fractaldna.dna_models.dnachain.DoubleDNAChain

class fractaldna.dna_models.dnachain.DoubleDNAChain(genome, separation)

Bases: DNAChain

Inherits from DNAChain

DoubleDNAChain(genome, separation) Construct four straight DNA chains Chain indices are assigned anticlockwise starting from the +y strand.

Parameters:

• genome – string of GATC specifying genome order

• separation – separation of each strand from the center in angstroms

__init__(genome, separation)

DoubleDNAChain(genome, separation)

Construct two parallel straight DNA chains

Methods

__init__(genome, separation)	DoubleDNAChain(genome, separation)
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