{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 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\n", "except (ImportError, ModuleNotFoundError):\n", " sys.path.append(str(Path.cwd().parent.parent.parent))\n", " from fractaldna.dna_models import dnachain\n", "\n", "import numpy as np\n", "from mayavi import mlab\n", "\n", "mlab.options.offscreen = True" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Single DNA Segments\n", "\n", "### Straight and Turned Segments for a 50nm box." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "%%capture\n", "bp_separation = dnachain.BP_SEPARATION # 3.32Å\n", "side_length_nm = 50 # nm\n", "num_basepairs_straight = int(side_length_nm / (0.1 * bp_separation))\n", "num_basepairs_turned = int((side_length_nm * np.pi / 4.0) / (0.1 * bp_separation))\n", "\n", "chain_straight = dnachain.DNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_straight))\n", ")\n", "\n", "chain_turned = dnachain.TurnedDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned))\n", ")\n", "\n", "chain_turned_twisted = dnachain.TurnedTwistedDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned))\n", ")\n", "\n", "chain_straight.to_frame().to_csv(\"results/50nm_straight.csv\", sep=\" \", index=False)\n", "chain_turned.to_frame().to_csv(\"results/50nm_turn.csv\", sep=\" \", index=False)\n", "chain_turned_twisted.to_frame().to_csv(\n", " \"results/50nm_turn_twist.csv\", sep=\" \", index=False\n", ")\n", "\n", "chain_straight.to_plot().savefig(\"results/50nm_straight.png\", sep=\" \", index=False)\n", "chain_turned.to_plot().savefig(\"results/50nm_turn.png\", sep=\" \", index=False)\n", "chain_turned_twisted.to_plot().savefig(\n", " \"results/50nm_turn_twist.png\", sep=\" \", index=False\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "### Multi Strand straight and turned segments" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "%%capture\n", "bp_separation = dnachain.BP_SEPARATION # 3.32Å\n", "side_length_nm = 50 # nm\n", "num_basepairs_straight = int(side_length_nm / (0.1 * bp_separation))\n", "num_basepairs_turned = int((side_length_nm * np.pi / 4.0) / (0.1 * bp_separation))\n", "strand_separation = 100 # angstroms\n", "\n", "chain4_straight = dnachain.FourStrandDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_straight)),\n", " strand_separation,\n", ")\n", "\n", "chain4_turned = dnachain.FourStrandTurnedDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned)),\n", " strand_separation,\n", ")\n", "\n", "chain4_turned_twisted = dnachain.FourStrandTurnedDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned)),\n", " strand_separation,\n", " twist=True,\n", ")\n", "\n", "chain4_straight.to_frame().to_csv(\"results/50nm_4_straight.csv\", sep=\" \", index=False)\n", "chain4_turned.to_frame().to_csv(\"results/50nm_4_turn.csv\", sep=\" \", index=False)\n", "chain4_turned_twisted.to_frame().to_csv(\n", " \"results/50nm_4_turn_twist.csv\", sep=\" \", index=False\n", ")\n", "\n", "chain4_straight.to_plot().savefig(\"results/50nm_4_straight.png\")\n", "chain4_turned.to_plot().savefig(\"results/50nm_4_turn.png\")\n", "chain4_turned_twisted.to_plot().savefig(\"results/50nm_4_turn_twist.png\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "%%capture\n", "bp_separation = dnachain.BP_SEPARATION # 3.32Å\n", "side_length_nm = 50 # nm\n", "num_basepairs_straight = int(side_length_nm / (0.1 * bp_separation))\n", "num_basepairs_turned = int((side_length_nm * np.pi / 4.0) / (0.1 * bp_separation))\n", "strand_separation_1 = 100 # angstroms\n", "strand_separation_2 = 250 # angstroms\n", "\n", "chain8_straight = dnachain.EightStrandDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_straight)),\n", " strand_separation_1,\n", " strand_separation_2,\n", " turn=False,\n", " twist=False,\n", ")\n", "\n", "chain8_turned = dnachain.EightStrandDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned)),\n", " strand_separation_1,\n", " strand_separation_2,\n", " turn=True,\n", " twist=False,\n", ")\n", "\n", "chain8_turned_twisted = dnachain.EightStrandDNAChain(\n", " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned)),\n", " strand_separation_1,\n", " strand_separation_2,\n", " turn=True,\n", " twist=True,\n", ")\n", "\n", "chain8_straight.to_frame().to_csv(\n", " \"results/50nm_8_straight.csv\",\n", " sep=\" \",\n", " index=False,\n", ")\n", "chain8_turned.to_frame().to_csv(\"results/50nm_8_turn.csv\", sep=\" \", index=False)\n", "chain8_turned_twisted.to_frame().to_csv(\n", " \"results/50nm_8_turn_twist.csv\", sep=\" \", index=False\n", ")\n", "\n", "chain8_straight.to_plot().savefig(\"results/50nm_8_straight.png\")\n", "chain8_turned.to_plot().savefig(\"results/50nm_8_turn.png\")\n", "chain8_turned_twisted.to_plot().savefig(\"results/50nm_8_turn_twist.png\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "## Making Solenoidal DNA\n", "\n", "### Single Solenoids" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "side_length = 750 # angstrom\n", "radius_solenoid = 100 # angstrom\n", "nhistones = 38 # histones\n", "\n", "solenoid_straight = dnachain.Solenoid(\n", " voxelheight=side_length, radius=radius_solenoid, nhistones=nhistones\n", ")\n", "solenoid_turned = dnachain.TurnedSolenoid(\n", " voxelheight=side_length, radius=radius_solenoid, nhistones=nhistones\n", ")\n", "solenoid_turned_twisted = dnachain.TurnedSolenoid(\n", " voxelheight=side_length, radius=radius_solenoid, nhistones=nhistones, twist=True\n", ")\n", "\n", "# centre around (x,y,z)=(0,0,0)\n", "solenoid_straight.translate([0, 0, -side_length / 2.0])\n", "solenoid_turned.translate([0, 0, -side_length / 2.0])\n", "solenoid_turned_twisted.translate([0, 0, -side_length / 2.0])\n", "\n", "solenoid_straight.to_frame().to_csv(\n", " \"results/solenoid_straight.csv\", sep=\" \", index=False\n", ")\n", "solenoid_turned.to_frame().to_csv(\"results/solenoid_turned.csv\", sep=\" \", index=False)\n", "solenoid_turned_twisted.to_frame().to_csv(\n", " \"results/solenoid_turned_twisted.csv\", sep=\" \", index=False\n", ")\n", "\n", "plot = solenoid_straight.to_line_plot()\n", "plot.scene.save_jpg(\"results/solenoid_straight.jpg\")\n", "\n", "plot = solenoid_turned.to_line_plot()\n", "distance = 1500\n", "mlab.view(azimuth=180, elevation=0, distance=distance, focalpoint=[0, 0, 0])\n", "mlab.move(up=-distance, forward=distance)\n", "mlab.pitch(90)\n", "plot.scene.save_jpg(\"results/solenoid_turned.jpg\")\n", "\n", "plot = solenoid_turned_twisted.to_line_plot()\n", "mlab.view(azimuth=180, elevation=0, distance=distance, focalpoint=[0, 0, 0])\n", "mlab.move(up=-distance, forward=distance)\n", "mlab.pitch(90)\n", "plot.scene.save_jpg(\"results/solenoid_turned_twisted.jpg\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Generating multiple solenoids in a Volume\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "side_length = 1000 # angstrom\n", "radius_solenoid = 100 # angstrom\n", "nhistones = 51 # histones\n", "separation = 250 # angstroms\n", "\n", "solenoid4_straight = dnachain.MultiSolenoidVolume(\n", " voxelheight=side_length,\n", " separation=separation,\n", " radius=radius_solenoid,\n", " nhistones=nhistones,\n", " chains=[1, 2, 3, 4],\n", " turn=False,\n", " twist=False,\n", ")\n", "\n", "solenoid4_turned = dnachain.MultiSolenoidVolume(\n", " voxelheight=side_length,\n", " separation=separation,\n", " radius=radius_solenoid,\n", " nhistones=nhistones,\n", " chains=[1, 2, 3, 4],\n", " turn=True,\n", " twist=False,\n", ")\n", "\n", "solenoid4_turned_twisted = dnachain.MultiSolenoidVolume(\n", " voxelheight=side_length,\n", " separation=separation,\n", " radius=radius_solenoid,\n", " nhistones=nhistones,\n", " chains=[1, 2, 3, 4],\n", " turn=True,\n", " twist=True,\n", ")\n", "\n", "# centre around (x,y,z)=(0,0,0)\n", "solenoid4_straight.translate([0, 0, -side_length / 2.0])\n", "solenoid4_turned.translate([0, 0, -side_length / 2.0])\n", "solenoid4_turned_twisted.translate([0, 0, -side_length / 2.0])\n", "\n", "solenoid4_straight.to_frame().to_csv(\n", " \"results/solenoid4_straight.csv\", sep=\" \", index=False\n", ")\n", "solenoid4_turned.to_frame().to_csv(\"results/solenoid4_turned.csv\", sep=\" \", index=False)\n", "solenoid4_turned_twisted.to_frame().to_csv(\n", " \"results/solenoid4_turned_twisted.csv\", sep=\" \", index=False\n", ")\n", "\n", "plot = solenoid4_straight.to_line_plot()\n", "plot.scene.save_jpg(\"results/solenoid4_straight.jpg\")\n", "\n", "plot = solenoid4_turned.to_line_plot()\n", "distance = 2500\n", "mlab.view(azimuth=180, elevation=0, distance=distance, focalpoint=[0, 0, 0])\n", "mlab.move(up=-distance, forward=distance)\n", "mlab.pitch(90)\n", "plot.scene.save_jpg(\"results/solenoid4_turned.jpg\")\n", "\n", "plot = solenoid4_turned_twisted.to_line_plot()\n", "mlab.view(azimuth=180, elevation=0, distance=distance, focalpoint=[0, 0, 0])\n", "mlab.move(up=-distance, forward=distance)\n", "mlab.pitch(90)\n", "plot.scene.save_jpg(\"results/solenoid4_turned_twisted.jpg\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " " ] } ], "metadata": { "language_info": { "name": "python", "pygments_lexer": "ipython3" } }, "nbformat": 4, "nbformat_minor": 4 }