)CCCC)CCC.[O:18]=[C:19]1[C@@H...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CC(Cl)Cl</td>\n",
       "      <td>None</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>392918</th>\n",
       "      <td>O=[Pt]=O</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-35c51552812941cda45194a013d34bb9</td>\n",
       "      <td>2015-01-01 00:08:00</td>\n",
       "      <td>True</td>\n",
       "      <td>2-Aminopropan-1-ol (5 g, 66.57 mmol) and 1-hyd...</td>\n",
       "      <td>CC(CO)NC(C)CO</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[NH2:1][CH:2]([CH3:5])[CH2:3][OH:4].[OH:6][CH2...</td>\n",
       "      <td>24.0</td>\n",
       "      <td>CCO</td>\n",
       "      <td>None</td>\n",
       "      <td>25.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>92455</th>\n",
       "      <td>[H-]</td>\n",
       "      <td>[Na+]</td>\n",
       "      <td>None</td>\n",
       "      <td>NaT</td>\n",
       "      <td>ord_dataset-c2ad1656a3ca4d08888ffb6e3f3a2742</td>\n",
       "      <td>1997-01-01 00:05:00</td>\n",
       "      <td>True</td>\n",
       "      <td>To a suspension of 12 g of 3,5-dibromopyridine...</td>\n",
       "      <td>COc1cncc(Br)c1</td>\n",
       "      <td>NULL</td>\n",
       "      <td>...</td>\n",
       "      <td>[Br:1][C:2]1[CH:3]=[N:4][CH:5]=[C:6](Br)[CH:7]...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>CN(C)C=O</td>\n",
       "      <td>None</td>\n",
       "      <td>60.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>387287 rows × 28 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                agent_000  \\\n",
       "index                                                       \n",
       "79574                                                [Pd]   \n",
       "148136                                    CCN=C=NCCCN(C)C   \n",
       "79634                                               [Na+]   \n",
       "329451  c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2...   \n",
       "359709                                               [H-]   \n",
       "...                                                   ...   \n",
       "182938                                               [H-]   \n",
       "123321                                              [Na+]   \n",
       "35293                    CC1(C)C2CCC1(CS(=O)(=O)O)C(=O)C2   \n",
       "392918                                           O=[Pt]=O   \n",
       "92455                                                [H-]   \n",
       "\n",
       "                        agent_001       agent_002 date_of_experiment  \\\n",
       "index                                                                  \n",
       "79574                         [C]            None                NaT   \n",
       "148136                         Cl  On1nnc2ccccc21                NaT   \n",
       "79634   [O-][I+3]([O-])([O-])[O-]            None                NaT   \n",
       "329451              O=C([O-])[O-]            [K+]                NaT   \n",
       "359709                      [Na+]            None                NaT   \n",
       "...                           ...             ...                ...   \n",
       "182938                      [Na+]            None                NaT   \n",
       "123321                      [OH-]            None                NaT   \n",
       "35293    CCCC[N+](CCCC)(CCCC)CCCC           other                NaT   \n",
       "392918                       None            None                NaT   \n",
       "92455                       [Na+]            None                NaT   \n",
       "\n",
       "                                 extracted_from_file          grant_date  \\\n",
       "index                                                                      \n",
       "79574   ord_dataset-a6643d22de674f30a85ba57198b82644 1995-01-01 00:03:00   \n",
       "148136  ord_dataset-82e842e611ef4a05b6e7f9ea0a46d52d 2003-01-01 00:07:00   \n",
       "79634   ord_dataset-a6643d22de674f30a85ba57198b82644 1995-01-01 00:03:00   \n",
       "329451  ord_dataset-cfad8b3f00044bcda60a96b019f09872 2013-01-01 00:08:00   \n",
       "359709  ord_dataset-a86112d52cd54525a5e36d41f18aced2 2014-01-01 00:07:00   \n",
       "...                                              ...                 ...   \n",
       "182938  ord_dataset-844a22e1fcab44a5b59c5e2922b2855a 2007-01-01 00:01:00   \n",
       "123321  ord_dataset-18e9ed24dbd44e98b33bdc22aa7580a8 2001-01-01 00:04:00   \n",
       "35293   ord_dataset-1895fe091c3f47afa1ee96a41a250de4 1986-01-01 00:05:00   \n",
       "392918  ord_dataset-35c51552812941cda45194a013d34bb9 2015-01-01 00:08:00   \n",
       "92455   ord_dataset-c2ad1656a3ca4d08888ffb6e3f3a2742 1997-01-01 00:05:00   \n",
       "\n",
       "        is_mapped                                  procedure_details  \\\n",
       "index                                                                  \n",
       "79574        True  In a mixture of 18 ml of ethanol and 9 ml of N...   \n",
       "148136       True  A mixture of 5-[5-(2,6-dichloro-phenylmethanes...   \n",
       "79634        True  A solution of sodium periodate (0.214 g.; 0.00...   \n",
       "329451       True  As depicted in Reaction 5, 15 g (46 mmol) of 3...   \n",
       "359709       True  Sodium hydride (60% in oil, 19.41 mg, 0.485 mm...   \n",
       "...           ...                                                ...   \n",
       "182938       True  In DMF (8.0 ml) was suspended sodium hydride (...   \n",
       "123321       True  A mixture of 6-benzyloxy-1,3-benzoxathiol-2-on...   \n",
       "35293        True  To a stirred solution of 3.58 g of (3S)-2-oxo-...   \n",
       "392918       True  2-Aminopropan-1-ol (5 g, 66.57 mmol) and 1-hyd...   \n",
       "92455        True  To a suspension of 12 g of 3,5-dibromopyridine...   \n",
       "\n",
       "                                              product_000 product_001  ...  \\\n",
       "index                                                                  ...   \n",
       "79574                     Nc1ccccc1Oc1cccc(-c2nnn[nH]2)c1        NULL  ...   \n",
       "148136  Cc1[nH]c(/C=C2\\C(=O)Nc3ccc(S(=O)(=O)Cc4c(Cl)cc...        NULL  ...   \n",
       "79634    COc1ccc2c(c1)C(CC(=O)O)=C(C)C2=Cc1ccc(S(C)=O)cc1        NULL  ...   \n",
       "329451       c1ccc(-c2ccc3[nH]c4ccc(-c5ccccc5)cc4c3c2)cc1        NULL  ...   \n",
       "359709       CC(C)(C)OC(=O)CN1C[C@@H]2COCCN2c2nc(Cl)ncc21        NULL  ...   \n",
       "...                                                   ...         ...  ...   \n",
       "182938                           CCn1cc(C(=O)OC)c2ccccc21        NULL  ...   \n",
       "123321                             Oc1cc(OCc2ccccc2)ccc1S        NULL  ...   \n",
       "35293                                 Oc1cccc2ccc[nH+]c12        NULL  ...   \n",
       "392918                                      CC(CO)NC(C)CO        NULL  ...   \n",
       "92455                                      COc1cncc(Br)c1        NULL  ...   \n",
       "\n",
       "                                                  rxn_str rxn_time  \\\n",
       "index                                                                \n",
       "79574   [N+:1]([C:4]1[CH:21]=[CH:20][CH:19]=[CH:18][C:...      NaN   \n",
       "148136  [Cl:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([Cl:8])[...     72.0   \n",
       "79634   I([O-])(=O)(=O)=O.[Na+].[OH2:7].[CH3:8][O:9][C...      8.0   \n",
       "329451  Br[C:2]1[CH:3]=[CH:4][C:5]2[NH:6][C:7]3[C:12](...      NaN   \n",
       "359709  [H-].[Na+].[Cl:3][C:4]1[N:13]=[CH:12][C:11]2[N...      0.5   \n",
       "...                                                   ...      ...   \n",
       "182938  [H-].[Na+].[NH:3]1[C:11]2[C:6](=[CH:7][CH:8]=[...      NaN   \n",
       "123321  [CH2:1]([O:8][C:9]1[CH:18]=[CH:17][C:12]2[S:13...     16.0   \n",
       "35293   C([N+](CCCC)(CCCC)CCCC)CCC.[O:18]=[C:19]1[C@@H...      NaN   \n",
       "392918  [NH2:1][CH:2]([CH3:5])[CH2:3][OH:4].[OH:6][CH2...     24.0   \n",
       "92455   [Br:1][C:2]1[CH:3]=[N:4][CH:5]=[C:6](Br)[CH:7]...      1.0   \n",
       "\n",
       "       solvent_000 solvent_001 temperature yield_000 yield_001 yield_002  \\\n",
       "index                                                                      \n",
       "79574          CCO    CN(C)C=O         NaN      96.9       NaN       NaN   \n",
       "148136    CN(C)C=O        None        40.0       NaN       NaN       NaN   \n",
       "79634      CC(C)=O          CO        25.0       NaN       NaN       NaN   \n",
       "329451   Cc1ccccc1        None         NaN      73.0       NaN       NaN   \n",
       "359709    CN(C)C=O           O        25.0      67.2       NaN       NaN   \n",
       "...            ...         ...         ...       ...       ...       ...   \n",
       "182938    CN(C)C=O           O         0.0       NaN       NaN       NaN   \n",
       "123321          CO        None        25.0       NaN       NaN       NaN   \n",
       "35293     CC(Cl)Cl        None         NaN       NaN       NaN       NaN   \n",
       "392918         CCO        None        25.0       NaN       NaN       NaN   \n",
       "92455     CN(C)C=O        None        60.0       NaN       NaN       NaN   \n",
       "\n",
       "       yield_003  yield_004  \n",
       "index                        \n",
       "79574        NaN        NaN  \n",
       "148136       NaN        NaN  \n",
       "79634        NaN        NaN  \n",
       "329451       NaN        NaN  \n",
       "359709       NaN        NaN  \n",
       "...          ...        ...  \n",
       "182938       NaN        NaN  \n",
       "123321       NaN        NaN  \n",
       "35293        NaN        NaN  \n",
       "392918       NaN        NaN  \n",
       "92455        NaN        NaN  \n",
       "\n",
       "[387287 rows x 28 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "train_2_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Download data from TDC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Downloading...\n",
      "100%|██████████| 795M/795M [01:29<00:00, 8.88MiB/s] \n",
      "Loading...\n",
      "Done!\n"
     ]
    }
   ],
   "source": [
    "# Inspect the retrosynthesis dataset\n",
    "\n",
    "from tdc.generation import RetroSyn\n",
    "data = RetroSyn(name = 'USPTO')\n",
    "split = data.get_split()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "997415"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(split['train'])+len(split['test'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Found local copy...\n",
      "Loading...\n",
      "Done!\n"
     ]
    }
   ],
   "source": [
    "from tdc.generation import Reaction\n",
    "data = Reaction(name = 'USPTO')\n",
    "split = data.get_split()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "997415"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(split['train'])+len(split['test'])"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "chemistry",
   "language": "python",
   "name": "python3"
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  "language_info": {
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    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.13"
  },
  "orig_nbformat": 4
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