paper_worked_examples.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Construction of a 4-arm PEG star polymer from single monomeric units"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "netcharge = 7.91033905045424e-16\n"
     ]
    }
   ],
   "source": [
    "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n",
    "\n",
    "# load in monomer topologies from ITP files\n",
    "ethanol = Topology.from_ITP(\"data_paper_examples/extended_ethanol.itp\") # main arm monomer\n",
    "methane = Topology.from_ITP(\"data_paper_examples/extended_methane.itp\") # terminal monomer\n",
    "neopentane = Topology.from_ITP(\"data_paper_examples/extended_neopentane.itp\") # central monomer\n",
    "\n",
    "# create junctions for each monomer with the bonding atom and then the leaving atom specified, in that order, with a unique name\n",
    "oxy_j1 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy1\")\n",
    "carb_j1 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb1\")\n",
    "oxy_j2 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy2\")\n",
    "carb_j2 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb2\")\n",
    "oxy_j3 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy3\")\n",
    "carb_j3 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb3\")\n",
    "oxy_j4 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy4\")\n",
    "carb_j4 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb4\")\n",
    "\n",
    "j1 = Junction(neopentane.get_atom(\"C1\"), neopentane.get_atom(\"O1\"), name = \"branch1\")\n",
    "j2 = Junction(neopentane.get_atom(\"C3\"), neopentane.get_atom(\"O2\"), name = \"branch2\")\n",
    "j3 = Junction(neopentane.get_atom(\"C4\"), neopentane.get_atom(\"O3\"), name = \"branch3\")\n",
    "j4 = Junction(neopentane.get_atom(\"C5\"), neopentane.get_atom(\"O4\"), name = \"branch4\")\n",
    "\n",
    "term_j = Junction(methane.get_atom(\"C1\"), methane.get_atom(\"O1\"), name = \"term\")\n",
    "\n",
    "# create monomers from their topologies and any specified junctions\n",
    "e1 = Monomer(ethanol, [oxy_j1, carb_j1])\n",
    "e2 = Monomer(ethanol, [oxy_j2, carb_j2])\n",
    "e3 = Monomer(ethanol, [oxy_j3, carb_j3])\n",
    "e4 = Monomer(ethanol, [oxy_j4, carb_j4])\n",
    "\n",
    "central = Monomer(neopentane, [j1, j2, j3, j4])\n",
    "\n",
    "terminal = Monomer(methane, [term_j]) # only needs one junction to join to the ends of each arm\n",
    "\n",
    "# start the polymer with the central monomer\n",
    "four_polymer = Polymer(central)\n",
    "\n",
    "# attach three ethanols to each of the four junctions (j1-j4) of the central monomer\n",
    "four_polymer.extend(e1, from_junction_name=\"branch1\", to_junction_name=\"oxy1\")\n",
    "four_polymer.extend(e2, from_junction_name=\"branch2\", to_junction_name=\"oxy2\")\n",
    "four_polymer.extend(e3, from_junction_name=\"branch3\", to_junction_name=\"oxy3\")\n",
    "four_polymer.extend(e4, from_junction_name=\"branch4\", to_junction_name=\"oxy4\")\n",
    "\n",
    "four_polymer.extend(e1, from_junction_name=\"carb1\", to_junction_name=\"oxy1\")\n",
    "four_polymer.extend(e2, from_junction_name=\"carb2\", to_junction_name=\"oxy2\")\n",
    "four_polymer.extend(e3, from_junction_name=\"carb3\", to_junction_name=\"oxy3\")\n",
    "four_polymer.extend(e4, from_junction_name=\"carb4\", to_junction_name=\"oxy4\")\n",
    "\n",
    "four_polymer.extend(e1, from_junction_name=\"carb1\", to_junction_name=\"oxy1\")\n",
    "four_polymer.extend(e2, from_junction_name=\"carb2\", to_junction_name=\"oxy2\")\n",
    "four_polymer.extend(e3, from_junction_name=\"carb3\", to_junction_name=\"oxy3\")\n",
    "four_polymer.extend(e4, from_junction_name=\"carb4\", to_junction_name=\"oxy4\")\n",
    "\n",
    "four_polymer.extend(terminal, from_junction_name=\"carb1\", to_junction_name=\"term\")\n",
    "four_polymer.extend(terminal, from_junction_name=\"carb2\", to_junction_name=\"term\")\n",
    "four_polymer.extend(terminal, from_junction_name=\"carb3\", to_junction_name=\"term\")\n",
    "four_polymer.extend(terminal, from_junction_name=\"carb4\", to_junction_name=\"term\")\n",
    "\n",
    "# check polymer charge and give it a descriptive name\n",
    "print(f\"netcharge = {four_polymer.topology.netcharge}\")\n",
    "four_polymer.topology.title = \"four arm star polymer - overlapped monomers\" # rename your ITP header and image name\n",
    "\n",
    "# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check\n",
    "four_polymer.save_to_file('data_paper_examples/four_arm_star_overlapped_monomers.json') # text dump\n",
    "four_polymer.topology.to_ITP('data_paper_examples/four_arm_star_overlapped_monomers.itp')\n",
    "Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data_paper_examples/four_arm_star_overlapped_monomers.png',(400,300))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Construction of an ethylamine dendrimer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-1.6653345369377348e-15\n"
     ]
    }
   ],
   "source": [
    "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n",
    "\n",
    "# load in monomer topologies from ITP files\n",
    "core_mono = Topology.from_ITP(\"data_paper_examples/dendrimer_core.itp\")\n",
    "bifurcating_mono = Topology.from_ITP(\"data_paper_examples/dendrimer_bifurcating.itp\")\n",
    "terminal_mono = Topology.from_ITP(\"data_paper_examples/dendrimer_terminal.itp\")\n",
    "\n",
    "# create junctions for different 'levels' of monomers, depending on what level of branching they exist at in the dendrimer\n",
    "# junctions are created with the bonding atom and then the leaving atom specified, in that order, and should be given a unique name\n",
    "central1 = Junction(core_mono.get_atom(\"N2\"), core_mono.get_atom(\"C9\"), name=\"C1\")\n",
    "central2 = Junction(core_mono.get_atom(\"N2\"), core_mono.get_atom(\"C7\"), name=\"C2\")\n",
    "central3 = Junction(core_mono.get_atom(\"N1\"), core_mono.get_atom(\"C2\"), name=\"C3\")\n",
    "central4 = Junction(core_mono.get_atom(\"N1\"), core_mono.get_atom(\"C3\"), name=\"C4\")\n",
    "\n",
    "b1 = Junction(bifurcating_mono.get_atom(\"C6\"), bifurcating_mono.get_atom(\"N2\"), name = \"to\")\n",
    "b2a = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C2\"), name = \"from1\")\n",
    "b2b = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C3\"), name = \"from2\")\n",
    "\n",
    "c1 = Junction(bifurcating_mono.get_atom(\"C6\"), bifurcating_mono.get_atom(\"N2\"), name = \"to2\")\n",
    "c2a = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C2\"), name = \"from12\")\n",
    "c2b = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C3\"), name = \"from22\")\n",
    "\n",
    "t = Junction(terminal_mono.get_atom(\"C1\"), terminal_mono.get_atom(\"N1\"), name = \"term\")\n",
    "\n",
    "# create monomers from their topologies and any specified junctions\n",
    "# note that different 'levels' of monomers have different names for their junctions.\n",
    "# This ensures that layers are added on sequentially. \n",
    "# If all monomers have the same junction names the polymerisation will be random and often defaults to a linear shape!\n",
    "central = Monomer(core_mono, [central1, central2, central3, central4])\n",
    "bifur1 = Monomer(bifurcating_mono, [b1, b2a, b2b])\n",
    "bifur2 = Monomer(bifurcating_mono, [c1, c2a, c2b])\n",
    "cap = Monomer(terminal_mono, [t])\n",
    "\n",
    "# start the polymer with the central monomer\n",
    "polymer = Polymer(central)\n",
    "\n",
    "# extend first layer of dendrimer\n",
    "polymer.extend(bifur1, from_junction_name=\"C1\", to_junction_name=\"to\")\n",
    "polymer.extend(bifur1, from_junction_name=\"C2\", to_junction_name=\"to\")\n",
    "polymer.extend(bifur1, from_junction_name=\"C3\", to_junction_name=\"to\")\n",
    "polymer.extend(bifur1, from_junction_name=\"C4\", to_junction_name=\"to\")\n",
    "\n",
    "# extend second layer of dendrimer\n",
    "# note how the first and second 'layers' have different monomers with different\n",
    "# Junction names to ensure the correct structure is always formed. Junction and\n",
    "# Monomer name ambiguity WILL cause formation of random, unreplicatable polymer topologies\n",
    "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n",
    "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n",
    "\n",
    "# finish polymer by extending on the capping monomer\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n",
    "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n",
    "\n",
    "# check netcharge of the monomers is preserved (in this case, close to 0)\n",
    "print(polymer.topology.netcharge)\n",
    "\n",
    "# save the dendrimer to a file and visualise the structure with RDKit for an easy visual structure check\n",
    "polymer.save_to_file('data_paper_examples/ethylamine_dendrimer.json') # text dump\n",
    "polymer.topology.to_ITP('data_paper_examples/ethylamine_dendrimer.itp')\n",
    "Visualize.polymer(polymer,infer_bond_order=False).draw2D('data_paper_examples/ethylamine_dendrimer.png',(400,300))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "-----------------------------------------------------------------------------------------------------------------------------------------\n",
    "\n",
    "ALL EXAMPLES FROM HERE DOWN DO *NOT* USE EXTENDED TOPOLOGIES AND THUS PRODUCE INCORRECT PARAMETERS - THEY ARE FOR INTEREST AND AS EXAMPLES FOR WORKFLOWS USED TO BUILD OTHER COMPLEX POLYMER TOPOLOGIES ONLY!\n",
    "\n",
    "-----------------------------------------------------------------------------------------------------------------------------------------"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Construction of an alternating homopolymer of polyester"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n",
    "\n",
    "# load in monomer topologies\n",
    "ethylene_glycol = Topology.from_ITP(\"data_paper_examples/ethylene_glycol.itp\")\n",
    "terephthalic_acid = Topology.from_ITP(\"data_paper_examples/terephthalic_acid.itp\")\n",
    "\n",
    "# define junctions for both monomers\n",
    "ej1 = Junction(ethylene_glycol.get_atom(\"O2\"), ethylene_glycol.get_atom(\"H6\"), name=\"ej1\")\n",
    "ej2 = Junction(ethylene_glycol.get_atom(\"O1\"), ethylene_glycol.get_atom(\"H5\"), name=\"ej2\")\n",
    "\n",
    "tj1 = Junction(terephthalic_acid.get_atom(\"C7\"), terephthalic_acid.get_atom(\"O4\"), name=\"tj1\")\n",
    "tj2 = Junction(terephthalic_acid.get_atom(\"C8\"), terephthalic_acid.get_atom(\"O3\"), name=\"tj2\")\n",
    "\n",
    "# create monomers from their respctive topologies and lists of junctions\n",
    "e_mono = Monomer(ethylene_glycol, [ej1, ej2])\n",
    "t_mono = Monomer(terephthalic_acid, [tj1, tj2])\n",
    "\n",
    "# start polymer\n",
    "polyester = Polymer(e_mono)\n",
    "\n",
    "# extend polymer in alternating fashion for a total length of 10\n",
    "for i in range(10):\n",
    "    if (i%2):\n",
    "        polyester.extend(e_mono, from_junction_name=\"tj2\", to_junction_name=\"ej1\")\n",
    "    else:\n",
    "        polyester.extend(t_mono, from_junction_name=\"ej2\", to_junction_name=\"tj1\")\n",
    "\n",
    "# save polymer topology to file and visualise with RDKit\n",
    "polyester.topology.to_ITP('data_paper_examples/polyester.itp')\n",
    "Visualize.polymer(polyester,infer_bond_order=False).draw2D('data_paper_examples/polyester.png',(400,300))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Construction of a 6-arm PEG star polymer from single monomeric units"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "netcharge = -1.6653345369377348e-16\n"
     ]
    }
   ],
   "source": [
    "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n",
    "\n",
    "# load in monomer topologies from ITP files\n",
    "ethanol = Topology.from_ITP(\"data_paper_examples/ethanol.itp\") # main monomer\n",
    "propanol = Topology.from_ITP(\"data_paper_examples/propanol.itp\") # terminal monomer\n",
    "\n",
    "# create junctions for each monomer with the bonding atom and then the leaving atom specified, in that order, with a unique name\n",
    "oxy_j = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"H6\"), name = \"oxy\")\n",
    "carb_j = Junction(ethanol.get_atom(\"C2\"), ethanol.get_atom(\"H3\"), name = \"carb\")\n",
    "extra_carb_j = Junction(ethanol.get_atom(\"C2\"), ethanol.get_atom(\"H4\"), name = \"carb2\")\n",
    "carb1_j = Junction(ethanol.get_atom(\"C1\"), ethanol.get_atom(\"H1\"), name = \"carb1\")\n",
    "bye_j = Junction(ethanol.get_atom(\"C1\"), ethanol.get_atom(\"O1\"), name = \"byeO\")\n",
    "\n",
    "term_j = Junction(propanol.get_atom(\"OAB\"), propanol.get_atom(\"HAH\"), name = \"term\")\n",
    "\n",
    "# create monomers from their topologies and any specified junctions\n",
    "main = Monomer(ethanol, [oxy_j, carb_j, extra_carb_j])\n",
    "extraC = Monomer(ethanol, [carb_j, bye_j, carb1_j])\n",
    "branch = Monomer(ethanol, [oxy_j, carb_j])\n",
    "terminal = Monomer(propanol, [term_j]) # only needs one junction to join to the backbone\n",
    "\n",
    "# build the arms\n",
    "arm_polymer = Polymer(branch)\n",
    "arm_polymer.extend(terminal, from_junction_name=\"carb\", to_junction_name=\"term\", keep_charge=True)\n",
    "arm = Monomer(arm_polymer.topology, arm_polymer.junctions)\n",
    "\n",
    "# start the polymer by building the linear backbone\n",
    "star_polymer = Polymer(main)\n",
    "star_polymer.extend(main, from_junction_name=\"oxy\", to_junction_name=\"carb\", keep_charge=True)\n",
    "star_polymer.extend(main, from_junction_name=\"oxy\", to_junction_name=\"carb\", keep_charge=True)\n",
    "star_polymer.extend(extraC, from_junction_name=\"oxy\", to_junction_name=\"byeO\", keep_charge=True)\n",
    "\n",
    "# join all six arms to the backbone to make 6-arm star polymer\n",
    "star_polymer.extend(arm, from_junction_name=\"carb\", to_junction_name=\"oxy\", keep_charge=True)\n",
    "star_polymer.extend(arm, from_junction_name=\"carb\", to_junction_name=\"oxy\", keep_charge=True)\n",
    "star_polymer.extend(arm, from_junction_name=\"carb2\", to_junction_name=\"oxy\", keep_charge=True)\n",
    "star_polymer.extend(arm, from_junction_name=\"carb2\", to_junction_name=\"oxy\", keep_charge=True)\n",
    "star_polymer.extend(arm, from_junction_name=\"carb2\", to_junction_name=\"oxy\", keep_charge=True)\n",
    "star_polymer.extend(arm, from_junction_name=\"carb1\", to_junction_name=\"oxy\", keep_charge=True)\n",
    "\n",
    "# check polymer charge and give it a descriptive name\n",
    "print(f\"netcharge = {star_polymer.topology.netcharge}\")\n",
    "star_polymer.topology.title = \"six arm star polymer - from monomers\" # rename your ITP header and image name\n",
    "\n",
    "# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check\n",
    "star_polymer.save_to_file('data_paper_examples/six_arm_star_monomer_build.json') # text dump\n",
    "star_polymer.topology.to_ITP('data_paper_examples/six_arm_star_monomer_build.itp')\n",
    "Visualize.polymer(star_polymer,infer_bond_order=False).draw2D('data_paper_examples/six_arm_star_monomer_build.png',(400,300))"
   ]
  }
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