descriptorus_example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2019.03.4\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit import rdBase\n",
    "print(rdBase.rdkitVersion)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:root:No kyotocabinet available\n"
     ]
    }
   ],
   "source": [
    "from descriptastorus.descriptors.DescriptorGenerator import MakeGenerator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "gen1 = MakeGenerator(('rdkit2d',))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "smi = 'c1ccncc1'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "data=gen1.process(smi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "RDKit2D_calculated\n",
      "BalabanJ\n",
      "BertzCT\n",
      "Chi0\n",
      "Chi0n\n",
      "Chi0v\n",
      "Chi1\n",
      "Chi1n\n",
      "Chi1v\n",
      "Chi2n\n",
      "Chi2v\n",
      "Chi3n\n",
      "Chi3v\n",
      "Chi4n\n",
      "Chi4v\n",
      "EState_VSA1\n",
      "EState_VSA10\n",
      "EState_VSA11\n",
      "EState_VSA2\n",
      "EState_VSA3\n",
      "EState_VSA4\n",
      "EState_VSA5\n",
      "EState_VSA6\n",
      "EState_VSA7\n",
      "EState_VSA8\n",
      "EState_VSA9\n",
      "ExactMolWt\n",
      "FpDensityMorgan1\n",
      "FpDensityMorgan2\n",
      "FpDensityMorgan3\n",
      "FractionCSP3\n",
      "HallKierAlpha\n",
      "HeavyAtomCount\n",
      "HeavyAtomMolWt\n",
      "Ipc\n",
      "Kappa1\n",
      "Kappa2\n",
      "Kappa3\n",
      "LabuteASA\n",
      "MaxAbsEStateIndex\n",
      "MaxAbsPartialCharge\n",
      "MaxEStateIndex\n",
      "MaxPartialCharge\n",
      "MinAbsEStateIndex\n",
      "MinAbsPartialCharge\n",
      "MinEStateIndex\n",
      "MinPartialCharge\n",
      "MolLogP\n",
      "MolMR\n",
      "MolWt\n",
      "NHOHCount\n",
      "NOCount\n",
      "NumAliphaticCarbocycles\n",
      "NumAliphaticHeterocycles\n",
      "NumAliphaticRings\n",
      "NumAromaticCarbocycles\n",
      "NumAromaticHeterocycles\n",
      "NumAromaticRings\n",
      "NumHAcceptors\n",
      "NumHDonors\n",
      "NumHeteroatoms\n",
      "NumRadicalElectrons\n",
      "NumRotatableBonds\n",
      "NumSaturatedCarbocycles\n",
      "NumSaturatedHeterocycles\n",
      "NumSaturatedRings\n",
      "NumValenceElectrons\n",
      "PEOE_VSA1\n",
      "PEOE_VSA10\n",
      "PEOE_VSA11\n",
      "PEOE_VSA12\n",
      "PEOE_VSA13\n",
      "PEOE_VSA14\n",
      "PEOE_VSA2\n",
      "PEOE_VSA3\n",
      "PEOE_VSA4\n",
      "PEOE_VSA5\n",
      "PEOE_VSA6\n",
      "PEOE_VSA7\n",
      "PEOE_VSA8\n",
      "PEOE_VSA9\n",
      "RingCount\n",
      "SMR_VSA1\n",
      "SMR_VSA10\n",
      "SMR_VSA2\n",
      "SMR_VSA3\n",
      "SMR_VSA4\n",
      "SMR_VSA5\n",
      "SMR_VSA6\n",
      "SMR_VSA7\n",
      "SMR_VSA8\n",
      "SMR_VSA9\n",
      "SlogP_VSA1\n",
      "SlogP_VSA10\n",
      "SlogP_VSA11\n",
      "SlogP_VSA12\n",
      "SlogP_VSA2\n",
      "SlogP_VSA3\n",
      "SlogP_VSA4\n",
      "SlogP_VSA5\n",
      "SlogP_VSA6\n",
      "SlogP_VSA7\n",
      "SlogP_VSA8\n",
      "SlogP_VSA9\n",
      "TPSA\n",
      "VSA_EState1\n",
      "VSA_EState10\n",
      "VSA_EState2\n",
      "VSA_EState3\n",
      "VSA_EState4\n",
      "VSA_EState5\n",
      "VSA_EState6\n",
      "VSA_EState7\n",
      "VSA_EState8\n",
      "VSA_EState9\n",
      "fr_Al_COO\n",
      "fr_Al_OH\n",
      "fr_Al_OH_noTert\n",
      "fr_ArN\n",
      "fr_Ar_COO\n",
      "fr_Ar_N\n",
      "fr_Ar_NH\n",
      "fr_Ar_OH\n",
      "fr_COO\n",
      "fr_COO2\n",
      "fr_C_O\n",
      "fr_C_O_noCOO\n",
      "fr_C_S\n",
      "fr_HOCCN\n",
      "fr_Imine\n",
      "fr_NH0\n",
      "fr_NH1\n",
      "fr_NH2\n",
      "fr_N_O\n",
      "fr_Ndealkylation1\n",
      "fr_Ndealkylation2\n",
      "fr_Nhpyrrole\n",
      "fr_SH\n",
      "fr_aldehyde\n",
      "fr_alkyl_carbamate\n",
      "fr_alkyl_halide\n",
      "fr_allylic_oxid\n",
      "fr_amide\n",
      "fr_amidine\n",
      "fr_aniline\n",
      "fr_aryl_methyl\n",
      "fr_azide\n",
      "fr_azo\n",
      "fr_barbitur\n",
      "fr_benzene\n",
      "fr_benzodiazepine\n",
      "fr_bicyclic\n",
      "fr_diazo\n",
      "fr_dihydropyridine\n",
      "fr_epoxide\n",
      "fr_ester\n",
      "fr_ether\n",
      "fr_furan\n",
      "fr_guanido\n",
      "fr_halogen\n",
      "fr_hdrzine\n",
      "fr_hdrzone\n",
      "fr_imidazole\n",
      "fr_imide\n",
      "fr_isocyan\n",
      "fr_isothiocyan\n",
      "fr_ketone\n",
      "fr_ketone_Topliss\n",
      "fr_lactam\n",
      "fr_lactone\n",
      "fr_methoxy\n",
      "fr_morpholine\n",
      "fr_nitrile\n",
      "fr_nitro\n",
      "fr_nitro_arom\n",
      "fr_nitro_arom_nonortho\n",
      "fr_nitroso\n",
      "fr_oxazole\n",
      "fr_oxime\n",
      "fr_para_hydroxylation\n",
      "fr_phenol\n",
      "fr_phenol_noOrthoHbond\n",
      "fr_phos_acid\n",
      "fr_phos_ester\n",
      "fr_piperdine\n",
      "fr_piperzine\n",
      "fr_priamide\n",
      "fr_prisulfonamd\n",
      "fr_pyridine\n",
      "fr_quatN\n",
      "fr_sulfide\n",
      "fr_sulfonamd\n",
      "fr_sulfone\n",
      "fr_term_acetylene\n",
      "fr_tetrazole\n",
      "fr_thiazole\n",
      "fr_thiocyan\n",
      "fr_thiophene\n",
      "fr_unbrch_alkane\n",
      "fr_urea\n",
      "qed\n"
     ]
    }
   ],
   "source": [
    "for col in gen1.GetColumns():\n",
    "    print(col[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "from descriptastorus.descriptors import rdDescriptors\n",
    "from descriptastorus.descriptors import rdNormalizedDescriptors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "gen2 = rdDescriptors.RDKit2D()\n",
    "gen3 = rdNormalizedDescriptors.RDKit2DNormalized()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "data2 = gen2.process(smi)\n",
    "data3 = gen3.process(smi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "True True\n",
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      "0 0.16704063109164155\n",
      "0 0.16649833422826882\n",
      "0 0.16648681554273437\n",
      "0 0.20286466138783588\n",
      "0 0.06936588086433818\n",
      "0 7.105427357601002e-15\n",
      "0 0.16834648002367886\n",
      "0 0.16798293243083\n",
      "1 0.277430427049584\n",
      "0 0.0011815729111892548\n",
      "0 0.16433263444740043\n",
      "0 0.0008377769174453542\n",
      "0 0.16632573432045866\n",
      "0 0.1630341420539464\n",
      "0 0.16507954777521783\n",
      "0 9.569704921590424e-08\n",
      "0 3.497089221619717e-08\n",
      "0 0.16820617469834753\n",
      "0 0.16580685767199677\n",
      "0 0.1673465945690054\n",
      "0 7.13964618592744e-07\n",
      "0 2.64115098167329e-12\n",
      "0 0.09991279113071351\n",
      "0 2.868092430219349e-10\n",
      "0 0.37773784802857724\n",
      "0 0.004506167784075659\n",
      "0 0.13325025138007268\n",
      "0 0.03472992844289974\n",
      "0 1.6148291592799069e-09\n",
      "0 1.875173153042101e-18\n",
      "0 2.0941053890943806e-07\n",
      "0 7.105427357601002e-15\n",
      "0 0.49926428135900186\n",
      "0 0.16492940199937894\n",
      "0 1.3174450829220094e-17\n",
      "0 2.1116435458495668e-16\n",
      "0 1.1681587528983658e-09\n",
      "0 3.2592359986208345e-22\n",
      "0 6.246014200977821e-10\n",
      "0 0.16814918247297933\n",
      "0 0.16545072935045158\n",
      "0 1.1711026222995016e-13\n",
      "0 0.0\n",
      "0 0.16466886776470133\n",
      "0 0.1669247276390117\n",
      "0 0.0\n",
      "0 5.1007132747942736e-08\n",
      "0 7.105427357601002e-15\n",
      "0 0.1546541084142275\n",
      "0 2.794209383371835e-22\n",
      "0 0.0\n",
      "0 0.16763973281840122\n",
      "0 6.314992660308343e-25\n",
      "0 0.16818612974609914\n",
      "0 0.009088502666434949\n",
      "0 0.16836320220350243\n",
      "0 8.265423131146944e-11\n",
      "0 0.15634635438381983\n",
      "0 0.0\n",
      "0 0.0\n",
      "0 0.021135423572131908\n",
      "0 0.021135423572131908\n",
      "0 2.388155749350249e-20\n",
      "0 0.0\n",
      "0 8.336724500779247e-25\n",
      "0 5.301380942484303e-05\n",
      "1 0.9999791214129063\n",
      "0 4.034345030660423e-08\n",
      "0 1.552591960229748e-23\n",
      "0 1.5930611717254445e-17\n",
      "0 5.766100772128885e-14\n",
      "0 2.957989408969297e-11\n",
      "0 0.16837836924209137\n",
      "0 0.167380186090632\n",
      "0 1.4815146472600273e-18\n",
      "0 2.3241499374144116e-16\n",
      "0 4.7035980879892365e-08\n",
      "0 0.16663339666347546\n",
      "0.4531479654842905 0.2945907992775366\n"
     ]
    }
   ],
   "source": [
    "for i in range(len(data2)):\n",
    "    print(data2[i], data3[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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