5. API Reference¶
- class sbml2julia.core.SBML2JuliaProblem(petab_yaml, t_steps=None, n_starts=1, infer_ic_from_sbml=False, optimizer_options={}, custom_code_dict={})¶
Class to create and solve an optimization and retreive the results
- property custom_code_dict¶
Get custom_code_dict
- Returns
custom code dict
- Return type
dict
- import_julia_code(file)¶
Summary
- Parameters
file (TYPE) – Description
- property infer_ic_from_sbml¶
Get infer_ic_from_sbml
- Returns
if missing initial conditions shall be infered from SBML model
- Return type
bool
- insert_custom_code(custom_code_dict)¶
Inserts custom code into Julia code
- Parameters
custom_code_dict (
dict) – dict with replaced code as keys and replacement code as values
- property julia_code¶
Get julia_code
- Returns
julia code for optimization
- Return type
str
- property n_starts¶
Get n_starts
- Returns
number of multistarts
- Return type
int
- optimize()¶
Optimize SBML2JuliaProblem
- Returns
- Results in a dict with keys ‘species’,
’observables’, ‘parameters’ and ‘par_est’
- Return type
dict
- property optimizer_options¶
Get optimizer_options
- Returns
optimization solver options
- Return type
dict
- property petab_problem¶
Get petab_problem
- Returns
petab problem
- Return type
petab.problem.Problem
- property petab_yaml_dict¶
Get petab_yaml_dict
- Returns
petab_yaml_dict
- Return type
dict
- plot_results(condition, path='./plot.pdf', observables=[], size=(6, 5))¶
Plot results
- Parameters
condition (
str) – experimental condition to plotpath (
str, optional) – path to output plotobservables (
list, optional) – list of observables to be plottedsize (
tuple, optional) – size of image
- Raises
ValueError – if observables is not a list
- property results¶
Get results
- Returns
optimization results
- Return type
dict
- property t_steps¶
Get t_steps
- Returns
number of time-discretiation steps
- Return type
t_steps (
int, optional)
- write_jl_file(path='./julia_code.jl')¶
Write code to julia file
- Parameters
path (
str, optional) – path to output Julia file
- write_optimized_parameter_table()¶
Writes a new parameter table were nominal values are replaced with optimized values
- write_results(path='./results', df_format='long')¶
Write results to excel file
- Parameters
path (
str, optional) – path of excel file to write results todf_format (
str, optional) – long or wide table format
- Raises
ValueError – if path is not a directory or Excel file