pycotools3.tasks.Scan

class pycotools3.tasks.Scan(model, **kwargs)

Interface to COPASI scan task

Scan Kwargs	Description
update_model	Default: False
subtask	Default: parameter_estimation
report_type	Default: profile_likelihood. Name of report from Reports class
output_in_subtask	Default: False
adjust_initial_conditions	Default: False
number_of_steps	Default: 10
maximum	Default: 100
minimum	Default: 0.01
log10	Default: False
distribution_type	Default: normal
scan_type	Default: scan
scheduled	Default: True
save	Default: False
clear_scans	Default: True. If true, will remove all scans present then add new scan
run	Default: False
<report_kwargs>	Arguments for report_kwargs are also accepted here

Args:

Returns:

__init__(model, **kwargs)

Parameters:

• model – Model
• kwargs –

Methods

__init__(model, **kwargs)	param model:
check_integrity(allowed, given)	Method to raise an error when a wrong kwarg is passed to a subclass
convert_bool_to_numeric(dct)	CopasiML uses 1’s and 0’s for True or False in some but not all places.
convert_bool_to_numeric2()	CopasiML uses 1’s and 0’s for True or False in some but not all places.
create_scan()	metabolite cn:
define_report()	Use Report class to create report :return:
execute()
get_report_key()
get_variable_from_string(m, v[, glob])	Use model entity name to get the pycotools3 variable
read_model(m)	param m:
remove_scans()	Remove all scans that have been defined.
set_scan_options()
update_properties(kwargs)	method for updating properties from kwargs

Attributes

schema

create_scan()

metabolite cn:

CN=Root,Model=New Model,Vector=Compartments[nuc],Vector=Metabolites[A],Reference=InitialConcentration”/>

Returns:

Args:

Returns:

define_report()

Use Report class to create report :return:

Args:

Returns:

execute()

get_report_key()

remove_scans()

Remove all scans that have been defined.

Returns:

Args:

Returns:

set_scan_options()