fractaldna.dna_models.dnachain.Histone

class fractaldna.dna_models.dnachain.Histone(position, rotation, genome=None, chain=0, histone_index=0)

Bases: PlottableSequence

Inherits from PlottableSequence

This class defines a histone.

Parameters:

• position (Union[List, array]) – 3-vector for histone position

• rotation (Union[List, array]) – 3-vector for histone rotation (euler angles)

• genome (Optional[str]) – string defining the genome for the histone

• chain (int) – Chain index for histone and basepairs therein

• histone_index (int) – An index for the histone (by default, order in the solenoid)

__init__(position, rotation, genome=None, chain=0, histone_index=0)

Create a Histone

Methods

__init__(position, rotation[, genome, ...])	Create a Histone
as_series()	Express the histone as a single molecule in a pandas series
setChain(chainIdx)	Set the Chain Index of all base pairs in the histone
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 histone spatially

Attributes

height
hist_bp_rotation
hist_bp_separation
histone_bps
histone_end_bp_rot
histone_start_bp_rot
histone_total_twist
histone_turns
pitch_dna
radius_dna
radius_histone
turn_per_bp
z_angle
z_offset
z_per_bp

as_series()

Express the histone as a single molecule in a pandas series

Return type:

Series

Returns:

Pandas Series for Histone

setChain(chainIdx)

Set the Chain Index of all base pairs in the histone

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 histone spatially

Parameters:

translation (Union[List, array]) – 3-vector for translation

Return type:

None