fractaldna.dna_models.dnachain.TurnedSolenoid

class fractaldna.dna_models.dnachain.TurnedSolenoid(voxelheight=750, radius=100, nhistones=38, histone_angle=50, twist=False, chain=0)

Bases: Solenoid

Inherits from Solenoid

Define Solenoidal DNA in a voxel (basically a box). This Solenoid will turn 90 degrees through the box

This method works by placing histones around the z-axis (≈6 histones per rotation) and then joining them together using SplineLinkers

Parameters:

voxelheight (float) – Height of ‘voxel’ in angstrom
radius (float) – Radius from Solenoid centre to histone centre
nhistones (int) – Number of histones to place
histone_angle (float) – tilt of histones from axis in degrees
twist (bool) – whether the DNA exiting the final spine should be rotated an extra pi/2.
chain (int) – Chain index for solenoid and basepairs therein

__init__(voxelheight=750, radius=100, nhistones=38, histone_angle=50, twist=False, chain=0): Constructor

Methods

`__init__`([voxelheight, radius, nhistones, ...])	Constructor
`histones_to_frame`()	Get Histones in Solenoid as a dataframe of their positions
`setChain`(chainIdx)	Set the Chain Index of all base pairs in the solenoid
`to_frame`([suppress_hash])	Return the molecules as a pandas data frame
`to_line_plot`([size])	Return a mayavi figure instance with histone and linkers shown
`to_plot`([plot_p, plot_b, plot_s])	Return a matplotlib.Figure instance with molecules plotted
`to_strand_plot`([plot_p, plot_b, plot_s, plot_bp])	Return a mayavi figure instance with strands plotted
`to_surface_plot`()	Plot the surfaces of each molecule in the chain.
`to_text`([seperator])	Return a description of the molecules in the chain as text
`translate`(translation)	Translate the solenoid spatially

histones_to_frame()

Get Histones in Solenoid as a dataframe of their positions

Return type:: DataFrame
Returns:: DataFrame of Histones

setChain(chainIdx)

Set the Chain Index of all base pairs in the solenoid

Parameters:: chainIdx (int) – Index for Chain
Return type:: None

to_frame(suppress_hash=False)

Return the molecules as a pandas data frame

Parameters:: suppress_hash (bool) – Hide the hash in front of the ‘name’ column which is kept for compatibiilty with the Geant4 DNA simulation format
Return type:: DataFrame
Returns:: Pandas data frame with molecule information

to_line_plot(size=(400, 350))

Return a mayavi figure instance with histone and linkers shown

Parameters:: size (Tuple[int, int]) – Figure size (width, height)
Returns:: mayavi figure
Raises:: ImportError – MayaVi likely Not installed

to_plot(plot_p=True, plot_b=True, plot_s=True)

Return a matplotlib.Figure instance with molecules plotted

Parameters:

plot_p (bool) – Show Phosphates in plot
plot_b (bool) – Show Bases in plot
plot_s (bool) – Show sugars in plot

Return type:

Figure

Returns:

Matplotlib Figure

to_strand_plot(plot_p=True, plot_b=True, plot_s=True, plot_bp=False)

Return a mayavi figure instance with strands plotted

:param plot_p : plot phosphate strands :param plot_s : plot sugar strands :param plot_b : plot base strands :param plot_bp : join base pairs together

Returns:: Mayavi Figure
Raises:: ImportError – MayaVi not imported

to_surface_plot()

Plot the surfaces of each molecule in the chain. Avoid this with large chains, this assumes each molecule is an ellipse

Return type:: Figure
Returns:: Matplotlib figure (contour plot)

to_text(seperator=' ')

Return a description of the molecules in the chain as text

Parameters:: seperator (str) – column seperator
Return type:: str

translate(translation)

Translate the solenoid spatially

Parameters:: translation (Union[List, array]) – 3-vector for translation
Return type:: None