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   "source": [
    "# Partial bond orders and benzene\n",
    "\n",
    "This notebook applies a SMIRNOFF FFXML involving partial bond orders (reducing the number of parameters) to assign bond parameters for benzene. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Import stuff we need\n",
    "from openff.toolkit.typing.engines.smirnoff import *\n",
    "import openeye.oechem as oechem\n",
    "import openeye.oeiupac as oeiupac\n",
    "import openeye.oeomega as oeomega"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# NBVAL_SKIP\n",
    "# Load our force field from this directory. Use of partial bond orders here means there is only one [#6X3]~[#6X3] \n",
    "# bond parameter line rather than three which otherwise would be required\n",
    "ffxml = 'Frosst_AlkEthOH_extracarbons.offxml'\n",
    "ff = ForceField(ffxml)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Initialize benzene as a test molecule\n",
    "mol = oechem.OEMol()\n",
    "oeiupac.OEParseIUPACName(mol, 'benzene')\n",
    "omega = oeomega.OEOmega()\n",
    "omega(mol)\n",
    "oechem.OETriposAtomNames(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Applying oechem.oequacpac.OEAssignPartialCharges with specified charge method \"OECharges_AM1BCCSym\".\n",
      "\n",
      "HarmonicBondGenerator:\n",
      "\n",
      "                                               [#6X4:1]-[#6X4:2] :        0 matches\n",
      "                                                 [#6X4:1]-[#1:2] :        0 matches\n",
      "                                                   [#8:1]~[#1:2] :        0 matches\n",
      "                                            [#6X4:1]-[O&X2&H1:2] :        0 matches\n",
      "                                            [#6X4:1]-[O&X2&H0:2] :        0 matches\n",
      "                                                 [#8X2:1]-[#1:2] :        0 matches\n",
      "                                              [#6X3:1]!#[#6X3:2] :       12 matches\n",
      "                                                 [#6X3:1]-[#1:2] :        6 matches\n",
      "\n",
      "12 bonds added (0 skipped due to constraints)\n",
      "\n",
      "HarmonicAngleGenerator:\n",
      "\n",
      "                                        [a,A:1]-[#6X4:2]-[a,A:3] :        0 matches\n",
      "                                          [#1:1]-[#6X4:2]-[#1:3] :        0 matches\n",
      "                                      [#6X4:1]-[#6X4:2]-[#6X4:3] :        0 matches\n",
      "                                      [#8X2:1]-[#6X4:2]-[#8X2:3] :        0 matches\n",
      "                                        [#6X4:1]-[#8X2:2]-[#1:3] :        0 matches\n",
      "                                      [#6X4:1]-[#8X2:2]-[#6X4:3] :        0 matches\n",
      "                                            [*:1]~[#6X3:2]~[*:3] :       36 matches\n",
      "                                           [#1:1]-[#6X3:2]~[*:3] :       12 matches\n",
      "                                          [#1:1]-[#6X3:2]-[#1:3] :        0 matches\n",
      "\n",
      "18 angles added (0 skipped due to constraints)\n",
      "\n",
      "PeriodicTorsionGenerator Propers:\n",
      "\n",
      "                               [a,A:1]-[#6X4:2]-[#6X4:3]-[a,A:4] :        0 matches\n",
      "                                [a,A:1]-[#6X4:2]-[#8X2:3]-[#1:4] :        0 matches\n",
      "                               [a,A:1]-[#6X4:2]-[#8X2:3]-[!#1:4] :        0 matches\n",
      "                                 [#1:1]-[#6X4:2]-[#6X4:3]-[#1:4] :        0 matches\n",
      "                               [#1:1]-[#6X4:2]-[#6X4:3]-[#6X4:4] :        0 matches\n",
      "                               [#6X4:1]-[#6X4:2]-[#8X2:3]-[#1:4] :        0 matches\n",
      "                             [#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4] :        0 matches\n",
      "                             [#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X4:4] :        0 matches\n",
      "                          [#6X4:1]-[#8X2:2]-[#6X4:3]-[O&X2&H0:4] :        0 matches\n",
      "                             [#8X2:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] :        0 matches\n",
      "                               [#8X2:1]-[#6X4:2]-[#6X4:3]-[#1:4] :        0 matches\n",
      "                                [#1:1]-[#6X4:2]-[#6X4:3]-[OX2:4] :        0 matches\n",
      "                                   [*:1]~[#6X3:2]-[#6X4:3]~[*:4] :        0 matches\n",
      "                               [#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] :        0 matches\n",
      "                                   [*:1]~[#6X3:2]-[#6X3:3]~[*:4] :        0 matches\n",
      "                                   [*:1]~[#6X3:2]:[#6X3:3]~[*:4] :       48 matches\n",
      "                                   [*:1]-[#6X3:2]=[#6X3:3]-[*:4] :        0 matches\n",
      "\n",
      "PeriodicTorsionGenerator Impropers:\n",
      "\n",
      "                               [a,A:1]~[#6X3:2]([a,A:3])~[OX1:4] :        0 matches\n",
      "\n",
      "24 torsions added\n",
      "0 impropers added, each applied in a six-fold manner\n",
      "\n",
      "NonbondedForceGenerator:\n",
      "\n",
      "                                                          [#1:1] :        6 matches\n",
      "                                                   [$([#1]-C):1] :        0 matches\n",
      "                               [$([#1]-C-[#7,#8,F,#16,Cl,Br]):1] :        0 matches\n",
      "         [$([#1]-C(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]):1] :        0 matches\n",
      "[$([#1]-C(-[#7,#8,F,#16,Cl,Br])(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]):1] :        0 matches\n",
      "                                                 [#1$(*-[#8]):1] :        0 matches\n",
      "                                                          [#6:1] :        6 matches\n",
      "                                                        [#6X4:1] :        0 matches\n",
      "                                                          [#8:1] :        0 matches\n",
      "                                                        [#8X2:1] :        0 matches\n",
      "                                             [#8X2+0$(*-[#1]):1] :        0 matches\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "topology = generateTopologyFromOEMol(mol)\n",
    "system = ff.createSystem(topology, [mol], chargeMethod = 'OECharges_AM1BCCSym', verbose = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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