cg_hexane.ipynb

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   "source": [
    "%%writeandexecute -i cg_hexane cg_hexane.py\n",
    "import mbuild as mb\n",
    "\n",
    "from mbuild.examples.alkane.alkane import Alkane\n",
    "\n",
    "\n",
    "class Propane(mb.Compound):\n",
    "    def __init__(self):\n",
    "        super(Propane, self).__init__()\n",
    "\n",
    "        c = Alkane(n=3, cap_front=True, cap_end=False)\n",
    "        self.add(c, 'propane')\n",
    "\n",
    "        self.add(c['down'], 'down', containment=False)\n",
    "\n",
    "class Hexane(mb.Compound):\n",
    "    def __init__(self):\n",
    "        super(Hexane, self).__init__()\n",
    "\n",
    "        self.add(Propane(), 'propane1')\n",
    "        self.add(Propane(), 'propane2')\n",
    "\n",
    "        mb.equivalence_transform(self['propane1'], \n",
    "                                 self['propane1']['down'], \n",
    "                                 self['propane2']['down'])"
   ]
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     "text": [
      "<Hexane 20 particles, non-periodic, 19 bonds, id: 4509515336>\n"
     ]
    }
   ],
   "source": [
    "hexane = Hexane()\n",
    "print(hexane)\n",
    "hexane.visualize()"
   ]
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     "text": [
      "<Hexane (proxy)  2 particles, non-periodic, 0 bonds, id: 4509512984>\n"
     ]
    }
   ],
   "source": [
    "particles = [Propane]\n",
    "cg = mb.coarse_grain(hexane, particle_classes=particles)\n",
    "print(cg)\n",
    "cg.visualize()"
   ]
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