fractaldna.dna_models.dnachain.TurnedDoubleDNAChain¶
- class fractaldna.dna_models.dnachain.TurnedDoubleDNAChain(genome, separation)¶
Bases:
TurnedDNAChain
,DoubleDNAChain
- __init__(genome, separation)¶
TurnedDNAChain(genome)
Construct a DNA chain from a genome of GATC that turns 90 degrees
Methods
__init__
(genome, separation)TurnedDNAChain(genome)
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
Plot the surfaces of each molecule in the chain.
to_text
([seperator])Return a description of the molecules in the chain as text
turnDNA
()- 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 plotplot_b (
bool
) – Show Bases in plotplot_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