Apposed-Cortex Model
Apposed-Cortex Model
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Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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M
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P
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R
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S
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T
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U
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V
A
activate_fast_adhesions() (cell_class.Cell method)
(eptm_class.Epithelium method)
activate_sidekick_adhesions() (eptm_class.Epithelium method)
activate_slow_adhesions() (eptm_class.Epithelium method)
adaptive_mesh_update() (cell_class.Cell method)
Adhesion (class in adhesion_class)
adhesion_class
module
adjust_intersections() (eptm_class.Epithelium method)
apply_prestretch_to_cell_identity_pairs() (eptm_class.Epithelium method)
apply_prestretch_to_whole_cells() (eptm_class.Epithelium method)
B
build_adhesion_tree() (cell_class.Cell method)
bvp_bcs() (cell_class.Cell method)
C
Cell (class in cell_class)
cell_class
module
cell_index_by_id() (adhesion_class.Adhesion method)
check_if_cell_intersects_adhesion_boundary() (cell_class.Cell method)
check_if_cells_share_a_vertex() (eptm_class.Epithelium method)
clear_adhesion_points() (cell_class.Cell method)
coarsen_mesh() (cell_class.Cell method)
create_14_cell_eptm_from_fitted_single_cell() (eptm_class.Epithelium method)
create_17_cell_eptm_from_fitted_single_cell() (eptm_class.Epithelium method)
create_19_cell_eptm_from_fitted_single_cell() (eptm_class.Epithelium method)
create_3_cell_eptm_from_fitted_single_cell() (eptm_class.Epithelium method)
create_apposed_cortex() (cell_class.Cell method)
create_disordered_tissue_in_ellipse() (eptm_class.Epithelium method)
D
decimate_all_cells_onto_new_grid() (eptm_class.Epithelium method)
decimate_all_variables_onto_new_grid() (cell_class.Cell method)
deform_elastic_boundary() (eptm_class.Epithelium method)
double_mesh() (cell_class.Cell method)
(eptm_class.Epithelium method)
duplicate_cell() (eptm_class.Epithelium method)
E
Epithelium (class in eptm_class)
Epithelium.OOMFormatter (class in eptm_class)
eptm_class
module
F
funcForScipyBVPSolver() (cell_class.Cell method)
G
get_adhesion_nodes_connected_to_xy() (cell_class.Cell method)
get_all_tissue_vertices() (eptm_class.Epithelium method)
get_all_vertices_for_cell() (eptm_class.Epithelium method)
get_angle_relative_to_cortices() (adhesion_class.Adhesion method)
get_area() (cell_class.Cell method)
get_bicellular_junctions_for_cell() (eptm_class.Epithelium method)
get_boundary_stress_tensor() (eptm_class.Epithelium method)
get_cartesian_coords_of_vertex_triangle() (eptm_class.Epithelium method)
get_cell_id_at_other_end() (adhesion_class.Adhesion method)
get_cell_sum_stress_tensor() (eptm_class.Epithelium method)
get_centroid() (cell_class.Cell method)
get_coordinates_of_junction_midpoint() (eptm_class.Epithelium method)
get_coordinates_of_nearest_points_between_cells() (eptm_class.Epithelium method)
get_cortex_coord_of_vertex_triangle() (eptm_class.Epithelium method)
get_cortex_forces() (cell_class.Cell method)
get_effective_pressure() (cell_class.Cell method)
get_fast_adhesion_forces_across_cortex() (cell_class.Cell method)
get_first_derivative_of_cortex_variables() (cell_class.Cell method)
get_force_magnitude() (adhesion_class.Adhesion method)
get_indices_of_points_within_distance() (eptm_class.Epithelium method)
get_indices_to_order_anticlockwise() (eptm_class.Epithelium static method)
get_intersection_indices() (cell_class.Cell method)
get_junction_cell_pairs() (eptm_class.Epithelium method)
get_length() (adhesion_class.Adhesion method)
(cell_class.Cell method)
get_length_of_adhesions() (cell_class.Cell method)
get_length_of_cortex_with_active_contractility() (cell_class.Cell method)
get_length_of_longest_adhesion() (cell_class.Cell method)
get_length_of_shared_junction() (eptm_class.Epithelium method)
get_length_of_shortest_adhesion() (cell_class.Cell method)
get_locations_of_cortex_adhesion_transition() (eptm_class.Epithelium method)
get_mesh_spacing() (cell_class.Cell method)
get_neighbours() (cell_class.Cell method)
get_normal_and_tangential_components_of_cortex_forces() (cell_class.Cell method)
get_prestrains() (cell_class.Cell method)
get_protrusion_force() (cell_class.Cell method)
get_sdk_forces_across_cortex() (cell_class.Cell method)
get_shape_tensor() (cell_class.Cell method)
get_shortest_distance_between_two_cells() (eptm_class.Epithelium method)
get_slow_adhesion_forces_across_cortex() (cell_class.Cell method)
get_spacing_at_other_end() (adhesion_class.Adhesion method)
get_stress_tensor() (cell_class.Cell method)
get_stress_tensor_around_cell_cluster_depreciated() (eptm_class.Epithelium method)
get_tissue_pressure() (eptm_class.Epithelium method)
get_tissue_width_and_height() (eptm_class.Epithelium method)
get_total_adhesion_force_across_cortex() (cell_class.Cell method)
get_total_adhesion_force_from_adhesion_indices() (cell_class.Cell method)
get_unbalanced_force_residual() (eptm_class.Epithelium method)
get_unit_direction() (adhesion_class.Adhesion method)
get_vector_force() (adhesion_class.Adhesion method)
get_vertex_circumcircle() (eptm_class.Epithelium method)
get_xy() (adhesion_class.Adhesion method)
get_xy_at_other_end() (adhesion_class.Adhesion method)
get_xy_at_this_end() (adhesion_class.Adhesion method)
get_xy_segment_lengths() (cell_class.Cell method)
(eptm_class.Epithelium method)
H
hand_of_god_distances_to_delta() (eptm_class.Epithelium method)
I
impose_pcp() (eptm_class.Epithelium method)
interpolate_variable_onto_new_grid() (cell_class.Cell method)
M
make_heatmap_from_array() (cell_class.Cell static method)
module
adhesion_class
cell_class
eptm_class
move_cortex_nodes_to_equilibrium_dist() (cell_class.Cell method)
P
pickle_self() (cell_class.Cell method)
(eptm_class.Epithelium method)
plot() (adhesion_class.Adhesion method)
plot_adhesion_points() (cell_class.Cell method)
plot_bijunction_tension_arrows() (eptm_class.Epithelium method)
plot_cortex() (cell_class.Cell method)
plot_cortex_variables() (cell_class.Cell method)
plot_medial_pressure() (cell_class.Cell method)
plot_principal_axes_of_shape() (cell_class.Cell method)
plot_protrusion_force() (cell_class.Cell method)
plot_stress() (cell_class.Cell method)
plot_xy_on_trijunction() (cell_class.Cell method)
(eptm_class.Epithelium method)
prune_adhesion_data() (cell_class.Cell method)
prune_slow_adhesions_by_length() (eptm_class.Epithelium method)
R
refine_mesh() (cell_class.Cell method)
relax_deformable_boundary() (eptm_class.Epithelium method)
relax_eptm_with_boundary() (eptm_class.Epithelium method)
relax_eptm_with_germband_bcs() (eptm_class.Epithelium method)
remesh_all_cortices() (eptm_class.Epithelium method)
remove_redundant_member_variables() (eptm_class.Epithelium method)
remove_sdk_from_a_junction() (eptm_class.Epithelium method)
rotate_curve_about_line() (eptm_class.Epithelium static method)
run_simulation_timestep() (eptm_class.Epithelium method)
S
scale_cells_to_fit_adhesion_to_delta() (eptm_class.Epithelium method)
scale_whole_cell_to_fit_adhesion_to_delta() (cell_class.Cell method)
set_adhesion_beta_scale_factor() (eptm_class.Epithelium method)
set_adhesion_search_radius() (eptm_class.Epithelium method)
set_adhesion_to_fixed_line_bool() (eptm_class.Epithelium method)
set_adhesion_type() (eptm_class.Epithelium method)
set_area_stiffness() (eptm_class.Epithelium method)
set_cables_in_eptm() (eptm_class.Epithelium method)
set_constitutive_model() (eptm_class.Epithelium method)
set_fast_adhesion_force_law() (eptm_class.Epithelium method)
set_max_num_adhesions_for_fast_force_calculation() (eptm_class.Epithelium method)
set_mesh_coarsening_fraction() (eptm_class.Epithelium method)
set_omega_for_cells() (eptm_class.Epithelium method)
set_pressure_on_off() (eptm_class.Epithelium method)
set_prestrain_type() (eptm_class.Epithelium method)
set_relax_tolerance_for_cells() (eptm_class.Epithelium method)
set_sdk_restlen() (eptm_class.Epithelium method)
set_sdk_stiffness() (eptm_class.Epithelium method)
set_verbose() (eptm_class.Epithelium method)
set_viscous_bluk() (eptm_class.Epithelium method)
set_viscous_cortex() (eptm_class.Epithelium method)
smooth_all_variables_with_spline() (eptm_class.Epithelium method)
smooth_variables() (cell_class.Cell method)
solve_bvp() (cell_class.Cell method)
solve_bvps_in_parallel() (eptm_class.Epithelium method)
solve_bvps_in_series() (eptm_class.Epithelium method)
T
truncate_colormap() (cell_class.Cell static method)
(eptm_class.Epithelium static method)
U
update_adhesion_distances_identifiers_and_indices() (cell_class.Cell method)
update_adhesion_distances_identifiers_and_indices_for_all_cortices() (eptm_class.Epithelium method)
update_adhesion_points() (cell_class.Cell method)
update_adhesion_points_between_all_cortices() (eptm_class.Epithelium method)
update_adhesions_for_hexagons() (eptm_class.Epithelium method)
update_all_max_adhesion_lengths() (eptm_class.Epithelium method)
update_all_missing_member_variables() (eptm_class.Epithelium method)
update_all_rest_lengths() (eptm_class.Epithelium method)
update_all_rest_lengths_and_areas() (eptm_class.Epithelium method)
update_deformed_mesh_spacing() (cell_class.Cell method)
update_fast_adhesions() (eptm_class.Epithelium method)
update_local_cell_indices_with_s() (adhesion_class.Adhesion method)
update_pref_areas() (eptm_class.Epithelium method)
update_pressures() (eptm_class.Epithelium method)
update_prestrains() (cell_class.Cell method)
update_reference_configuration_to_current() (cell_class.Cell method)
update_s_by_local_cell_indices() (adhesion_class.Adhesion method)
update_sidekick_adhesions() (eptm_class.Epithelium method)
update_slow_adhesions() (eptm_class.Epithelium method)
upsample_all_variables_onto_new_grid() (cell_class.Cell method)
V
verboseprint() (cell_class.Cell method)
(eptm_class.Epithelium method)