Molecule.ipynb 14.9 KB
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{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Molecule representation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2020-07-16 17:34:25,168 chemicalchecker.util.config.config.Config [DEBUG   ] Loading config from: /aloy/home/mbertoni/cc_config.json\n",
      "2020-07-16 17:34:25,170 chemicalchecker.core.chemcheck.ChemicalChecker [DEBUG   ] ChemicalChecker with root: /aloy/web_checker/current/\n",
      "2020-07-16 17:34:25,710 chemicalchecker.core.chemcheck.ChemicalChecker [WARNING ] Logging level WARNING for logger 'chemicalchecker'.\n"
     ]
    }
   ],
   "source": [
    "from chemicalchecker import ChemicalChecker\n",
    "cc = ChemicalChecker()\n",
    "cc.set_verbosity('warning') # suppress debug ouput"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Initialize a molecule object"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from chemicalchecker.core import Mol\n",
    "mol1 = Mol(cc, 'RZVAJINKPMORJF-UHFFFAOYSA-N', 'inchikey')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "and visualize it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7fae6f580570>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'CC(O)=Nc1ccc(O)cc1'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1.smiles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11H,1H3,(H,9,10)'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1.inchi"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'RZVAJINKPMORJF-UHFFFAOYSA-N'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1.inchikey"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "When not specifying the type of identifier we do our best to guess it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol2 = Mol(cc, 'CC(O)=Nc1ccc(O)cc1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol2.inchi == mol1.inchi"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Query the CC for signature where this molecules is available"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'full': {'A1.001': ['sign1'],\n",
       "  'A2.001': ['sign1'],\n",
       "  'A3.001': ['sign1'],\n",
       "  'A4.001': ['sign1'],\n",
       "  'A5.001': ['sign1'],\n",
       "  'B1.001': ['sign1'],\n",
       "  'B2.001': ['sign1'],\n",
       "  'B3.001': ['sign1'],\n",
       "  'B4.001': ['sign1'],\n",
       "  'B5.001': ['sign1'],\n",
       "  'C1.001': ['sign1'],\n",
       "  'C2.001': ['sign1'],\n",
       "  'C3.001': ['sign1'],\n",
       "  'C4.001': ['sign1'],\n",
       "  'C5.001': ['sign1'],\n",
       "  'D1.001': ['sign1'],\n",
       "  'E1.001': ['sign1'],\n",
       "  'E2.001': ['sign1'],\n",
       "  'E3.001': ['sign1'],\n",
       "  'E4.001': ['sign1'],\n",
       "  'E5.001': ['sign1']}}"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol1.report_available(cctype='sign1')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Obtain the signature for our molcule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol_signature = mol1.signature('sign1','E5.001')"
   ]
  }
 ],
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