{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Placing volumes that contain multiple DNA solenoids\n",
    "\n",
    "Multiple solenoid volumes allow for the densest DNA geometries we generate here.\n",
    "\n",
    "Up to 9 solenoids can be placed in a voxel by the methods shown in this example.\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`"
   ]
  },
  {
   "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",
    "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 Multiple Solenoids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Multi-Solenoidal Volumes contain 8 chromatin strands.\n",
    "chain = dna.MultiSolenoidVolume(voxelheight=750)\n",
    "# MayaVI plots are best for visualisation here\n",
    "plot = chain.to_strand_plot()\n",
    "plot.scene.save_jpg(\"multi_solenoid_strand_plot.jpg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![multi_solenoid_strand_plot](multi_solenoid_strand_plot.jpg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# They can be turned, and only select chains can be generated\n",
    "chain = dna.MultiSolenoidVolume(\n",
    "    voxelheight=1500, separation=400, turn=True, chains=[0, 3, 7]\n",
    ")\n",
    "plot = chain.to_line_plot()\n",
    "plot.scene.save_jpg(\"multi_solenoid_turned_plot.jpg\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![multi_solenoid_turned_plot](multi_solenoid_turned_plot.jpg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Exporting multiple solenoids as text"
   ]
  },
  {
   "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 base pair of histones\n",
    "chain.histones_to_frame()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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