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    "# Single DNA Solenoids\n",
    "\n",
    "This example shows how to generate single DNA Solenoids, and either plot them in MayaVI\n",
    "or export them to text\n",
    "\n",
    "*It is recommended that you run this example inside a Jupyter environment*\n",
    "*rather than a VSCode or similar environment*\n",
    "\n",
    "This requires the mayavi jupyter extension\n",
    "`jupyter nbextension install --py mayavi --user`# Generating Geometries for Geant4\n",
    "\n",
    "This notebook contains code blocks used to generate sample\n",
    "geometries used in Geant4 simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "from pathlib import Path\n",
    "\n",
    "try:\n",
    "    from fractaldna.dna_models import dnachain as dna\n",
    "except (ImportError, ModuleNotFoundError):\n",
    "    sys.path.append(str(Path.cwd().parent.parent.parent))\n",
    "    from fractaldna.dna_models import dnachain as dna\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "from mayavi import mlab\n",
    "\n",
    "# Disable this option for interactive rendering\n",
    "mlab.options.offscreen = True\n",
    "\n",
    "# Enable this option for an interactive notebook\n",
    "# mlab.init_notebook()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Making a straight Solenoidal DNA strand"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Make a straight solenoid in a 750 Å box\n",
    "chain = dna.Solenoid(voxelheight=750)\n",
    "# MayaVI plots are best for visualisation here\n",
    "plot = chain.to_strand_plot()\n",
    "\n",
    "# Save the figure\n",
    "plot.scene.save_jpg(\"single_solenoid_strand_plot.jpg\")\n",
    "\n",
    "# In an interactive notebook, you can refer to the figure to\n",
    "# interact with it.\n",
    "# plot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = chain.to_line_plot()\n",
    "plot.scene.save_jpg(\"single_solenoid_line_plot.jpg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![single_solenoid_strand_plot](single_solenoid_strand_plot.jpg) ![single_solenoid_line_plot](single_solenoid_line_plot.jpg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Making a turned Solenoidal DNA Strand"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Make a turned solenoid in a 750 Å box\n",
    "chain = dna.TurnedSolenoid(voxelheight=750)\n",
    "# MayaVI plots are best for visualisation here\n",
    "plot = chain.to_strand_plot()\n",
    "plot.scene.save_jpg(\"single_solenoid_strand_plot_turned.jpg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![single_solenoid_strand_plot_turned](single_solenoid_strand_plot_turned.jpg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# The line plot method is well adapted to plotting chromatin\n",
    "plot = chain.to_line_plot()\n",
    "plot.scene.save_jpg(\"single_solenoid_line_plot_turned.jpg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![single_solenoid_line_plot_turned](single_solenoid_line_plot_turned.jpg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Centering the DNA\n",
    "By default, solenoids are generated starting near (0, 0, 0). If you are running a simulation in \n",
    "Geant4, you will want to use the chain.translate method to move the whole unit down."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print(\"Default bounds\")\n",
    "print(chain.to_frame()[[\"pos_x\", \"pos_y\", \"pos_z\"]].min())\n",
    "\n",
    "print(\"After Translation\")\n",
    "chain.translate([0, 0, -750.0 / 2])\n",
    "print(chain.to_frame()[[\"pos_x\", \"pos_y\", \"pos_z\"]].min())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Exporting Solenoidal DNA to CSV"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# This too can be exported to a dataframe of basepairs\n",
    "chain.to_frame()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# And a second data frame of histones\n",
    "# This can be joined to the base pairs frame, assuming a sufficient handling of\n",
    "# the missing strand index, and the relation between the base pair and histone index.\n",
    "chain.histones_to_frame()"
   ]
  }
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