fractaldna.dna_models.dnachain.EightStrandDNAChain¶

class fractaldna.dna_models.dnachain.EightStrandDNAChain(genome, sep1, sep2, turn=False, twist=False)¶

Bases: DNAChain

Construct eight DNA chains that can turn 90 degrees if turn=True

Chain indices are assigned anticlockwise starting from the +y strand, first to the inner four strands, then two the outer four strands. i.e.:

____________________
|                  |
|        4         |
|        0         |
|  5  1     3  7   |
|        2         |
|        6         |
|__________________|

Strands 1 and 3, 0 and 2 are separated by sep1 Strands 4 and 6, 5 and 7 are separated by sep2

Parameters:

genome (str) – string of GATC specifying genome order
sep1 (float) – separation of inner strands from the center in angstroms
sep2 (float) – separation of outer strands from the center in angstroms
turn (bool) – boolean, turn strands 90 degrees along box
twist (bool) – boolean, add a 90 deg twist to each chain

__init__(genome, sep1, sep2, turn=False, twist=False)¶: EightStrandTurnedDNAChain(genome, sep1, sep2, turn=False, twist=False)

Methods

`__init__`(genome, sep1, sep2[, turn, twist])	EightStrandTurnedDNAChain(genome, sep1, sep2, turn=False, twist=False)
`center_in_z`()	Center the molecule around the z=0 plane
`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

center_in_z()¶: Center the molecule around the z=0 plane

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