{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "45d54f76-45c5-46c1-aeb2-dde40c63e8fc",
   "metadata": {},
   "source": [
    "**Requirements** \n",
    "* According to this [paper](https://arxiv.org/pdf/1904.01561.pdf), features are computed with [descriptastorus](https://github.com/bp-kelley/descriptastorus) package\n",
    "* Install via: `pip install git+https://github.com/bp-kelley/descriptastorus`"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fa137ded",
   "metadata": {},
   "source": [
    "## General imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "6c950b63",
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "\n",
    "# this depends on the notebook depth and must be adapted per notebook\n",
    "sys.path.insert(0, \"/\")  \n",
    "from chemCPA.paths import DATA_DIR, EMBEDDING_DIR"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4643260d",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from joblib import Parallel, delayed\n",
    "from tqdm.notebook import tqdm"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db8608d6",
   "metadata": {},
   "source": [
    "## Load Smiles list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "db1601d1",
   "metadata": {},
   "outputs": [],
   "source": [
    "import scanpy as sc\n",
    "from chemCPA.helper import canonicalize_smiles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "842d22c4",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/nfs/staff-hdd/hetzell/miniconda3/envs/chemical_CPA/lib/python3.7/site-packages/anndata/_core/anndata.py:1828: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n",
      "  utils.warn_names_duplicates(\"obs\")\n"
     ]
    }
   ],
   "source": [
    "adata = sc.read(DATA_DIR/ \"adata_biolord_split_30.h5ad\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "734a3db6",
   "metadata": {},
   "outputs": [],
   "source": [
    "smiles_list = adata.obs[\"smiles\"].unique()\n",
    "# exclude nan from smiles_list \n",
    "smiles_list = [canonicalize_smiles(s) for s in smiles_list if s !=\"nan\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "653d99cf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of smiles strings: 186\n"
     ]
    }
   ],
   "source": [
    "print(f'Number of smiles strings: {len(smiles_list)}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "a5dc19a2-d321-49e6-a62d-e6024073146e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "RDKit2D_calculated(bool)\n",
      "BalabanJ(float64)\n",
      "BertzCT(float64)\n",
      "Chi0(float64)\n",
      "Chi0n(float64)\n",
      "Chi0v(float64)\n",
      "Chi1(float64)\n",
      "Chi1n(float64)\n",
      "Chi1v(float64)\n",
      "Chi2n(float64)\n",
      "Chi2v(float64)\n",
      "Chi3n(float64)\n",
      "Chi3v(float64)\n",
      "Chi4n(float64)\n",
      "Chi4v(float64)\n",
      "EState_VSA1(float64)\n",
      "EState_VSA10(float64)\n",
      "EState_VSA11(float64)\n",
      "EState_VSA2(float64)\n",
      "EState_VSA3(float64)\n",
      "EState_VSA4(float64)\n",
      "EState_VSA5(float64)\n",
      "EState_VSA6(float64)\n",
      "EState_VSA7(float64)\n",
      "EState_VSA8(float64)\n",
      "EState_VSA9(float64)\n",
      "ExactMolWt(float64)\n",
      "FpDensityMorgan1(float64)\n",
      "FpDensityMorgan2(float64)\n",
      "FpDensityMorgan3(float64)\n",
      "FractionCSP3(float64)\n",
      "HallKierAlpha(float64)\n",
      "HeavyAtomCount(float64)\n",
      "HeavyAtomMolWt(float64)\n",
      "Ipc(float64)\n",
      "Kappa1(float64)\n",
      "Kappa2(float64)\n",
      "Kappa3(float64)\n",
      "LabuteASA(float64)\n",
      "MaxAbsEStateIndex(float64)\n",
      "MaxAbsPartialCharge(float64)\n",
      "MaxEStateIndex(float64)\n",
      "MaxPartialCharge(float64)\n",
      "MinAbsEStateIndex(float64)\n",
      "MinAbsPartialCharge(float64)\n",
      "MinEStateIndex(float64)\n",
      "MinPartialCharge(float64)\n",
      "MolLogP(float64)\n",
      "MolMR(float64)\n",
      "MolWt(float64)\n",
      "NHOHCount(float64)\n",
      "NOCount(float64)\n",
      "NumAliphaticCarbocycles(float64)\n",
      "NumAliphaticHeterocycles(float64)\n",
      "NumAliphaticRings(float64)\n",
      "NumAromaticCarbocycles(float64)\n",
      "NumAromaticHeterocycles(float64)\n",
      "NumAromaticRings(float64)\n",
      "NumHAcceptors(float64)\n",
      "NumHDonors(float64)\n",
      "NumHeteroatoms(float64)\n",
      "NumRadicalElectrons(float64)\n",
      "NumRotatableBonds(float64)\n",
      "NumSaturatedCarbocycles(float64)\n",
      "NumSaturatedHeterocycles(float64)\n",
      "NumSaturatedRings(float64)\n",
      "NumValenceElectrons(float64)\n",
      "PEOE_VSA1(float64)\n",
      "PEOE_VSA10(float64)\n",
      "PEOE_VSA11(float64)\n",
      "PEOE_VSA12(float64)\n",
      "PEOE_VSA13(float64)\n",
      "PEOE_VSA14(float64)\n",
      "PEOE_VSA2(float64)\n",
      "PEOE_VSA3(float64)\n",
      "PEOE_VSA4(float64)\n",
      "PEOE_VSA5(float64)\n",
      "PEOE_VSA6(float64)\n",
      "PEOE_VSA7(float64)\n",
      "PEOE_VSA8(float64)\n",
      "PEOE_VSA9(float64)\n",
      "RingCount(float64)\n",
      "SMR_VSA1(float64)\n",
      "SMR_VSA10(float64)\n",
      "SMR_VSA2(float64)\n",
      "SMR_VSA3(float64)\n",
      "SMR_VSA4(float64)\n",
      "SMR_VSA5(float64)\n",
      "SMR_VSA6(float64)\n",
      "SMR_VSA7(float64)\n",
      "SMR_VSA8(float64)\n",
      "SMR_VSA9(float64)\n",
      "SlogP_VSA1(float64)\n",
      "SlogP_VSA10(float64)\n",
      "SlogP_VSA11(float64)\n",
      "SlogP_VSA12(float64)\n",
      "SlogP_VSA2(float64)\n",
      "SlogP_VSA3(float64)\n",
      "SlogP_VSA4(float64)\n",
      "SlogP_VSA5(float64)\n",
      "SlogP_VSA6(float64)\n",
      "SlogP_VSA7(float64)\n",
      "SlogP_VSA8(float64)\n",
      "SlogP_VSA9(float64)\n",
      "TPSA(float64)\n",
      "VSA_EState1(float64)\n",
      "VSA_EState10(float64)\n",
      "VSA_EState2(float64)\n",
      "VSA_EState3(float64)\n",
      "VSA_EState4(float64)\n",
      "VSA_EState5(float64)\n",
      "VSA_EState6(float64)\n",
      "VSA_EState7(float64)\n",
      "VSA_EState8(float64)\n",
      "VSA_EState9(float64)\n",
      "fr_Al_COO(float64)\n",
      "fr_Al_OH(float64)\n",
      "fr_Al_OH_noTert(float64)\n",
      "fr_ArN(float64)\n",
      "fr_Ar_COO(float64)\n",
      "fr_Ar_N(float64)\n",
      "fr_Ar_NH(float64)\n",
      "fr_Ar_OH(float64)\n",
      "fr_COO(float64)\n",
      "fr_COO2(float64)\n",
      "fr_C_O(float64)\n",
      "fr_C_O_noCOO(float64)\n",
      "fr_C_S(float64)\n",
      "fr_HOCCN(float64)\n",
      "fr_Imine(float64)\n",
      "fr_NH0(float64)\n",
      "fr_NH1(float64)\n",
      "fr_NH2(float64)\n",
      "fr_N_O(float64)\n",
      "fr_Ndealkylation1(float64)\n",
      "fr_Ndealkylation2(float64)\n",
      "fr_Nhpyrrole(float64)\n",
      "fr_SH(float64)\n",
      "fr_aldehyde(float64)\n",
      "fr_alkyl_carbamate(float64)\n",
      "fr_alkyl_halide(float64)\n",
      "fr_allylic_oxid(float64)\n",
      "fr_amide(float64)\n",
      "fr_amidine(float64)\n",
      "fr_aniline(float64)\n",
      "fr_aryl_methyl(float64)\n",
      "fr_azide(float64)\n",
      "fr_azo(float64)\n",
      "fr_barbitur(float64)\n",
      "fr_benzene(float64)\n",
      "fr_benzodiazepine(float64)\n",
      "fr_bicyclic(float64)\n",
      "fr_diazo(float64)\n",
      "fr_dihydropyridine(float64)\n",
      "fr_epoxide(float64)\n",
      "fr_ester(float64)\n",
      "fr_ether(float64)\n",
      "fr_furan(float64)\n",
      "fr_guanido(float64)\n",
      "fr_halogen(float64)\n",
      "fr_hdrzine(float64)\n",
      "fr_hdrzone(float64)\n",
      "fr_imidazole(float64)\n",
      "fr_imide(float64)\n",
      "fr_isocyan(float64)\n",
      "fr_isothiocyan(float64)\n",
      "fr_ketone(float64)\n",
      "fr_ketone_Topliss(float64)\n",
      "fr_lactam(float64)\n",
      "fr_lactone(float64)\n",
      "fr_methoxy(float64)\n",
      "fr_morpholine(float64)\n",
      "fr_nitrile(float64)\n",
      "fr_nitro(float64)\n",
      "fr_nitro_arom(float64)\n",
      "fr_nitro_arom_nonortho(float64)\n",
      "fr_nitroso(float64)\n",
      "fr_oxazole(float64)\n",
      "fr_oxime(float64)\n",
      "fr_para_hydroxylation(float64)\n",
      "fr_phenol(float64)\n",
      "fr_phenol_noOrthoHbond(float64)\n",
      "fr_phos_acid(float64)\n",
      "fr_phos_ester(float64)\n",
      "fr_piperdine(float64)\n",
      "fr_piperzine(float64)\n",
      "fr_priamide(float64)\n",
      "fr_prisulfonamd(float64)\n",
      "fr_pyridine(float64)\n",
      "fr_quatN(float64)\n",
      "fr_sulfide(float64)\n",
      "fr_sulfonamd(float64)\n",
      "fr_sulfone(float64)\n",
      "fr_term_acetylene(float64)\n",
      "fr_tetrazole(float64)\n",
      "fr_thiazole(float64)\n",
      "fr_thiocyan(float64)\n",
      "fr_thiophene(float64)\n",
      "fr_unbrch_alkane(float64)\n",
      "fr_urea(float64)\n",
      "qed(float64)\n"
     ]
    }
   ],
   "source": [
    "from descriptastorus.descriptors.DescriptorGenerator import MakeGenerator\n",
    "generator = MakeGenerator((\"RDKit2D\",))\n",
    "for name, numpy_type in generator.GetColumns():\n",
    "    print(f\"{name}({numpy_type.__name__})\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "003cc588-e4dd-4dcc-98ec-4d3fcdd5432b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "3cdbc7fd2ace48aa960a1f81738956bc",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/186 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "n_jobs = 16\n",
    "data = Parallel(n_jobs=n_jobs)(delayed(generator.process)(smiles) for smiles in tqdm(smiles_list, position=0, leave=True) )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "055b3661",
   "metadata": {},
   "outputs": [],
   "source": [
    "data = [d[1:] for d in data]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "ba76cf35-7e75-4b53-8e82-9ea09a90f01a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(186, 200)"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "embedding = np.array(data)\n",
    "embedding.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f784e11a-82e8-4b63-90c0-5b835bd1f1a5",
   "metadata": {},
   "source": [
    "## Check `nans` and `infs`"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9296ab55-04e8-47c7-8624-bf68330c5553",
   "metadata": {},
   "source": [
    "Check for `nans`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "71e23bf2-e2dc-4cf7-a2f2-253a3a35ff99",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "drug_idx:\n",
      " []\n",
      "feature_idx:\n",
      " []\n"
     ]
    }
   ],
   "source": [
    "drug_idx, feature_idx = np.where(np.isnan(embedding))\n",
    "print(f'drug_idx:\\n {drug_idx}')\n",
    "print(f'feature_idx:\\n {feature_idx}')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ac8119cb-4f13-4498-a21d-3c100727ec71",
   "metadata": {},
   "source": [
    "Check for `infs` and add to idx lists"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "5ed78575-5351-433a-934d-fb969f33a9a6",
   "metadata": {},
   "outputs": [],
   "source": [
    "drug_idx_infs, feature_idx_infs = np.where(np.isinf(embedding))\n",
    "\n",
    "drug_idx = np.concatenate((drug_idx, drug_idx_infs))\n",
    "feature_idx = np.concatenate((feature_idx, feature_idx_infs))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ed64de53-ff22-4f86-839e-9fb70c0558db",
   "metadata": {},
   "source": [
    "Features that have these invalid values:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "eba4e112-e676-4816-9fe4-d2ba9b464b1d",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([], shape=(0, 2), dtype=object)"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.array(generator.GetColumns())[np.unique(feature_idx)]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a851a96f-27d3-42b6-a74c-db5c6fa6a257",
   "metadata": {},
   "source": [
    "Set values to `0`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "0a7fb00f-468b-4957-96cc-ae0974c54780",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([], dtype=float64)"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "embedding[drug_idx, feature_idx] "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "1ee85449-5515-4d93-94ae-b3a4845e088b",
   "metadata": {},
   "outputs": [],
   "source": [
    "embedding[drug_idx, feature_idx] = 0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cf768d83",
   "metadata": {},
   "source": [
    "## Save"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "a6291a01",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Deleting columns with std<=0.01: ['latent_60', 'latent_89', 'latent_102', 'latent_137', 'latent_145', 'latent_146', 'latent_147', 'latent_149', 'latent_151', 'latent_152', 'latent_159', 'latent_160', 'latent_163', 'latent_164', 'latent_167', 'latent_174', 'latent_177', 'latent_182', 'latent_186', 'latent_188', 'latent_193', 'latent_195']\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "df = pd.DataFrame(data=embedding,index=smiles_list,columns=[f'latent_{i}' for i in range(embedding.shape[1])]) \n",
    "\n",
    "# Drop first feature from generator (RDKit2D_calculated)\n",
    "df.drop(columns=['latent_0'], inplace=True)\n",
    "\n",
    "# Drop columns with 0 standard deviation\n",
    "threshold = 0.01\n",
    "columns=[f'latent_{idx+1}' for idx in np.where(df.std() <= threshold)[0]]\n",
    "print(f'Deleting columns with std<={threshold}: {columns}')\n",
    "df.drop(columns=[f'latent_{idx+1}' for idx in np.where(df.std() <= 0.01)[0]], inplace=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0f14068e-51b8-40a9-b9c6-043c12b082ee",
   "metadata": {},
   "source": [
    "Check that correct columns were deleted: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "c92f8a87-ce38-4309-a6c4-4e5b828b59c7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(array([], dtype=int64),)"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.where(df.std() <= threshold)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d0d8c60-79ae-4451-ae5c-321f533bed48",
   "metadata": {},
   "source": [
    "### Normalise dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "721590cd-67bb-4c70-bef4-268fbfa9a7cc",
   "metadata": {},
   "outputs": [],
   "source": [
    "normalized_df=(df-df.mean())/df.std()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "f4b63954-a11e-4384-945d-c94e2b629026",
   "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>latent_1</th>\n",
       "      <th>latent_2</th>\n",
       "      <th>latent_3</th>\n",
       "      <th>latent_4</th>\n",
       "      <th>latent_5</th>\n",
       "      <th>latent_6</th>\n",
       "      <th>latent_7</th>\n",
       "      <th>latent_8</th>\n",
       "      <th>latent_9</th>\n",
       "      <th>latent_10</th>\n",
       "      <th>...</th>\n",
       "      <th>latent_187</th>\n",
       "      <th>latent_189</th>\n",
       "      <th>latent_190</th>\n",
       "      <th>latent_191</th>\n",
       "      <th>latent_192</th>\n",
       "      <th>latent_194</th>\n",
       "      <th>latent_196</th>\n",
       "      <th>latent_197</th>\n",
       "      <th>latent_198</th>\n",
       "      <th>latent_199</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>O=C([O-])CCCc1ccccc1.[Na+]</th>\n",
       "      <td>-1.666455</td>\n",
       "      <td>-1.600675</td>\n",
       "      <td>-1.385933</td>\n",
       "      <td>-1.134785</td>\n",
       "      <td>-1.605154</td>\n",
       "      <td>-1.460731</td>\n",
       "      <td>-1.536649</td>\n",
       "      <td>-1.465486</td>\n",
       "      <td>-1.543553</td>\n",
       "      <td>-1.452940</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.121276</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)cccn4n3)c2)CC1</th>\n",
       "      <td>0.863033</td>\n",
       "      <td>0.376632</td>\n",
       "      <td>0.455178</td>\n",
       "      <td>0.475603</td>\n",
       "      <td>0.463247</td>\n",
       "      <td>0.462348</td>\n",
       "      <td>0.777506</td>\n",
       "      <td>0.503243</td>\n",
       "      <td>0.879424</td>\n",
       "      <td>0.503081</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>3.977884</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.060135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccncc3)ccc2c1</th>\n",
       "      <td>0.944786</td>\n",
       "      <td>0.248064</td>\n",
       "      <td>0.295501</td>\n",
       "      <td>0.318775</td>\n",
       "      <td>0.412792</td>\n",
       "      <td>0.268612</td>\n",
       "      <td>0.506380</td>\n",
       "      <td>0.178487</td>\n",
       "      <td>0.384114</td>\n",
       "      <td>0.284651</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.496321</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc23)c(Cl)cc1Cl</th>\n",
       "      <td>0.603507</td>\n",
       "      <td>0.746555</td>\n",
       "      <td>0.789836</td>\n",
       "      <td>0.920548</td>\n",
       "      <td>0.783927</td>\n",
       "      <td>0.701164</td>\n",
       "      <td>0.700273</td>\n",
       "      <td>0.582936</td>\n",
       "      <td>0.573394</td>\n",
       "      <td>0.651072</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>0.628009</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.508369</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O</th>\n",
       "      <td>-0.393464</td>\n",
       "      <td>-0.067916</td>\n",
       "      <td>-0.163103</td>\n",
       "      <td>-0.268156</td>\n",
       "      <td>-0.140663</td>\n",
       "      <td>-0.313933</td>\n",
       "      <td>-0.456744</td>\n",
       "      <td>-0.450171</td>\n",
       "      <td>-0.621424</td>\n",
       "      <td>-0.534237</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.379172</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>CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c3[nH]c4ncc(C)cc4c23)c1</th>\n",
       "      <td>1.286344</td>\n",
       "      <td>0.740428</td>\n",
       "      <td>0.887842</td>\n",
       "      <td>0.900547</td>\n",
       "      <td>0.732054</td>\n",
       "      <td>0.910649</td>\n",
       "      <td>1.136028</td>\n",
       "      <td>1.014856</td>\n",
       "      <td>1.426770</td>\n",
       "      <td>1.140227</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>3.977884</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.325822</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2c1.Cl.O</th>\n",
       "      <td>0.123124</td>\n",
       "      <td>0.267321</td>\n",
       "      <td>0.453349</td>\n",
       "      <td>0.473807</td>\n",
       "      <td>0.289093</td>\n",
       "      <td>0.295629</td>\n",
       "      <td>0.117262</td>\n",
       "      <td>0.090182</td>\n",
       "      <td>-0.130664</td>\n",
       "      <td>0.137535</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.746358</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2ccccc21</th>\n",
       "      <td>-0.028239</td>\n",
       "      <td>-0.011372</td>\n",
       "      <td>0.230844</td>\n",
       "      <td>0.391784</td>\n",
       "      <td>0.111804</td>\n",
       "      <td>0.200441</td>\n",
       "      <td>0.027626</td>\n",
       "      <td>0.214944</td>\n",
       "      <td>-0.017353</td>\n",
       "      <td>0.364936</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.495217</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4)cc3)c3ccccc3)c2c1</th>\n",
       "      <td>1.115222</td>\n",
       "      <td>0.770763</td>\n",
       "      <td>0.847426</td>\n",
       "      <td>0.860852</td>\n",
       "      <td>0.884172</td>\n",
       "      <td>0.997570</td>\n",
       "      <td>1.217879</td>\n",
       "      <td>0.869661</td>\n",
       "      <td>1.210711</td>\n",
       "      <td>0.882431</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>3.638151</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-1.140448</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(O)C1.Cl</th>\n",
       "      <td>0.252492</td>\n",
       "      <td>-0.041707</td>\n",
       "      <td>-0.056939</td>\n",
       "      <td>0.099009</td>\n",
       "      <td>-0.050176</td>\n",
       "      <td>-0.053351</td>\n",
       "      <td>-0.110797</td>\n",
       "      <td>0.095547</td>\n",
       "      <td>0.002473</td>\n",
       "      <td>0.210616</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.466665</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>186 rows × 177 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    latent_1  latent_2  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.666455 -1.600675   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.863033  0.376632   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.944786  0.248064   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.603507  0.746555   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.393464 -0.067916   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  1.286344  0.740428   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.123124  0.267321   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc... -0.028239 -0.011372   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  1.115222  0.770763   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...  0.252492 -0.041707   \n",
       "\n",
       "                                                    latent_3  latent_4  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.385933 -1.134785   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.455178  0.475603   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.295501  0.318775   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.789836  0.920548   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.163103 -0.268156   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  0.887842  0.900547   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.453349  0.473807   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...  0.230844  0.391784   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  0.847426  0.860852   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(... -0.056939  0.099009   \n",
       "\n",
       "                                                    latent_5  latent_6  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.605154 -1.460731   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.463247  0.462348   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.412792  0.268612   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.783927  0.701164   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.140663 -0.313933   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  0.732054  0.910649   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.289093  0.295629   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...  0.111804  0.200441   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  0.884172  0.997570   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(... -0.050176 -0.053351   \n",
       "\n",
       "                                                    latent_7  latent_8  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.536649 -1.465486   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.777506  0.503243   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.506380  0.178487   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.700273  0.582936   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.456744 -0.450171   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  1.136028  1.014856   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.117262  0.090182   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...  0.027626  0.214944   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  1.217879  0.869661   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(... -0.110797  0.095547   \n",
       "\n",
       "                                                    latent_9  latent_10  ...  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.543553  -1.452940  ...   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.879424   0.503081  ...   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.384114   0.284651  ...   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.573394   0.651072  ...   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.621424  -0.534237  ...   \n",
       "...                                                      ...        ...  ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  1.426770   1.140227  ...   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2... -0.130664   0.137535  ...   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc... -0.017353   0.364936  ...   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  1.210711   0.882431  ...   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...  0.002473   0.210616  ...   \n",
       "\n",
       "                                                    latent_187  latent_189  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.535847    -0.19722   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...    1.457503    -0.19722   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...    1.457503    -0.19722   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...    1.457503    -0.19722   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.535847    -0.19722   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...    1.457503    -0.19722   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.535847    -0.19722   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.535847    -0.19722   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...   -0.535847    -0.19722   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.535847    -0.19722   \n",
       "\n",
       "                                                    latent_190  latent_191  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.273387   -0.250038   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...   -0.273387    3.977884   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...   -0.273387   -0.250038   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...   -0.273387   -0.250038   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.273387   -0.250038   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...   -0.273387    3.977884   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.273387   -0.250038   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.273387   -0.250038   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...    3.638151   -0.250038   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.273387   -0.250038   \n",
       "\n",
       "                                                    latent_192  latent_194  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.073324   -0.199302   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...   -0.073324   -0.199302   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...   -0.073324   -0.199302   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...   -0.073324   -0.199302   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.073324   -0.199302   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...   -0.073324   -0.199302   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.073324   -0.199302   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.073324   -0.199302   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...   -0.073324   -0.199302   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.073324   -0.199302   \n",
       "\n",
       "                                                    latent_196  latent_197  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                            -0.19722   -0.270527   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...    -0.19722   -0.270527   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...    -0.19722   -0.270527   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...    -0.19722    0.628009   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O         -0.19722   -0.270527   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...    -0.19722   -0.270527   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...    -0.19722   -0.270527   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...    -0.19722   -0.270527   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...    -0.19722   -0.270527   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...    -0.19722   -0.270527   \n",
       "\n",
       "                                                    latent_198  latent_199  \n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.284531    0.121276  \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...   -0.284531    0.060135  \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...   -0.284531   -0.496321  \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...   -0.284531   -0.508369  \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.284531    0.379172  \n",
       "...                                                        ...         ...  \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...   -0.284531   -0.325822  \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.284531   -0.746358  \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.284531   -0.495217  \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...   -0.284531   -1.140448  \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.284531    0.466665  \n",
       "\n",
       "[186 rows x 177 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normalized_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7c216a71-a174-4f0b-8fea-0fe4a1f47fcb",
   "metadata": {},
   "source": [
    "Check destination folder"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "39bfb2ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_name = \"rdkit2D\"\n",
    "dataset_name= \"biolord\"\n",
    "fname = f'{model_name}_embedding_{dataset_name}.parquet'\n",
    "\n",
    "directory = EMBEDDING_DIR /'rdkit' / 'data' /'embeddings'\n",
    "directory.mkdir(parents=True, exist_ok=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ee361ecd-2224-4c58-b3fc-5879cb3a6488",
   "metadata": {},
   "source": [
    "Save normalised version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "f330b59f-798b-420f-9ca8-07d6049dc26a",
   "metadata": {},
   "outputs": [],
   "source": [
    "normalized_df.to_parquet(directory / fname)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "85180ed5",
   "metadata": {},
   "source": [
    "Check that it worked"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "9620dae5",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>latent_1</th>\n",
       "      <th>latent_2</th>\n",
       "      <th>latent_3</th>\n",
       "      <th>latent_4</th>\n",
       "      <th>latent_5</th>\n",
       "      <th>latent_6</th>\n",
       "      <th>latent_7</th>\n",
       "      <th>latent_8</th>\n",
       "      <th>latent_9</th>\n",
       "      <th>latent_10</th>\n",
       "      <th>...</th>\n",
       "      <th>latent_187</th>\n",
       "      <th>latent_189</th>\n",
       "      <th>latent_190</th>\n",
       "      <th>latent_191</th>\n",
       "      <th>latent_192</th>\n",
       "      <th>latent_194</th>\n",
       "      <th>latent_196</th>\n",
       "      <th>latent_197</th>\n",
       "      <th>latent_198</th>\n",
       "      <th>latent_199</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>O=C([O-])CCCc1ccccc1.[Na+]</th>\n",
       "      <td>-1.666455</td>\n",
       "      <td>-1.600675</td>\n",
       "      <td>-1.385933</td>\n",
       "      <td>-1.134785</td>\n",
       "      <td>-1.605154</td>\n",
       "      <td>-1.460731</td>\n",
       "      <td>-1.536649</td>\n",
       "      <td>-1.465486</td>\n",
       "      <td>-1.543553</td>\n",
       "      <td>-1.452940</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.121276</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)cccn4n3)c2)CC1</th>\n",
       "      <td>0.863033</td>\n",
       "      <td>0.376632</td>\n",
       "      <td>0.455178</td>\n",
       "      <td>0.475603</td>\n",
       "      <td>0.463247</td>\n",
       "      <td>0.462348</td>\n",
       "      <td>0.777506</td>\n",
       "      <td>0.503243</td>\n",
       "      <td>0.879424</td>\n",
       "      <td>0.503081</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>3.977884</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.060135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccncc3)ccc2c1</th>\n",
       "      <td>0.944786</td>\n",
       "      <td>0.248064</td>\n",
       "      <td>0.295501</td>\n",
       "      <td>0.318775</td>\n",
       "      <td>0.412792</td>\n",
       "      <td>0.268612</td>\n",
       "      <td>0.506380</td>\n",
       "      <td>0.178487</td>\n",
       "      <td>0.384114</td>\n",
       "      <td>0.284651</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.496321</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc23)c(Cl)cc1Cl</th>\n",
       "      <td>0.603507</td>\n",
       "      <td>0.746555</td>\n",
       "      <td>0.789836</td>\n",
       "      <td>0.920548</td>\n",
       "      <td>0.783927</td>\n",
       "      <td>0.701164</td>\n",
       "      <td>0.700273</td>\n",
       "      <td>0.582936</td>\n",
       "      <td>0.573394</td>\n",
       "      <td>0.651072</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>0.628009</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.508369</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O</th>\n",
       "      <td>-0.393464</td>\n",
       "      <td>-0.067916</td>\n",
       "      <td>-0.163103</td>\n",
       "      <td>-0.268156</td>\n",
       "      <td>-0.140663</td>\n",
       "      <td>-0.313933</td>\n",
       "      <td>-0.456744</td>\n",
       "      <td>-0.450171</td>\n",
       "      <td>-0.621424</td>\n",
       "      <td>-0.534237</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.379172</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>CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c3[nH]c4ncc(C)cc4c23)c1</th>\n",
       "      <td>1.286344</td>\n",
       "      <td>0.740428</td>\n",
       "      <td>0.887842</td>\n",
       "      <td>0.900547</td>\n",
       "      <td>0.732054</td>\n",
       "      <td>0.910649</td>\n",
       "      <td>1.136028</td>\n",
       "      <td>1.014856</td>\n",
       "      <td>1.426770</td>\n",
       "      <td>1.140227</td>\n",
       "      <td>...</td>\n",
       "      <td>1.457503</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>3.977884</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.325822</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2c1.Cl.O</th>\n",
       "      <td>0.123124</td>\n",
       "      <td>0.267321</td>\n",
       "      <td>0.453349</td>\n",
       "      <td>0.473807</td>\n",
       "      <td>0.289093</td>\n",
       "      <td>0.295629</td>\n",
       "      <td>0.117262</td>\n",
       "      <td>0.090182</td>\n",
       "      <td>-0.130664</td>\n",
       "      <td>0.137535</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.746358</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2ccccc21</th>\n",
       "      <td>-0.028239</td>\n",
       "      <td>-0.011372</td>\n",
       "      <td>0.230844</td>\n",
       "      <td>0.391784</td>\n",
       "      <td>0.111804</td>\n",
       "      <td>0.200441</td>\n",
       "      <td>0.027626</td>\n",
       "      <td>0.214944</td>\n",
       "      <td>-0.017353</td>\n",
       "      <td>0.364936</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-0.495217</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4)cc3)c3ccccc3)c2c1</th>\n",
       "      <td>1.115222</td>\n",
       "      <td>0.770763</td>\n",
       "      <td>0.847426</td>\n",
       "      <td>0.860852</td>\n",
       "      <td>0.884172</td>\n",
       "      <td>0.997570</td>\n",
       "      <td>1.217879</td>\n",
       "      <td>0.869661</td>\n",
       "      <td>1.210711</td>\n",
       "      <td>0.882431</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>3.638151</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>-1.140448</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(O)C1.Cl</th>\n",
       "      <td>0.252492</td>\n",
       "      <td>-0.041707</td>\n",
       "      <td>-0.056939</td>\n",
       "      <td>0.099009</td>\n",
       "      <td>-0.050176</td>\n",
       "      <td>-0.053351</td>\n",
       "      <td>-0.110797</td>\n",
       "      <td>0.095547</td>\n",
       "      <td>0.002473</td>\n",
       "      <td>0.210616</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.535847</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.273387</td>\n",
       "      <td>-0.250038</td>\n",
       "      <td>-0.073324</td>\n",
       "      <td>-0.199302</td>\n",
       "      <td>-0.19722</td>\n",
       "      <td>-0.270527</td>\n",
       "      <td>-0.284531</td>\n",
       "      <td>0.466665</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>186 rows × 177 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    latent_1  latent_2  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.666455 -1.600675   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.863033  0.376632   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.944786  0.248064   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.603507  0.746555   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.393464 -0.067916   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  1.286344  0.740428   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.123124  0.267321   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc... -0.028239 -0.011372   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  1.115222  0.770763   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...  0.252492 -0.041707   \n",
       "\n",
       "                                                    latent_3  latent_4  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.385933 -1.134785   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.455178  0.475603   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.295501  0.318775   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.789836  0.920548   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.163103 -0.268156   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  0.887842  0.900547   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.453349  0.473807   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...  0.230844  0.391784   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  0.847426  0.860852   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(... -0.056939  0.099009   \n",
       "\n",
       "                                                    latent_5  latent_6  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.605154 -1.460731   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.463247  0.462348   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.412792  0.268612   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.783927  0.701164   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.140663 -0.313933   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  0.732054  0.910649   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.289093  0.295629   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...  0.111804  0.200441   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  0.884172  0.997570   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(... -0.050176 -0.053351   \n",
       "\n",
       "                                                    latent_7  latent_8  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.536649 -1.465486   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.777506  0.503243   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.506380  0.178487   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.700273  0.582936   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.456744 -0.450171   \n",
       "...                                                      ...       ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  1.136028  1.014856   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...  0.117262  0.090182   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...  0.027626  0.214944   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  1.217879  0.869661   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(... -0.110797  0.095547   \n",
       "\n",
       "                                                    latent_9  latent_10  ...  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                         -1.543553  -1.452940  ...   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...  0.879424   0.503081  ...   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...  0.384114   0.284651  ...   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...  0.573394   0.651072  ...   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O      -0.621424  -0.534237  ...   \n",
       "...                                                      ...        ...  ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...  1.426770   1.140227  ...   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2... -0.130664   0.137535  ...   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc... -0.017353   0.364936  ...   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...  1.210711   0.882431  ...   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...  0.002473   0.210616  ...   \n",
       "\n",
       "                                                    latent_187  latent_189  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.535847    -0.19722   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...    1.457503    -0.19722   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...    1.457503    -0.19722   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...    1.457503    -0.19722   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.535847    -0.19722   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...    1.457503    -0.19722   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.535847    -0.19722   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.535847    -0.19722   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...   -0.535847    -0.19722   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.535847    -0.19722   \n",
       "\n",
       "                                                    latent_190  latent_191  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.273387   -0.250038   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...   -0.273387    3.977884   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...   -0.273387   -0.250038   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...   -0.273387   -0.250038   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.273387   -0.250038   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...   -0.273387    3.977884   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.273387   -0.250038   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.273387   -0.250038   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...    3.638151   -0.250038   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.273387   -0.250038   \n",
       "\n",
       "                                                    latent_192  latent_194  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.073324   -0.199302   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...   -0.073324   -0.199302   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...   -0.073324   -0.199302   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...   -0.073324   -0.199302   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.073324   -0.199302   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...   -0.073324   -0.199302   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.073324   -0.199302   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.073324   -0.199302   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...   -0.073324   -0.199302   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.073324   -0.199302   \n",
       "\n",
       "                                                    latent_196  latent_197  \\\n",
       "O=C([O-])CCCc1ccccc1.[Na+]                            -0.19722   -0.270527   \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...    -0.19722   -0.270527   \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...    -0.19722   -0.270527   \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...    -0.19722    0.628009   \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O         -0.19722   -0.270527   \n",
       "...                                                        ...         ...   \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...    -0.19722   -0.270527   \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...    -0.19722   -0.270527   \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...    -0.19722   -0.270527   \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...    -0.19722   -0.270527   \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...    -0.19722   -0.270527   \n",
       "\n",
       "                                                    latent_198  latent_199  \n",
       "O=C([O-])CCCc1ccccc1.[Na+]                           -0.284531    0.121276  \n",
       "CN1CCN(c2cccc(Nc3nc4c(-c5ccc(S(C)(=O)=O)cc5)ccc...   -0.284531    0.060135  \n",
       "COc1ccc2cc(-c3nc(-c4ccc(S(C)=O)cc4)[nH]c3-c3ccn...   -0.284531   -0.496321  \n",
       "COc1cc(Nc2c(C#N)cnc3cc(OCCCN4CCN(C)CC4)c(OC)cc2...   -0.284531   -0.508369  \n",
       "COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O        -0.284531    0.379172  \n",
       "...                                                        ...         ...  \n",
       "CCS(=O)(=O)c1cccc(-c2cc(C(=O)NC3CCN(C)CC3)c(C)c...   -0.284531   -0.325822  \n",
       "CCN(CC)Cc1ccc2cc(COC(=O)Nc3ccc(C(=O)NO)cc3)ccc2...   -0.284531   -0.746358  \n",
       "Cl.Cl.Cn1cc(CNCC2CCN(c3ncc(C(=O)NO)cn3)CC2)c2cc...   -0.284531   -0.495217  \n",
       "CCS(=O)(=O)Nc1ccc2[nH]c(O)c(C(=Nc3ccc(CN4CCCCC4...   -0.284531   -1.140448  \n",
       "CN1CCC(c2c(O)cc(O)c3c(=O)cc(-c4ccccc4Cl)oc23)C(...   -0.284531    0.466665  \n",
       "\n",
       "[186 rows x 177 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_parquet(directory/ fname)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "201edd5b-832b-4350-b82d-8e6a4da099ac",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "PosixPath('/nfs/staff-ssd/hetzell/code/chemCPA_v2/project_folder/embeddings/rdkit/data/embeddings/rdkit2D_embedding_biolord.parquet')"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "directory/ fname"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8494453a",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "interpreter": {
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.12"
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 },
 "nbformat": 4,
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