Index _ | A | B | C | D | F | G | H | I | K | M | N | O | P | R | S | T | U _ __post_init__() (neurorosettes.grid.UniformGrid method) __version__ (in module neurorosettes) A add_grid() (neurorosettes.utilities.Animator method) adhesion_coefficient (neurorosettes.physics.ContactForces attribute) advance_clock() (neurorosettes.clocks.Clock method) advance_clocks() (neurorosettes.clocks.CellClocks method) advance_cycles() (neurorosettes.simulation.Container method) Animator (class in neurorosettes.utilities) B block_all_clocks() (neurorosettes.clocks.CellClocks method) C ccw() (in module neurorosettes.simulation) cell_interaction_factor (neurorosettes.config.ObjectValidator attribute) (neurorosettes.subcellular.ObjectFactory attribute) cell_radius (neurorosettes.config.ObjectValidator attribute) (neurorosettes.neurons.Neuron property) (neurorosettes.subcellular.ObjectFactory attribute) CellBody (class in neurorosettes.subcellular) CellClocks (class in neurorosettes.clocks) CellDensityCheck (class in neurorosettes.grid) check_max_density() (neurorosettes.grid.CellDensityCheck method) (neurorosettes.grid.OneLevelDensityCheck method) (neurorosettes.grid.TwoLevelsDensityCheck method) Clock (class in neurorosettes.clocks) clocks_factory (neurorosettes.neurons.NeuronFactory attribute) ClocksFactory (class in neurorosettes.clocks) ClocksValidator (class in neurorosettes.config) compute_adhesion() (neurorosettes.physics.ContactForces method) (neurorosettes.physics.PotentialsContact method) (neurorosettes.physics.SimpleContact method) compute_displacements() (neurorosettes.simulation.Container method) compute_repulsion() (neurorosettes.physics.ContactForces method) (neurorosettes.physics.PotentialsContact method) (neurorosettes.physics.SimpleContact method) ConfigParser (class in neurorosettes.config) ContactFactory (class in neurorosettes.physics) ContactForces (class in neurorosettes.physics) Container (class in neurorosettes.simulation) create_first_neurite() (neurorosettes.neurons.Neuron method) create_neurite_representation() (neurorosettes.subcellular.Neurite method) create_neuron() (neurorosettes.neurons.NeuronFactory method) create_new_neuron() (neurorosettes.simulation.Container method) create_secondary_neurite() (neurorosettes.neurons.Neuron method) current_length (neurorosettes.subcellular.Neurite property) current_time (neurorosettes.simulation.Timer attribute) cylinder_cylinder_adhesion (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) (neurorosettes.physics.SimpleFactory attribute) cylinder_cylinder_repulsion (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) (neurorosettes.physics.SimpleFactory attribute) cylinder_cylinder_smoothness (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) CylinderProperties (class in neurorosettes.physics) D death_rate (neurorosettes.clocks.ClocksFactory attribute) (neurorosettes.config.ClocksValidator attribute) differentiate() (neurorosettes.simulation.Container method) differentiation_rate (neurorosettes.clocks.ClocksFactory attribute) (neurorosettes.config.ClocksValidator attribute) divide() (neurorosettes.simulation.Container method) DomainValidator (class in neurorosettes.config) draw_sphere() (neurorosettes.utilities.Animator method) draw_spring() (neurorosettes.utilities.Animator method) F flag() (neurorosettes.clocks.Clock method) from_file() (neurorosettes.simulation.Simulation class method) G get_2d_status() (neurorosettes.config.ConfigParser method) get_cell_body() (neurorosettes.subcellular.ObjectFactory method) get_cell_neighbor_force() (neurorosettes.subcellular.Neurite method) get_cells_in_radius() (neurorosettes.grid.UniformGrid method) get_clock_rates() (neurorosettes.clocks.CellClocks method) get_clocks() (neurorosettes.clocks.ClocksFactory method) get_clocks_data() (neurorosettes.config.ConfigParser method) get_close_cells() (neurorosettes.grid.UniformGrid method) get_close_objects() (neurorosettes.grid.UniformGrid method) get_coordinates() (neurorosettes.utilities.HexagonalTissue method) (neurorosettes.utilities.RectangularTissue method) (neurorosettes.utilities.Tissue method) get_cylinder_cylinder_interactions() (neurorosettes.physics.ContactFactory method) (neurorosettes.physics.PotentialsFactory method) (neurorosettes.physics.SimpleFactory method) get_cylinder_intersection() (in module neurorosettes.physics) get_displacement_from_force() (neurorosettes.simulation.Container method) get_distance_components() (in module neurorosettes.physics) get_domain_data() (neurorosettes.config.ConfigParser method) get_drag_coefficient() (neurorosettes.config.ConfigParser method) get_growth_force() (neurorosettes.subcellular.Neurite method) get_interactions_data() (neurorosettes.config.ConfigParser method) get_max_number_of_neurites() (neurorosettes.config.ConfigParser method) get_neighbor_force() (neurorosettes.subcellular.CellBody method) get_neurite() (neurorosettes.subcellular.ObjectFactory method) get_neurite_neighbor_force() (neurorosettes.subcellular.Neurite method) get_neurite_position_on_cell_surface() (neurorosettes.neurons.Neuron method) get_objects_data() (neurorosettes.config.ConfigParser method) get_objects_in_voxel() (neurorosettes.grid.UniformGrid method) get_progress_bar() (neurorosettes.simulation.Timer method) get_random_position() (in module neurorosettes.utilities) get_random_unit_vector() (in module neurorosettes.utilities) get_sphere_cylinder_interactions() (neurorosettes.physics.ContactFactory method) (neurorosettes.physics.PotentialsFactory method) (neurorosettes.physics.SimpleFactory method) get_sphere_cylinder_intersection() (in module neurorosettes.physics) get_sphere_overlap() (in module neurorosettes.physics) get_sphere_sphere_interactions() (neurorosettes.physics.ContactFactory method) (neurorosettes.physics.PotentialsFactory method) (neurorosettes.physics.SimpleFactory method) get_spring_force() (neurorosettes.subcellular.Neurite method) get_spring_tension() (neurorosettes.physics.CylinderProperties method) get_time_data() (neurorosettes.config.ConfigParser method) grid (neurorosettes.grid.UniformGrid attribute) grid_values (neurorosettes.grid.UniformGrid attribute) H HexagonalTissue (class in neurorosettes.utilities) I idx_values (neurorosettes.grid.UniformGrid attribute) interaction_factor (neurorosettes.physics.PhysicalProperties property) interaction_radius (neurorosettes.physics.PhysicalProperties property) InteractionsValidator (class in neurorosettes.config) interpolate_idx() (neurorosettes.grid.UniformGrid method) intersect() (in module neurorosettes.simulation) K kill() (neurorosettes.simulation.Container method) M max (neurorosettes.config.DomainValidator attribute) (neurorosettes.grid.UniformGrid attribute) max_number_of_neurites (neurorosettes.neurons.NeuronFactory attribute) min (neurorosettes.config.DomainValidator attribute) (neurorosettes.grid.UniformGrid attribute) module neurorosettes neurorosettes.clocks neurorosettes.config neurorosettes.grid neurorosettes.neurons neurorosettes.physics neurorosettes.simulation neurorosettes.subcellular neurorosettes.utilities move_cell() (neurorosettes.simulation.Container method) move_distal_point() (neurorosettes.subcellular.Neurite method) move_neurite() (neurorosettes.simulation.Container method) move_proximal_point() (neurorosettes.subcellular.Neurite method) N Neurite (class in neurorosettes.subcellular) neurite_default_length (neurorosettes.config.ObjectValidator attribute) (neurorosettes.subcellular.ObjectFactory attribute) neurite_interaction_factor (neurorosettes.config.ObjectValidator attribute) (neurorosettes.subcellular.ObjectFactory attribute) neurite_radius (neurorosettes.config.ObjectValidator attribute) (neurorosettes.subcellular.ObjectFactory attribute) neurite_spring_constant (neurorosettes.config.ObjectValidator attribute) (neurorosettes.subcellular.ObjectFactory attribute) Neuron (class in neurorosettes.neurons) NeuronFactory (class in neurorosettes.neurons) neurorosettes module neurorosettes.clocks module neurorosettes.config module neurorosettes.grid module neurorosettes.neurons module neurorosettes.physics module neurorosettes.simulation module neurorosettes.subcellular module neurorosettes.utilities module normalize_vector() (in module neurorosettes.physics) not_negative() (neurorosettes.config.ClocksValidator method) (neurorosettes.config.DomainValidator method) (neurorosettes.config.InteractionsValidator method) (neurorosettes.config.ObjectValidator method) (neurorosettes.config.TimerValidator method) O ObjectFactory (class in neurorosettes.subcellular) objects_factory (neurorosettes.neurons.NeuronFactory attribute) ObjectValidator (class in neurorosettes.config) OneLevelDensityCheck (class in neurorosettes.grid) P PhysicalProperties (class in neurorosettes.physics) place_neurite_on_cell_surface() (neurorosettes.neurons.Neuron method) PotentialsContact (class in neurorosettes.physics) PotentialsFactory (class in neurorosettes.physics) proliferation_rate (neurorosettes.clocks.ClocksFactory attribute) (neurorosettes.config.ClocksValidator attribute) R radius (neurorosettes.physics.PhysicalProperties property) ready_for_differentiation (neurorosettes.neurons.Neuron property) ready_for_division (neurorosettes.neurons.Neuron property) ready_to_die (neurorosettes.neurons.Neuron property) RectangularTissue (class in neurorosettes.utilities) register_cell() (neurorosettes.grid.UniformGrid method) register_neurite() (neurorosettes.grid.UniformGrid method) register_neuron() (neurorosettes.simulation.Container method) remove_cell() (neurorosettes.grid.UniformGrid method) remove_flag() (neurorosettes.clocks.Clock method) remove_neurite() (neurorosettes.grid.UniformGrid method) representation_grid_values (neurorosettes.grid.UniformGrid property) repulsion_coefficient (neurorosettes.physics.ContactForces attribute) run() (neurorosettes.simulation.Simulation method) S save_meshes() (neurorosettes.simulation.Simulation method) save_screenshot() (neurorosettes.utilities.Animator method) set_camera() (neurorosettes.utilities.Animator method) set_center_position() (neurorosettes.subcellular.CellBody method) set_clocks() (neurorosettes.clocks.CellClocks method) set_death_clock() (neurorosettes.clocks.CellClocks method) set_density_check() (neurorosettes.simulation.Container method) set_differentiation_clock() (neurorosettes.clocks.CellClocks method) set_force_from_daughter() (neurorosettes.subcellular.CellBody method) (neurorosettes.subcellular.Neurite method) set_mechanics() (neurorosettes.subcellular.CellBody method) set_outgrowth_axis() (neurorosettes.neurons.Neuron method) set_proliferation_clock() (neurorosettes.clocks.CellClocks method) set_rate() (neurorosettes.clocks.Clock method) set_sphere_representation() (neurorosettes.subcellular.CellBody method) show() (neurorosettes.utilities.Animator method) SimpleContact (class in neurorosettes.physics) SimpleFactory (class in neurorosettes.physics) Simulation (class in neurorosettes.simulation) smoothness_factor (neurorosettes.physics.PotentialsContact attribute) solve_mechanics() (neurorosettes.simulation.Container method) sphere_cylinder_adhesion (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) (neurorosettes.physics.SimpleFactory attribute) sphere_cylinder_repulsion (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) (neurorosettes.physics.SimpleFactory attribute) sphere_cylinder_smoothness (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) sphere_sphere_adhesion (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) (neurorosettes.physics.SimpleFactory attribute) sphere_sphere_repulsion (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) (neurorosettes.physics.SimpleFactory attribute) sphere_sphere_smoothness (neurorosettes.config.InteractionsValidator attribute) (neurorosettes.physics.PotentialsFactory attribute) SphereProperties (class in neurorosettes.physics) spring_axis (neurorosettes.subcellular.Neurite property) step (neurorosettes.config.DomainValidator attribute) (neurorosettes.config.TimerValidator attribute) (neurorosettes.grid.UniformGrid attribute) (neurorosettes.simulation.Timer attribute) T tension (neurorosettes.subcellular.Neurite property) Timer (class in neurorosettes.simulation) TimerValidator (class in neurorosettes.config) Tissue (class in neurorosettes.utilities) total_time (neurorosettes.config.TimerValidator attribute) (neurorosettes.simulation.Timer attribute) trigger_block() (neurorosettes.clocks.Clock method) TwoLevelsDensityCheck (class in neurorosettes.grid) type (neurorosettes.config.InteractionsValidator attribute) U UniformGrid (class in neurorosettes.grid) update_cell_positions() (neurorosettes.simulation.Container method) update_clock() (neurorosettes.utilities.Animator method) update_drawings() (neurorosettes.simulation.Container method) update_representation() (neurorosettes.subcellular.CellBody method) (neurorosettes.subcellular.Neurite method) use_2d (neurorosettes.grid.UniformGrid attribute)