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"# Building Polyphenylene\n",
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"In this tutorial we will build the first reported dendrimer polyphenylene By Mullen et al. \n",
"\n",
"\n",
"\n",
"\"Single-Crystal Structures of Polyphenylene Dendrimers\". Chemistry: A European Journal. 8 (17): 3858–3864. 2002. doi:10.1002/1521-3765(20020902)8:17<3858::AID-CHEM3858>3.0.CO;2-5."
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"benzene = bb.get_compound(\"benzene\")\n",
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"# set up the linkage instructions\n",
"link = bb.linkage(\"C1\", \"C1\")\n",
"\n",
"# start with the centrla benzene ring\n",
"periphery = benzene.copy()\n",
"\n",
"for carbon in range(1, 6):\n",
"\n",
" # update the linkage to the next carbon\n",
" link.atom1 = f\"C{carbon}\"\n",
"\n",
" # attach one benzene to the central one\n",
" periphery.attach(benzene, link, at_residue=1)\n",
"\n",
"periphery.show()"
]
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"metadata": {},
"source": [
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]
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"source": [
"# setup a new linkage\n",
"link2 = bb.linkage(\"C1\", \"C4\")\n",
"\n",
"# set a new attach residue for the periphery (now it's the second residue)\n",
"periphery.set_attach_residue(2)\n",
"\n",
"# now make the central core\n",
"core = benzene.copy()\n",
"\n",
"# and attach the periphery to the core\n",
"for carbon in core.get_atoms(\"C\", by=\"element\"):\n",
" link2.atom1 = carbon.id\n",
"\n",
" core.attach(periphery, link2, at_residue=1)\n",
"\n",
"core.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now that looks fancy! But it is quite cramped still. So let's optimize the structure. "
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
"graph = core.get_atom_graph()\n",
"edges = core.get_residue_connections()\n",
"edges = graph.direct_edges(graph.central_node, edges)\n",
"\n",
"env = bb.optimizers.DistanceRotatron(graph, edges)"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {},
"outputs": [],
"source": [
"core_opt = bb.optimizers.optimize(core.copy(), env, \"swarm\")"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
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"text/html": [
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},
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],
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},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now that looks better! Let's save it to a PDB file."
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [],
"source": [
"core_opt.to_pdb(\"polyphenylene.pdb\")"
]
}
],
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