simularium_readdy_models package¶
Subpackages¶
- simularium_readdy_models.actin package
- Submodules
- simularium_readdy_models.actin.actin_analyzer module
ActinAnalyzerActinAnalyzer.analyze_average_for_series()ActinAnalyzer.analyze_branch_angles()ActinAnalyzer.analyze_daughter_filament_lengths()ActinAnalyzer.analyze_filament_straightness()ActinAnalyzer.analyze_free_actin_concentration_over_time()ActinAnalyzer.analyze_lateral_bond_lengths()ActinAnalyzer.analyze_long_helix_pitches()ActinAnalyzer.analyze_longitudinal_bond_lengths()ActinAnalyzer.analyze_mother_filament_lengths()ActinAnalyzer.analyze_pointed_end_displacement()ActinAnalyzer.analyze_ratio_of_bound_ATP_actin_to_total_actin()ActinAnalyzer.analyze_ratio_of_bound_to_total_arp23()ActinAnalyzer.analyze_ratio_of_capped_ends_to_total_ends()ActinAnalyzer.analyze_ratio_of_daughter_to_total_actin()ActinAnalyzer.analyze_ratio_of_filamentous_to_total_actin()ActinAnalyzer.analyze_reaction_rate_over_time()ActinAnalyzer.analyze_short_helix_pitches()ActinAnalyzer.analyze_stddev_for_series()ActinAnalyzer.analyze_total_twist()ActinAnalyzer.neighbor_types_to_string()ActinAnalyzer.positions_to_string()
- simularium_readdy_models.actin.actin_generator module
ActinGeneratorActinGenerator.add_bound_arp_monomers()ActinGenerator.attach_daughter_fiber_to_mother_fiber()ActinGenerator.check_shift_branch_actin_numbers()ActinGenerator.get_actin_number()ActinGenerator.get_actins_for_linear_fiber()ActinGenerator.get_cropped_fibers()ActinGenerator.get_extents()ActinGenerator.get_intersection_point_with_extents()ActinGenerator.get_main_monomers_for_fiber()ActinGenerator.get_monomers()ActinGenerator.get_monomers_for_daughter_fiber()ActinGenerator.get_monomers_for_fiber()ActinGenerator.get_neighbor_actin_id()ActinGenerator.get_next_fiber_id()ActinGenerator.get_next_monomer_id()ActinGenerator.get_nucleated_arp_monomer_positions()ActinGenerator.get_point_on_plane_of_intersecting_extent()ActinGenerator.particles_to_string()ActinGenerator.position_is_in_bounds()ActinGenerator.remove_mid_from_actin()ActinGenerator.remove_mother_mid_at_junction()ActinGenerator.set_next_fiber_id()ActinGenerator.set_next_monomer_id()ActinGenerator.set_particle_type_name()ActinGenerator.setup_fixed_monomers()
- simularium_readdy_models.actin.actin_reactions module
- simularium_readdy_models.actin.actin_simulation module
ActinSimulationActinSimulation.add_constraints()ActinSimulation.add_crystal_structure_monomers()ActinSimulation.add_fibers_from_data()ActinSimulation.add_monomers_from_data()ActinSimulation.add_obstacles()ActinSimulation.add_particle_types()ActinSimulation.add_random_linear_fibers()ActinSimulation.add_random_monomers()ActinSimulation.add_reactions()ActinSimulation.create_actin_system()ActinSimulation.do_pointed_end_translation()ActinSimulation.get_current_monomers()ActinSimulation.get_pointed_end_displacements()ActinSimulation.simulate()
- simularium_readdy_models.actin.actin_structure module
ActinStructureActinStructure.actin_distance_from_axis()ActinStructure.actin_to_actin_angle()ActinStructure.actin_to_actin_angle_degreesActinStructure.actin_to_actin_axis_angle()ActinStructure.actin_to_actin_axis_distanceActinStructure.actin_to_actin_dihedral_angle()ActinStructure.actin_to_actin_distance()ActinStructure.actin_to_actin_repulsion_distance()ActinStructure.arp2_daughter1_daughter2_angle()ActinStructure.arp2_daughter1_daughter2_daughter3_dihedral_angle()ActinStructure.arp2_mother1_mother2_arp3_dihedral_angle()ActinStructure.arp2_positionActinStructure.arp2_to_arp3_distance()ActinStructure.arp2_to_daughter_distance()ActinStructure.arp2_to_mother_distance()ActinStructure.arp3_arp2_daughter1_angle()ActinStructure.arp3_arp2_daughter1_daughter2_dihedral_angle()ActinStructure.arp3_positionActinStructure.arp3_to_mother_distance()ActinStructure.bound_arp_orientation()ActinStructure.branch_angle()ActinStructure.branch_monomer_position()ActinStructure.branch_positions()ActinStructure.branch_shift()ActinStructure.daughter_axis_directionActinStructure.daughter_axis_pointActinStructure.daughter_positionsActinStructure.mother0_mother1_arp2_angle()ActinStructure.mother0_mother1_arp2_daughter1_dihedral_angle()ActinStructure.mother1_arp2_daughter1_daughter2_dihedral_angle()ActinStructure.mother1_mother2_arp3_angle()ActinStructure.mother1_mother2_arp3_arp2_dihedral_angle()ActinStructure.mother1_to_arp2_vector()ActinStructure.mother1_to_arp3_vector()ActinStructure.mother1_to_branch_actin_vectors()ActinStructure.mother1_to_mother3_vector()ActinStructure.mother1_to_mother_vector()ActinStructure.mother2_arp3_arp2_daughter1_dihedral_angle()ActinStructure.mother3_mother2_arp3_angle()ActinStructure.mother3_mother2_arp3_arp2_dihedral_angle()ActinStructure.mother4_mother3_mother2_arp3_dihedral_angle()ActinStructure.mother_axis_directionActinStructure.mother_axis_pointActinStructure.mother_branch_position()ActinStructure.mother_fiber()ActinStructure.mother_mother0_mother1_arp2_dihedral_angle()ActinStructure.mother_positionsActinStructure.nucleated_arp_orientation()ActinStructure.orientation()ActinStructure.vector_to_axis()
- simularium_readdy_models.actin.actin_test_data module
- simularium_readdy_models.actin.actin_util module
ActinUtilActinUtil.add_actin_dimer()ActinUtil.add_actin_dimers()ActinUtil.add_actin_monomers()ActinUtil.add_actin_nucleotide_exchange_reaction()ActinUtil.add_actin_types()ActinUtil.add_arp23_bind_reaction()ActinUtil.add_arp23_dimers()ActinUtil.add_arp23_nucleotide_exchange_reaction()ActinUtil.add_arp23_types()ActinUtil.add_arp23_unbind_reaction()ActinUtil.add_barbed_growth_reaction()ActinUtil.add_barbed_shrink_reaction()ActinUtil.add_bonds_between_actins()ActinUtil.add_box_potential()ActinUtil.add_branch_angles()ActinUtil.add_branch_bonds()ActinUtil.add_branch_dihedrals()ActinUtil.add_cap_angles()ActinUtil.add_cap_bind_reaction()ActinUtil.add_cap_bonds()ActinUtil.add_cap_dihedrals()ActinUtil.add_cap_types()ActinUtil.add_cap_unbind_reaction()ActinUtil.add_capping_protein()ActinUtil.add_debranch_reaction()ActinUtil.add_dimerize_reaction()ActinUtil.add_dimerize_reverse_reaction()ActinUtil.add_fibers_from_data()ActinUtil.add_filament_twist_angles()ActinUtil.add_filament_twist_dihedrals()ActinUtil.add_hydrolyze_reaction()ActinUtil.add_monomer_box_potentials()ActinUtil.add_monomers_from_data()ActinUtil.add_nucleate_branch_reaction()ActinUtil.add_nucleate_reaction()ActinUtil.add_particle_types()ActinUtil.add_pointed_growth_reaction()ActinUtil.add_pointed_shrink_reaction()ActinUtil.add_random_linear_fibers()ActinUtil.add_repulsions()ActinUtil.add_translate_reaction()ActinUtil.add_trimerize_reaction()ActinUtil.add_trimerize_reverse_reaction()ActinUtil.check_add_global_box_potential()ActinUtil.check_arp3_attached_to_neighbors()ActinUtil.do_arp23_unbind()ActinUtil.do_debranching()ActinUtil.do_finish_grow()ActinUtil.do_shrink()ActinUtil.get_actin_axis_position()ActinUtil.get_actin_number()ActinUtil.get_actin_rotation()ActinUtil.get_actins_near_branch()ActinUtil.get_all_actin_particle_types()ActinUtil.get_all_arp23_particle_types()ActinUtil.get_all_cap_particle_types()ActinUtil.get_all_fixed_actin_particle_types()ActinUtil.get_all_particle_types()ActinUtil.get_all_polymer_actin_types()ActinUtil.get_box_positions()ActinUtil.get_branch_orientation_vertices_and_offset()ActinUtil.get_new_arp23()ActinUtil.get_new_vertex()ActinUtil.get_next_actin()ActinUtil.get_position_for_new_vertex()ActinUtil.get_position_for_radial_translation()ActinUtil.get_position_for_tangent_translation()ActinUtil.get_prev_branch_actin()ActinUtil.get_random_arp2()ActinUtil.reaction_function_arp23_unbind_ADP()ActinUtil.reaction_function_arp23_unbind_ATP()ActinUtil.reaction_function_barbed_shrink_ADP()ActinUtil.reaction_function_barbed_shrink_ATP()ActinUtil.reaction_function_cap_unbind()ActinUtil.reaction_function_cleanup_shrink()ActinUtil.reaction_function_debranching_ADP()ActinUtil.reaction_function_debranching_ATP()ActinUtil.reaction_function_finish_arp_bind()ActinUtil.reaction_function_finish_barbed_grow()ActinUtil.reaction_function_finish_cap_bind()ActinUtil.reaction_function_finish_pointed_grow()ActinUtil.reaction_function_finish_start_branch()ActinUtil.reaction_function_finish_trimerize()ActinUtil.reaction_function_hydrolyze_actin()ActinUtil.reaction_function_hydrolyze_arp()ActinUtil.reaction_function_nucleotide_exchange_actin()ActinUtil.reaction_function_nucleotide_exchange_arp()ActinUtil.reaction_function_pointed_shrink_ADP()ActinUtil.reaction_function_pointed_shrink_ATP()ActinUtil.reaction_function_reverse_dimerize()ActinUtil.reaction_function_reverse_trimerize()ActinUtil.reaction_function_translate()ActinUtil.set_actin_mid_flag()ActinUtil.set_actin_mid_flags_at_new_branch()ActinUtil.set_actin_mid_flags_at_removed_branch()ActinUtil.set_arp23_vertex_position()ActinUtil.set_end_vertex_position()ActinUtil.set_new_trimer_vertex_position()
set_displacements()set_parameters()
- simularium_readdy_models.actin.arp_data module
ArpDataArpData.arp_idArpData.assignedArpData.boundArpData.daughter_fiberArpData.distance_from_mother_pointedArpData.get_bound_arp_rotation()ArpData.get_bound_monomer_position()ArpData.get_closest_actin_index()ArpData.get_local_nucleated_monomer_position()ArpData.get_nucleated_arp_rotation()ArpData.nucleatedArpData.positionArpData.rotate_position_to_match_branch_angle()
- simularium_readdy_models.actin.fiber_data module
FiberDataFiberData.barbed_point()FiberData.bound_arpsFiberData.direction()FiberData.fiber_idFiberData.get_first_segment_direction()FiberData.get_index_of_closest_point()FiberData.get_index_of_curve_start_point()FiberData.get_indices_of_closest_points()FiberData.get_nearest_position()FiberData.get_nearest_segment_direction()FiberData.get_tangents()FiberData.is_daughterFiberData.nucleated_arpsFiberData.pointed_point()FiberData.pointsFiberData.points_reversedFiberData.reversed_points()FiberData.reversed_tangents()FiberData.tangentsFiberData.tangents_reversedFiberData.type_name
- Module contents
- simularium_readdy_models.common package
- Submodules
- simularium_readdy_models.common.particle_data module
- simularium_readdy_models.common.readdy_util module
ReaddyUtilReaddyUtil.add_angle()ReaddyUtil.add_bond()ReaddyUtil.add_dihedral()ReaddyUtil.add_polymer_angle_1D()ReaddyUtil.add_polymer_angle_2D()ReaddyUtil.add_polymer_bond_1D()ReaddyUtil.add_polymer_bond_2D()ReaddyUtil.add_polymer_dihedral_1D()ReaddyUtil.add_polymer_dihedral_2D()ReaddyUtil.add_repulsion()ReaddyUtil.analyze_frame_get_chain_of_types()ReaddyUtil.analyze_frame_get_count_of_topologies_of_type()ReaddyUtil.analyze_frame_get_id_for_neighbor_of_types()ReaddyUtil.analyze_frame_get_ids_for_types()ReaddyUtil.analyze_frame_get_neighbor_ids_of_types()ReaddyUtil.analyze_reaction_count_over_time()ReaddyUtil.calculate_concentration()ReaddyUtil.calculate_diffusionCoefficient()ReaddyUtil.calculate_nParticles()ReaddyUtil.calculate_polymer_number()ReaddyUtil.clamp_polymer_offsets_2D()ReaddyUtil.create_readdy_simulation()ReaddyUtil.get_angle_between_vectors()ReaddyUtil.get_box_size()ReaddyUtil.get_current_monomers()ReaddyUtil.get_current_particle_edges()ReaddyUtil.get_first_neighbor()ReaddyUtil.get_first_vertex_of_types()ReaddyUtil.get_neighbor_of_type()ReaddyUtil.get_neighbor_of_types()ReaddyUtil.get_neighbors_of_type()ReaddyUtil.get_non_periodic_boundary_position()ReaddyUtil.get_orientation_from_positions()ReaddyUtil.get_orientation_from_vectors()ReaddyUtil.get_perpendicular_components_of_vector()ReaddyUtil.get_random_boundary_position()ReaddyUtil.get_random_perpendicular_vector()ReaddyUtil.get_random_unit_vector()ReaddyUtil.get_random_vertex_of_type()ReaddyUtil.get_random_vertex_of_types()ReaddyUtil.get_rotation_matrix()ReaddyUtil.get_types_with_polymer_numbers_1D()ReaddyUtil.get_types_with_polymer_numbers_2D()ReaddyUtil.get_vertex_of_type()ReaddyUtil.get_vertex_position()ReaddyUtil.get_vertex_with_id()ReaddyUtil.get_vertices_of_type()ReaddyUtil.load_reactions()ReaddyUtil.monomer_data_and_reactions_from_file()ReaddyUtil.normalize()ReaddyUtil.particle_type_with_flags()ReaddyUtil.rate_function_infinity()ReaddyUtil.reaction_function_reset_state()ReaddyUtil.rotate()ReaddyUtil.set_flags()ReaddyUtil.topology_to_string()ReaddyUtil.try_remove_edge()ReaddyUtil.vector_is_invalid()ReaddyUtil.vertex_not_found()ReaddyUtil.vertex_satisfies_type()ReaddyUtil.vertex_to_string()ReaddyUtil.vertices_are_connected()ReaddyUtil.vertices_are_equal()
- simularium_readdy_models.common.repeated_timer module
- Module contents
- simularium_readdy_models.kinesin package
- Submodules
- simularium_readdy_models.kinesin.kinesin_simulation module
- simularium_readdy_models.kinesin.kinesin_util module
KinesinUtilKinesinUtil.add_angles_between_tubulins()KinesinUtil.add_kinesin()KinesinUtil.add_kinesin_angles_and_dihedrals()KinesinUtil.add_kinesin_bonds_and_repulsions()KinesinUtil.add_motor_bind_ATP_reaction()KinesinUtil.add_motor_bind_tubulin_reaction()KinesinUtil.add_motor_release_tubulin_reaction()KinesinUtil.add_motor_tubulin_interactions()KinesinUtil.add_tubulin_bonds_and_repulsions()KinesinUtil.rate_function_motor_bind_ATP()KinesinUtil.rate_function_motor_release_tubulin()KinesinUtil.reaction_function_cleanup_release_tubulin()KinesinUtil.reaction_function_motor_bind_ATP()KinesinUtil.reaction_function_motor_bind_tubulin()KinesinUtil.reaction_function_motor_release_tubulin()KinesinUtil.set_kinesin_state()
set_parameters()
- Module contents
- simularium_readdy_models.microtubules package
- Submodules
- simularium_readdy_models.microtubules.microtubules_analyzer module
- simularium_readdy_models.microtubules.microtubules_reactions module
- simularium_readdy_models.microtubules.microtubules_simulation module
MicrotubulesSimulationMicrotubulesSimulation.add_microtubule_seed()MicrotubulesSimulation.add_microtubules_constraints()MicrotubulesSimulation.add_microtubules_reactions()MicrotubulesSimulation.add_microtubules_types()MicrotubulesSimulation.add_random_tubulin_dimers()MicrotubulesSimulation.create_microtubules_system()
- simularium_readdy_models.microtubules.microtubules_util module
MicrotubulesUtilMicrotubulesUtil.add_angles_between_tubulins()MicrotubulesUtil.add_attach_reaction()MicrotubulesUtil.add_bent_site_angles()MicrotubulesUtil.add_bent_site_bonds()MicrotubulesUtil.add_bonds_between_tubulins()MicrotubulesUtil.add_detach_reaction()MicrotubulesUtil.add_edge_site_angles()MicrotubulesUtil.add_edges()MicrotubulesUtil.add_growth_reaction()MicrotubulesUtil.add_hydrolyze_reaction()MicrotubulesUtil.add_microtubule()MicrotubulesUtil.add_polymer_repulsion()MicrotubulesUtil.add_polymer_topology_species()MicrotubulesUtil.add_shrink_reaction()MicrotubulesUtil.add_tubulin_dimers()MicrotubulesUtil.add_tubulin_site_angles()MicrotubulesUtil.add_tubulin_site_bonds()MicrotubulesUtil.add_tubulin_sites()MicrotubulesUtil.add_tubulin_types()MicrotubulesUtil.cancel_attach()MicrotubulesUtil.check_add_tubulin_sites()MicrotubulesUtil.check_remove_tubulin_sites()MicrotubulesUtil.connect_sites_between_tubulins()MicrotubulesUtil.do_grow1()MicrotubulesUtil.do_grow2()MicrotubulesUtil.do_shrink1()MicrotubulesUtil.filament_is_crosslinked()MicrotubulesUtil.get_all_polymer_tubulin_types()MicrotubulesUtil.get_all_tubulin_types()MicrotubulesUtil.get_attaching_sites()MicrotubulesUtil.get_filament_lengths()MicrotubulesUtil.get_microtubule_positions_and_types()MicrotubulesUtil.get_neighboring_tubulin()MicrotubulesUtil.get_new_sites()MicrotubulesUtil.get_polymer_indices()MicrotubulesUtil.get_polymer_offsets()MicrotubulesUtil.get_random_tubulin_neighbors()MicrotubulesUtil.get_tubulin_sites()MicrotubulesUtil.increment_polymer_indices()MicrotubulesUtil.polymer_indices_to_string()MicrotubulesUtil.rate_function_detach_ring()MicrotubulesUtil.rate_function_hydrolyze()MicrotubulesUtil.rate_function_shrink_GDP()MicrotubulesUtil.rate_function_shrink_GTP()MicrotubulesUtil.reaction_function_attach()MicrotubulesUtil.reaction_function_detach1()MicrotubulesUtil.reaction_function_detach2()MicrotubulesUtil.reaction_function_grow1_GDP()MicrotubulesUtil.reaction_function_grow1_GTP()MicrotubulesUtil.reaction_function_grow2_GDP()MicrotubulesUtil.reaction_function_grow2_GTP()MicrotubulesUtil.reaction_function_hydrolyze()MicrotubulesUtil.reaction_function_shrink2()MicrotubulesUtil.reaction_function_shrink_GDP()MicrotubulesUtil.reaction_function_shrink_GTP()MicrotubulesUtil.remove_bent_filament_site_bonds()MicrotubulesUtil.remove_tubulin_sites()MicrotubulesUtil.set_free()MicrotubulesUtil.setup_sites()MicrotubulesUtil.topology_is_microtubule()MicrotubulesUtil.tubulin_has_sites()MicrotubulesUtil.tubulin_is_crosslinked()MicrotubulesUtil.tubulin_is_not_crosslinked()MicrotubulesUtil.tubulins_can_attach()
set_parameters()
- Module contents
- simularium_readdy_models.visualization package
- Submodules
- simularium_readdy_models.visualization.actin_visualization module
ActinVisualizationActinVisualization.generate_bend_twist_plots()ActinVisualization.generate_polymerization_plots()ActinVisualization.get_avg_length_plot()ActinVisualization.get_bond_length_plot()ActinVisualization.get_bound_monomers_plot()ActinVisualization.get_branch_angle_plot()ActinVisualization.get_capped_ends_plot()ActinVisualization.get_filament_straightness_plot()ActinVisualization.get_growth_reactions_plot()ActinVisualization.get_growth_reactions_vs_actin_plot()ActinVisualization.get_helix_pitch_plot()ActinVisualization.get_structural_reactions_plot()ActinVisualization.get_total_twist_plot()ActinVisualization.visualize_actin()
- simularium_readdy_models.visualization.kinesin_visualization module
- simularium_readdy_models.visualization.microtubules_visualization module
MicrotubulesVisualizationMicrotubulesVisualization.generate_plots()MicrotubulesVisualization.get_attach_reactions_plot()MicrotubulesVisualization.get_avg_microtubule_length_plot()MicrotubulesVisualization.get_display_data_for_all_polymer_types()MicrotubulesVisualization.get_growth_reactions_plot()MicrotubulesVisualization.get_protofilament_length_plot()MicrotubulesVisualization.get_shrink_reactions_plot()MicrotubulesVisualization.visualize_microtubules()
main()
- Module contents
Module contents¶
Top-level package for Simularium Models Util.