notebooks/test_skfp.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9e6b21c3",
   "metadata": {},
   "outputs": [],
   "source": [
    "import torch\n",
    "import numpy as np\n",
    "import os\n",
    "from torch import nn\n",
    "import sys\n",
    "import polars as pl\n",
    "import sklearn\n",
    "import shap\n",
    "from functools import partial\n",
    "import pandas as pd\n",
    "import random\n",
    "from matplotlib import pyplot as plt\n",
    "import time\n",
    "from rdkit.Chem import DataStructs\n",
    "from tqdm import tqdm\n",
    "from joblib import Parallel, delayed\n",
    "import math\n",
    "from skfp import fingerprints as skfps\n",
    "\n",
    "\n",
    "sys.path.append('../')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "6c855685",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.07109459023922682 GB\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_56723/3396396263.py:8: DeprecationWarning: `count` is deprecated. It has been renamed to `len`.\n",
      "  test_df.group_by('mol_group').count().sort('mol_group')\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div><style>\n",
       ".dataframe > thead > tr,\n",
       ".dataframe > tbody > tr {\n",
       "  text-align: right;\n",
       "  white-space: pre-wrap;\n",
       "}\n",
       "</style>\n",
       "<small>shape: (4, 2)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>mol_group</th><th>count</th></tr><tr><td>i64</td><td>u32</td></tr></thead><tbody><tr><td>0</td><td>369039</td></tr><tr><td>1</td><td>486390</td></tr><tr><td>2</td><td>11271</td></tr><tr><td>3</td><td>11322</td></tr></tbody></table></div>"
      ],
      "text/plain": [
       "shape: (4, 2)\n",
       "┌───────────┬────────┐\n",
       "│ mol_group ┆ count  │\n",
       "│ ---       ┆ ---    │\n",
       "│ i64       ┆ u32    │\n",
       "╞═══════════╪════════╡\n",
       "│ 0         ┆ 369039 │\n",
       "│ 1         ┆ 486390 │\n",
       "│ 2         ┆ 11271  │\n",
       "│ 3         ┆ 11322  │\n",
       "└───────────┴────────┘"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test_df = pl.scan_csv('/home/dangnh36/datasets/competitions/leash_belka/processed/test_v4.csv').with_row_index('index').select(\n",
    "        pl.col('molecule'),\n",
    "        pl.col('index', 'mol_group'),\n",
    "#         pl.col('bb1', 'bb2', 'bb3').cast(pl.UInt16),\n",
    "        # pl.col('BRD4', 'HSA', 'sEH').cast(pl.UInt8),\n",
    "    ).collect()\n",
    "print(test_df.estimated_size('gb'), 'GB')\n",
    "test_df.group_by('mol_group').count().sort('mol_group')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b751a7e9",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ba547e62",
   "metadata": {},
   "outputs": [],
   "source": [
    "def test_fp(fp_class):\n",
    "    try:\n",
    "        start = time.time()\n",
    "        smiles = test_df[:200, 'molecule']\n",
    "        fp = fp_class()\n",
    "        fps = fp.transform(smiles)\n",
    "        end = time.time()\n",
    "        take = round((end - start) * 1000, 2)\n",
    "        print('Take:', take, 'ms')\n",
    "        # assert (0 <= fps).all() and (1 >= fps).all()\n",
    "        print(type(fps), fps.dtype, fps.shape)\n",
    "        print(fps)\n",
    "        return take, fps.dtype, fps.shape, ''\n",
    "    except Exception as e:\n",
    "        return None, None, None, str(e)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "1ed63fe1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[skfp.fingerprints.atom_pair.AtomPairFingerprint,\n",
       " skfp.fingerprints.autocorr.AutocorrFingerprint,\n",
       " skfp.fingerprints.avalon.AvalonFingerprint,\n",
       " skfp.fingerprints.e3fp_fp.E3FPFingerprint,\n",
       " skfp.fingerprints.ecfp.ECFPFingerprint,\n",
       " skfp.fingerprints.erg.ERGFingerprint,\n",
       " skfp.fingerprints.estate.EStateFingerprint,\n",
       " skfp.fingerprints.functional_groups.FunctionalGroupsFingerprint,\n",
       " skfp.fingerprints.getaway.GETAWAYFingerprint,\n",
       " skfp.fingerprints.ghose_crippen.GhoseCrippenFingerprint,\n",
       " skfp.fingerprints.klekota_roth.KlekotaRothFingerprint,\n",
       " skfp.fingerprints.laggner.LaggnerFingerprint,\n",
       " skfp.fingerprints.layered.LayeredFingerprint,\n",
       " skfp.fingerprints.lingo.LingoFingerprint,\n",
       " skfp.fingerprints.maccs.MACCSFingerprint,\n",
       " skfp.fingerprints.map.MAPFingerprint,\n",
       " skfp.fingerprints.mhfp.MHFPFingerprint,\n",
       " skfp.fingerprints.morse.MORSEFingerprint,\n",
       " skfp.fingerprints.mqns.MQNsFingerprint,\n",
       " skfp.fingerprints.mordred_fp.MordredFingerprint,\n",
       " skfp.fingerprints.pattern.PatternFingerprint,\n",
       " skfp.fingerprints.pharmacophore.PharmacophoreFingerprint,\n",
       " skfp.fingerprints.physiochemical_properties.PhysiochemicalPropertiesFingerprint,\n",
       " skfp.fingerprints.pubchem.PubChemFingerprint,\n",
       " skfp.fingerprints.rdf.RDFFingerprint,\n",
       " skfp.fingerprints.rdk.RDKitFingerprint,\n",
       " skfp.fingerprints.secfp.SECFPFingerprint,\n",
       " skfp.fingerprints.topological_torsion.TopologicalTorsionFingerprint,\n",
       " skfp.fingerprints.usrcat.USRCATFingerprint,\n",
       " skfp.fingerprints.usr.USRFingerprint,\n",
       " skfp.fingerprints.whim.WHIMFingerprint]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from skfp.bases import BaseFingerprintTransformer\n",
    "import inspect\n",
    "\n",
    "all_skfp_classes = []\n",
    "for e in dir(skfps):\n",
    "    att = getattr(skfps, e)\n",
    "    if inspect.isclass(att) and issubclass(att, BaseFingerprintTransformer):\n",
    "        all_skfp_classes.append(att)\n",
    "\n",
    "all_skfp_classes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "id": "a4c68b82",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  6%|██▊                                        | 2/31 [00:00<00:03,  8.74it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 128.21 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [1 0 0 ... 0 0 0]\n",
      " ...\n",
      " [1 0 0 ... 0 0 0]\n",
      " [1 1 0 ... 0 0 0]\n",
      " [1 1 0 ... 0 0 0]]\n",
      "Take: 102.16 ms\n",
      "<class 'numpy.ndarray'> float64 (200, 192)\n",
      "[[4.012 4.202 4.446 ... 1.174 0.68  1.323]\n",
      " [4.145 4.379 4.589 ... 1.152 0.87  1.108]\n",
      " [4.036 4.286 4.524 ... 1.07  0.874 1.473]\n",
      " ...\n",
      " [4.28  4.512 4.668 ... 1.089 0.821 1.109]\n",
      " [4.288 4.519 4.685 ... 1.161 0.814 0.929]\n",
      " [4.226 4.464 4.653 ... 1.034 0.991 0.848]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 10%|████▏                                      | 3/31 [00:00<00:09,  3.00it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 591.92 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 512)\n",
      "[[0 0 0 ... 1 0 0]\n",
      " [1 0 0 ... 1 1 1]\n",
      " [0 0 0 ... 1 0 0]\n",
      " ...\n",
      " [1 0 0 ... 1 1 1]\n",
      " [0 1 0 ... 1 1 0]\n",
      " [1 0 0 ... 1 1 1]]\n",
      "Take: 94.46 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 1 0 ... 0 0 0]\n",
      " [0 1 0 ... 0 0 0]\n",
      " [0 1 0 ... 0 0 0]\n",
      " ...\n",
      " [0 1 0 ... 0 0 0]\n",
      " [0 1 0 ... 0 0 0]\n",
      " [0 1 0 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 19%|████████▎                                  | 6/31 [00:01<00:04,  6.10it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 134.01 ms\n",
      "<class 'numpy.ndarray'> float64 (200, 315)\n",
      "[[0.  0.3 1.9 ... 0.  0.  0. ]\n",
      " [0.  0.3 1.9 ... 0.  0.  0. ]\n",
      " [0.  0.6 2.9 ... 0.  0.  0. ]\n",
      " ...\n",
      " [0.  0.3 2.2 ... 0.  0.  0. ]\n",
      " [0.  0.3 1.9 ... 0.  0.  0. ]\n",
      " [0.  0.3 2.2 ... 0.  0.  0. ]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      " 26%|███████████                                | 8/31 [00:01<00:04,  4.91it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 341.23 ms\n",
      "<class 'numpy.ndarray'> float64 (200, 79)\n",
      "[[0. 0. 0. ... 0. 0. 0.]\n",
      " [0. 0. 0. ... 0. 0. 0.]\n",
      " [0. 0. 0. ... 0. 0. 0.]\n",
      " ...\n",
      " [0. 0. 0. ... 0. 0. 0.]\n",
      " [0. 0. 0. ... 0. 0. 0.]\n",
      " [0. 0. 0. ... 0. 0. 0.]]\n",
      "Take: 192.67 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 85)\n",
      "[[0 0 0 ... 0 1 0]\n",
      " [0 1 1 ... 0 1 0]\n",
      " [0 1 0 ... 0 1 0]\n",
      " ...\n",
      " [0 0 0 ... 0 1 0]\n",
      " [0 0 0 ... 0 1 0]\n",
      " [0 1 1 ... 0 1 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 32%|█████████████▌                            | 10/31 [00:01<00:03,  5.93it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 238.62 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 110)\n",
      "[[0 0 1 ... 0 0 0]\n",
      " [0 1 1 ... 0 0 0]\n",
      " [0 1 1 ... 0 0 0]\n",
      " ...\n",
      " [0 0 1 ... 0 0 0]\n",
      " [0 0 1 ... 0 0 0]\n",
      " [0 1 1 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 35%|██████████████▉                           | 11/31 [00:10<00:41,  2.05s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 8255.99 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 4860)\n",
      "[[1 0 0 ... 0 0 0]\n",
      " [1 0 0 ... 0 0 0]\n",
      " [1 0 0 ... 0 0 0]\n",
      " ...\n",
      " [1 0 0 ... 0 0 0]\n",
      " [1 0 0 ... 0 0 0]\n",
      " [1 0 0 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 39%|████████████████▎                         | 12/31 [00:11<00:34,  1.82s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 1100.49 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 307)\n",
      "[[0 1 0 ... 0 0 1]\n",
      " [1 1 0 ... 0 0 1]\n",
      " [1 1 0 ... 0 0 1]\n",
      " ...\n",
      " [1 1 0 ... 0 0 1]\n",
      " [1 1 0 ... 0 0 1]\n",
      " [1 1 0 ... 0 0 1]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 42%|█████████████████▌                        | 13/31 [00:12<00:28,  1.57s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 884.91 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 1 1 ... 0 0 0]\n",
      " [0 1 1 ... 0 0 0]\n",
      " [0 1 1 ... 1 0 0]\n",
      " ...\n",
      " [0 1 1 ... 0 0 1]\n",
      " [0 1 1 ... 0 0 1]\n",
      " [0 1 1 ... 0 0 0]]\n",
      "Take: 31.18 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 1024)\n",
      "[[0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " ...\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 48%|████████████████████▎                     | 15/31 [00:12<00:15,  1.01it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 391.64 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 167)\n",
      "[[0 0 0 ... 1 1 0]\n",
      " [0 0 0 ... 1 1 0]\n",
      " [0 0 0 ... 1 1 0]\n",
      " ...\n",
      " [0 0 0 ... 1 1 0]\n",
      " [0 0 0 ... 1 1 0]\n",
      " [0 0 0 ... 1 1 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 52%|█████████████████████▋                    | 16/31 [00:13<00:15,  1.05s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 1251.15 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 1024)\n",
      "[[0 0 1 ... 0 1 1]\n",
      " [0 0 1 ... 0 0 1]\n",
      " [0 0 1 ... 0 0 1]\n",
      " ...\n",
      " [0 0 1 ... 0 0 1]\n",
      " [0 0 1 ... 1 0 1]\n",
      " [0 0 1 ... 0 0 1]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 55%|███████████████████████                   | 17/31 [00:15<00:15,  1.08s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 1174.15 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[1 0 0 ... 1 1 1]\n",
      " [1 0 0 ... 1 1 1]\n",
      " [1 0 0 ... 0 1 1]\n",
      " ...\n",
      " [1 0 1 ... 1 1 1]\n",
      " [1 0 1 ... 1 1 1]\n",
      " [1 0 1 ... 1 1 1]]\n",
      "Take: 76.25 ms\n",
      "<class 'numpy.ndarray'> uint32 (200, 42)\n",
      "[[26  0  0 ...  0  0  0]\n",
      " [26  0  0 ...  0  2  1]\n",
      " [26  0  0 ...  0  0  0]\n",
      " ...\n",
      " [34  0  0 ...  0  2  1]\n",
      " [33  0  0 ...  0  2  1]\n",
      " [27  0  0 ...  0  2  1]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 65%|███████████████████████████               | 20/31 [04:05<07:23, 40.35s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 230641.02 ms\n",
      "<class 'numpy.ndarray'> float32 (200, 1613)\n",
      "[[ 26.231901  19.772808   0.       ... 192.        11.25       8.194445]\n",
      " [ 30.572     23.001709   0.       ... 233.        12.833333   9.111111]\n",
      " [ 27.32103   21.888456   0.       ... 210.        12.902778   8.131945]\n",
      " ...\n",
      " [ 37.01684   25.19043    0.       ... 275.        13.944445  10.805555]\n",
      " [ 36.976402  25.503395   0.       ... 276.        13.944445  10.833333]\n",
      " [ 33.538326  25.528872   0.       ... 253.        14.444445  10.      ]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 68%|████████████████████████████▍             | 21/31 [04:06<05:25, 32.54s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 863.47 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 1 0 ... 1 1 0]\n",
      " [0 1 0 ... 1 1 0]\n",
      " [0 1 1 ... 1 1 0]\n",
      " ...\n",
      " [0 1 0 ... 1 1 0]\n",
      " [0 1 0 ... 1 1 0]\n",
      " [0 1 1 ... 1 1 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 71%|█████████████████████████████▊            | 22/31 [04:50<05:15, 35.01s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 43720.44 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 39972)\n",
      "[[0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " ...\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 74%|███████████████████████████████▏          | 23/31 [04:50<03:33, 26.70s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 312.74 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " ...\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 77%|████████████████████████████████▌         | 24/31 [04:55<02:27, 21.05s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 4525.36 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 881)\n",
      "[[1 1 1 ... 0 0 0]\n",
      " [1 1 1 ... 0 0 0]\n",
      " [1 1 1 ... 0 0 0]\n",
      " ...\n",
      " [1 1 1 ... 0 0 0]\n",
      " [1 1 1 ... 0 0 0]\n",
      " [1 1 1 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\r",
      " 84%|███████████████████████████████████▏      | 26/31 [04:55<01:01, 12.31s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 587.81 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 0 0 ... 0 0 1]\n",
      " [1 0 0 ... 0 0 1]\n",
      " [0 0 0 ... 0 0 1]\n",
      " ...\n",
      " [1 0 1 ... 0 0 1]\n",
      " [1 0 0 ... 1 0 1]\n",
      " [1 1 1 ... 1 1 1]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████████████████████████████████████| 31/31 [04:58<00:00,  9.62s/it]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Take: 2124.91 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " ...\n",
      " [0 0 0 ... 0 0 1]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]]\n",
      "Take: 185.57 ms\n",
      "<class 'numpy.ndarray'> uint8 (200, 2048)\n",
      "[[0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " ...\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]\n",
      " [0 0 0 ... 0 0 0]]\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>class</th>\n",
       "      <th>dtype</th>\n",
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       "      <th>error</th>\n",
       "      <th>take</th>\n",
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       "      <th>0</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>128.21</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>float64</td>\n",
       "      <td>(200, 192)</td>\n",
       "      <td></td>\n",
       "      <td>102.16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
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       "      <td></td>\n",
       "      <td>591.92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
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       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>94.46</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>float64</td>\n",
       "      <td>(200, 315)</td>\n",
       "      <td></td>\n",
       "      <td>134.01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>float64</td>\n",
       "      <td>(200, 79)</td>\n",
       "      <td></td>\n",
       "      <td>341.23</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 85)</td>\n",
       "      <td></td>\n",
       "      <td>192.67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 110)</td>\n",
       "      <td></td>\n",
       "      <td>238.62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 4860)</td>\n",
       "      <td></td>\n",
       "      <td>8255.99</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 307)</td>\n",
       "      <td></td>\n",
       "      <td>1100.49</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>884.91</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 1024)</td>\n",
       "      <td></td>\n",
       "      <td>31.18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 167)</td>\n",
       "      <td></td>\n",
       "      <td>391.64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 1024)</td>\n",
       "      <td></td>\n",
       "      <td>1251.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>1174.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint32</td>\n",
       "      <td>(200, 42)</td>\n",
       "      <td></td>\n",
       "      <td>76.25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>float32</td>\n",
       "      <td>(200, 1613)</td>\n",
       "      <td></td>\n",
       "      <td>230641.02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>863.47</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 39972)</td>\n",
       "      <td></td>\n",
       "      <td>43720.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>312.74</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 881)</td>\n",
       "      <td></td>\n",
       "      <td>4525.36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>587.81</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>2124.91</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>185.57</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>&lt;class 'abc.ABCMeta'&gt;</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    class    dtype         shape  \\\n",
       "0   <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "1   <class 'abc.ABCMeta'>  float64    (200, 192)   \n",
       "2   <class 'abc.ABCMeta'>    uint8    (200, 512)   \n",
       "3   <class 'abc.ABCMeta'>     None          None   \n",
       "4   <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "5   <class 'abc.ABCMeta'>  float64    (200, 315)   \n",
       "6   <class 'abc.ABCMeta'>  float64     (200, 79)   \n",
       "7   <class 'abc.ABCMeta'>    uint8     (200, 85)   \n",
       "8   <class 'abc.ABCMeta'>     None          None   \n",
       "9   <class 'abc.ABCMeta'>    uint8    (200, 110)   \n",
       "10  <class 'abc.ABCMeta'>    uint8   (200, 4860)   \n",
       "11  <class 'abc.ABCMeta'>    uint8    (200, 307)   \n",
       "12  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "13  <class 'abc.ABCMeta'>    uint8   (200, 1024)   \n",
       "14  <class 'abc.ABCMeta'>    uint8    (200, 167)   \n",
       "15  <class 'abc.ABCMeta'>    uint8   (200, 1024)   \n",
       "16  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "17  <class 'abc.ABCMeta'>     None          None   \n",
       "18  <class 'abc.ABCMeta'>   uint32     (200, 42)   \n",
       "19  <class 'abc.ABCMeta'>  float32   (200, 1613)   \n",
       "20  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "21  <class 'abc.ABCMeta'>    uint8  (200, 39972)   \n",
       "22  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "23  <class 'abc.ABCMeta'>    uint8    (200, 881)   \n",
       "24  <class 'abc.ABCMeta'>     None          None   \n",
       "25  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "26  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "27  <class 'abc.ABCMeta'>    uint8   (200, 2048)   \n",
       "28  <class 'abc.ABCMeta'>     None          None   \n",
       "29  <class 'abc.ABCMeta'>     None          None   \n",
       "30  <class 'abc.ABCMeta'>     None          None   \n",
       "\n",
       "                                                error       take  \n",
       "0                                                         128.21  \n",
       "1                                                         102.16  \n",
       "2                                                         591.92  \n",
       "3   Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "4                                                          94.46  \n",
       "5                                                         134.01  \n",
       "6                                                         341.23  \n",
       "7                                                         192.67  \n",
       "8   Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "9                                                         238.62  \n",
       "10                                                       8255.99  \n",
       "11                                                       1100.49  \n",
       "12                                                        884.91  \n",
       "13                                                         31.18  \n",
       "14                                                        391.64  \n",
       "15                                                       1251.15  \n",
       "16                                                       1174.15  \n",
       "17  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "18                                                         76.25  \n",
       "19                                                     230641.02  \n",
       "20                                                        863.47  \n",
       "21                                                      43720.44  \n",
       "22                                                        312.74  \n",
       "23                                                       4525.36  \n",
       "24  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "25                                                        587.81  \n",
       "26                                                       2124.91  \n",
       "27                                                        185.57  \n",
       "28  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "29  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "30  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  "
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_dtypes = []\n",
    "all_shapes = []\n",
    "all_errs = []\n",
    "all_class_name = []\n",
    "takes = []\n",
    "\n",
    "for fp_class in tqdm(all_skfp_classes):\n",
    "    take, dtype, shape, err = test_fp(fp_class)\n",
    "    all_class_name.append(fp_class.__name__)\n",
    "    all_dtypes.append(dtype)\n",
    "    all_shapes.append(shape)\n",
    "    all_errs.append(err)\n",
    "    takes.append(take)\n",
    "\n",
    "df = pd.DataFrame({\n",
    "    'class': all_class_name,\n",
    "    'dtype': all_dtypes,\n",
    "    'shape': all_shapes,\n",
    "    'error': all_errs,\n",
    "    'take': takes\n",
    "})\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "id": "c951619c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "172.79999999999998"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "24 * 60 * 60 / 100_000_000 * 200 * 1000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "id": "e6a95860",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
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       "      <th></th>\n",
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       "      <th>take</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AtomPairFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>128.21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AutocorrFingerprint</td>\n",
       "      <td>float64</td>\n",
       "      <td>(200, 192)</td>\n",
       "      <td></td>\n",
       "      <td>102.16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AvalonFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 512)</td>\n",
       "      <td></td>\n",
       "      <td>591.92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>E3FPFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ECFPFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>94.46</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ERGFingerprint</td>\n",
       "      <td>float64</td>\n",
       "      <td>(200, 315)</td>\n",
       "      <td></td>\n",
       "      <td>134.01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>EStateFingerprint</td>\n",
       "      <td>float64</td>\n",
       "      <td>(200, 79)</td>\n",
       "      <td></td>\n",
       "      <td>341.23</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>FunctionalGroupsFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 85)</td>\n",
       "      <td></td>\n",
       "      <td>192.67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>GETAWAYFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>GhoseCrippenFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 110)</td>\n",
       "      <td></td>\n",
       "      <td>238.62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>KlekotaRothFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 4860)</td>\n",
       "      <td></td>\n",
       "      <td>8255.99</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>LaggnerFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 307)</td>\n",
       "      <td></td>\n",
       "      <td>1100.49</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>LayeredFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>884.91</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>LingoFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 1024)</td>\n",
       "      <td></td>\n",
       "      <td>31.18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>MACCSFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 167)</td>\n",
       "      <td></td>\n",
       "      <td>391.64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>MAPFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 1024)</td>\n",
       "      <td></td>\n",
       "      <td>1251.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>MHFPFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>1174.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>MORSEFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>MQNsFingerprint</td>\n",
       "      <td>uint32</td>\n",
       "      <td>(200, 42)</td>\n",
       "      <td></td>\n",
       "      <td>76.25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>MordredFingerprint</td>\n",
       "      <td>float32</td>\n",
       "      <td>(200, 1613)</td>\n",
       "      <td></td>\n",
       "      <td>230641.02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>PatternFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>863.47</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>PharmacophoreFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 39972)</td>\n",
       "      <td></td>\n",
       "      <td>43720.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>PhysiochemicalPropertiesFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>312.74</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>PubChemFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 881)</td>\n",
       "      <td></td>\n",
       "      <td>4525.36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>RDFFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>RDKitFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>587.81</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>SECFPFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>2124.91</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>TopologicalTorsionFingerprint</td>\n",
       "      <td>uint8</td>\n",
       "      <td>(200, 2048)</td>\n",
       "      <td></td>\n",
       "      <td>185.57</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>USRCATFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>USRFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>WHIMFingerprint</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>Passed data must be molecules (rdkit.Chem.rdCh...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  class    dtype         shape  \\\n",
       "0                   AtomPairFingerprint    uint8   (200, 2048)   \n",
       "1                   AutocorrFingerprint  float64    (200, 192)   \n",
       "2                     AvalonFingerprint    uint8    (200, 512)   \n",
       "3                       E3FPFingerprint     None          None   \n",
       "4                       ECFPFingerprint    uint8   (200, 2048)   \n",
       "5                        ERGFingerprint  float64    (200, 315)   \n",
       "6                     EStateFingerprint  float64     (200, 79)   \n",
       "7           FunctionalGroupsFingerprint    uint8     (200, 85)   \n",
       "8                    GETAWAYFingerprint     None          None   \n",
       "9               GhoseCrippenFingerprint    uint8    (200, 110)   \n",
       "10               KlekotaRothFingerprint    uint8   (200, 4860)   \n",
       "11                   LaggnerFingerprint    uint8    (200, 307)   \n",
       "12                   LayeredFingerprint    uint8   (200, 2048)   \n",
       "13                     LingoFingerprint    uint8   (200, 1024)   \n",
       "14                     MACCSFingerprint    uint8    (200, 167)   \n",
       "15                       MAPFingerprint    uint8   (200, 1024)   \n",
       "16                      MHFPFingerprint    uint8   (200, 2048)   \n",
       "17                     MORSEFingerprint     None          None   \n",
       "18                      MQNsFingerprint   uint32     (200, 42)   \n",
       "19                   MordredFingerprint  float32   (200, 1613)   \n",
       "20                   PatternFingerprint    uint8   (200, 2048)   \n",
       "21             PharmacophoreFingerprint    uint8  (200, 39972)   \n",
       "22  PhysiochemicalPropertiesFingerprint    uint8   (200, 2048)   \n",
       "23                   PubChemFingerprint    uint8    (200, 881)   \n",
       "24                       RDFFingerprint     None          None   \n",
       "25                     RDKitFingerprint    uint8   (200, 2048)   \n",
       "26                     SECFPFingerprint    uint8   (200, 2048)   \n",
       "27        TopologicalTorsionFingerprint    uint8   (200, 2048)   \n",
       "28                    USRCATFingerprint     None          None   \n",
       "29                       USRFingerprint     None          None   \n",
       "30                      WHIMFingerprint     None          None   \n",
       "\n",
       "                                                error       take  \n",
       "0                                                         128.21  \n",
       "1                                                         102.16  \n",
       "2                                                         591.92  \n",
       "3   Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "4                                                          94.46  \n",
       "5                                                         134.01  \n",
       "6                                                         341.23  \n",
       "7                                                         192.67  \n",
       "8   Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "9                                                         238.62  \n",
       "10                                                       8255.99  \n",
       "11                                                       1100.49  \n",
       "12                                                        884.91  \n",
       "13                                                         31.18  \n",
       "14                                                        391.64  \n",
       "15                                                       1251.15  \n",
       "16                                                       1174.15  \n",
       "17  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "18                                                         76.25  \n",
       "19                                                     230641.02  \n",
       "20                                                        863.47  \n",
       "21                                                      43720.44  \n",
       "22                                                        312.74  \n",
       "23                                                       4525.36  \n",
       "24  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "25                                                        587.81  \n",
       "26                                                       2124.91  \n",
       "27                                                        185.57  \n",
       "28  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "29  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  \n",
       "30  Passed data must be molecules (rdkit.Chem.rdCh...        NaN  "
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "id": "98df7dde",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.',\n",
       " 'Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.',\n",
       " 'Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.',\n",
       " 'Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.',\n",
       " 'Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.',\n",
       " 'Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.',\n",
       " 'Passed data must be molecules (rdkit.Chem.rdChem.Mol instances) and each must have conf_id property set. You can use ConformerGenerator to add them.']"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df[df.error.str.len() > 0]['error'].to_list()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "359be02e",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "97eed535",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "8f064fa2",
   "metadata": {},
   "outputs": [],
   "source": [
    "def replace_dy(smiles):\n",
    "    mol = Chem.MolFromSmiles(smiles)\n",
    "    #Create a mol object to replace the Dy atom with.\n",
    "    new_attachment = Chem.MolFromSmiles('C')\n",
    "    #Get the pattern for the Dy atom\n",
    "    dy_pattern = Chem.MolFromSmiles('[Dy]')\n",
    "    #This returns a tuple of all possible replacements, but we know there will only be one.\n",
    "    new_mol = AllChem.ReplaceSubstructs(mol, dy_pattern, new_attachment)[0]\n",
    "    #Good idea to clean it up\n",
    "    Chem.SanitizeMol(new_mol)\n",
    "    # Since you want 3D mols later, I'd suggest adding hydrogens. Note: this takes up a lot more memory for the obj.\n",
    "    # Chem.AddHs(new_mol)\n",
    "    return Chem.MolToSmiles(new_mol, canonical=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "3dfe3354",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>#sk-container-id-6 {\n",
       "  /* Definition of color scheme common for light and dark mode */\n",
       "  --sklearn-color-text: black;\n",
       "  --sklearn-color-line: gray;\n",
       "  /* Definition of color scheme for unfitted estimators */\n",
       "  --sklearn-color-unfitted-level-0: #fff5e6;\n",
       "  --sklearn-color-unfitted-level-1: #f6e4d2;\n",
       "  --sklearn-color-unfitted-level-2: #ffe0b3;\n",
       "  --sklearn-color-unfitted-level-3: chocolate;\n",
       "  /* Definition of color scheme for fitted estimators */\n",
       "  --sklearn-color-fitted-level-0: #f0f8ff;\n",
       "  --sklearn-color-fitted-level-1: #d4ebff;\n",
       "  --sklearn-color-fitted-level-2: #b3dbfd;\n",
       "  --sklearn-color-fitted-level-3: cornflowerblue;\n",
       "\n",
       "  /* Specific color for light theme */\n",
       "  --sklearn-color-text-on-default-background: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, black)));\n",
       "  --sklearn-color-background: var(--sg-background-color, var(--theme-background, var(--jp-layout-color0, white)));\n",
       "  --sklearn-color-border-box: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, black)));\n",
       "  --sklearn-color-icon: #696969;\n",
       "\n",
       "  @media (prefers-color-scheme: dark) {\n",
       "    /* Redefinition of color scheme for dark theme */\n",
       "    --sklearn-color-text-on-default-background: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, white)));\n",
       "    --sklearn-color-background: var(--sg-background-color, var(--theme-background, var(--jp-layout-color0, #111)));\n",
       "    --sklearn-color-border-box: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, white)));\n",
       "    --sklearn-color-icon: #878787;\n",
       "  }\n",
       "}\n",
       "\n",
       "#sk-container-id-6 {\n",
       "  color: var(--sklearn-color-text);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 pre {\n",
       "  padding: 0;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 input.sk-hidden--visually {\n",
       "  border: 0;\n",
       "  clip: rect(1px 1px 1px 1px);\n",
       "  clip: rect(1px, 1px, 1px, 1px);\n",
       "  height: 1px;\n",
       "  margin: -1px;\n",
       "  overflow: hidden;\n",
       "  padding: 0;\n",
       "  position: absolute;\n",
       "  width: 1px;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-dashed-wrapped {\n",
       "  border: 1px dashed var(--sklearn-color-line);\n",
       "  margin: 0 0.4em 0.5em 0.4em;\n",
       "  box-sizing: border-box;\n",
       "  padding-bottom: 0.4em;\n",
       "  background-color: var(--sklearn-color-background);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-container {\n",
       "  /* jupyter's `normalize.less` sets `[hidden] { display: none; }`\n",
       "     but bootstrap.min.css set `[hidden] { display: none !important; }`\n",
       "     so we also need the `!important` here to be able to override the\n",
       "     default hidden behavior on the sphinx rendered scikit-learn.org.\n",
       "     See: https://github.com/scikit-learn/scikit-learn/issues/21755 */\n",
       "  display: inline-block !important;\n",
       "  position: relative;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-text-repr-fallback {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       "div.sk-parallel-item,\n",
       "div.sk-serial,\n",
       "div.sk-item {\n",
       "  /* draw centered vertical line to link estimators */\n",
       "  background-image: linear-gradient(var(--sklearn-color-text-on-default-background), var(--sklearn-color-text-on-default-background));\n",
       "  background-size: 2px 100%;\n",
       "  background-repeat: no-repeat;\n",
       "  background-position: center center;\n",
       "}\n",
       "\n",
       "/* Parallel-specific style estimator block */\n",
       "\n",
       "#sk-container-id-6 div.sk-parallel-item::after {\n",
       "  content: \"\";\n",
       "  width: 100%;\n",
       "  border-bottom: 2px solid var(--sklearn-color-text-on-default-background);\n",
       "  flex-grow: 1;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-parallel {\n",
       "  display: flex;\n",
       "  align-items: stretch;\n",
       "  justify-content: center;\n",
       "  background-color: var(--sklearn-color-background);\n",
       "  position: relative;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-parallel-item {\n",
       "  display: flex;\n",
       "  flex-direction: column;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-parallel-item:first-child::after {\n",
       "  align-self: flex-end;\n",
       "  width: 50%;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-parallel-item:last-child::after {\n",
       "  align-self: flex-start;\n",
       "  width: 50%;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-parallel-item:only-child::after {\n",
       "  width: 0;\n",
       "}\n",
       "\n",
       "/* Serial-specific style estimator block */\n",
       "\n",
       "#sk-container-id-6 div.sk-serial {\n",
       "  display: flex;\n",
       "  flex-direction: column;\n",
       "  align-items: center;\n",
       "  background-color: var(--sklearn-color-background);\n",
       "  padding-right: 1em;\n",
       "  padding-left: 1em;\n",
       "}\n",
       "\n",
       "\n",
       "/* Toggleable style: style used for estimator/Pipeline/ColumnTransformer box that is\n",
       "clickable and can be expanded/collapsed.\n",
       "- Pipeline and ColumnTransformer use this feature and define the default style\n",
       "- Estimators will overwrite some part of the style using the `sk-estimator` class\n",
       "*/\n",
       "\n",
       "/* Pipeline and ColumnTransformer style (default) */\n",
       "\n",
       "#sk-container-id-6 div.sk-toggleable {\n",
       "  /* Default theme specific background. It is overwritten whether we have a\n",
       "  specific estimator or a Pipeline/ColumnTransformer */\n",
       "  background-color: var(--sklearn-color-background);\n",
       "}\n",
       "\n",
       "/* Toggleable label */\n",
       "#sk-container-id-6 label.sk-toggleable__label {\n",
       "  cursor: pointer;\n",
       "  display: block;\n",
       "  width: 100%;\n",
       "  margin-bottom: 0;\n",
       "  padding: 0.5em;\n",
       "  box-sizing: border-box;\n",
       "  text-align: center;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 label.sk-toggleable__label-arrow:before {\n",
       "  /* Arrow on the left of the label */\n",
       "  content: \"▸\";\n",
       "  float: left;\n",
       "  margin-right: 0.25em;\n",
       "  color: var(--sklearn-color-icon);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 label.sk-toggleable__label-arrow:hover:before {\n",
       "  color: var(--sklearn-color-text);\n",
       "}\n",
       "\n",
       "/* Toggleable content - dropdown */\n",
       "\n",
       "#sk-container-id-6 div.sk-toggleable__content {\n",
       "  max-height: 0;\n",
       "  max-width: 0;\n",
       "  overflow: hidden;\n",
       "  text-align: left;\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-0);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-toggleable__content.fitted {\n",
       "  /* fitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-0);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-toggleable__content pre {\n",
       "  margin: 0.2em;\n",
       "  border-radius: 0.25em;\n",
       "  color: var(--sklearn-color-text);\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-0);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-toggleable__content.fitted pre {\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-0);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 input.sk-toggleable__control:checked~div.sk-toggleable__content {\n",
       "  /* Expand drop-down */\n",
       "  max-height: 200px;\n",
       "  max-width: 100%;\n",
       "  overflow: auto;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 input.sk-toggleable__control:checked~label.sk-toggleable__label-arrow:before {\n",
       "  content: \"▾\";\n",
       "}\n",
       "\n",
       "/* Pipeline/ColumnTransformer-specific style */\n",
       "\n",
       "#sk-container-id-6 div.sk-label input.sk-toggleable__control:checked~label.sk-toggleable__label {\n",
       "  color: var(--sklearn-color-text);\n",
       "  background-color: var(--sklearn-color-unfitted-level-2);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-label.fitted input.sk-toggleable__control:checked~label.sk-toggleable__label {\n",
       "  background-color: var(--sklearn-color-fitted-level-2);\n",
       "}\n",
       "\n",
       "/* Estimator-specific style */\n",
       "\n",
       "/* Colorize estimator box */\n",
       "#sk-container-id-6 div.sk-estimator input.sk-toggleable__control:checked~label.sk-toggleable__label {\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-2);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-estimator.fitted input.sk-toggleable__control:checked~label.sk-toggleable__label {\n",
       "  /* fitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-2);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-label label.sk-toggleable__label,\n",
       "#sk-container-id-6 div.sk-label label {\n",
       "  /* The background is the default theme color */\n",
       "  color: var(--sklearn-color-text-on-default-background);\n",
       "}\n",
       "\n",
       "/* On hover, darken the color of the background */\n",
       "#sk-container-id-6 div.sk-label:hover label.sk-toggleable__label {\n",
       "  color: var(--sklearn-color-text);\n",
       "  background-color: var(--sklearn-color-unfitted-level-2);\n",
       "}\n",
       "\n",
       "/* Label box, darken color on hover, fitted */\n",
       "#sk-container-id-6 div.sk-label.fitted:hover label.sk-toggleable__label.fitted {\n",
       "  color: var(--sklearn-color-text);\n",
       "  background-color: var(--sklearn-color-fitted-level-2);\n",
       "}\n",
       "\n",
       "/* Estimator label */\n",
       "\n",
       "#sk-container-id-6 div.sk-label label {\n",
       "  font-family: monospace;\n",
       "  font-weight: bold;\n",
       "  display: inline-block;\n",
       "  line-height: 1.2em;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-label-container {\n",
       "  text-align: center;\n",
       "}\n",
       "\n",
       "/* Estimator-specific */\n",
       "#sk-container-id-6 div.sk-estimator {\n",
       "  font-family: monospace;\n",
       "  border: 1px dotted var(--sklearn-color-border-box);\n",
       "  border-radius: 0.25em;\n",
       "  box-sizing: border-box;\n",
       "  margin-bottom: 0.5em;\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-0);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-estimator.fitted {\n",
       "  /* fitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-0);\n",
       "}\n",
       "\n",
       "/* on hover */\n",
       "#sk-container-id-6 div.sk-estimator:hover {\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-2);\n",
       "}\n",
       "\n",
       "#sk-container-id-6 div.sk-estimator.fitted:hover {\n",
       "  /* fitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-2);\n",
       "}\n",
       "\n",
       "/* Specification for estimator info (e.g. \"i\" and \"?\") */\n",
       "\n",
       "/* Common style for \"i\" and \"?\" */\n",
       "\n",
       ".sk-estimator-doc-link,\n",
       "a:link.sk-estimator-doc-link,\n",
       "a:visited.sk-estimator-doc-link {\n",
       "  float: right;\n",
       "  font-size: smaller;\n",
       "  line-height: 1em;\n",
       "  font-family: monospace;\n",
       "  background-color: var(--sklearn-color-background);\n",
       "  border-radius: 1em;\n",
       "  height: 1em;\n",
       "  width: 1em;\n",
       "  text-decoration: none !important;\n",
       "  margin-left: 1ex;\n",
       "  /* unfitted */\n",
       "  border: var(--sklearn-color-unfitted-level-1) 1pt solid;\n",
       "  color: var(--sklearn-color-unfitted-level-1);\n",
       "}\n",
       "\n",
       ".sk-estimator-doc-link.fitted,\n",
       "a:link.sk-estimator-doc-link.fitted,\n",
       "a:visited.sk-estimator-doc-link.fitted {\n",
       "  /* fitted */\n",
       "  border: var(--sklearn-color-fitted-level-1) 1pt solid;\n",
       "  color: var(--sklearn-color-fitted-level-1);\n",
       "}\n",
       "\n",
       "/* On hover */\n",
       "div.sk-estimator:hover .sk-estimator-doc-link:hover,\n",
       ".sk-estimator-doc-link:hover,\n",
       "div.sk-label-container:hover .sk-estimator-doc-link:hover,\n",
       ".sk-estimator-doc-link:hover {\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-3);\n",
       "  color: var(--sklearn-color-background);\n",
       "  text-decoration: none;\n",
       "}\n",
       "\n",
       "div.sk-estimator.fitted:hover .sk-estimator-doc-link.fitted:hover,\n",
       ".sk-estimator-doc-link.fitted:hover,\n",
       "div.sk-label-container:hover .sk-estimator-doc-link.fitted:hover,\n",
       ".sk-estimator-doc-link.fitted:hover {\n",
       "  /* fitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-3);\n",
       "  color: var(--sklearn-color-background);\n",
       "  text-decoration: none;\n",
       "}\n",
       "\n",
       "/* Span, style for the box shown on hovering the info icon */\n",
       ".sk-estimator-doc-link span {\n",
       "  display: none;\n",
       "  z-index: 9999;\n",
       "  position: relative;\n",
       "  font-weight: normal;\n",
       "  right: .2ex;\n",
       "  padding: .5ex;\n",
       "  margin: .5ex;\n",
       "  width: min-content;\n",
       "  min-width: 20ex;\n",
       "  max-width: 50ex;\n",
       "  color: var(--sklearn-color-text);\n",
       "  box-shadow: 2pt 2pt 4pt #999;\n",
       "  /* unfitted */\n",
       "  background: var(--sklearn-color-unfitted-level-0);\n",
       "  border: .5pt solid var(--sklearn-color-unfitted-level-3);\n",
       "}\n",
       "\n",
       ".sk-estimator-doc-link.fitted span {\n",
       "  /* fitted */\n",
       "  background: var(--sklearn-color-fitted-level-0);\n",
       "  border: var(--sklearn-color-fitted-level-3);\n",
       "}\n",
       "\n",
       ".sk-estimator-doc-link:hover span {\n",
       "  display: block;\n",
       "}\n",
       "\n",
       "/* \"?\"-specific style due to the `<a>` HTML tag */\n",
       "\n",
       "#sk-container-id-6 a.estimator_doc_link {\n",
       "  float: right;\n",
       "  font-size: 1rem;\n",
       "  line-height: 1em;\n",
       "  font-family: monospace;\n",
       "  background-color: var(--sklearn-color-background);\n",
       "  border-radius: 1rem;\n",
       "  height: 1rem;\n",
       "  width: 1rem;\n",
       "  text-decoration: none;\n",
       "  /* unfitted */\n",
       "  color: var(--sklearn-color-unfitted-level-1);\n",
       "  border: var(--sklearn-color-unfitted-level-1) 1pt solid;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 a.estimator_doc_link.fitted {\n",
       "  /* fitted */\n",
       "  border: var(--sklearn-color-fitted-level-1) 1pt solid;\n",
       "  color: var(--sklearn-color-fitted-level-1);\n",
       "}\n",
       "\n",
       "/* On hover */\n",
       "#sk-container-id-6 a.estimator_doc_link:hover {\n",
       "  /* unfitted */\n",
       "  background-color: var(--sklearn-color-unfitted-level-3);\n",
       "  color: var(--sklearn-color-background);\n",
       "  text-decoration: none;\n",
       "}\n",
       "\n",
       "#sk-container-id-6 a.estimator_doc_link.fitted:hover {\n",
       "  /* fitted */\n",
       "  background-color: var(--sklearn-color-fitted-level-3);\n",
       "}\n",
       "</style><div id=\"sk-container-id-6\" class=\"sk-top-container\"><div class=\"sk-text-repr-fallback\"><pre>E3FPFingerprint(n_jobs=-1)</pre><b>In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. <br />On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.</b></div><div class=\"sk-container\" hidden><div class=\"sk-item\"><div class=\"sk-estimator fitted sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"sk-estimator-id-6\" type=\"checkbox\" checked><label for=\"sk-estimator-id-6\" class=\"sk-toggleable__label fitted sk-toggleable__label-arrow fitted\">&nbsp;E3FPFingerprint<span class=\"sk-estimator-doc-link fitted\">i<span>Fitted</span></span></label><div class=\"sk-toggleable__content fitted\"><pre>E3FPFingerprint(n_jobs=-1)</pre></div> </div></div></div></div>"
      ],
      "text/plain": [
       "E3FPFingerprint(n_jobs=-1)"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from skfp.fingerprints import E3FPFingerprint\n",
    "from skfp.preprocessing import MolFromSmilesTransformer, ConformerGenerator\n",
    "smiles = test_df[:10_000, 'molecule']\n",
    "smiles = [replace_dy(e) for e in smiles]\n",
    "fp = E3FPFingerprint(n_jobs=-1)\n",
    "fp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "d6d55e7a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 34min 19s, sys: 7.6 s, total: 34min 27s\n",
      "Wall time: 35min 47s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([[0, 0, 0, ..., 0, 0, 0],\n",
       "       [0, 0, 0, ..., 0, 0, 0],\n",
       "       [0, 0, 0, ..., 0, 0, 0],\n",
       "       ...,\n",
       "       [0, 0, 0, ..., 0, 0, 0],\n",
       "       [0, 0, 0, ..., 0, 0, 0],\n",
       "       [1, 0, 0, ..., 1, 0, 0]], dtype=uint8)"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "mol_from_smiles = MolFromSmilesTransformer()\n",
    "mols = mol_from_smiles.transform(smiles)\n",
    "conf_gen = ConformerGenerator()\n",
    "mols = conf_gen.transform(mols)\n",
    "ret = fp.transform(mols)\n",
    "ret"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "896a3424",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.216"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "36 * 60 / 10_000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "a828e057",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "93.75"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "90_000_000 * 0.3 / 3600 / 80"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "ed107b03",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2.8125"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "90_000_000 * 0.216 / 3600 / 80 / 24"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b2eb8527",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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