Module ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias Import alias ImportFrom alias Import alias identifier FunctionDef arguments args defaults body Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad Str BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Assign NameStore Num Assign NameStore Call NameLoad NameLoad keyword Num keyword NameLoad Expr Call NameLoad CompareEq Call NameLoad SubscriptLoad NameLoad Index Str BinOpAdd NameLoad Num Expr Call NameLoad CompareEq Call NameLoad SubscriptLoad NameLoad Index Str BinOpAdd NameLoad Num Expr Call NameLoad CompareEq SubscriptLoad SubscriptLoad NameLoad Index Str Index Num Num Expr Call NameLoad CompareEq SubscriptLoad Call NameLoad SubscriptLoad NameLoad Index Str Index Num Num decorator_list NameLoad FunctionDef arguments args defaults body Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str Num Expr Call NameLoad Str BinOpDiv Num NameLoad Expr Call NameLoad Call NameLoad keyword Str NameLoad Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str BinOpMod Call NameLoad keyword TupleLoad Str Num Call NameLoad keyword TupleLoad Str Num NameLoad Expr Call NameLoad Str BinOpRShift BinOpMod Call NameLoad keyword TupleLoad Str Num Call NameLoad keyword TupleLoad Str Num BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str NameLoad Expr Call NameLoad NameLoad keyword Num Expr Call NameLoad Str BinOpRShift Call NameLoad keyword TupleLoad Str NameLoad NameLoad NameLoad Expr Call NameLoad Str Call NameLoad keyword TupleLoad Str NameLoad Expr Call NameLoad NameLoad keyword Num decorator_list NameLoad FunctionDef arguments args defaults body Expr Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num NameLoad Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num NameLoad Expr Call NameLoad Str BinOpMod BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num keyword Num Call NameLoad keyword Num Expr Call NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Assign NameStore Call NameLoad NameLoad keyword Num keyword Num keyword NameLoad keyword Str keyword NameLoad keyword NameLoad Assign NameStore AttributeLoad NameLoad attr Expr Call NameLoad CompareEq Call NameLoad SubscriptLoad NameLoad Index Str Num Expr Call NameLoad CompareEq Call NameLoad SubscriptLoad NameLoad Index Str Num Expr Call NameLoad CompareEq SubscriptLoad SubscriptLoad NameLoad Index Str Index Num Num Expr Call NameLoad CompareEq SubscriptLoad Call NameLoad SubscriptLoad NameLoad Index Str Index Num Num Assign NameStore AttributeLoad NameLoad attr Expr Call NameLoad Call NameLoad NameLoad AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args defaults body Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword NameLoad Call NameLoad Str Num Expr Call NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift Call NameLoad keyword AttributeLoad NameLoad attr NameLoad Call NameLoad Str Num Expr Call NameLoad Str Call NameLoad Expr Call NameLoad NameLoad keyword Num decorator_list NameLoad FunctionDef arguments args defaults body Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Call NameLoad Str Num Expr Call NameLoad Str BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad keyword Str decorator_list Call NameLoad NameLoad NameLoad FunctionDef arguments args defaults body Expr Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Call NameLoad Str Num Expr Call NameLoad Str BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad keyword Str Expr Call NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call NameLoad CompareIs AttributeLoad NameLoad attr NameLoad decorator_list NameLoad FunctionDef arguments args defaults body Expr Str Expr Call NameLoad Str ListLoad Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Str Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Str Expr Call NameLoad Call NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad Call NameLoad keyword Str BinOpAdd Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str Call NameLoad Str Num Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad keyword Str Expr Call NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call NameLoad CompareIs AttributeLoad NameLoad attr NameLoad decorator_list NameLoad FunctionDef arguments args defaults body Expr Str Expr Call NameLoad Str ListLoad Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Str Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Str Expr Call NameLoad Call NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad Call NameLoad keyword Str BinOpAdd Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str Call NameLoad Str Num Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad keyword Str Expr Call NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args defaults body Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str ListLoad Str Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword NameLoad Call NameLoad keyword NameLoad BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Call NameLoad Str Num Expr Call NameLoad Str BinOpMod Call NameLoad keyword Num Call NameLoad keyword Num Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword Str Expr Call NameLoad Call NameLoad NameLoad AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args defaults body Expr Call NameLoad Str ListLoad Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Str Expr Call NameLoad Str ListLoad Str Dict Str ListLoad Str Str Expr Call NameLoad Call NameLoad Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad Call NameLoad keyword Str BinOpAdd Call NameLoad Call NameLoad keyword Str Call NameLoad Str Num Expr Call NameLoad Str BinOpRShift BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str BinOpAdd Call NameLoad keyword Str Call NameLoad keyword Str Call NameLoad Str Num Assign NameStore Call NameLoad NameLoad keyword NameLoad Expr Call NameLoad Call NameLoad NameLoad AttributeLoad NameLoad attr decorator_list NameLoad
N/A pysb.testing * pysb * pysb.kappa * pysb.bng generate_network N/A subprocess re split N/A pygraphviz pgv test_kappa_simulation_results N/A N/A N/A N/A N/A N/A Monomer A N/A b N/A N/A Monomer B N/A b N/A N/A Initial N/A A b None N/A Parameter A_0 100 N/A N/A Initial N/A B b None N/A Parameter B_0 100 N/A N/A Rule A_binds_B N/A N/A N/A A b None N/A B b None N/A N/A A b 1 N/A B b 1 N/A Parameter kf 1 N/A N/A Rule A_binds_B_rev N/A N/A N/A A b 1 N/A B b 1 N/A N/A A b None N/A B b None N/A Parameter kr 1 N/A N/A Observable AB N/A N/A A b 1 N/A B b 1 N/A npts 200 N/A kres N/A run_simulation model time 100 points npts N/A N/A ok_ N/A N/A len N/A kres N/A time N/A npts 1 N/A N/A ok_ N/A N/A len N/A kres N/A AB N/A npts 1 N/A N/A ok_ N/A N/A N/A kres N/A time N/A 0 0 N/A N/A ok_ N/A N/A N/A sorted N/A kres N/A time N/A -1 100 N/A with_model test_kappa_expressions N/A N/A N/A N/A N/A N/A Monomer A N/A site N/A site N/A u N/A N/A Parameter two 2 N/A N/A Parameter kr 0.1 N/A N/A Parameter num_A 1000 N/A N/A Expression kf N/A 1e-05 two N/A N/A Initial N/A A site u num_A N/A N/A Rule dimerize_fwd N/A N/A N/A A site u N/A A site u N/A N/A A site N/A u 1 N/A A site N/A u 1 kf N/A N/A Rule dimerize_rev N/A N/A N/A A site N/A u 1 N/A A site N/A u 1 N/A N/A A site u N/A A site u kr N/A N/A run_simulation model time 0 N/A N/A Rule degrade_dimer N/A N/A A site N/A u ANY None kr N/A N/A Observable dimer N/A A site N/A u ANY N/A N/A run_simulation model time 0 N/A with_model test_flux_map N/A N/A N/A N/A N/A Test kappa simulation with flux map (returns tuple with graph) N/A N/A Monomer A N/A b N/A N/A Monomer B N/A a c N/A N/A Monomer C N/A b N/A N/A Parameter k 0.001 N/A N/A Rule A_binds_B N/A N/A N/A A b None N/A B a None N/A N/A A b 1 N/A B a 1 k N/A N/A Rule C_binds_B N/A N/A N/A C b None N/A B c None N/A N/A C b 1 N/A B c 1 k N/A N/A Observable ABC N/A N/A N/A A b 1 N/A B a 1 c 2 N/A C b 2 N/A N/A Initial N/A A b None N/A Parameter A_0 100 N/A N/A Initial N/A B a None c None N/A Parameter B_0 100 N/A N/A Initial N/A C b None N/A Parameter C_0 100 N/A res N/A run_simulation model time 10 points 100 flux_map True output_dir . cleanup True verbose False N/A simdata N/A res timecourse N/A N/A ok_ N/A N/A len N/A simdata N/A time 101 N/A N/A ok_ N/A N/A len N/A simdata N/A ABC 101 N/A N/A ok_ N/A N/A N/A simdata N/A time N/A 0 0 N/A N/A ok_ N/A N/A N/A sorted N/A simdata N/A time N/A -1 10 N/A fluxmap N/A res flux_map N/A N/A ok_ N/A isinstance fluxmap N/A pgv AGraph N/A with_model test_kappa_wild N/A N/A N/A N/A N/A N/A Monomer A N/A site N/A N/A Monomer B N/A site N/A N/A Initial N/A A site None N/A Parameter A_0 100 N/A N/A Initial N/A B site None N/A Parameter B_0 100 N/A N/A Initial N/A N/A A site 1 N/A B site 1 N/A Parameter AB_0 1000 N/A N/A Rule deg_A N/A N/A A site N/A pysb WILD None N/A Parameter k 1 N/A N/A Observable A_ N/A A N/A N/A run_simulation model time 0 N/A with_model test_run_static_analysis_valueerror N/A N/A N/A N/A N/A N/A Monomer A N/A b N/A N/A Monomer B N/A b N/A N/A Rule A_binds_B N/A N/A N/A A b None N/A B b None N/A N/A A b 1 N/A B b 1 N/A Parameter k_A_binds_B 1 N/A N/A Observable AB N/A N/A A b 1 N/A B b 1 N/A res N/A run_static_analysis model contact_map False influence_map False output_dir . N/A N/A raises ValueError with_model test_run_static_analysis_cmap N/A N/A N/A N/A N/A Test generation of contact map by run_static_analysis N/A N/A Monomer A N/A b N/A N/A Monomer B N/A b N/A N/A Rule A_binds_B N/A N/A N/A A b None N/A B b None N/A N/A A b 1 N/A B b 1 N/A Parameter k_A_binds_B 1 N/A N/A Observable AB N/A N/A A b 1 N/A B b 1 N/A res N/A run_static_analysis model contact_map True influence_map False output_dir . N/A N/A ok_ N/A isinstance N/A res contact_map N/A pgv AGraph N/A N/A ok_ N/A N/A res influence_map None N/A with_model test_run_static_analysis_imap N/A N/A N/A N/A N/A Test generation of influence map by run_static_analysis N/A N/A Monomer A N/A N/A N/A Monomer B N/A active N/A active N/A y n N/A N/A Monomer C N/A active N/A active N/A y n N/A N/A Initial N/A A N/A Parameter A_0 100 N/A N/A Initial N/A B active n N/A Parameter B_0 100 N/A N/A Initial N/A C active n N/A Parameter C_0 100 N/A N/A Rule A_activates_B N/A N/A N/A A N/A B active n N/A N/A A N/A B active y N/A Parameter k_A_activates_B 1 N/A N/A Rule B_activates_C N/A N/A N/A B active y N/A C active n N/A N/A B active y N/A C active y N/A Parameter k_B_activates_C 1 N/A res N/A run_static_analysis model contact_map False influence_map True output_dir . N/A N/A ok_ N/A isinstance N/A res influence_map N/A pgv AGraph N/A N/A ok_ N/A N/A res contact_map None N/A with_model test_run_static_analysis_both N/A N/A N/A N/A N/A Test generation of both influence and contact map by run_static_analysis N/A N/A Monomer A N/A N/A N/A Monomer B N/A active N/A active N/A y n N/A N/A Monomer C N/A active N/A active N/A y n N/A N/A Initial N/A A N/A Parameter A_0 100 N/A N/A Initial N/A B active n N/A Parameter B_0 100 N/A N/A Initial N/A C active n N/A Parameter C_0 100 N/A N/A Rule A_activates_B N/A N/A N/A A N/A B active n N/A N/A A N/A B active y N/A Parameter k_A_activates_B 1 N/A N/A Rule B_activates_C N/A N/A N/A B active y N/A C active n N/A N/A B active y N/A C active y N/A Parameter k_B_activates_C 1 N/A res N/A run_static_analysis model contact_map True influence_map True output_dir . N/A N/A ok_ N/A isinstance N/A res influence_map N/A pgv AGraph N/A N/A ok_ N/A isinstance N/A res contact_map N/A pgv AGraph N/A with_model test_contact_map N/A N/A N/A N/A N/A N/A Monomer A N/A b N/A N/A Monomer B N/A b N/A N/A Rule A_binds_B N/A N/A N/A A b None N/A B b None N/A N/A A b 1 N/A B b 1 N/A Parameter k_A_binds_B 1 N/A N/A Observable AB N/A N/A A b 1 N/A B b 1 N/A res N/A contact_map model cleanup True output_dir . N/A N/A ok_ N/A isinstance res N/A pgv AGraph N/A with_model test_influence_map_kasa N/A N/A N/A N/A N/A N/A Monomer A N/A N/A N/A Monomer B N/A active N/A active N/A y n N/A N/A Monomer C N/A active N/A active N/A y n N/A N/A Initial N/A A N/A Parameter A_0 100 N/A N/A Initial N/A B active n N/A Parameter B_0 100 N/A N/A Initial N/A C active n N/A Parameter C_0 100 N/A N/A Rule A_activates_B N/A N/A N/A A N/A B active n N/A N/A A N/A B active y N/A Parameter k_A_activates_B 1 N/A N/A Rule B_activates_C N/A N/A N/A B active y N/A C active n N/A N/A B active y N/A C active y N/A Parameter k_B_activates_C 1 N/A res N/A influence_map model cleanup True N/A N/A ok_ N/A isinstance res N/A pgv AGraph N/A with_model