Simularium Models Util
0.0.0
Contents:
Overview
Installation
Stable release
From sources
Package modules
simularium_readdy_models package
Subpackages
simularium_readdy_models.actin package
simularium_readdy_models.common package
simularium_readdy_models.kinesin package
simularium_readdy_models.microtubules package
simularium_readdy_models.visualization package
Module contents
get_module_version()
Contributing
Get Started!
Deploying
Simularium Models Util
»
Index
Index
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V
A
actin_distance_from_axis() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
actin_to_actin_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
actin_to_actin_angle_degrees (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
actin_to_actin_axis_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
actin_to_actin_axis_distance (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
actin_to_actin_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
actin_to_actin_distance() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
actin_to_actin_repulsion_distance() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
ActinAnalyzer (class in simularium_readdy_models.actin.actin_analyzer)
ActinGenerator (class in simularium_readdy_models.actin.actin_generator)
ActinSimulation (class in simularium_readdy_models.actin.actin_simulation)
ActinStructure (class in simularium_readdy_models.actin.actin_structure)
ActinTestData (class in simularium_readdy_models.actin.actin_test_data)
ActinUtil (class in simularium_readdy_models.actin.actin_util)
ActinVisualization (class in simularium_readdy_models.visualization.actin_visualization)
add_actin_dimer() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_actin_dimers() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_actin_monomers() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_actin_nucleotide_exchange_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_actin_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_angle() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_angles_between_tubulins() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
(simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_arp23_bind_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_arp23_dimers() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_arp23_nucleotide_exchange_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_arp23_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_arp23_unbind_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_attach_reaction() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_barbed_growth_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_barbed_shrink_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_bent_site_angles() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_bent_site_bonds() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_bond() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_bonds_between_actins() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_bonds_between_tubulins() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_bound_arp_monomers() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
add_box_potential() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_branch_angles() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_branch_bonds() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_branch_dihedrals() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_cap_angles() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_cap_bind_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_cap_bonds() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_cap_dihedrals() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_cap_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_cap_unbind_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_capping_protein() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_constraints() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
add_crystal_structure_monomers() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
add_debranch_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_detach_reaction() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_dihedral() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_dimerize_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_dimerize_reverse_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_edge_site_angles() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_edges() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_fibers_from_data() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
(simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_filament_twist_angles() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_filament_twist_dihedrals() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_growth_reaction() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_hydrolyze_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
(simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_kinesin() (simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation method)
(simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_kinesin_angles_and_dihedrals() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_kinesin_bonds_and_repulsions() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_kinesin_constraints() (simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation method)
add_kinesin_reactions() (simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation method)
add_kinesin_types() (simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation method)
add_microtubule() (simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation method)
(simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_microtubule_seed() (simularium_readdy_models.microtubules.microtubules_simulation.MicrotubulesSimulation method)
add_microtubules_constraints() (simularium_readdy_models.microtubules.microtubules_simulation.MicrotubulesSimulation method)
add_microtubules_reactions() (simularium_readdy_models.microtubules.microtubules_simulation.MicrotubulesSimulation method)
add_microtubules_types() (simularium_readdy_models.microtubules.microtubules_simulation.MicrotubulesSimulation method)
add_monomer_box_potentials() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_monomers_from_data() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
(simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_motor_bind_ATP_reaction() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_motor_bind_tubulin_reaction() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_motor_release_tubulin_reaction() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_motor_tubulin_interactions() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_nucleate_branch_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_nucleate_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_obstacles() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
add_particle_types() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
(simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_pointed_growth_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_pointed_shrink_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_polymer_angle_1D() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_polymer_angle_2D() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_polymer_bond_1D() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_polymer_bond_2D() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_polymer_dihedral_1D() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_polymer_dihedral_2D() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_polymer_repulsion() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_polymer_topology_species() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_random_linear_fibers() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
(simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_random_monomers() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
add_random_tubulin_dimers() (simularium_readdy_models.microtubules.microtubules_simulation.MicrotubulesSimulation method)
add_reactions() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
add_repulsion() (simularium_readdy_models.common.readdy_util.ReaddyUtil method)
add_repulsions() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_shrink_reaction() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_translate_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_trimerize_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_trimerize_reverse_reaction() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
add_tubulin_bonds_and_repulsions() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
add_tubulin_dimers() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_tubulin_site_angles() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_tubulin_site_bonds() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_tubulin_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
add_tubulin_types() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
analyze_average_for_series() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_branch_angles() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_daughter_filament_lengths() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_filament_straightness() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_frame_get_chain_of_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
analyze_frame_get_count_of_topologies_of_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
analyze_frame_get_id_for_neighbor_of_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
analyze_frame_get_ids_for_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
analyze_frame_get_neighbor_ids_of_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
analyze_free_actin_concentration_over_time() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_lateral_bond_lengths() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_long_helix_pitches() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_longitudinal_bond_lengths() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_mother_filament_lengths() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_pointed_end_displacement() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_protofilament_lengths() (simularium_readdy_models.microtubules.microtubules_analyzer.MicrotubulesAnalyzer static method)
analyze_ratio_of_bound_ATP_actin_to_total_actin() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_ratio_of_bound_to_total_arp23() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_ratio_of_capped_ends_to_total_ends() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_ratio_of_daughter_to_total_actin() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_ratio_of_filamentous_to_total_actin() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_reaction_count_over_time() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
analyze_reaction_rate_over_time() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_short_helix_pitches() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_stddev_for_series() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
analyze_total_twist() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
arp2_daughter1_daughter2_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp2_daughter1_daughter2_daughter3_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp2_mother1_mother2_arp3_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp2_position (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
arp2_to_arp3_distance() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp2_to_daughter_distance() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp2_to_mother_distance() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp3_arp2_daughter1_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp3_arp2_daughter1_daughter2_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp3_position (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
arp3_to_mother_distance() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
arp_id (simularium_readdy_models.actin.arp_data.ArpData attribute)
ArpData (class in simularium_readdy_models.actin.arp_data)
assigned (simularium_readdy_models.actin.arp_data.ArpData attribute)
attach_daughter_fiber_to_mother_fiber() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
B
barbed_point() (simularium_readdy_models.actin.fiber_data.FiberData method)
bound (simularium_readdy_models.actin.arp_data.ArpData attribute)
bound_arp_orientation() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
bound_arps (simularium_readdy_models.actin.fiber_data.FiberData attribute)
branch_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
branch_monomer_position() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
branch_positions() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
branch_shift() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
C
calculate_concentration() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
calculate_diffusionCoefficient() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
calculate_nParticles() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
calculate_polymer_number() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
cancel_attach() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
check_add_global_box_potential() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
check_add_tubulin_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
check_arp3_attached_to_neighbors() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
check_remove_tubulin_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
check_shift_branch_actin_numbers() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
clamp_polymer_offsets_2D() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
complex_branched_actin_fiber() (simularium_readdy_models.actin.actin_test_data.ActinTestData method)
complex_branched_actin_monomers() (simularium_readdy_models.actin.actin_test_data.ActinTestData method)
connect_sites_between_tubulins() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
create_actin_system() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
create_kinesin_system() (simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation method)
create_microtubules_system() (simularium_readdy_models.microtubules.microtubules_simulation.MicrotubulesSimulation method)
create_readdy_simulation() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
D
daughter_axis_direction (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
daughter_axis_point (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
daughter_fiber (simularium_readdy_models.actin.arp_data.ArpData attribute)
daughter_positions (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
direction() (simularium_readdy_models.actin.fiber_data.FiberData method)
distance_from_mother_pointed (simularium_readdy_models.actin.arp_data.ArpData attribute)
do_arp23_unbind() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
do_debranching() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
do_finish_grow() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
do_grow1() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
do_grow2() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
do_pointed_end_translation() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
do_shrink() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
do_shrink1() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
F
fiber_id (simularium_readdy_models.actin.fiber_data.FiberData attribute)
FiberData (class in simularium_readdy_models.actin.fiber_data)
filament_is_crosslinked() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
G
generate_bend_twist_plots() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
generate_plots() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
generate_polymerization_plots() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_actin_axis_position() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_actin_number() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
(simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_actin_rotation() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_actins_for_linear_fiber() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_actins_near_branch() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_actin_particle_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_arp23_particle_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_cap_particle_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_fixed_actin_particle_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_particle_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_polymer_actin_types() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_all_polymer_tubulin_types() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_all_tubulin_types() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_angle_between_vectors() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_attach_reactions_plot() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
get_attaching_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_avg_length_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_avg_microtubule_length_plot() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
get_bond_length_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_bound_arp_rotation() (simularium_readdy_models.actin.arp_data.ArpData method)
get_bound_monomer_position() (simularium_readdy_models.actin.arp_data.ArpData method)
get_bound_monomers_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_box_positions() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_box_size() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_branch_angle_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_branch_orientation_vertices_and_offset() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_capped_ends_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_closest_actin_index() (simularium_readdy_models.actin.arp_data.ArpData method)
get_cropped_fibers() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_current_monomers() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
(simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_current_particle_edges() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_display_data_for_all_polymer_types() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
get_extents() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_filament_lengths() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_filament_straightness_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_first_neighbor() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_first_segment_direction() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_first_vertex_of_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_growth_reactions_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
(simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
get_growth_reactions_vs_actin_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_helix_pitch_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_index_of_closest_point() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_index_of_curve_start_point() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_indices_of_closest_points() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_intersection_point_with_extents() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_local_nucleated_monomer_position() (simularium_readdy_models.actin.arp_data.ArpData method)
get_main_monomers_for_fiber() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_mapping_for_all_polymer_types() (simularium_readdy_models.visualization.kinesin_visualization.KinesinVisualization static method)
get_microtubule_positions_and_types() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_module_version() (in module simularium_readdy_models)
get_monomers() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_monomers_for_daughter_fiber() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_monomers_for_fiber() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_nearest_position() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_nearest_segment_direction() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_neighbor_actin_id() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_neighbor_of_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_neighbor_of_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_neighboring_tubulin() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_neighbors_of_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_new_arp23() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_new_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_new_vertex() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_next_actin() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_next_fiber_id() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_next_monomer_id() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_non_periodic_boundary_position() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_nucleated_arp_monomer_positions() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_nucleated_arp_rotation() (simularium_readdy_models.actin.arp_data.ArpData method)
get_orientation_from_positions() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_orientation_from_vectors() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_perpendicular_components_of_vector() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_plus_and_minus_end_neighbors() (simularium_readdy_models.microtubules.microtubules_analyzer.MicrotubulesAnalyzer static method)
get_point_on_plane_of_intersecting_extent() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
get_pointed_end_displacements() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
get_polymer_indices() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_polymer_offsets() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_position_for_new_vertex() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_position_for_radial_translation() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_position_for_tangent_translation() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_prev_branch_actin() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_protofilament_length_plot() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
get_protofilaments() (simularium_readdy_models.microtubules.microtubules_analyzer.MicrotubulesAnalyzer static method)
get_random_arp2() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
get_random_boundary_position() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_random_perpendicular_vector() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_random_tubulin_neighbors() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_random_unit_vector() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_random_vertex_of_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_random_vertex_of_types() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_rotation_matrix() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_shrink_reactions_plot() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)
get_structural_reactions_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_tangents() (simularium_readdy_models.actin.fiber_data.FiberData method)
get_total_twist_plot() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
get_tubulin_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
get_types_with_polymer_numbers_1D() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_types_with_polymer_numbers_2D() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_vertex_of_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_vertex_position() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_vertex_with_id() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
get_vertices_of_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
I
increment_polymer_indices() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
is_daughter (simularium_readdy_models.actin.fiber_data.FiberData attribute)
K
KinesinSimulation (class in simularium_readdy_models.kinesin.kinesin_simulation)
KinesinUtil (class in simularium_readdy_models.kinesin.kinesin_util)
KinesinVisualization (class in simularium_readdy_models.visualization.kinesin_visualization)
L
linear_actin_fiber() (simularium_readdy_models.actin.actin_test_data.ActinTestData method)
linear_actin_monomers() (simularium_readdy_models.actin.actin_test_data.ActinTestData method)
load_reactions() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
M
main() (in module simularium_readdy_models.visualization.kinesin_visualization)
(in module simularium_readdy_models.visualization.microtubules_visualization)
MicrotubulesAnalyzer (class in simularium_readdy_models.microtubules.microtubules_analyzer)
MicrotubulesSimulation (class in simularium_readdy_models.microtubules.microtubules_simulation)
MicrotubulesUtil (class in simularium_readdy_models.microtubules.microtubules_util)
MicrotubulesVisualization (class in simularium_readdy_models.visualization.microtubules_visualization)
module
simularium_readdy_models
simularium_readdy_models.actin
simularium_readdy_models.actin.actin_analyzer
simularium_readdy_models.actin.actin_generator
simularium_readdy_models.actin.actin_reactions
simularium_readdy_models.actin.actin_simulation
simularium_readdy_models.actin.actin_structure
simularium_readdy_models.actin.actin_test_data
simularium_readdy_models.actin.actin_util
simularium_readdy_models.actin.arp_data
simularium_readdy_models.actin.fiber_data
simularium_readdy_models.common
simularium_readdy_models.common.particle_data
simularium_readdy_models.common.readdy_util
simularium_readdy_models.common.repeated_timer
simularium_readdy_models.kinesin
simularium_readdy_models.kinesin.kinesin_simulation
simularium_readdy_models.kinesin.kinesin_util
simularium_readdy_models.microtubules
simularium_readdy_models.microtubules.microtubules_analyzer
simularium_readdy_models.microtubules.microtubules_reactions
simularium_readdy_models.microtubules.microtubules_simulation
simularium_readdy_models.microtubules.microtubules_util
simularium_readdy_models.visualization
simularium_readdy_models.visualization.actin_visualization
simularium_readdy_models.visualization.kinesin_visualization
simularium_readdy_models.visualization.microtubules_visualization
monomer_data_and_reactions_from_file() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
mother0_mother1_arp2_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother0_mother1_arp2_daughter1_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_arp2_daughter1_daughter2_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_mother2_arp3_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_mother2_arp3_arp2_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_to_arp2_vector() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_to_arp3_vector() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_to_branch_actin_vectors() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_to_mother3_vector() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother1_to_mother_vector() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother2_arp3_arp2_daughter1_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother3_mother2_arp3_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother3_mother2_arp3_arp2_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother4_mother3_mother2_arp3_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother_axis_direction (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
mother_axis_point (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
mother_branch_position() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother_fiber() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother_mother0_mother1_arp2_dihedral_angle() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
mother_positions (simularium_readdy_models.actin.actin_structure.ActinStructure attribute)
N
neighbor_ids (simularium_readdy_models.common.particle_data.ParticleData attribute)
neighbor_types_to_string() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
normalize() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
nucleated (simularium_readdy_models.actin.arp_data.ArpData attribute)
nucleated_arp_orientation() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
nucleated_arps (simularium_readdy_models.actin.fiber_data.FiberData attribute)
O
orientation() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
P
particle_type_with_flags() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
ParticleData (class in simularium_readdy_models.common.particle_data)
particles_to_string() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
pointed_point() (simularium_readdy_models.actin.fiber_data.FiberData method)
points (simularium_readdy_models.actin.fiber_data.FiberData attribute)
points_reversed (simularium_readdy_models.actin.fiber_data.FiberData attribute)
polymer_indices_to_string() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
position (simularium_readdy_models.actin.arp_data.ArpData attribute)
(simularium_readdy_models.common.particle_data.ParticleData attribute)
position_is_in_bounds() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
positions_to_string() (simularium_readdy_models.actin.actin_analyzer.ActinAnalyzer static method)
R
rate_function_detach_ring() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
rate_function_hydrolyze() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
rate_function_infinity() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
rate_function_motor_bind_ATP() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
rate_function_motor_release_tubulin() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
rate_function_shrink_GDP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
rate_function_shrink_GTP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_arp23_unbind_ADP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_arp23_unbind_ATP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_attach() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_barbed_shrink_ADP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_barbed_shrink_ATP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_cap_unbind() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_cleanup_release_tubulin() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
reaction_function_cleanup_shrink() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_debranching_ADP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_debranching_ATP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_detach1() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_detach2() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_finish_arp_bind() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_finish_barbed_grow() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_finish_cap_bind() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_finish_pointed_grow() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_finish_start_branch() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_finish_trimerize() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_grow1_GDP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_grow1_GTP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_grow2_GDP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_grow2_GTP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_hydrolyze() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_hydrolyze_actin() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_hydrolyze_arp() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_motor_bind_ATP() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
reaction_function_motor_bind_tubulin() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
reaction_function_motor_release_tubulin() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
reaction_function_nucleotide_exchange_actin() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_nucleotide_exchange_arp() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_pointed_shrink_ADP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_pointed_shrink_ATP() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_reset_state() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
reaction_function_reverse_dimerize() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_reverse_trimerize() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
reaction_function_shrink2() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_shrink_GDP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_shrink_GTP() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
reaction_function_translate() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
ReaddyUtil (class in simularium_readdy_models.common.readdy_util)
remove_bent_filament_site_bonds() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
remove_mid_from_actin() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
remove_mother_mid_at_junction() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
remove_tubulin_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
RepeatedTimer (class in simularium_readdy_models.common.repeated_timer)
reversed_points() (simularium_readdy_models.actin.fiber_data.FiberData method)
reversed_tangents() (simularium_readdy_models.actin.fiber_data.FiberData method)
rotate() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
rotate_position_to_match_branch_angle() (simularium_readdy_models.actin.arp_data.ArpData static method)
S
set_actin_mid_flag() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
set_actin_mid_flags_at_new_branch() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
set_actin_mid_flags_at_removed_branch() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
set_arp23_vertex_position() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
set_displacements() (in module simularium_readdy_models.actin.actin_util)
set_end_vertex_position() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
set_flags() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
set_free() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
set_kinesin_state() (simularium_readdy_models.kinesin.kinesin_util.KinesinUtil static method)
set_new_trimer_vertex_position() (simularium_readdy_models.actin.actin_util.ActinUtil static method)
set_next_fiber_id() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
set_next_monomer_id() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
set_parameters() (in module simularium_readdy_models.actin.actin_util)
(in module simularium_readdy_models.kinesin.kinesin_util)
(in module simularium_readdy_models.microtubules.microtubules_util)
set_particle_type_name() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
setup_fixed_monomers() (simularium_readdy_models.actin.actin_generator.ActinGenerator static method)
setup_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
simple_branched_actin_fiber() (simularium_readdy_models.actin.actin_test_data.ActinTestData method)
simularium_readdy_models
module
simularium_readdy_models.actin
module
simularium_readdy_models.actin.actin_analyzer
module
simularium_readdy_models.actin.actin_generator
module
simularium_readdy_models.actin.actin_reactions
module
simularium_readdy_models.actin.actin_simulation
module
simularium_readdy_models.actin.actin_structure
module
simularium_readdy_models.actin.actin_test_data
module
simularium_readdy_models.actin.actin_util
module
simularium_readdy_models.actin.arp_data
module
simularium_readdy_models.actin.fiber_data
module
simularium_readdy_models.common
module
simularium_readdy_models.common.particle_data
module
simularium_readdy_models.common.readdy_util
module
simularium_readdy_models.common.repeated_timer
module
simularium_readdy_models.kinesin
module
simularium_readdy_models.kinesin.kinesin_simulation
module
simularium_readdy_models.kinesin.kinesin_util
module
simularium_readdy_models.microtubules
module
simularium_readdy_models.microtubules.microtubules_analyzer
module
simularium_readdy_models.microtubules.microtubules_reactions
module
simularium_readdy_models.microtubules.microtubules_simulation
module
simularium_readdy_models.microtubules.microtubules_util
module
simularium_readdy_models.visualization
module
simularium_readdy_models.visualization.actin_visualization
module
simularium_readdy_models.visualization.kinesin_visualization
module
simularium_readdy_models.visualization.microtubules_visualization
module
simulate() (simularium_readdy_models.actin.actin_simulation.ActinSimulation method)
start() (simularium_readdy_models.common.repeated_timer.RepeatedTimer method)
stop() (simularium_readdy_models.common.repeated_timer.RepeatedTimer method)
T
tangents (simularium_readdy_models.actin.fiber_data.FiberData attribute)
tangents_reversed (simularium_readdy_models.actin.fiber_data.FiberData attribute)
to_string() (simularium_readdy_models.common.particle_data.ParticleData method)
topology_is_microtubule() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
topology_to_string() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
try_remove_edge() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
tubulin_has_sites() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
tubulin_is_crosslinked() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
tubulin_is_not_crosslinked() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
tubulins_can_attach() (simularium_readdy_models.microtubules.microtubules_util.MicrotubulesUtil static method)
type_name (simularium_readdy_models.actin.fiber_data.FiberData attribute)
(simularium_readdy_models.common.particle_data.ParticleData attribute)
U
unique_id (simularium_readdy_models.common.particle_data.ParticleData attribute)
V
vector_is_invalid() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
vector_to_axis() (simularium_readdy_models.actin.actin_structure.ActinStructure static method)
vertex_not_found() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
vertex_satisfies_type() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
vertex_to_string() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
vertices_are_connected() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
vertices_are_equal() (simularium_readdy_models.common.readdy_util.ReaddyUtil static method)
visualize_actin() (simularium_readdy_models.visualization.actin_visualization.ActinVisualization static method)
visualize_kinesin() (simularium_readdy_models.visualization.kinesin_visualization.KinesinVisualization static method)
visualize_microtubules() (simularium_readdy_models.visualization.microtubules_visualization.MicrotubulesVisualization static method)