How to make a Other DNA Structure

Structures can also be built from paths, or as random placements.

Paths can be used to seed a measured geometry, while random placements serve well when generating isotropic DNA damage measurements

import sys
from pathlib import Path

try:
    # The voxelisation library produces the cubic voxelisation that
    # can be used to build DNA
    from fractaldna.structure_models import voxelisation as v
    from fractaldna.structure_models import random_placements as rp

except (ImportError, ModuleNotFoundError):
    sys.path.append(str(Path.cwd().parent.parent.parent))
    from fractaldna.structure_models import voxelisation as v
    from fractaldna.structure_models import random_placements as rp

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

Producing Voxels from Random Placements

This method generates a random collection of prisms inside a ball. It places candidate prisms in the volume of interest, ensuring there are no overlaps.

placements = rp.generate_non_overlapping_prisms(
    10, np.array([100, 100, 200]), 500, early_exit=-1, verbose=True
)

100%|██████████| 10/10 [00:00<00:00, 575.44it/s]

# A single prism can be plotted as a diagnostic,
# using random points inside the prism
# Arrows show the cardinal axes of the prism

placements.prisms[0].to_plot(n=500, arrows=True)

# Multiple prisms can be plotted together

fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
for prism in placements.prisms:
    prism.to_plot(ax=ax)

# And the output can be extracted as a Data Frame
placements.to_frame()

	IDX	TYPE	POS_X	POS_Y	POS_Z	EUL_PSI	EUL_THETA	EUL_PHI
0	0	prism	415.348520	219.712351	-114.423994	2.839435	0.720987	-2.984271
1	1	prism	-432.076027	-237.553875	-24.083225	-2.963485	0.275591	2.982139
2	2	prism	-159.592674	-392.947419	78.121664	1.882360	0.062193	-2.492313
3	3	prism	125.804152	179.063631	112.421050	0.192454	0.851023	1.541503
4	4	prism	396.528057	-50.657998	135.188644	1.464938	-0.688803	2.440295
5	5	prism	23.628732	402.649308	123.393114	-2.756459	-0.737142	0.798266
6	6	prism	-137.302603	106.387584	-328.511381	-0.239809	-0.454546	-0.187761
7	7	prism	-263.391776	91.491565	242.850182	-3.066083	-0.120225	-0.347392
8	8	prism	83.777441	-340.462284	-76.226070	0.010002	0.670432	-2.375796
9	9	prism	336.420935	-355.243091	35.149724	-0.356458	0.604563	-2.353776
10	10	prism	-50.563102	-104.805623	389.180301	2.528837	0.120697	-2.753579