pycotools3.tasks.TimeCourse¶
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class
pycotools3.tasks.TimeCourse(model, **kwargs)[source]¶ Simulate a time course
A class for running a time course from python using a copasi model. All but one of copasi’s solvers are supported and available via the method kwarg.
TimeCourse Kwargs Description intervals Default: 100 step_size Default: 0.01 end Default: 1 start Default: 0 update_model Default: False method Default: deterministic output_event Default: False scheduled Default: True automatic_step_size Default: False start_in_steady_state Default: False integrate_reduced_model Default: False relative_tolerance Default: 1e-6 absolute_tolerance Default: 1e-12 max_internal_steps Default: 10000 max_internal_step_size Default: 0 subtype Default: 2 use_random_seed Default: True random_seed Default: 1 epsilon Default: 0.001 lower_limit Default: 800 upper_limit Default: 1000 partitioning_interval Default: 1 runge_kutta_step_size Default: 0.001 run Default: True correct_headers Default: True save Default: False <report_kwargs> Arguments for :ref:` report_kwargs <report_kwargs>` are also accepted here Args:
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Methods
__init__(model, **kwargs)Initialize self. adaptive_tau_leap()return: 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_task()Begin creating the segment of xml needed for a time course. deterministic():return:lxml.etree._Element direct()return: get_report_key()cross reference the timecourse task with the newly created time course reort to get the key get_variable_from_string(m, v[, glob])Use model entity name to get the pycotools3 variable gibson_bruck()return: hybrid_lsoda()return: hybrid_rk45()return: hybrid_runge_kutta()return: read_model(m)param m: set_report()ser a time course report containing time and all species or global quantities defined by the user. set_timecourse()Set method specific sections of xml. simulate()tau_leap()return: update_properties(kwargs)method for updating properties from kwargs Attributes
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create_task()[source]¶ Begin creating the segment of xml needed for a time course. Define task and problem definition. This section of xml is common to all methods :return: lxml.etree._Element
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get_report_key()[source]¶ cross reference the timecourse task with the newly created time course reort to get the key
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set_report()[source]¶ ser a time course report containing time and all species or global quantities defined by the user.
Returns: pycotools3.model.Model Args:
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