src.infer.fourmer_trajectory_from_rate_constants module

fourmer_trajectory_from_rate_constants(motif_production_rate_constants: MotifProductionVector, motif_production_log_rate_constants: MotifProductionVector, breakage_rate_constants: MotifBreakageVector, initial_motif_concentrations_vector: MotifVector, times: TimesVector, complements: list, mass_correction_rate_constant: float = 0.0, concentrations_are_logarithmized: bool = True, ode_integration_method: str = 'DOP853', execution_time_path: str = None, pseudo_count_concentration: float = 1e-12, soft_reactant_threshold: float = None, hard_reactant_threshold: float = None, first_step: float = None, ivp_atol: float = 1e-06, ivp_rtol: float = 0.001) → MotifTrajectory

performs a fourmer reactor with the stated rate constants and initial conditions, i.e. integrates the motif ode with stated parameters.

Parameters:

motif_production_rate_constants : MotifProductionVector, motif_production_log_rate_constants : MotifProductionVector, breakage_rate_constants : MotifBreakageVector, initial_motif_concentrations_vector : MotifVector, times : TimesVector, complements : list, mass_correction_rate_constant : float

Rate constant for compensation of numerical mass fluctuations, default 0.

ode_integration_methodstr

default ‘DOP853’,

execution_time_pathstr

if not None, the execution time of the ode integration is saved here default None,

pseudo_count_concentrationfloat

default 1.e-12,

first_stepfloat

default None

ivp_atolfloat

atol for scipy.integrate.solve_ivp default 1.e-6

ivp_rtolfloat

rtol for scipy.integrate.solve_ivp default 1.e-3

Returns:

motif_trajectory : MotifTrajectory