simularium_readdy_models.visualization package

Submodules

simularium_readdy_models.visualization.actin_visualization module

class simularium_readdy_models.visualization.actin_visualization.ActinVisualization[source]

Bases: object

visualize an actin trajectory in Simularium

static generate_bend_twist_plots(path_to_readdy_h5, box_size, stride=1, periodic_boundary=True, plots=None)[source]

Use an ActinAnalyzer to generate plots of observables for actin being bent or twisted

static generate_polymerization_plots(path_to_readdy_h5, box_size, stride=1, periodic_boundary=True, plots=None)[source]

Use an ActinAnalyzer to generate plots of observables for polymerizing actin

static get_avg_length_plot(monomer_data, times)[source]

Add a plot of average mother and daughter filament length

static get_bond_length_plot(monomer_data, box_size, periodic_boundary, times)[source]

Add a plot of bond lengths (lat and long) vs end displacement (normalize bond lengths relative to theoretical lengths, plot average ± std)

static get_bound_monomers_plot(monomer_data, times)[source]

Add a plot of percent actin in filaments

static get_branch_angle_plot(monomer_data, box_size, periodic_boundary, times)[source]

Add a plot of branch angle mean and std dev

static get_capped_ends_plot(monomer_data, times)[source]

Add a plot of percent barbed ends that are capped

static get_filament_straightness_plot(monomer_data, box_size, periodic_boundary, times)[source]

Add a plot of how many nm each monomer is away from ideal position in a straight filament

static get_growth_reactions_plot(reactions, times)[source]

Add a plot of reaction events over time for each total growth reaction

static get_growth_reactions_vs_actin_plot(reactions, monomer_data, box_size)[source]

Add a plot of average reaction events over time for each total growth reaction

static get_helix_pitch_plot(monomer_data, box_size, periodic_boundary, times)[source]

Add a plot of average helix pitch for both the short and long helices ideal Ref: http://www.jbc.org/content/266/1/1.full.pdf

static get_structural_reactions_plot(reactions, times)[source]

Add a plot of the number of times a structural reaction was triggered over time Note: triggered != completed, the reaction may have failed to find the required reactants

static get_total_twist_plot(monomer_data, box_size, periodic_boundary, times)[source]

Add a plot of total twist vs end displacement

static visualize_actin(path_to_readdy_h5, box_size, total_steps, plots=None)[source]

visualize an actin trajectory in Simularium

simularium_readdy_models.visualization.kinesin_visualization module

class simularium_readdy_models.visualization.kinesin_visualization.KinesinVisualization[source]

Bases: object

visualize a kinesin trajectory in Simularium

static get_mapping_for_all_polymer_types(types_mapping)[source]

creates a dictionary mapping particle type for all polymer types to a value for a dictionary of types and values

returns dictionary mapping all types to values

static visualize_kinesin(path_to_readdy_h5, box_size, plots)[source]

visualize a kinesin trajectory in Simularium

simularium_readdy_models.visualization.kinesin_visualization.main()[source]

simularium_readdy_models.visualization.microtubules_visualization module

class simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization[source]

Bases: object

visualize a microtubules trajectory in Simularium

static generate_plots(path_to_readdy_h5, box_size, stride=1, periodic_boundary=True, save_pickle_file=False, pickle_file_path=None)[source]

Use an MicrotubulesAnalyzer to generate plots of observables

static get_attach_reactions_plot(reactions, times)[source]

Add a plot of attachment events over time for each total attach reaction

static get_avg_microtubule_length_plot(monomer_data, times)[source]

Add a plot of average microtubule length

static get_display_data_for_all_polymer_types(raw_display_data)[source]

creates a dictionary mapping particle type for all polymer types to a value for a dictionary of types and values

returns dictionary mapping all types to values

static get_growth_reactions_plot(reactions, times)[source]

Add a plot of reaction events over time for each total growth reaction

static get_protofilament_length_plot(monomer_data, times)[source]

Add a plot of protofilament lengths

static get_shrink_reactions_plot(reactions, times)[source]

Add a plot of reaction events over time for each total shrink reaction

static visualize_microtubules(path_to_readdy_h5, box_size, scaled_time_step_us, plots)[source]

visualize a microtubule trajectory in Simularium

simularium_readdy_models.visualization.microtubules_visualization.main()[source]

Module contents