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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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"# (this is technically not necessary, since BuildAMol will automatically\n",
"# query PubChem for any unloaded compounds, but it's a good practice to load the molecules\n",
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"/Users/noahhk/anaconda3/envs/glyco2/lib/python3.11/site-packages/plotly/express/_core.py:1985: FutureWarning:\n",
"\n",
"When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.\n",
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"# set up the linkage instructions\n",
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" # the at_residue is important to make sure we \n",
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"# setup a new linkage\n",
"link2 = bam.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",
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"# now make the central core\n",
"core = benzene.copy()\n",
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"# and attach the periphery to the core\n",
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},
{
"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": 7,
"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 = bam.optimizers.DistanceRotatron(graph, edges)"
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},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
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]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
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"name": "stderr",
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"text": [
"/Users/noahhk/anaconda3/envs/glyco2/lib/python3.11/site-packages/plotly/express/_core.py:1985: FutureWarning:\n",
"\n",
"When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.\n",
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"title": {
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"automargin": true,
"gridcolor": "rgb(232,232,232)",
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}
},
"text/html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"core_opt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now that looks better! Let's save it to a PDB file."
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"core_opt.to_pdb(\"./files/polyphenylene.pdb\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "glyco2",
"language": "python",
"name": "python3"
},
"language_info": {
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"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
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}