Index

B

build_cycles() (KineticModel method) build_directional_diagrams() (KineticModel method)

build_flux_diagrams() (KineticModel method) build_partial_diagrams() (KineticModel method) build_state_probabilities() (KineticModel method)

C

calc_cycle_flux() (in module kda.calculations) calc_pi_difference() (in module kda.calculations) calc_sigma() (in module kda.calculations) calc_sigma_K() (in module kda.calculations)

calc_state_probs() (in module kda.calculations) calc_thermo_force() (in module kda.calculations) construct_lambda_funcs() (in module kda.expressions) construct_sympy_net_cycle_flux_func() (in module kda.expressions) construct_sympy_prob_funcs() (in module kda.expressions)

D

draw_cycles() (in module kda.plotting)

draw_diagrams() (in module kda.plotting) draw_ode_results() (in module kda.plotting)

E

enumerate_partial_diagrams() (in module kda.diagrams)

F

find_all_unique_cycles() (in module kda.graph_utils)

G

generate_all_flux_diagrams() (in module kda.diagrams) generate_directional_diagrams() (in module kda.diagrams) generate_edges() (in module kda.graph_utils) generate_flux_diagrams() (in module kda.diagrams) generate_K_string_matrix() (in module kda.graph_utils)

generate_partial_diagrams() (in module kda.diagrams) get_ccw_cycle() (in module kda.graph_utils) get_directional_diagram_count() (KineticModel method) get_flux_diagrams() (KineticModel method) get_partial_diagram_count() (KineticModel method) get_transition_flux() (KineticModel method)

K

kda.calculations module kda.core module kda.diagrams module kda.expressions module

kda.graph_utils module kda.ode module kda.plotting module kda.svd module KineticModel (class in kda.core)

M

matrix_solver() (in module kda.svd) module kda.calculations kda.core kda.diagrams kda.expressions kda.graph_utils kda.ode kda.plotting kda.svd

O

ode_solver() (in module kda.ode)

R

retrieve_rate_matrix() (in module kda.graph_utils)

S

svd_solver() (in module kda.svd)