01 Calculating All RDKit and Mordred Descriptors.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pickle # to open RDKit molecules' lists\n",
    "\n",
    "import numpy as np # to store data in numpy arrays for future use in ML algorithms\n",
    "import pandas as pd # to work with Mordred descriptors dataframes\n",
    "\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import Draw\n",
    "IPythonConsole.ipython_useSVG=True # all of the above – to draw molecules in case I need it\n",
    "from rdkit.Chem import Descriptors # to get the names of all the RDKit descriptors\n",
    "from rdkit.ML.Descriptors import MoleculeDescriptors # the names of all desc-s get passed here\n",
    "\n",
    "from mordred import Calculator, descriptors # this calculates other descriptors"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Loading data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"./data/0_all_active_all_inactive/python_lists/all_active.pickle\", \"rb\") as file1:\n",
    "    all_active_list = pickle.load(file1)\n",
    "\n",
    "with open(\"./data/0_all_active_all_inactive/python_lists/all_inactive.pickle\", \"rb\") as file2:\n",
    "    all_inactive_list = pickle.load(file2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculating RDKit descriptors for all active compounds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "names_of_all_rdkit_descriptors = [x[0] for x in Descriptors._descList]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "rdkit_descriptors_calculator = MoleculeDescriptors.MolecularDescriptorCalculator(names_of_all_rdkit_descriptors)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "rdkit_descriptors_for_all_active_molecules = np.array([rdkit_descriptors_calculator.CalcDescriptors(active_molecule) for active_molecule in all_active_list])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(366, 200)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdkit_descriptors_for_all_active_molecules.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"./data/0_all_active_all_inactive/all_active_descriptors.pickle\", \"wb\") as out_file:\n",
    "    pickle.dump(rdkit_descriptors_for_all_active_molecules, out_file)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculating RDKit descriptors for all inactive compounds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "rdkit_descriptors_for_all_inactive_molecules = np.array([rdkit_descriptors_calculator.CalcDescriptors(inactive_molecule) for inactive_molecule in all_inactive_list])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(59422, 200)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdkit_descriptors_for_all_inactive_molecules.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"./data/0_all_active_all_inactive/all_inactive_descriptors.pickle\", \"wb\") as out_file2:\n",
    "    pickle.dump(rdkit_descriptors_for_all_inactive_molecules, out_file2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculating RDKit descriptors for 366 randomly selected inactive molecules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"./data/1_all_active_random_inactive/python_lists/random_inactive.pickle\", \"rb\") as file3:\n",
    "    random_inactive_list = pickle.load(file3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "rdkit_descriptors_for_366_random_inactive_molecules = np.array([rdkit_descriptors_calculator.CalcDescriptors(rand_inactive_molecule) for rand_inactive_molecule in random_inactive_list])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(366, 200)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdkit_descriptors_for_366_random_inactive_molecules.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"./data/1_all_active_random_inactive/random_inactive_descriptors.pickle\", \"wb\") as out_file3:\n",
    "    pickle.dump(rdkit_descriptors_for_366_random_inactive_molecules, out_file3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculating all Mordred descriptors (except for networkx-based ones) for all active molecules "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_calculator = Calculator(descriptors, ignore_3D=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 366/366 [00:37<00:00,  9.67it/s]\n"
     ]
    }
   ],
   "source": [
    "mordred_desc_for_all_active_df = mordred_desc_calculator.pandas(all_active_list)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The result is a dataframe. It mostly contains correct descriptors, however, there are some strings there as well. These are, first of all, due to the fall of networkx-2.3 on my machine, and also because some of the counter descriptors cannot be calculated for a given molecule. So let's process the resulting dataframe further."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(366, 1613)"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mordred_desc_for_all_active_df.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Dropping all detourn-matrix based descriptors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_active_dropped = mordred_desc_for_all_active_df.drop([\"SpAbs_Dt\", \"SpMax_Dt\", \"SpDiam_Dt\", \"SpAD_Dt\", \"SpMAD_Dt\", \"LogEE_Dt\", \n",
    "               \"SM1_Dt\", \"VE1_Dt\", \"VE2_Dt\", \"VE3_Dt\", \"VR1_Dt\", \"VR2_Dt\", \"VR3_Dt\", \n",
    "               \"DetourIndex\"], axis = 1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(366, 1599)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mordred_desc_for_all_active_dropped.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_active_final = mordred_desc_for_all_active_dropped.apply(pd.to_numeric, errors='coerce').fillna(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_active_final.to_csv(\"./data/0_all_active_all_inactive/Mordred/all_active_mordred.csv\", index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculating all Mordred descriptors (except for networkx-based ones) for all inactive molecules "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  3%|▎         | 1623/59422 [03:05<1:50:20,  8.73it/s]Process ForkPoolWorker-8:\n",
      "\n",
      "Process ForkPoolWorker-7:\n",
      "Traceback (most recent call last):\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 99, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\", line 121, in worker\n",
      "    result = (True, func(*args, **kwds))\n",
      "Traceback (most recent call last):\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 99, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\", line 121, in worker\n",
      "    result = (True, func(*args, **kwds))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\", line 17, in worker\n",
      "    r = list(calculator._calculate(cxt))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 273, in _calculate\n",
      "    _, r = self._calculate_one(cxt, desc, True)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 239, in _calculate_one\n",
      "    ok, r = self._calculate_one(cxt, dep, False)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 247, in _calculate_one\n",
      "    r = desc.calculate(**args)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/ExtendedTopochemicalAtom.py\", line 81, in calculate\n",
      "    ai.GetAtomicNum() != 6 or aj.GetAtomicNum() != 6\n",
      "Process ForkPoolWorker-9:\n",
      "Process ForkPoolWorker-6:\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\", line 17, in worker\n",
      "    r = list(calculator._calculate(cxt))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 273, in _calculate\n",
      "    _, r = self._calculate_one(cxt, desc, True)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 239, in _calculate_one\n",
      "    ok, r = self._calculate_one(cxt, dep, False)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 247, in _calculate_one\n",
      "    r = desc.calculate(**args)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/Chi.py\", line 148, in calculate\n",
      "    dfs.reset(bonds)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/Chi.py\", line 84, in reset\n",
      "    ns[b].add(a)\n",
      "KeyboardInterrupt\n",
      "KeyboardInterrupt\n",
      "Traceback (most recent call last):\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 99, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\", line 121, in worker\n",
      "    result = (True, func(*args, **kwds))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\", line 17, in worker\n",
      "    r = list(calculator._calculate(cxt))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 273, in _calculate\n",
      "    _, r = self._calculate_one(cxt, desc, True)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 239, in _calculate_one\n",
      "    ok, r = self._calculate_one(cxt, dep, False)\n",
      "Traceback (most recent call last):\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 247, in _calculate_one\n",
      "    r = desc.calculate(**args)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n",
      "    self.run()\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/PathCount.py\", line 81, in calculate\n",
      "    bond = self.mol.GetBondBetweenAtoms(before, i)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/process.py\", line 99, in run\n",
      "    self._target(*self._args, **self._kwargs)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\", line 121, in worker\n",
      "    result = (True, func(*args, **kwds))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\", line 17, in worker\n",
      "    r = list(calculator._calculate(cxt))\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 273, in _calculate\n",
      "    _, r = self._calculate_one(cxt, desc, True)\n",
      "KeyboardInterrupt\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 239, in _calculate_one\n",
      "    ok, r = self._calculate_one(cxt, dep, False)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\", line 247, in _calculate_one\n",
      "    r = desc.calculate(**args)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 78, in calculate\n",
      "    return [1 + aid.get_atomic_id(i) / 2.0 for i in range(self.mol.GetNumAtoms())]\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 78, in <listcomp>\n",
      "    return [1 + aid.get_atomic_id(i) / 2.0 for i in range(self.mol.GetNumAtoms())]\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 36, in get_atomic_id\n",
      "    self._search(s)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 52, in _search\n",
      "    self._search(v)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 52, in _search\n",
      "    self._search(v)\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 52, in _search\n",
      "    self._search(v)\n",
      "  [Previous line repeated 3 more times]\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/MolecularId.py\", line 42, in _search\n",
      "    for v, d in self.G[u].items():\n",
      "  File \"/anaconda3/envs/chem/lib/python3.7/_collections_abc.py\", line 678, in items\n",
      "    return ItemsView(self)\n",
      "KeyboardInterrupt\n"
     ]
    },
    {
     "ename": "FileNotFoundError",
     "evalue": "[Errno 2] No such file or directory",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\u001b[0m in \u001b[0;36mparallel\u001b[0;34m(calc, mols, nproc, nmols, quiet, ipynb, id)\u001b[0m\n\u001b[1;32m     78\u001b[0m     \u001b[0;32mwith\u001b[0m \u001b[0mMolPool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcalc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnproc\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpool\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcalc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_progress\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mquiet\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnmols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mipynb\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mbar\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 79\u001b[0;31m         \u001b[0;32mfor\u001b[0m \u001b[0mmol\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mpool\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mid\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     80\u001b[0m             \u001b[0;32mfor\u001b[0m \u001b[0me\u001b[0m \u001b[0;32min\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\u001b[0m in \u001b[0;36m__next__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     69\u001b[0m             \u001b[0mmol\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfut\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfutures\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpopleft\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 70\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mmol\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfut\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     71\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mIndexError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    650\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 651\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    652\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mready\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    647\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 648\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_event\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    649\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/threading.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    551\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0msignaled\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 552\u001b[0;31m                 \u001b[0msignaled\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_cond\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    553\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0msignaled\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/threading.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m    295\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mtimeout\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 296\u001b[0;31m                 \u001b[0mwaiter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0macquire\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    297\u001b[0m                 \u001b[0mgotit\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: ",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[0;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-20-2b7f50cf5b5b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmordred_desc_for_all_inactive_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmordred_desc_calculator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpandas\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mall_inactive_list\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\u001b[0m in \u001b[0;36mpandas\u001b[0;34m(self, mols, nproc, nmols, quiet, ipynb, id)\u001b[0m\n\u001b[1;32m    398\u001b[0m             \u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mr\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnproc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnmols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mquiet\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mipynb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mid\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    399\u001b[0m             \u001b[0mcolumns\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0md\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0md\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdescriptors\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 400\u001b[0;31m             \u001b[0mindex\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    401\u001b[0m         )\n\u001b[1;32m    402\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.7/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, data, index, columns, dtype, copy)\u001b[0m\n\u001b[1;32m    443\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mabc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mIterable\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbytes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    444\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mabc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSequence\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 445\u001b[0;31m                 \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    446\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    447\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0mis_list_like\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"ndim\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/calculator.py\u001b[0m in \u001b[0;36m<genexpr>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m    396\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    397\u001b[0m         return MordredDataFrame(\n\u001b[0;32m--> 398\u001b[0;31m             \u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mr\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnproc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnmols\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mquiet\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mipynb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mid\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    399\u001b[0m             \u001b[0mcolumns\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0md\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0md\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdescriptors\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    400\u001b[0m             \u001b[0mindex\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\u001b[0m in \u001b[0;36mparallel\u001b[0;34m(calc, mols, nproc, nmols, quiet, ipynb, id)\u001b[0m\n\u001b[1;32m     86\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     87\u001b[0m             \u001b[0;32myield\u001b[0m \u001b[0mcalc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_wrap_result\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmol\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 88\u001b[0;31m             \u001b[0mbar\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/site-packages/mordred/_base/parallel.py\u001b[0m in \u001b[0;36m__exit__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     33\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     34\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m__exit__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 35\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpool\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mterminate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     36\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmgr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__exit__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     37\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\u001b[0m in \u001b[0;36mterminate\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    546\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_state\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTERMINATE\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    547\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_worker_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_state\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTERMINATE\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 548\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_terminate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    549\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    550\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/util.py\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, wr, _finalizer_registry, sub_debug, getpid)\u001b[0m\n\u001b[1;32m    199\u001b[0m                 sub_debug('finalizer calling %s with args %s and kwargs %s',\n\u001b[1;32m    200\u001b[0m                           self._callback, self._args, self._kwargs)\n\u001b[0;32m--> 201\u001b[0;31m                 \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_callback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_args\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    202\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_weakref\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_callback\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_args\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    203\u001b[0m                             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_kwargs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_key\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\u001b[0m in \u001b[0;36m_terminate_pool\u001b[0;34m(cls, taskqueue, inqueue, outqueue, pool, worker_handler, task_handler, result_handler, cache)\u001b[0m\n\u001b[1;32m    579\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    580\u001b[0m         \u001b[0mutil\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdebug\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'helping task handler/workers to finish'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 581\u001b[0;31m         \u001b[0mcls\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_help_stuff_finish\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minqueue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtask_handler\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpool\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    582\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    583\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0;32mnot\u001b[0m \u001b[0mresult_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_alive\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcache\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/pool.py\u001b[0m in \u001b[0;36m_help_stuff_finish\u001b[0;34m(inqueue, task_handler, size)\u001b[0m\n\u001b[1;32m    566\u001b[0m         \u001b[0minqueue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_rlock\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0macquire\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    567\u001b[0m         \u001b[0;32mwhile\u001b[0m \u001b[0mtask_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_alive\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0minqueue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_reader\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpoll\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 568\u001b[0;31m             \u001b[0minqueue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_reader\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    569\u001b[0m             \u001b[0mtime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msleep\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    570\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/connection.py\u001b[0m in \u001b[0;36mrecv\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    249\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_readable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    250\u001b[0m         \u001b[0mbuf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_recv_bytes\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 251\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0m_ForkingPickler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbuf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetbuffer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    252\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    253\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mpoll\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0.0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/managers.py\u001b[0m in \u001b[0;36mRebuildProxy\u001b[0;34m(func, token, serializer, kwds)\u001b[0m\n\u001b[1;32m    941\u001b[0m         \u001b[0;32mnot\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprocess\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcurrent_process\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'_inheriting'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    942\u001b[0m         )\n\u001b[0;32m--> 943\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtoken\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mserializer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mincref\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mincref\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    944\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    945\u001b[0m \u001b[0;31m#\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/managers.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, token, serializer, manager, authkey, exposed, incref, manager_owned)\u001b[0m\n\u001b[1;32m    791\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    792\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mincref\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 793\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_incref\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    794\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    795\u001b[0m         \u001b[0mutil\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mregister_after_fork\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mBaseProxy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_after_fork\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/managers.py\u001b[0m in \u001b[0;36m_incref\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    845\u001b[0m             \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    846\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 847\u001b[0;31m         \u001b[0mconn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_Client\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_token\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maddress\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mauthkey\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_authkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    848\u001b[0m         \u001b[0mdispatch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'incref'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_id\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    849\u001b[0m         \u001b[0mutil\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdebug\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'INCREF %r'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_token\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mid\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/connection.py\u001b[0m in \u001b[0;36mClient\u001b[0;34m(address, family, authkey)\u001b[0m\n\u001b[1;32m    490\u001b[0m         \u001b[0mc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mPipeClient\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maddress\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    491\u001b[0m     \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 492\u001b[0;31m         \u001b[0mc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSocketClient\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maddress\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    493\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    494\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mauthkey\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mauthkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbytes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/anaconda3/envs/chem/lib/python3.7/multiprocessing/connection.py\u001b[0m in \u001b[0;36mSocketClient\u001b[0;34m(address)\u001b[0m\n\u001b[1;32m    617\u001b[0m     \u001b[0;32mwith\u001b[0m \u001b[0msocket\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msocket\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msocket\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfamily\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    618\u001b[0m         \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetblocking\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 619\u001b[0;31m         \u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconnect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maddress\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    620\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mConnection\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdetach\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    621\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory"
     ]
    }
   ],
   "source": [
    "mordred_desc_for_all_inactive_df = mordred_desc_calculator.pandas(all_inactive_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_inactive_dropped = mordred_desc_for_all_inactive_df.drop([\"SpAbs_Dt\", \"SpMax_Dt\", \"SpDiam_Dt\", \"SpAD_Dt\", \"SpMAD_Dt\", \"LogEE_Dt\", \n",
    "               \"SM1_Dt\", \"VE1_Dt\", \"VE2_Dt\", \"VE3_Dt\", \"VR1_Dt\", \"VR2_Dt\", \"VR3_Dt\", \n",
    "               \"DetourIndex\"], axis = 1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_inactive_dropped.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_inactive_final = mordred_desc_for_all_inactive_dropped.apply(pd.to_numeric, errors='coerce').fillna(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mordred_desc_for_all_inactive_final.to_csv(\"./data/0_all_active_all_inactive/Mordred/all_inactive_mordred.csv\", index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Calculating all Mordred descriptors (except for networkx-based ones) for 366 random inactive molecules "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"./data/1_all_active_random_inactive/python_lists/random_inactive.pickle\", \"rb\") as file4:\n",
    "    random_inactive_molecules = pickle.load(file4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      " 66%|██████▌   | 242/366 [00:30<00:15,  7.81it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/mancy/.local/lib/python3.7/site-packages/numpy/core/fromnumeric.py:90: RuntimeWarning: overflow encountered in reduce\n",
      "  return ufunc.reduce(obj, axis, dtype, out, **passkwargs)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 366/366 [00:47<00:00,  7.76it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(366, 1599)\n"
     ]
    }
   ],
   "source": [
    "mordred_desc_for_366_random_inactive_mols_df = mordred_desc_calculator.pandas(random_inactive_molecules)\n",
    "\n",
    "# drop the ones that cannot be calculated\n",
    "mordred_desc_for_366_random_inactive_mols_dropped = mordred_desc_for_366_random_inactive_mols_df.drop([\"SpAbs_Dt\", \"SpMax_Dt\", \"SpDiam_Dt\", \"SpAD_Dt\", \"SpMAD_Dt\", \"LogEE_Dt\", \n",
    "               \"SM1_Dt\", \"VE1_Dt\", \"VE2_Dt\", \"VE3_Dt\", \"VR1_Dt\", \"VR2_Dt\", \"VR3_Dt\", \n",
    "               \"DetourIndex\"], axis = 1)\n",
    "\n",
    "print(mordred_desc_for_366_random_inactive_mols_dropped.shape)\n",
    "\n",
    "mordred_desc_for_366_random_inactive_mols_final = mordred_desc_for_366_random_inactive_mols_dropped.apply(pd.to_numeric, errors='coerce').fillna(0)\n",
    "\n",
    "mordred_desc_for_366_random_inactive_mols_final.to_csv(\"./data/1_all_active_random_inactive/Mordred/random_inactive_mordred.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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