fractaldna.dna_models.dnachain.MultiSolenoidVolume

class fractaldna.dna_models.dnachain.MultiSolenoidVolume(voxelheight=1500.0, separation=400, twist=False, turn=False, chains=[0, 1, 2, 3, 4, 5, 6, 7, 8], nhistones=None, radius=100, histone_angle=50)

Bases: PlottableSequence

Class to build placement volumes that contain multiple solenoidal DNA strands.

Constructor:

MultiSolenoidVolume(voxelheight=1500., separation=400, twist=False,

turn=False)

voxelheight: size of placement volume separation: separation between DNA strands

The class can contain up to 9 strands with indices as follows

0: central strand 1: x = separation, y = 0 2: x = 0, y = separation 3: x = -separation, y = 0 4: x = separation, y = separation 5: x = separation, y = separation 6: x = -separation, y = separation 7: x = -separation, y = -separation 8: x = separation, y = -seperation

Try: dna = MultiSolenoidVolume() dna.to_line_plot() dna.to_text()

Parameters:

• voxelheight (float) – Height of ‘voxel’ in angstrom

• separation (float) – separation between DNA strands

• twist (bool) – whether the DNA exiting the final spine should be rotated an extra pi/2.

• turn (bool) – make a turned volume (turn strand 90°)

• chains (List) – List of chains to plot, e.g. [0, 1, 2, 3, 4] for a central strand (0) and 4 strands along the X/Y axes.

• radius (float) – Radius from Solenoid centre to histone centre

• nhistones (Optional[int]) – Number of histones to place (if None, will default) to int(38 * voxelheight / 750.0)

• histone_angle (float) – tilt of histones from axis in degrees

__init__(voxelheight=1500.0, separation=400, twist=False, turn=False, chains=[0, 1, 2, 3, 4, 5, 6, 7, 8], nhistones=None, radius=100, histone_angle=50)

Methods

__init__([voxelheight, separation, twist, ...])
histones_to_frame()	Get Histones in Solenoid as a dataframe of their positions
to_frame()	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

to_frame()

Return the molecules as a pandas data frame

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