BioMASS model object (biomass.model_object
)
- class biomass.model_object.ModelObject(path, biomass_model)
The BioMASS model object.
Examples
>>> from biomass import create_model >>> from biomass.models import mapk_cascade >>> model = create_model(mapk_cascade.__package__) >>> type(model) <class 'biomass.model_object.ModelObject'> >>> print('Parameters:', len(model.parameters)) Parameters: 22 >>> print('Species:', len(model.species)) Species: 8 >>> print('Observables:', len(model.observables)) Observables: 2
- gene2val(indiv_gene)
Convert gene to actual value. Mainly used in parameter estimation.
- Parameters:
indiv_gene (
numpy.ndarray
) – Individual gene.- Returns:
indiv_values – Corresponding values.
- Return type:
numpy.ndarray
- get_executable()
Get executable parameter sets from optimization results.
- Return type:
List
[int
]
- get_individual(paramset_id)
Get estimated parameter values from optimization results.
- Parameters:
paramset_id (int) – Index of parameter set.
- Returns:
best_individual – Estimated parameter values.
- Return type:
numpy.ndarray
- get_obj_val(indiv_gene)
An objective function to minimize in parameter estimation.
- Parameters:
indiv_gene (
numpy.ndarray
) – Genes, not parameter values.- Returns:
obj_val – Objective function value.
- Return type:
float
- load_param(paramset)
Load a parameter set from optimization results.
- Parameters:
paramset (int) – Index of parameter set.
- Returns:
optimized_values – Optimized parameter/initial values.
- Return type:
biomass.model_object.OptimizedValues